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1. int index index 0 vexbuf index SWITCH_STIM vexbuf index 1 number of objects vexbuf index 1 object number vexbuf index OBJ_ON turn object on to_vex index return 0 int start_ramp int index index 0 vexbuf index START_RAMP vexbuf index 1 number of ramps to start vexbuf index 1 ramp number vexbuf index 1 number of object on ramp vexbuf index RA_ONCE run ramp once to_vex index return 0 int object_location short index index 0 vexbuf index REPORT_LOCATION tells REX where VEX target is vexbuf index 1 object number Page 315 to_vex index return 0 int vex_gate long flag if flag rampFlag RAMP_ON else rampFlag RAMP_DONE return 0 int resetSwitch vexMessage amp TARG_SWITCH return 0 pp Subroutine that tests the return message from vex I int tstVexMsg unsigned char msg unsigned char code msg vex_message retrieve message from GLvex if msg if message is not null code vex_code msg returned code if code FLOW_RAMP_STOP rampFlag RAMP_DONE else if code FLOW_RAMP_CHANGE vexMessage TARG_SWITCH else if code OBJECT_LOCATION vexMessage LOCATE vex_location msg unpack x and y values to globals vx vy gi else vexMessage 0 return 0
2. A prev do action to state state do PvexSetStimColors amp num objects foreRed foreGreen foreBlue backRed backGreen backBlue to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 174 PvexSetGrayScale sets up a gray scale for all objects in each objectis color lookup table SYNOPSIS PvexSetGrayScale int start int length start index into color lookup table to start gray scale can be 0 to 255 length number of gray levels in gray scale can be 1 to 255 DESCRIPTION This action sets up a gray scale in all objects color lookup tables The sum of the start and length parameters cannot exceed 255 The luminance range of the gray scale is always 0 to 255 The size of the steps between luminances is determined by the length of the gray scale This command is used to initialize a gray scale for continuous tone stimuli RETURN VALUE Glvex will return the signal BATCH DONE 241 after completing this action EXAMPLE int start 64 int length 128 A state do PvexSetGrayScale amp start amp length to nextstate on 0 tst_rx_new FILES rex act vexActions c Page 175 PvexSetObjectGrayScale sets up a gray scale for each specified object in that objectis color lookup table SYNOPSIS PvexSetObjectGrayScale int nObjects int objList int startList int lengthList nObjects number of objects to set objList list of the object numbers to set startList index into each objectis color lookup
3. 1001 1002 1003 1004 1005 1006 short ptrlst 6 0 y short ob 3 5 2 short size 4 draw_rgb_user unsigned short index short i j static int rs_shift 10 static int tricntr 6 for i 0 i lt tricntr i ptrist i i shuffle tricntr rs_shift ptrist index 0 vexbuf index DRAW_RGB_USER_PATTERN vexbuf index 3 number of objects for i 0 i lt 3 i j ptrist i vexbuf index obli object number vexbuf index hibyte patterns j high byte of pattern number vexbuf index lobyte patterns j low of pattern number vexbuf index size pattern check size vexbuf index 1 positive contrast other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not Page 279 DRAW_TIFF_IMAGE This is a batchable command that draws a TIFF image in an object The image is taken from a file named Inumber tif where number is the image number you are going to use for that image I chose to have file names start with I because they contain images not patterns The reason for requiring the tif extension is so that other windows programs can recognize the file as a TIFF file Though TIFF image files may contain multiple images currently GLvex will only draw the first
4. Page 159 object 1 forgrnd rgb 255 255 255 backgrnd rgb 0 0 0 object 2 forgrnd rgb 255 0 0 backgrnd rgb 0 255 0 The letters r g b in brackets stand for the values of red green and blue to use for the object foreground or background These values can range from 0 to 255 Example commands of 25500 ob 0 255 0 These two commands will make the active object have a red foreground and a green background This command will have no effect if the active object has a continuous tone stimulus P Copy pattern This command copies the pattern in one object to a second object If you type P lt return gt you will get the following help message P s d coPy pattern from Source object to Destination object P s d x y coPy pattern from Source object to Destination object and scale width by X and height by Y The letter s in brackets stands for the number of the source object and the letter d in brackets stands for the number of the destination object In the second example of the command the letter x in brackets stands for the percentage to scale the width of the copied object and the letter y in brackets stands for the percentage to scale the height of the copied object To increase the size of the copied object use x and y values greater than 100 To decrease the size of the copied object use x and y values less than 100 Example command P12 This command will copy the stimulus pattern in object 1 to object 2 The main purpose of th
5. Page 286 LOAD_PIXEL_RAMP This is a batchable command that loads a user defined ramp from Rex The command is for users who want ramps that are not linear or circular The first parameter is the number of ramps to load Each ramp requires four parameters the number of the ramp the end action high byte of the number of steps in the ramp and the low byte of the number of steps in the ramp Each step requires eight parameters the four bytes of the X coordinate of the step and the four bytes of the Y coordinate of the step This command is the same as LOAD_RAMP except that the step coordinates are in screen pixels rather than in Rex units Spot files that define user loaded ramps do not need to include the rex hdr ramp h header file End action defines what happens to the object on the ramp after the ramp stops OFF AFTER RAMP 0 object turns off after the end of the ramp ON AFTER RAMP 1 object stays on after the end of the ramp Example action I This action loads a ramp computed in Rex to GLvex struct ramp float x float y struct ramp thisRamp 300 loadRamp unsigned short index int i j steps char flbuf JEFTERRERRR RARE NENE ERRE RERERRERRS You would put code to load the ramp steps here DRA steps 300 index 0 vexbuf index LOAD_RAMP vexbuf index 1 number of ramps to load vexbuf index 1 this ramp number vexbuf index ON_AFTER_RAMP I object stays on after end
6. vexbuf index hibyte direction 1 high byte of ramp direction vexbuf index lobyte direction 1 low byte of ramp direction vexbuf index hibyte speed 1 high byte of ramp speed vexbuf index lobyte speed low byte of ramp speed vexbuf index hibyte rfx I high byte of X offset vexbuf index lobyte rfx I low byte of X offset vexbuf index hibyte rfy 1 high byte of Y offset vexbuf index lobyte rfy 1 low byte of Y offset vexbuf index RA_CENPT reference is center of ramp vexbuf index ON_AFTER_RAMP I object stays on after end of ramp F other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not The hibyte and lobyte functions are defined in GLvex_com c Page 284 NEW_RAMP_FROM _FP This is a batchable command that defines a new ramp or redefines an old ramp relative to the fixation point The first parameter is the number of ramps to define Each ramp requires 13 parameters the ramp number the hi and lo bytes of the length the hi and lo bytes of the angle the hi and lo bytes of the velocity the hi and lo bytes of the horizontal distance from the fixation point the hi and lo bytes of the vertical distance from the fixation point the ramp type and the end action Lengt
7. Example action E this action displays two movie clips of 20 frames each each frame is shown for 2 video fields and the movie loops 5 times clp1 1 clp2 21 nframes 20 interval 2 cycles 5 start_movie short index index 0 vexbuf index SHOW_MOVIE_CLIP vexbuf index 2 number of movie clips vexbuf index clp1 number of the first object in clip 1 vexbuf index clp2 number of the first object in clip 2 vexbuf index nframes number of frames each in clip vexbuf index interval I video fields to show each frame vexbuf index cycles number of times to loop through movie to_vex index return 0 If the digital sync is enabled GLvex will return the signal MOVIE_START 226 at the beginning of the video field in which movie starts and the signal MOVIE STOP 225 at the beginning of the first video field after the movie stops Also GLvex will return the signal MOVIE CHANGE 237 at each frame specified in the SET TRIGGERS command see below If the digital sync is not enabled GLvex will not return any digital signal in this command If the video sync is enabled the rex video sync square will flash white for the first field of the movie and for the first field after the movie stops Also the rex video sync square will flash white for one field at each frame specified in the SET_ TRIGGERS command see below Page 300 STOP_ MOVIE Th
8. Interfacing with Experimental Control 337 Waveform Data 338 Antidromic Data 338 Page x Rex At a Glance Data Acquisition Rex continually acquires samples from the a d converter and stores the data to a circular memory buffer This data is stored to disk when a window is opened Data is stored until the window is closed Each window has an associated pre time and post time These times specify additional data that will be saved before the window is opened and after the window is closed Data stored to disk can originate either from an a d converter or from global memory variables a d sample rate acquire rate and disk store rate can be different e g a signal can be sampled at 1000Hz and stored to disk at 250Hz All rates acquire rate and store rate can be independently set on a per signal basis all signals are not required to be acquired or stored at the same rate Maximum a d sample rate acquire rate per channel 2000Hz Overall throughput to disk has been tested to at least 16k samples sec on a 486 33 with SCSI disk Each signal can be identified with an ascii string that is available to analysis programs Data File Format Rex produces only two types of files the E file and the A file The E file contains short fixed records that identify epochs or times of occurrence The A file is composed of variable length data records The E file indexes the A file Both files include additional information such as se
9. Q vgazeh Q vgazev Q cgazeh Q cgazev afd aquirerate 2000Hz 1000Hz 500Hz 250Hz signal store rate 2000 Hz 1000Hz 500Hz 250 Hz a d calibration 204 102 O51 025 O12 O6 16 bit a d noise test signal you want to modify from the Signal List at the left Rex can store either the input from the A D converters a memory location or a computed signal as an analog signal Set the signal type by clicking on either the a d or mem buttons in the Signal Type panel Selecting the off button will disable that signal The dialog will disable or enable the a d variable set of buttons or the memory source set of buttons depending on which of the Signal Type buttons you select For A D signals the dialog provides options for setting the a d channel the a d delay and the a d acquire rate If you have a low frequency Page 87 signal you can reduce the size of the analog files in your experiments by selecting one of the lower signal store rates Beginning with Version 7 4 Rex can compute several types of analog signals Vergence signals vergh vergv are computed by subtracting the oeye signals oeyeh oeyev from the eye signals eyeh eyev Cyclopean version signals cycloph cyclopv are computed by summing the eye and oeye signals and dividing by 2 The gaze signals gazeh gazev are computed by the other signals otherh otherv from the eye signals The ogaze signals ogazeh ogazev are computed by subtracting the
10. Sv Current limiting resisto determines brightness Odd Numbered Terminals Even Numbered Terminals DC Ouptut Module Red 10k resistor in parallel with LED is required to shunt leakage current from 1 0 module Figure 7 Single LED Page 129 Figure 8 shows an LED which can be dimmed This circuit requires two I O modules and two pots Current limiting resistor in case brightness pot is turned all the way down Brightness adjusts bright and dim together Dim adjust Odd Numbered Terminals Odd Numbered Terminals Even Numbered Terminals DC Ouptut DC Ouptut Module Red Module Red This module is turned on This module is turned on for bright ALONG WITH THE FIRST MODULE for dim 10k resistor in parallel with LED is required to shunt leakage current from I O module Figure 8 Dimmable LED Page 130 The last two figures show how to physically connect the above circuits on the I O rack panel Figure 9 shows the connection diagrams for a single LED either variable brightness or fixed brightness I O Module Rack Pot or resistor determines brightness Variable brightness LED Fixed brightness LED Note solder 18 ga solid wire to pot The stiffness of this wire will hold pot in place 10k resistor in parallel with LED is required to shunt leakage current from 1 0 module Figure 9 Single LED Connections Page 131 Figure 10 shows the connection diagram f
11. Waveform Generator MN MN 40 ST deg 2 s comp Mirror output 40 ST deg 2 s comp Macros xmout ymout_ Convert to 40 ST deg by gt make D A specific conversions shifting left by 2 MN Absolute coordinates for window check Page 118 Configuring PC Systems for Running REX Arthur V Hays Revised 7 Apr 94 REX Software Configuration REX for the PC runs on the QNX operating system QNX is a distributed real time operating system that is POSIX compliant We chose the QNX operating system because it provides an application programming interface that closely parallels the Unix environment that REX runs under on the pdpd11 It is also a 32 bit protected mode operating system that has real time support QNX provides real time features such as attaching to interrupts and fast service times and context switches It has proven very reliable and robust Through POSIX compatibility Unix programs are easily ported The C compiler used under QNX is Watcom C REX does not run on DOS DOS programs however can be run under QNX by using an additional product called RUNDOS This is a DOS emulator This emulator is quite good and will run Windows 3 1 in f2standard f1 mode QNX is a product of QNX Software in Canada We usually place our orders with Florida Datamation QNX Software also sells a TCP IP option for QNX This permits communication via ethernet to other machines NFS and X windows are also available
12. buttons is set to blue You can freeze the dialog by toggling the Debug button to off This makes it very easy to see which states your paradigm enters and when It also makes it easy to see where your paradigm gets stuck If you click on a state button Rex will display a dialog similar to the States Menu that allows you to modify parameters of the state Preset Time Random Time msec M8 msec Running Line Value Abs Rel B FirstArgument Dec Hex 117833792 E Second Argument Dec Hex Third Argument Dec Hex m Data Displays Rex provides three types of data display The Window display shows cursors representing six analog signals and eight eye window positions in X Y coordinates The Running Line display shows eight channels of analog signals unit activity and running line level over time The Raster display shows rasters and spike density functions of unit activity Window Display You launch the window display by selecting the Window Display item from the Displays menu in the Process Switching tool bar In this display eye offsets are displayed in the numerical fields at the top of the display panel The scales at the left and bottom of the display show the spatial extent of the display in degrees The horizontal and vertical extents are always the same so if you resize the display to a rectangular shape square eye windows will appear rectangular The toggle buttons in the bottom Page 92 panel control wh
13. define the flow movie vexbuf index 2 number of objects containing movies vexbuf index nframes number of frames in the movies for i 0 i lt 2 i vexbuf index fobili object number other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not The hibyte and lobyte functions are defined in GLvex_com c Page 294 TO_FLOW_MOVIE_START This is a batchable that sets the flow fields in flow field objects to the starting frame of a flow field movie The first parameter is the number of objects to set up You must build a flow field movie for each of these objects before using this command see above The second parameter is the starting frame of the movie All objects must start on the same frame For each object only one parameter is needed the object number Example action set_movie short index index 0 vexbuf index TO_FLOW_MOVIE_START vexbuf index 2 number of objects to set up vexbuf index 50 frame at which the flow move will start vexbuf index 1 I first object with flow field movie vexbuf index 2 second object with flow field movie other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all comm
14. return memSacList currstim ecode Beginning with Rex 7 2 actions can have up to 10 arguments The arguments can be either type long constants or pointers to global variables User defined menus You may build menus to allow modification of variables at run time The menus are accessed from a dialog launched from the int process tool bar Prior to version 7 0 Rex allowed user menus to access submenus Submenus are no longer supported because they are no longer needed Default Menu Spot will build one menu automatically This menu is named state_vars All that is needed for this menu is a list of variables to display The list of variables is defined in an array of structures of type VLIST and must be named state _vl For example VLIST state_vi clear_all_da amp clear_all NP clearVaf ME_AFT ME_DEC do_two_ramps amp do_two_ramps NP NP 0 ME_DEC ramp0_xda amp r0_xda NP NP 0 ME_DEC ramp0_yda amp r0_yda NP NP 0 ME_DEC ramp1_xda amp r1_xda NP NP 0 ME_DEC ramp1_yda amp r1_yda NP NP 0 ME_DEC fix_xwind amp fxwd NP NP 0 ME_DEC Page 13 fix_ywind amp fywd NP NP 0 ME_DEC fix_oxwind amp foxwd NP NP 0 ME_DEC fix_oywind amp foywd NP NP 0 ME_DEC user_msg amp tst_user NP NP 0 ME_DEC single_trace amp tst_single NP singleVaf ME_AFT ME_DEC NS The VLIST structure has the following format VI_name
15. unpack coordinates into vx and vy wd_pos WIND1 vx vy wd_siz WIND1 tarsiz tarsiz wd_cntrl WIND1 WD_ON return 0 One way to use this command is to set up a second state chain Example state chain E Object location query state set where_set status ON begin start to halt Page 262 halt to qrywts on PSTOP amp drinput qrywts to query on 0 tst_tx_rdy query do object_location to qryack on 0 tst_rx_new qryack do pcm_ack 0 to stgwnd stgwnd do targ_wnd time 200 to halt GLvex will return two floating point values representing the X and Y coordinates of the selected object packed into an array of 8 bytes regardless of whether digital synchronization is enabled or not The rex video sync square will not flash for this command The vex_message subroutine retrieves the last message from GLvex The vex_code char subroutine gets the code value from the msg argument The vex_location char subroutine unpacks the coordinates from the byte array msg and loads them into the long variables vx and vy Vex_message vex_code char vex_location char vx and vy are all defined in GLvex_com c Page 263 SET_ACTIVE_ OBJECT This is a batchable command that changes the active object Subsequent keyboard commands or movements of the mouse will affect the object specified by this command The REPORT LOCATION command will report the location of this object This command has a single
16. 3 object number vexbuf index 2 ramp number other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not Page 288 START_RAMP This is a non batchable command that places objects on ramps and starts the ramps moving The first parameter is the number of ramps to start Each ramp requires three parameters the number of the ramp the number of the object to place on that ramp and the type of cycle There are three types of ramp cycle RA_ ONCE 0 ramp runs once RA_OSCIL 1 ramp goes back and forth until stopped RA_LOOP 2 ramp runs over and over until stopped Ramps of differing speeds lengths or cycle may be started together Switching the object and moving the object are independent actions Each object must be positioned at the beginning of the ramp and then turned on or must have its switch set to ON to be displayed If the object placed on a ramp is switched off the ramp will run but nothing will be displayed Example action E This action starts two ramps short rmp 1 2 short obi 1 2 y get_going void unsigned short index short i index 0 vexbuf index START_RAMP vexbuf index 2 number of ramps to start for i 0 i lt 2 i vexbuf index rmp i ramp number vexbuf index obil
17. A state do PvexClipRectSet amp num objArray widthArray heightArray xArray yArray to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 194 PvexClearClipRect remove the clipping rectangles from a number of objects SYNOPSIS PvexClearClipRect int nObjects int objList nObjects number of objects to clear objList array of object numbers DESCRIPTION This action clears the clipping rectangles that were set by the previous actions RETURN VALUE GLvex will return the signal BATCH_DONE 241 when it completes this action EXAMPLE int num int objArray 4 int setup int i num 4 for i 0 i lt num i objArray i i 1 return 0 A prev do setup to state state do PvexClearClipRect amp num objArray to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 195 PvexDrawWalsh draws patterns based on Walsh functions in a number of objects SYNOPSIS PvexDrawWalsh int nObjects int objList int patList int sizList int cntrstList nObjects number of objects to draw in objList array of object numbers patList array of Walsh function numbers on which to base patterns can be 0 to 255 sizList array of sizes of the pattern checks in screen pixels can be 1 to 255 cntrstList array of the contrasts of the patterns in each object can be 1 or 1 DESCRIPTION This action draws patterns based on Walsh functions in objects Walsh patterns are 16 rows by 16 columns The
18. Conversion of paradigms to REX 3 10 requires one change in the Spot file A help message string for the state_vars menu must now be defined in the spot file The help message is the information that appears on the right side of the screen when some menus are accessed If a help message for the state_vars menu is not desired it must at least be defined as a null string The following example of a state_vars declaration at the end of a Spot file also includes a definition for a help message to be printed on the right side of the screen lo pp Declaration of statelist menu extern int tstate tloop VLIST state_vi tstate amp tstate NP NP 0 ME_DEC tloop amp tloop NP NP 0 ME_DEC NS E Help message char hm_sv_vl tstate n norm no error n pri lt 6 panic halt n signal stack n sup stack n kernel stack n sys call n seg violation oOahwhd o If a help message is not desired the following definition MUST appear to avoid an error message when compiling E Null help message char hm_sv_vi The VO page in the lower level of the interrupt routine is now mapped with memory management register 6 instead of 7 All device addresses defined in the header device h have been changed to reflect this see macro d_ addr declared at beginning of device h If you have added new devices to REX redefine their addresses using this macro just as
19. EXAMPLE int num int objects 255 int fore 255 int back 255 int setup int i num 15 for i 0 i lt num i objects i i 2 fore i 255 back i 0 return 0 A prev do setup to state state do PvexSetStimLuminances amp num objects fore back to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 173 PvexSetStimColors sets the foreground and background colors of one and two tone stimuli SYNOPSIS PvexSetStimColors int nObjects int objList int fgrList int fggList fgbList int bgrList int bggList int bgbList nObjects number of objects to set objList array of object numbers to set fgrList fggList fgbList arrays of foreground red green and blue values can be 0 to 255 bgrList bggList bgbList arrays of background red green and blue values can be 0 to 255 DESCRIPTION This function allows you to specify the colors of the foreground and background checks of a number of objects RETURN VALUE Glvex will return the signal BATCH DONE 241 after completing this action EXAMPLE int num int objects 255 int foreRed 255 foreGreen 255 foreBlue 255 int backRed 255 backGreen 255 backBlue 255 int setup int i num 15 for i 0 i lt num i objects i i 2 foreRed i 255 i 15 foreGreen i 0 i 15 foreBlue i 127 backRed i 127 backGreen i 0 i 15 backBlue i 255 i 15 return 0
20. Page 150 1 For random check stimuli this key reduces the percentage of white checks by 1 For flow field stimuli this key changes the xy angle of motion by 10 degrees PAGE DOWN This key is the opposite of PAGE UP For Walsh Haar user and TIFF stimuli this key increases the stimulus number by one For bar stimuli this key changes the orientation of the bar by 10 degrees For annulus and circle stimuli this key increases the outer radius by 1 For random check stimuli this key increases the percentage of white checks by 1 For flow field stimuli this key changes the xy angle of motion by 10 degrees You can type these two keys while the flow field is running and the checks will change direction immediately If you have defined a number of user patterns or TIFF images in files with consecutive numbers p100 p101 p102 p103 1100 tif 1101 tif 1102 tif etc you can display each pattern in sequence with these keys UP ARROW Moves the active object up one video pixel DOWN ARROW Moves the active object down one video pixel LEFT ARROW Moves the active object left one video pixel RIGHT ARROW Moves the active object right one video pixel Keyboard commands terminated by a lt return gt b Set screen background color This command sets the screen background color or luminance This command is not case sensitive If you type b lt return gt you will get a help message similar to the following b r g b set Backgroun
21. wd_src_check pos wd_cntrl wd_cursor wd_disp wd_siz FILE rex act wd_set c Page 68 wd siz set eye window size SYNOPSIS wd_siz long wdnum long xsiz long ysiz wdnum window number xsiz ysiz size in tenths of degree of distance from center of window to side i e one half window size ADDITIONAL HEADERS REQUIRED None DESCRIPTION wd_siz specifies the size of a window The sizes can be different values for horizontal and vertical Size is specified as length from center of window to one side RETURN VALUE Returns 0 EXAMPLE wd_siz 0 100 200 Set window number 0 size to 20 degrees across horizontal and 40 degrees vertical SEE ALSO wd_center wd_src_check pos wd_cntrl wd_cursor wd_disp wd_pos FILE rex act wd_set c Page 69 wd_sre_pos wd_src_check specify source for window position and source for window to check SYNOPSIS wd_src_pos long wdnum long x_src long x_src_num long y_src long y_src_num wd_src_check long wdnum long x_src long x_src_num long y_src long y_src_num wdnum window number X_src x source X_src_num x source number specifier y_src y source y_src_num y source number specifier ADDITIONAL HEADERS REQUIRED None DESCRIPTION REX provides a two dimensional window capability A window is characterized by an x and y size an x and y position and an x and y source to check A set of flags is maintained in the global variable eyeflag These flags can be tested
22. End action defines what happens to the object on the ramp after the ramp stops OFF AFTER RAMP 0 object turns off after the end of the ramp ON AFTER RAMP 1 object stays on after the end of the ramp Example action I This action loads a ramp computed in Rex to GLvex struct ramp float x float y struct ramp thisRamp 300 loadRamp unsigned short index int i j steps char flbuf JOERSRERHARE NETA RARE REF REN ERE SES You would put code to load the ramp steps here NHREEEEREREEEES ES ERERERERERE RENE steps 300 index 0 vexbuf index LOAD_RAMP vexbuf index 1 number of ramps to load vexbuf index 1 this ramp number vexbuf index ON_AFTER_RAMP I object stays on after end of ramp vexbuf index hibyte steps I hi byte of number of ramp steps vexbuf index lobyte steps I lo byte of number of ramp steps for i 0 i lt steps i flbuf float2byte thisRamplTi x for j 0 j lt 4 j vexbuf index flbuf j flbuf float2byte thisRampl i y for j 0 j lt 4 j vexbuf index flbuf j other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not The hibyte and lobyte functions are defined in GLvex_com c The float2byte function is defined in GLvex_com c
23. NP eye_winds amp eyewnds_vl NP ral_maf ME_BEF ral_agf hm_eyewnds_vi eye_offsets amp eyeoffs_vl NP ral_maf ME_BEF ral_agf hm_eyeoffs_vl NS Declaration of ramp reset function void f_rampReset void int i i 0 while listO i len gt 0 listO i len 200 listO i xoff 0 listO i y off 0 i list0 0 ang 315 list0 1 ang 90 list0 2 ang 225 list0 3 ang 0 list0 4 ang 180 list0 5 ang 45 list0 6 ang 270 list0 7 ang 135 list0 8 ang 0 list0 9 ang 315 list0 10 ang 45 list0 11 ang 225 Page 30 list0 12 ang 90 list0 13 ang 180 list0 14 ang 135 list0 15 ang 270 return F Declaration of ramp length function void f_rampLength int length int i for i 0 i lt 16 i listO i len length return Declaration of ramp angle function void f_rampAngle int angle int i for i 0 i lt 16 i listO i ang angle return Declaration of ramp offset function void f_rampOffset int Xoff int Yoff int i for i 0 i lt 16 i listO i xoff Xoff listO i yoff Y off return E User supplied function table USER_FUNC ufuncs reset amp f_rampReset void length amp f_rampLength d angle amp f_rampAngle d offset amp f_rampOffset d d NS it User supplied real time varia
24. This is a non batchable command that presents one list of objects for a given number of video fields switches them off waits for a given number of video fields and then presents a second list of objects for a given number of video fields The first parameter is the number of objects in the first list Each of these objects requires one parameter the object number The next two parameters are the number of fields to present the first list and the number of fields to wait between lists The value for the number of fields to wait between lists can be 0 The next parameter is the number objects in the second list Each of these objects requires one parameter the object number The last parameter is the number of fields to present the second list Example action I This action will present object 1 for 60 fields wait 10 fields and then present objects 3 4 and 5 for 120 fields gi short fld1 60 short fld2 10 short fld3 120 short n_in_frst 1 short frst_Ist 1 y short n_in_scnd 3 short scnd_Ist 3 4 5 sequence void unsigned short index short i index 0 vexbuf index SEQUENCE_STIM vexbuf index n_in_frst number of objects in first list for i 0 i lt n_in_frst vexbuf index frst_Ist i object number vexbuf index fld1 number of fields to present first list vexbuf index fld2 number of fields in gap can be 0 vexbuf index n_in_scnd numb
25. b other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not Page 240 SET_FP_ON_CLR This is a batchable command that sets what the color or luminance of the fixation point will be when it is switch on It requires three parameters the values for the red green and blue guns These parameters can range from 0 to 255 Example action p This action will set the fixation point to a specified gray luminance int lum fpon_lum void value may be set in Rex state variables menu unsigned short index index 0 vexbuf index SET_FP_ON_CLR vexbuf index lum vexbuf index lum vexbuf index lum other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not Page 241 SET_FP_DIM_CLR This is a batchable command that sets what the color or luminance of the fixation point will be when it is dimmed It requires three parameters the values for the red green and blue guns These parameters can range from 0 to 255 Example action E This action will set the fixation point dim level to a specified color fpdim_cir long r long g long b unsigned short index index 0 vexbuf i
26. high byte of ramp speed vexbuf index lobyte speed low byte of ramp speed vexbuf index hibyte rfx 1 high byte of horiz distance from FP vexbuf index lobyte rfx 1 low byte of horiz distance from FP vexbuf index hibyte rfy F high byte of vertical distance from FP vexbuf index lobyte rfy F low byte of vertical distance from FP vexbuf index RA_CENPT reference is center of ramp vexbuf index OFF_AFTER_RAMP object turns off after end of ramp F other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not The hibyte and lobyte functions are defined in GLvex_com c Page 285 LOAD_RAMP This is a batchable command that loads a user defined ramp from Rex The command is for users who want ramps that are not linear or circular The first parameter is the number of ramps to load Each ramp requires four parameters the number of the ramp the end action high byte of the number of steps in the ramp and the low byte of the number of steps in the ramp Each step requires eight parameters the four bytes of the X coordinate of the step and the four bytes of the Y coordinate of the step The step coordinates are in Rex units Spot files that define user loaded ramps do not need to include the rex hdr ramp h header file
27. int dest 2 int rows 50 int cols 50 int size 4 int pwhite 50 int xScale 150 int yScale 100 return 0 A state do PvexDrawRandom amp num amp source amp cols amp rows amp size amp pwhite to copystate on 0 tst_rx_new copystate do PvexCopyObject amp source amp dest amp xScale amp yScale to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 212 PvexRotateObject rotates objects around the X Y or Z axes SYNOPSIS PvexRotateObject int nObjects int obList float Xlist float Ylist float Zlist nObjects number of objects to rotate objList array of object numbers to rotate Xlist array of angles of rotation about the X axis Ylist array of angles of rotation about the Y axis Zlist array of angles of rotation about the Z axis DESCRIPTION This action allows you rotate patterns made up of checks such as random patterns or walsh patterns about the three cardinal axes Note tiff images cannot be rotated because they are bitmaps not arrays of checks RETURN VALUE GLvex will return the signal BATCH _DONE 241 when it completes this action EXAMPLE int nObjects 2 int objList 1 2 float Xrot 0 0 0 0 float Yrot 0 0 0 0 float Zrot 25 0 25 0 lo state do PvexRotateObject amp nObjects objList Xrot Yrot Zrot to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 213 Actions That Control Ram
28. lt num i objArray i i 1 if i 2 swtchArray i OBJ_ON else swtchArray i OBJ_OFF return 0 A prev do setup to state state do PvexSwitchStim amp num objArray swtchArray to nextstate on 0 tst_rx_new if digital sync to nextstate on PHOTO_CELL amp drinput if video sync FILE rex act vexActions c Page 185 PvexTimeStim presents a number of objects for a fixed interval SYNOPSIS PvexTimeStim int nObjects int objList int nFields nObjects number of objects to time objList array of object numbers nFields number of video fields to display objects can be 1 to 255 DESCRIPTION This action allows you to present a number of objects for a precise interval The interval will be more precise than that you can achieve if you use Rexis clock RETURN VALUE If the digital sync is enabled GLvex will return the signal TIME ON 248 at the beginning of the first video field in which the objects are on and the signal TIME OFF 247 at the beginning of the first video field in which the objects are off If the video sync is enabled the video sync object will flash white in the first video field in which the objects are on and again in the first video field in which the objects are off EXAMPLE int num int objects 4 int fields int setup int i num 4 fields 8 for i 0 i lt num i objects i i 10 return 0 A prev do setup to state state do Pv
29. s command described below Sometimes the object will not go to the edges of the screen In this case re specify the active object using the s command The keyboard and rex protocols are described below Page 145 Communications with Rex GLvex can use either of two protocols to communicate with Rex The first method is to use a parallel I O card and the subroutines in pemsg This communication algorithm is fully handshaked and has no timing dependencies The code on either the TX_PC transmitting side or the RX_PC receiving side can be interrupted indefinitely at any point and the algorithm will still function properly when execution is resumed The algorithm would be simpler if the handshaking lines were latched However the 8255 chip on the PIO board was not designed to talk directly to another 8255 It does not permit an efficient algorithm without external glue logic to latch the handshake lines If the receiving PC encounters an error the ERROR line is set The transmitting PC then aborts the transfer and returns an error to the caller Error conditions are therefore passed from the receiving end back to the transmitting end Errors are not sent from the transmitting end to the receiving end However the transmitting end reports an error to the caller if message receiving is not enabled on the receiving end Synchronizing parallel I O communications To ensure that messages between rex and GLvex are not garbled when you are using the
30. these variables should not be written or changed only read The header rex hdr ramp h defines the ramp structure Some variables of interest ramp rnum ra_timeleft time left on ramp ramp rnum ra_rampflag state of ramp generator ramp rnum ra_x ra_pos current X position of ramp ramp rnum ra_y ra_pos current Y position of ramp The ra_compute_ time and ramptd functions can be used to vary the length of ramps in a random fashion RETURN VALUE Returns 0 EXAMPLE ra_new 0 100 90 10 0 0 0 RA BEGINPT RA_NO25MS Specifies new ramp number 0 which begins at offset 0 0 and moves vertically from bottom to top for 20 degrees There is no 25 milliseconds acceleration time SEE ALSO ira_phistart ra_phiend ra_start ra_stop ra_tostart NOTES The ramp is the only built in waveform generator in REX To drive the d a s with other types of waveforms e g sinusoids the waveform is pre computed and stored in a memory buffer This buffer can than be used to drive the d a directly by specifying the DA_MEM source see da_cntrl_1 2 FILE rex act ramp_act c Page 50 ra_compute_time Pra_compute_time Compute the time remaining before current ramp completes based on specified preset and random percentages SYNOPSIS ra_compute_time long rnum long presetper long randper Pra_compute_time long rnum long presetper long randper RA_RAMP_TIME ra_time This function computes the time remaining before the ramp completes bas
31. wd_src_pos WIND1 WD_DA r1_xda WD_DA r1_yda wd_src_check WINDO WD_SIGNAL EYEH_SIG WD_SIGNAL EYEV_SIG wd_src_check WIND1 WD_SIGNAL OEYEH_SIG WD_SIGNAL OEYEV_SIG wd_siz WINDO fxwd fywd wd_siz WIND1 foxwd foywd wd_pos WINDO O 0 wd_pos WINDY1 0 0 wd_cntrl WINDO WD_ON wd_cntrl WIND1 WD_ON rlp amp listO 0 wd_test 1 put windows in test mode ustatus REX test paradigm int clear_all_da void da_set_2 r0_xda 0 r0_yda 0 da_set_2 r1_xda 0 r1_yda 0 return 0 int marknum 1 int newmark RL_CHAN rcp if marknum gt 4 marknum 1 sd_mark marknum 1 marknum marknum return 0 int tst_user 0 int strcount 0 int newstring if tst_user return 0 if strcount 0 ustatus Change 1 strcount 1 else ustatus Back to test strcount 0 return 0 pragma off unreferenced Page 27 int do_clear_vaf int flag MENU mp char astr VLIST vip int tvadd pragma on unreferenced clear_all_da return 0 static int rl_valid 0 pragma off unreferenced int setup_single_vaf int flag MENU mp char astr VLIST vip int tvadd pragma on unreferenced if tst_single Setup single trace mode Save current rl struct rl_sav i_b gt rl rl_valid 1 i_b gt d_flags D_RL_SINGLE single_step 0 else Return to continuous mode if rl_valid i
32. 1 and earlier an action can be called with up to six arguments These arguments are long integers If the action is listed in a state the arguments must be constants In rex versions 7 2 and later an action can be called with up to ten arguments In the standard versions of the actions i e ra_ new the arguments must be long integers In the P versions of the actions i e Pra_new all arguments are pointers to variables State set description files or Spot files usually contain source for some actions that are specific to the particular paradigm Spot files also call other actions that are general in nature and common to many paradigms These commonly used actions are stored in a system library and are automatically searched whenever a new paradigm is linked The following pages document the actions that are provided in the system actions library Page 35 State Set Controls reset_s call the abort list SYNOPSIS reset_s long flag flag constant ADDITIONAL HEADERS REQUIRED None DESCRIPTION reset_s causes the abort list to be executed If flag is negative abort lists of all chains are executed If flag is zero or positive the abort list of only the current chain is executed Note do not place a state that calls this action in the abort list You will create an endless loop RETURN VALUE Returns 0 EXAMPLE reset_s 1 Abort lists of all state chains are executed FILE rex act scntrl c Page 36 set_times Pset_time
33. 1 to 99 The random number generator is given a new seed number on each call so each call will produce a different pattern of checks Example action E This action draws two different random patterns with the same resolution and percentage of white checks in two objects short horizontal 60 1 60 columns short vertical 120 120 rows 7200 checks short pwhite 20 1440 of 7200 checks to be white short ob 1 2 short size 4 pattern check size draw_random unsigned short index short i index 0 vexbuf index DRAW_RANDOM_PATTERN vexbuf index 2 number of objects for i 0 i lt 2 i vexbuf index obli object number vexbuf index horizontal horizontal resolution vexbuf index vertical vertical resolution vexbuf index size pattern check size vexbuf index pwhite percentage of white checks other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not Page 271 DRAW_ANNULUS This is a batchable command that draws an annulus in an object The first parameter is the number of objects to draw in Each object requires four parameters the object number the outer radius of the annulus the inner radius of the annulus and the contrast If the inner rad
34. 14 15 For REX a new QNX kernel build must be built specifying the flag i 5 to Proc by editing the build file in boot build This changes the assignment of the highest priority interrupt to level 5 and results in a priority order of 5 6 7 8 9 10 11 12 13 14 15 0 1 2 3 4 The idea is to make the A D interrupt the highest If your A D cannot be set to level 5 place it somewhere else Be careful to keep it s priority the highest Also note that COM4 on a Vectra cannot be used with an ATI Graphics Ultra The 8514 A part of the ATI card uses I O addresses at 2e8 Note that REX requires a dumb tty that can emulate a VT100 At NIH I connect this tty to COM3 I use COM 1 for a modem This tty can be connected to any port however If you change it from COM3 you must edit etc config sysinit 1 to make sure a login is started on the terminal Page 122 Table 2 DMA Channels 8 bit channels 16 bit channels 0 Unused 4 Unused 1 Unused 5 Adaptec 1740 2 Floppy 6 A D 3 Archive 1 4 tape 7 A d when using dual DMA Table 3 Addresses I O Port Addresses in Hex Memory Address in Hex Address What Address Size What 170 178 IDE disk a0000 affff 64k ATI video 180 19f d a board a 200 207 Archive 1 4 b0000 b7fff 32k Unused tape b8000 bffff 32k ATI text 23c 23f Mouse c0000 c7fff 32k
35. 7 Shared Data Str ctures AAA AA AA A 7 EVADIR a 7 Analog BUE A indeed aoe Ha ed a ne ae as 8 Men Sy Stem ext cites casio A Te ee eee wt 8 Data File Formats etapa traida 8 Rex Header Block oo ii edhe eke eka oe eA La ee 8 Exile Ema e See eis WS AS Ghee E 9 ARS Ford a bat ats sev cg tava ree aim rasan Garey aise 9 Data File Consistency 24 5 2 a doen 9 Data File Portability ss 2 0048 255 A ee OR te oa 9 DISCUSS ON e naa aean EA Paes Wen tnd Sah Se A a KOSS Sima SN 10 A A arity MEd Se AM Ae td ed he ated bee 2 10 SPOT State Process Translator for REX 11 TOUCH a O oe cay seas Sareea aS 11 Page i Process Controlan tosis Sue a asd ta Seed awh nla cd tte Bee at ee 11 Spot Language Specification asias ladda paa genau 11 Spot file s ctions 2 2 420 404 hie ht de Sak Adee tele ttt dee 11 Include ES Geet hy ohh Ohh LAL Ee Sh te ttle ae het 12 User defined actions 52 33 rotiers oe tena teach eye Beets odour ee eeey 12 User defined menus ii di babs 13 User defined functions ee est aie naa Peat A ea Be oat eae ees 18 Real time variables 00 0 ccc ccc nee nee eens 19 Comment 2 55 24 A cee emai eae eee eee 19 State s tideclaration oda r See phases lar 19 A RI E O a a t 20 ESCAPES a ea 21 Error Handling Abort List oooo ccocooccooccooccn ro 22 General Considerations 0 0 cece cence nee teens 22 Examples Scere Se bee he ech Bt be Ga EO ee 23 REX Actions Library 35 State Set Control
36. ATI BIOS 240 25f a d board ony pr eee c8000 cbfff 16k Unused o AAA cc000 cfff 16k SMC 8013 A PUE d0000 d3 tF 16k Adaptec 330 333 Adaptec 1740 1740 378 371 LPT1 d4000 dffff 48k Unused 311 317 Floppy 3e8 3ef COM3 318 31f COM1 Page 123 EISA Configuration for HP Vectra obvious settings not listed System board Cache memory enabled Enhanced video performance copy BIOS to RAM at E0000 AFTER init Mouse and serial port board Serial port COM3 used for VT100 Serial port and parallel port board Serial port COM1 used for modem Parallel port LPT1 i Adaptec 1740 Note you should have received a floppy from Adaptec with your 1740 It has the EISA cfg file needed for configuration Interface mode Use standard mode with interrupt level 11 T O Port 330h DMA 5 Host adapter BIOS DOOOOH Host ID 7 SCSI reset enable SCSI configuration standard mode parity on sync negation on disconnection on Vectra memory board Reserved memory 384k 0 KB remapped Analogics DAS 12 50 The Analogics board should be jumpered for address 0x240 Other jumper options are for differential inputs and full scale range The vector and DMA are set by software The DAS 12 50 has a 26 pin f3High Density f1 D connector This type of connector is somewhat unusual It is a f2high density f1 version of the regular D style and has one more pin 26 instead of 25 One can order the connector from Digikey The other opti
37. CIO DAC08 CIO DACI6 124 Industrial Computer Source PCDIO 0 0 ee 124 AA ae aaa arado 125 Digital I O Rack Panels and Circuits 0 0 eee ee eee 125 Appendix A Example Orders cota sees b a sees 133 Following are copies of the orders we used at NIH 00005 133 FOTONES A oon gee ee ate eee eee ee 135 Noise tests of Adac 5508SHR National ATMIOI6 X 4 136 Appendix B REX License Agreement 00 0002 eee eee 137 GLVEX User s Manual 139 Ovas ee 139 Whats NEW capiet benas Pee tated aa ea Pena 139 Additions oi hesitate ae back Beek Pek BRE EES HE aA Perdis 139 SUbITACHONS y Maw Meese Sens bey ee ht els Pon A 140 Statne GEV X AA A Pe A gE 141 Coordinate System Ae Aida 142 Video Fields iii A A AAA 142 Y A A A A eh teddies 142 SI A AAA AAA EA e 143 Calibration pattem acia as ns ad ours Loe IA 144 Blow fields css uigumer A soca iene elie oe alerts 144 ODE ao O Seema yee O e A oie ees 145 COMMUNICATIONS a al E EE E 145 Communications with Rex 2 0 eee o 146 Synchronizing parallel I O communications 0 00 c ee eee eee 146 Page v Ethernet communications 0 00000 ccc eect eens 147 Synchronizing ethernet communications 0 00 cee eee eee eee 148 Synchronizing stimuli 2 0 tte etn enes 148 Parallel I O Communication errors uesa 0 0 e eee eee eee 149 KEYBOARD COMMANDS israse i yea A 150 Keyboard commands not terminated by
38. FAX 508 261 1094 Table 5 Item Order Number Description Qty Price ea 1 CIO DDA06 6 channel 1 349 D A card 2 CIO DACOS 8 channel 1 549 D A card 3 CIO DAC16 16 channel 1 899 D A card NOTE Donit order all 3 Choose which one you need based on how many d ais you want Analogics may have another representative for your area Call 508 977 3000 to ask Page 133 Rep tron Inc 6925 D Oakland Mills Road Columbia MD 21045 Attn Darrell Covell 410 995 6322 FAX 410 995 6325 Table 6 Item Order Number Description Qty Price ea 1 DAS 12 50 50KHz 12 1 449 bit a d con verter 2 ACAB 22 2 meter 1 90 cable NOTE This is the 12 bit a d Order only one a d either this one or the 16 bit one National Instruments 15851 A Crabbs Branch Way Rockville MD 20855 Attn Linda Provencher 301 258 0125 Item Order Number Description QtyPrice ea Table 7 Item Order Number Description Qty Price ea 1 AT MIO16 X 16 bit A D 8 2000 converter NOTE This is the 16 bit a d Order only one a d either this one or the 12 bit one MS Electronics 8031 Cessna Ave Gaithersburg MD 20879 301 921 0200 FAX 301 921 4996 Attn John Heyden Page 134 Item Order Number Description QtyPrice ea Table 8 Item Order Number Description
39. Properties O Dialog Disabled Ramp 0 Override M Ramp Anchor oeeie O CENPT O BEGPT O ENDPT O 25MS PRE CENPT NO25MS Menu Ramp Number Length Tenths of a degree A 100 Menu Override o Menu Override 100 Menu Override O Ramp 0 O Angle Degrees Velocity Degrees second X Offset Tenths of a degree Menu Override Menu o Override 1037 Phi Device memi Y Offset Tenths of a degree Menu Override Phi Off Time msec Pah values for variables or values set by the spot file are displayed in the Actual panel to the right The override controls are displayed in the Override panels to the left To change parameters select the ramp Phi On Time msec Page 81 number from the list at the left Click the Dialog button changing the indicator from red to green and the label to i Dialog Enabled This will enable the Menu Override widgets for this ramp Enter the values you want in the appropriate numerical boxes The values will not take effect until you click on the blue Menu Override buttons to the left of the numerical boxes When set the Menu Override buttons will display a large yellow check mark If you un check a Menu Override button the override is removed but the value of the parameter will not change until your spot file changes it The other control dialogs have a similar format The Ramp Summary dialog is shown as an example of summary dialogs The other summaries have a similar format R
40. action allows you to set the red green and blue values of a number of entries in the color lookup tables of all objects Each object has a color look up table of 255 entries RETURN VALUE Glvex will return the signal BATCH DONE 241 after completing this action EXAMPLE int num int list 32 int red 32 int green 32 int blue 32 int setup int i for i 0 i lt 32 i list i i 32 red i i 8 green i i 4 blue i 127 return 0 A prev do setup to state state do PvexSetLutEntryClr amp num list red green blue to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 177 PvexSetObjectLutEntryClr sets the color of the specified entry in the specified objectis color look up table SYNOPSIS PvexSetObjectLutEntryClir int nObjects int objectList int nEntries int entryList int rList int gList int bList nObjects number of objects to set objList list of object numbers to set nEntries number of entries to set can be 1 to 255 entryList array of look up table indices to set can be 0 to 255 rList array of red values can be 0 to 255 gList array of green values can be 0 to 255 bList array of blue values can be 0 to 255 DESCRIPTION This action allows you to set the red green and blue values of a number of entries in the color lookup tables of a number of objects Each object has a color look up table of 255 entries The sizes of the entryList rL
41. along the Z axis would be equivalent to movement of 10 centimeters second To use flow field stimuli you must first define the flow field pattern After defining the pattern you may define an occluding mask if you wish The last step is to define the movement parameters of the flow field Only after fully defining the flow field may you start the flow fields Failure to follow this sequence will result in error messages or may cause the GLvex computer to crash Starting and stopping the movement of the flow fields is independent of switching the objects on or off After a flow field movement has started the object in which it is drawn may be turned off and then on again to produce a blink stimulus While the object is off the positions of the points in the flow field will be continuously update according to the transformation matrix so that when the object is Page 144 turned back on the points will be in the positions that they would have been in had they not been turned off Also an object containing a flow field pattern may be switched on and off without putting the flow field in motion allowing you use flow field patterns as static stimuli When you stop the movement of groups of flow fields you should stop all the flow fields that are running If you start flow fields moving in 4 objects and then stop the flow fields in two of the objects the checks in the stopped flow fields will jitter back and forth as long as the flow fields in the rem
42. an ecode when Rex receives the signal to allow you to align data across trials This digital form of synchronization may not be possible for some digital displays In some LCD and DLP projectors the video display is not phase locked to the vertical sync pulse Its true just don t ask me why Therefore GLvex includes a video synchronizing signal This signal is a small black square By default it is located in the upper left corner of the screen but you can place it anywhere you wish This square will flash white for one video field when synchronization is be needed You can tape a photo diode over the square and use its signal to align data Included in this documentation is a schematic for a trigger system that we use in the LSR The video sync object will be displayed only when you send commands from rex that require timing It will not be displayed for batchable commands from rex or for keyboard commands By default both digital and video sync signals are enabled but you can disable either or both by command line arguments keyboard commands or rex commands There is a practical difference between the digital and video synchronization signals Each digital synchronization signal must be acknowledged If your spot file doesn t wait for the digital sync signal using the tst_rx_new function and doesn t acknowledge the signal with the pem ack function communications between GLvex and rex will get screwed up and your paradigm will hang The video sy
43. and 4 and bits 5 6 and 7 in port B of group 0 Mex signals the 12 neurons from electrodes 4 through 7 by toggling bits 2 through 7 in port A and in port B of group 1 Each bit is set for 250 microseconds Waveform Data Mex saves waveform data to disk in a binary format The format consists of records of 512 bytes Each record consists of the following items A four byte pointer to the trigger element and a four byte pointer to the end of the data array These are of no use in the save data but Mex needs them for the online classification The third element is an unsigned long integer that contains the time that the waveform crossed the trigger If you are using Mex with Rex this time is the Rex time stamp Otherwise it is a number starting with 0 This element occupies 4 bytes Following the time are 10 short integers each occupying 2 bytes These are the electrode number the neuron number the trigger index the valley amplitude the valley time the peak amplitude the peak time the peak to peak amplitude the wave width and the number of elements in the waveform array Following the data length element is an array of 240 short integers holding the waveform itself This array occupies 480 bytes The length of the array was chosen to be long enough to hold a 4 millisecond waveform and to bring the size of the record to 512 bytes Saving data to disk is more efficient if the amount written is a multiple of 512 bytes Therefore the waveform may not
44. another process is run it will see the rootflag and try to read the non existent root giving another error message REX 3 2 Release 3 2 is the first general release of Version 3 REX It was debugged during Summer 84 running experiments conducted by Bob Wurtz and Bill Newsome on Bob s 11 34 system Page 114 Current bugs of Release 3 2 1 3 2 Afile Efile overflow when no more space remains on disk not reported with an error 2 3 2 Bug in string compare function used in distinguishing process names A process name that is a subset of another process name is compared as equal 3 3 2 The JHU Unix kernel sometimes swaps out all swappable processes and then hangs up it cannot swap anyone back in This bug appears primarily when running new REX interrupt processes or changing the current interrupt process One can verify this bug by typing control t when the keyboard stops responding All non locked processes data scribe and int are normally locked will be swapped out identified by a by the process id An interim fix has been put into comm to help mitigate the effect of this bug During some of the process control operations comm locks itself in memory to guarantee it will not be locked out on the swap device This works most of the time 4 3 2 The window on the window display will sometimes flicker briefly at its last position when being changed to a new position For example if the window is at 0 0 then is turned off a
45. any signal after this command If the video sync is enabled the rex video sync square will flash white for the first field in which the movie starts and again for the first field in which the movie stops Page 296 START_FLOW_RAMP This is a non batchable command that runs ramps and flow fields simultaneously The first parameter is the number of flow fields to run Each flow field requires one parameter the object in which the flow field was drawn After listing the flow field objects the next parameter is the number of ramps to run Each ramp requires two parameters the number of the ramp to run and the number of the object to put on the ramp This display works best if the objects on the ramps have a higher priority 1 e lower numbers than the objects containing flow fields Before using this command you must call DRAW_FLOW_PATTERN and NEW_FLOW for each of the objects that will hold flow fields and you must call NEW_RAMP for each of the ramps you use Example action This action runs a flow field and a ramp flow_ramp void unsigned short index short i index 0 vexbuf index START_FLOW_RAMP vexbuf index 2 number of flow fields to start for i 0 i lt 2 i vexbuf index i 5 flow field object numbers 5 and 6 vexbuf index 2 number of ramps to start for i 0 i lt 2 i vexbuf index i 1 run ramps 1 and 2 vexbuf index i 3 put objects 3 and 4 on t
46. array of structures of type USER_ FUNC The name of the USER_FUNC array must be ufuncs The functions themselves are ordinary C functions They should be of type int or void The functions may have up to sixteen arguments and the arguments may be of type int float or char The functions are called by entering values for their arguments in the user functions dialog that can be displayed from a pull down menu in the int process tool bar User defined functions must be defined then listed in the ufuncs array For example void f_rampReset void body of function return void f_rampOffset int Xoff int Yoff body of function return USER_FUNC ufuncs reset amp f_rampReset void offset amp f_rampOffset d d NS Y The USER_FUNC structure has the format N_name is a character string that identifies the function in the dialog This Table 3 USER_FUNC Structure string may have imbedded spaces N_ptr is the name of the function that will be called To get the function called you enter values for the arguments in the dialogis text widget then enter a carriage return Format is a character string consisting of tokens that are used to int n_ptr f rampOffset convert the text you enter in the widget to the values that are P F assed to the function The tokens are separated by a a space enone as The meaning of the tokens is the same a aC cnt pean i e d indicates conversion to an
47. below If the video sync is enabled the sync object will flash white when the ramps start when the ramps stop and at each step specified by the PvexSetTriggers action EXAMPLE int num 5 int ramps 5 objects 5 cycles 5 int setup int i for i 0 i lt num i ramps i i 1 objects i i 1 cycles i RA_ONCE return 0 A prev do setup to state state do PvexStartRamp amp num ramps objects cycles to run on 0 tst_rx_new run to stop on 0 tst_rx_new stop to nextstate FILE rex act vexActions c Page 217 PvexResetRamps resets RA_ONCE ramps to their starting positions SYNOPSIS PvexResetRamps void DESCRIPTION You may have experimental conditions in which you have some ramps running in one of the continuous modes RA_OSCIL or RA_LOOP and others running in RA_ ONCE mode You may also have experimental conditions in which you have a flow field stimulus running continuously in conjunction with a ramp running in RA ONCE mode In either of these cases you can restart the RA_ONCE ramps without affecting the continuously running ramps or the flow field by calling this action RETURN VALUE If the digital sync is enabled GLvex will return the signal FLOW _ RAMP CHANGE 234 when the ramps restart If the video sync is enabled the sync object will flash white when the ramps restart EXAMPLE A state do PvexResetRamps to nextstate on 0 tst_rx_new FILE rex act vex
48. button a brief message pops up to the right of the button Files Settings Oscilloscope Display describing what the button does Clock The left most button with the red octagon starts and stops the Mex clock When the clock is stopped the icon for this button is a red octagon When the clock is running the icon for this button is a green circle Displays The next five buttons launch Mexis displays The first display button brings up Mex s oscilloscope displays Use the oscilloscope displays to set the trigger levels and slopes for detecting neuron waveforms and to set the latency for antidromic stimulation The second display button brings up Mex s waveform displays The waveform displays show each waveform extracted from an electrode s signal and how Mex has classified it as unclassified or as belonging to neuron 1 2 or 3 If you save waveform data this display shows all of the waveforms that Mex saves to disk The third display button launches Mexis time and amplitude discrimination window This display plots each waveform extracted from an electrodeis signal and allows you to place windows that Mex can use to classify the waveform as belonging to a specific neuron Page 327 The forth display button launches Mexis parameter cluster window Mex plots the parameters of the waveforms it extracts an electrodeis signal in this window and allows you to place boxes around clusters of points to specify neurons The f
49. bytes of the vertical distance of the center of the clipping rectangle from the fixation point the hi and lo bytes of the width of the clipping rectangle and the hi and lo bytes of the height of the clipping rectangle All four of the clipping rectangle parameters are in REX units 1 e tenths of a degree You must use clipping rectangles if you want to place random patterns on ramps to display translational flow fields Example action E This action will clipping rectangles in two objects int rfx 100 X coordinate of receptive field int rfy 30 Y coordinate of receptive field int clipx 300 100 width of surround texture aperture int clipy 300 100 height of surround texture aperture int ob 1 1 set_obj void unsigned short index short i surround clipping rectangle vexbuf index CLIP_RECT_SET_FROM_FP vexbuf index 2 number of apertures for i 0 i lt 2 i vexbuf index ob i surround object number vexbuf index hibyte rfx high byte of center x vexbuf index lobyte rfx low byte of center x vexbuf index hibyte rfy high byte of center y vexbuf index lobyte rfy low byte of center y vexbuf index hibyte clipx i high byte of width vexbuf index lobyte clipx i low byte of width vexbuf index hibyte clipy i high byte of height vexbuf index lobyte
50. compare signals with the window Clicking the Off toggle will prevent Rex from comparing signals with the window To override position size or source numbers enter the values you want in the numerical fields then click the blue Menu Override buttons The Page 85 buttons will display a yellow check mark when the override is in effect If none of the Position or Check toggles are selected these parameters are controlled by your spot file To override the spot file click the appropriate button To disable the override unselect the button When you disable an override control of that parameter is returned to your spot file but the parameter itself will not change until you call the appropriate action Eye Window Parameters Dialog Enabled Window On Off Eye Window 0 Eye Win Check Rate 10msec Override Actual Position Tenths of a dgree E okii ol Height Size Tenths of a degree i om Qe o o Source Name Source Number Name Number AEA o F Ea oa dl ee E o op A a Teme sy O tiga Quico n A Eye Offset Controls When monitoring the positions of both of a subjectis eyes it is often the case that the two eyes do not seem to be looking at the same point even when the subject is fixating a small point This offset may be an artifact introduced by the eye monitoring system rather than a true reflection of the subject s direction of gaze To overcome this artifact Rex allows an offset to be applied to eit
51. controls the saving of this data on the disk with actions in the state set These actions control the opening closing and canceling of a data keeping window Scribe keeps all data collected from the time the window is opened until the window closes no matter how many times the buffer wraps around within the limits of the computer s capacity If a high water mark is hit scribe writes out a partial data record marked with a continuation flag The user also specifies the number of samples to be kept before the window is opened and the number of samples to be kept after the window is closed The user need only be concerned with opening and closing the data keeping window The Rex system performs the bookkeeping necessary to store the data on disk In addition every time an analog record is written out an event is generated that indexes the analog record see below Menu System Rex provides a menu system that allows variables to be accessed and changed at run time Variables have different types including char string octal decimal etc A function can be created to be called when a menu or menu variable is accessed This function may be called before access after access or both This function can affect how the variable is accessed For example the function might prohibit a variable from being changed if the new value is not legal or perform necessary initialization when a variable is set to a new value Data File Formats Rex data is stor
52. converter number for x position of cursor y_danum d a converter number for y position of cursor cursor d a cursor ADDITIONAL HEADERS REQUIRED None DESCRIPTION The REX window display incorporates two cursors for d a converters excessive cpu time would be required to support more than two d a cursors These cursors are represented by an octagon symbol and a cross sign symbol The da_cursor action is used to specify the d a converter numbers corresponding to each of these two cursors Arguments are x_danum d a number for x component of cursor position y_danum d a number for y component of cursor position cursor specifies one of the two available cursors CU_DA_ONE cursor shaped like an octagon CU_DA TWO cursor shaped like an X By default the CU_DA_ONE cursor is connected to d a converters 0 and 1 and the CU_DA TWO cursor is connected to d a converters 2 and 3 RETURN VALUE Returns 0 EXAMPLE da _cursor 4 5 CU_DA ONE Set the octagon cursor X position to d a number 4 and the Y position to d a number 5 SEE ALSO da cntrl_1 2 da mode da_offset da set _1 2 FILE rex act da_cursor c Page 48 Ramp Controls Rex can generate up to 10 linear arrays of values called ramps These arrays can be used to control the d a converters ra_new Pra_new specify new ramp SYNOPSIS ra_new int rnum int len int angle int vel int xoff int yoff int ecode int type Pra_new int rnum int len int angle int vel in
53. could be superimposed With Rex 7 0 and later you can have multiple copies of each display active simultaneously The only limitation is that you can have only 32 processes loaded at one time Each type of display counts as one process The Rex data displays are described in detail below Cntrl B The Cntrl B button provides the function for Rex 7 0 that entering cntrl b provided for earlier versions of Rex Clicking this button stops data collection closes the data file and kills the current running process Rex will also present a dialog asking whether you want to exit rex Data The process switching tool bar has a panel labeled Keep Data that contains two toggle buttons Events Analog and Events Only These buttons turn data saving on and off Rex saves data in two files an A file and an file The E file contains the times of event codes and neuron spike activity The A file contains analog data Most likely you will want to save both event and analog data but if you are not interested in eye movements you can conserve disk space by saving Events Only You can save data only if Rexis millisecond clock is running and you can start Rex s millisecond clock only if you have an int process running So why are the data file and data saving functions in the process switching tool bar instead of in the int process tool bar Though most people don t do it Rex can save data from multiple int processes into the same data file The purpose of
54. d a converters SYNOPSIS ma_start int num Pma_start int num num memory array number ADDITIONAL HEADERS REQUIRED None DESCRIPTION ma start initiates output of the memory array The argument specifies that array to initiate You must define and register the array before calling ma_start Also before calling ma_start you must make sure that the array resources are in their initial states by calling ma_cntrl or ma_reset Once Rex begins to play the memory array it sets the MA_RUN bit in ma num ma_ status After Rex has play the array requisite number of repeats it clears the MA_RUN bit in ma num ma_status This allows you to define escapes on the beginning and end of the memory array output RETURN VALUE returns 0 EXAMPLE ma start 0 This command starts playing memory array 0 SEE ALSO ma _cntrl ma_reset ma_stop FILE rex act ma_set c Page 60 ma_stop Pma_stop stop memory array SYNOPSIS ma_stop int num Pma_stop int num num number of memory array to stop ADDITIONAL HEADERS REQUIRED None DESCRIPTION ma_stop stops a previously started memory array The argument specifies that array to stop After Rex stops the array it clears the MA_RUN bit in ma num ma_ status This allows you to define escapes on the beginning and end of the memory array output RETURN VALUE returns 0 EXAMPLE ma_stop 0 This command stops playing memory array 0 SEE ALSO ma _cntrl ma_reset ma_start FILE rex act ma_
55. during the previous 16 milliseconds Electrode 0 is drawn at the top with each successive electrode drawn below If you are recording from more than two electrodes you will need to use the scroll bar to view all of the inputs You can also stretch the display vertically to view more inputs Stretching the display horizontally will show more detail will not display more than the previous 16 milliseconds of data If the other displays seem to have stopped responding you can use this display to get an idea of the problem Note if the user interface seems sluggish in cases where the signal does not reach threshold change the trigger slope Saving Data Interfacing with Experimental Control Mex indicates waveform classification by toggling bits in ports A and B of the parallel I O card If you record from more than 4 electrodes Mex will use the A and B ports of groups 0 and 1 If you use Mex with Rex Rex interprets the bits in these ports and automatically assigns ecodes corresponding to Page 337 the different neurons If you use Mex in stand alone mode then you must make the connections with your experiment control system manually as follows Mex signals the purple green and blue neurons from electrode 0 by toggling bits 2 3 and 4 respectively in port A of group 0 Mex signals the 3 neurons from electrode 1 by toggling bits 5 6 and 7 respectively in port A of group 0 Mex signals the 6 neurons from electrodes 2 and 3 by toggling bits 2 3
56. et Aa wets 59 ma Start Pma Start 3 sc Aco a ia Rese nce eee ee 60 mazstop Pma SOPA Hey OES 61 Running bine Controls ui A IR 62 O oe 62 A tae Lak oh oak a TRL a WAE Se Se Pel S 63 Th asetspike xe ad eo de e ns E te EE eed alee 64 sd make it data 65 saccade Detector Controls iii Ra ds 66 dd nh crn cate ss Set Mn a RA th 66 Eye Window Controls siii 67 Wd CHIT is rere tere A PA RE okay os A 67 A bets eats AAS Bla hdl Le EE E Ee alk sed 68 WO SIZ6 3 Ghee an e EG Bhatt oot G nt Bete SL ete oes 69 wd_src_ pos wd_src_check 0 0 cece ete ees 70 Obsolete ACTIONS ia ls aa Cid lle ae tat A 71 TIO eee he Bei he tala acetal ph ada oe 71 A eR ee Gee ea ee ee Se aa 71 O edad doe eda ag Hida Bae bee eee eee eee 71 WE GISPisa as ds oe she wad oan Hebron Vi 71 WO SCUISOT ies fe of ase ices A ern de ici 71 A O ace aR 71 When Things Don t Work in REX 73 When and what to recompile 0 0 0 0 0c ccc een eens 73 No return value specified from actions 0 00 e eee eee eee 173 Where is the moving display Turia 65 lastra da aad 73 Paradigm not behaving or operating properly times arguments to actions incorrect menu variables mysteriously changed nothing corresponds to initialized values 73 Roots take longer and longer to read 0 2 eee ee 73 Data Keeping WINdOWSS cP ars oras da das 73 Astate named IDE A A ARDER Se WLS 74 Menu variable names cannot have embedded spaces symptom can write a root but then notreadiit back ihr
57. for 5 video and the movie will repeat 5 times m Link two objects on mouse This command links or unlinks two objects to be moved with the mouse The purpose of this command is to allow mapping of binocular receptive fields If you type m lt return gt you will get a help message similar to the following m m s mouse acts on two objects Master amp Slave m m mouse acts on Master only default The letter m in brackets stands for the number of the master object and the letter s in brackets stands for the number of the slave object Even if you link two objects with this command the arrow keys will move only the slave object and the x command will move only the master object Changing the active object with the s command or entering a single parameter in the m command will break the master slave bond Example command m12 This command links object 2 to object 1 for action by the mouse Page 156 O Flow fields The commands beginning with O allow you to set up and run flow fields If you type O lt return gt you will get the following help message Compute Optic flow field for active object Op w h nf p s set flow field Pattern Om w h x y set flow field Mask Ot x z v r p y s c set Translation of flow field Ov o I make a flow field moVie Os o n Set the first field of a flow field movie OB 01 02 Begin flow fields in objects 01 through 02 Ob begin flow field in active object Oe end flow fields Or r o
58. fpdim vexbuf index fpdim vexbuf index SET_FP_LOCATION flbuf float2byte fpx convert a float to a string of 4 bytes for i 0 i lt 4 i vexbuf index flbuf i flbuf float2byte fpy for i 0 i lt 4 i vexbuf index flbuf i to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not The float2byte function is defined in GLvex_com c Page 265 CLIP_RECT_SET This is a batchable command sets an object s clipping rectangle The first parameter is the number of objects to set Each object requires nine parameters the object number the hi and lo bytes of the X coordinate of the center of the clipping rectangle the hi and lo bytes of the Y coordinate of the center of the clipping rectangle the hi and lo bytes of the width of the clipping rectangle and the hi and lo bytes of the height of the clipping rectangle All four of the clipping rectangle parameters are in REX units i e tenths of a degree You must use clipping rectangles if you want to place random patterns on ramps to display translational flow fields Example action r This action will set clipping rectangles in two objects int rfx 100 X coordinate of receptive field int rfy 30 Y coordinate of receptive field int clipx 300 100 width of surround texture aperture
59. indicate the number of rows and columns in the pattern The maximum number of rows or columns is 255 The pattern may be rectangular i e you do not need to have the same number of rows and columns The letters n indicate the values for the individual checks in the pattern If equals 1 the object s foreground color will be used in that check If n equals 1 the object s background color will be used in that check If n equals 0 the screen s background color will be used in that check If n equals 2 255 color lookup table entries 2 255 will be used in that check Page 161 The format of the RGB template file is rc3 rg b rgb r 9 b rgb The letters r and c indicate the number of rows and columns in the pattern and the number 3 indicates that there are 3 values for each check You must use a 3 in this location and no other number The maximum number of rows or columns is 255 The pattern may be rectangular i e you do not need to have the same number of rows and columns The letters r g b indicate the red green and blue values for the individual checks in the pattern The 7 g and b values must be separated by at least 1 space but the triplets may be separated by more than 1 space for readability Example of a file for a user defined pattern with 3 rows and 8 cols This file defines a horizontal white bar flanked by two black bars The name of the file might be P1 38 1 1 1 1 1 1 1 1 11111111 Exa
60. int running line window or raster processes The boundaries imposed by distributing Rex among multiple processes afford some protection against code becoming excessively intertwined and difficult to modify Rex is written in C a structured high level language Laboratory control is accomplished with a state based interpreter in the int process A state set description language is translated into tables which drive the interpreter Rex stores sampled analog data in rotating buffers in a common memory area shared by all processes Inter process communication messages are also passed through this area Rex produces only two types of data files One stores information characterized by epochs and contains long integer times of occurrence the other stores variable length records such as analog data or experimental parameters The epoch file indexes the data file Both files contain additional information inserted by scribe that can be used to verify their integrity or aid in their reconstruction in case of partial loss or corruption The original version of Rex ran on the pdp11 using a V6 V7 Unix kernel that was modified to support real time applications The PC version of Rex currently runs with the Photon Window Manager on the QNX operating system a POSIX compliant real time system Rex Structure Rex is designed for an environment composed of multiple laboratories each equipped with PCs These computers are devoted entirely to the on line tasks in ea
61. int clipy 300 100 height of surround texture aperture int ob 1 2 set_obj void unsigned short index short i surround clipping rectangle vexbuf index CLIP_RECT_SET vexbuf index 2 number of apertures for i 0 i lt 2 i vexbuf index 1 surround object number vexbuf index hibyte rfx high byte of center x vexbuf index lobyte rfx low byte of center x vexbuf index hibyte rfy high byte of center y vexbuf index lobyte rfy low byte of center y vexbuf index hibyte clipx i high byte of width vexbuf index lobyte clipx i low byte of width vexbuf index hibyte clipy i high byte of height vexbuf index lobyte clipy i low byte of height other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not The hibyte and lobyte functions are defined in GLvex_com c Page 266 CLIP_RECT_SET_FROM FP This is a batchable command sets an object s clipping rectangle relative to the fixation point The first parameter is the number of objects to set Each object requires nine parameters the object number the hi and lo bytes of the horizontal distance of the center of the clipping rectangle from the fixation point the hi and lo
62. integer value f indicates conversion to a floating point value etc Currently Rex supports conversion to integer floating point and character strings i e 2 d f and s You must enter one token for each argument in your function This allows Rex to do some error checking If your function doesn t take any arguments they you should set the format string to void If you want to write functions that take a variable number of arguments leave the format character string blank This will cause Rex to parse what you enter in the function s widget into two character strings The first will be all of the characters up to the first space Member name Example char n name offset Page 18 The second will be the rest of the string Rex will call your function with pointers to these two character strings In this case you must define your function to take two char arguments i e void function char str1 char str2 You will need to add code to your function to parse the two character strings to extract the arguments As with the arrays of VLIST and MENU structures the last entry in the ufuncs array must be NS Failure to end the ufuncs definition with an NS line will cause Rex to crash when it attempts to display the user functions dialog Real time variables Prior to Rex 7 0 values of variables could only be displayed by bringing up a menu or by typing a command such as type trials Once displayed
63. is anything other than DA_STBY e g when the source is the signal for eyeh da_mode 0 DA OFFSET CONN DA OFFSET STBY Set d a converter 0 to apply offset to each output value for all connected sources and also when source is DA_STBY SEE ALSO da cntrl_1 2 da_cursor da_offset da _set_1 2 FILE rex act da_mode c Page 46 da_offset Pda_offset specify offset for d a converter SYNOPSIS da_offset long danum long offset Pda_offset long danum long offset danum d a converter number offset offset value ADDITIONAL HEADERS REQUIRED None DESCRIPTION The da_ offset action specifies an offset for a d a converter This offset will not be applied however unless the d a is set to one of the offset modes see da_mode action The Pda_offset action takes pointers to values as arguments By default the offset of all d a converters is initialized to 0 unless changed by calling this action RETURN VALUE Returns 0 EXAMPLE da _offset 0 100 Set offset for d a converter number 0 to 100 Note that this offset will not be applied unless the d a converter is set to one of the offset modes see da_mode action SEE ALSO da cntrl_1 2 da_cursor da mode da set _1 2 FILE rex act da_offset c Page 47 da_cursor Pda_cursor specify d a numbers for the two d a window display cursors SYNOPSIS da_cursor long x_danum long y_danum long cursor Pda_cursor long x_danum long y_danum long cursor x_danum d a
64. k 0 k lt nCols k checks I getRand return 0 A prev do setup to state state do PvexLoadPatterns amp num objArray stimArray sizArray rows cols checks to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 210 PvexLoadPointArray loads an array of locations to place checks in an object SYNOPSYS PvexLoadPointArray int obj int nPoints int size int pointArray obj the number of the object that will draw the point array this function loads only one object nPoints the number of squares to be drawn size the size of each of the squares pointArray an array of X and Y coordinate pairs in tenths of a degree relative to the object location DESCRIPTION This action allows you to define an array of locations for an object to place checks The purpose is to add visual noise to the background of a display Depending on the algorithm you use to choose check coordinates the noise may be a regular array or a random array Further you may define the checks to lie within an irregular boundary Though the pointArray variable is a simple array the elements are assumed to be X Y coordinate pairs The even numbered elements are defined to be X coordinates the odd numbered elements are defined to be Y coordinates Thus pointArray 0 X1 pointArray 1 Y1 pointArray 2 X2 pointArray 3 Y2 etc RETURN VALUE GLvex will return the signal BATCH _DONE 241 when it completes this act
65. lower half of the third port on the digital I O card to signal Rex to send time information Rex will send time information over an ethernet connection and will strobe the time stamp using the upper half of the digital I O card If you select the Stand Alone radio button Mex will run with a four kilohertz temporal resolution with the PCI DAS4020 12 A D card It will toggle bits on the digital I O corresponding to how it classifies input waveforms The bits will remain set for 250 microseconds In stand alone mode Mex will not increment the sequence bits or look for timing information If you are going to use Rex mode and if you are going to save waveforms for later classification you need to establish a TCP IP socket with your Rex machine so that Mex can receive time information from Rex You will also need to use Rex version 7 6 or later This time information is needed to align the waveforms with the rest of the data that Rex collects From the Files menu select the Connect Rex item This will bring up a dialog in which you enter the name of your Rex computer After entering the Connect Rex i NS Write Root SS Read Root AL Spike Waveforms Close Waveform File NN Antidromic Waveforms name hit the Enter key on the keyboard or click the OK button in the dialog Mex will establish the E Rex Connection Rex Computer socket and remove the dialog Note you must enter the name of the Rex machine not the IP address To test if th
66. mode toggle The bits in the output port will remain set until you click on the Reset mode toggle Control Panel Below the menu bar in the int process tool bar is a panel containing 5 buttons Reset Clock The Clock button starts and stops Rexis millisecond clock To start or stop the clock click on the button When the clock is running the indicator is green and the button label reads i Clock Oni When the clock is stopped the indicator is red and the label reads i Clock Offi This button implements the begin clock and end clock commands Paradigm The Paradigm button sets the value of the softswitch variable When softswitch is on the indicator is green and the label reads i Paradigm Runningi When softswitch is off the indicator is red and the and the label reads i Paradigm Stoppedi This button implements the ps so command To make your paradigm use this information you need to have escapes such as ito state on PSTOP softswitchi and ito state on PSTOP amp softswitchi instead of ito state on PSTOP amp drinputi Reset States The Reset States button implements the ir si or reset states command When you click on the button the indicator turns green and a ireset statesi command is issued The indicator turns red as soon as you release the mouse button Windows The Windows button controls whether or not Rex checks analog signals against the electronic eye windows When Rex is checking signals the indicator is green and the la
67. mouse cursor over a button a brief dialog will pop up describing what the button does The scroll bars around the display allow you to set the threshold level display interval display gain and latency of antidromic stimulation The vertical white line in the display shows the time of threshold crossing To the left of the line is the half millisecond of pre threshold data The scroll bar on the left together with the slope button in the menu bar controls the threshold conditions You can set the threshold by moving the mouse cursor over the scroll bar slider pressing the left mouse button and moving the mouse up or down A yellow horizontal line will appear indicating the threshold level This line will disappear as soon as you release the left mouse button If you want to Page 329 have the threshold level line to remain on the display set the level by clicking the left mouse button in the scroll bar trough above or below the slider Pick a level and slope combination that best displays the waveform The scroll bar on the bottom controls the display interval You can set the interval by moving the mouse cursor over the scroll bar slider pressing the left mouse button and moving the mouse left or right A value will appear indicating the display interval in milliseconds This value will disappear as soon as you release the left mouse button If you want to the display interval value to remain on the display set the interval by clicking the l
68. n set Fixation diM level to n Fm r g b set Fixation diM color to r g b Fx n m move Fixation point to nX mY Fz n set Fixation point size to n pixels In the two Fc commands the letter n in brackets stands for the on luminance of the fixation point and the letters r g b in brackets stand for the on color of the fixation point Similarly in the two Fm commands the letter n in brackets stands for the dim luminance of the fixation point and the letters r g b in brackets stand for the dim color of the fixation point In both the Fc and Fm commands the values for n and for r g and b can range from 0 to 255 In the Fx command the letters n m in brackets stand for the X and Y coordinates of the fixation point location In the Fz command the letter n stands for the size of the fixation point in video pixels Example commands Fc 64 This command will make the fixation point dark gray when it is turned on Fm 12800 This command will make the fixation point turn medium red when it is dimmed Fx 200 200 This command moves the fixation point into the upper right part of the screen Fz 4 This command makes the fixation point 4 video pixels high and 4 video pixels wide f Switch fixation point set video frame rate These commands switch and dim the fixation point and tell GLvex the vertical refresh rate of your monitor If you type f lt return gt you will get the following help message fpon turn Fixation point on fpoff turn Fixat
69. objects to draw in oList array of object numbers cList array of the numbers of columns in the random patterns can be 1 to 255 rList array of the numbers of rows in the random patterns can be 1 to 255 sList array of the sizes of the individual checks in the patterns in screen pixels can be 1 to 255 pList array of the percentage of white checks in the pattern can be 1 to 99 DESCRIPTION This action draws random check patterns in objects The checks are either white or black White checks are drawn in the objectis foreground color black checks are drawn in the objectis background color The patterns may be square or rectangular To have equal numbers of white and black checks the pList parameter should be 50 If the pList parameter is less than 50 there will be fewer white than black checks If the pList parameter is more than 50 there will be more white than black checks RETURN VALUE GLvex will return the signal BATCH DONE 241 when it completes this action EXAMPLE int num int objects 4 int rows 4 int cols 4 int size 4 int pwhite 4 int setup int i num 4 for i 0 i lt num i objects i i 1 rows i 50 cols i 75 size i 4 pwhite i 50 return 0 A prev do setup to state state do PvexDrawRandom amp num objects cols rows size pwhite to nexstate on 0 tst_rx_new FILE rex act vexActions c Page 198 PvexDrawAnnulus draws circular stimuli in o
70. of flow field objects flwList array of flow field object numbers nRamps number of ramps rmpList array of ramp numbers objList array of object numbers to be carried on the ramps DESCRIPTION This action allows you to start a number of flow fields and a number of ramps simultaneously This allows you to study the effects of pursuit with a moving background You must define all of the flow fields translation matrices and ramps before calling this action RETURN VALUE If the digital sync is enabled GLvex will return the signal FLOW RAMP START 236 when the checks and ramps begin to move If the video sync is enabled the sync object will flash white when the checks and ramps begin to move EXAMPLE int nFlows 2 int flows 2 1 2 y int nRamps 2 int ramps 2 1 2 int objects 2 3 4 y o state do PvexStartFlowRamp amp nFlows flows amp nRamps ramps objects to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 228 PvexStopFlowRamp stops all ramps and flow fields SYNOPSIS PvexStopFlowRamp void DESCRIPTION This actions stops all of the flow fields and ramps that you have running RETURN VALUE If the digital sync is enabled GLvex will return the signal FLOW RAMP STOP 235 after all movement has stopped If the video sync is enabled the sync object will flash white after all movement has stopped EXAMPLE lo state do PvexStopFlowRamp nextstate on 0 tst_rx_new FILE re
71. only be 3 The maximum number of rows or columns is 255 The pattern may be rectangular i e you do not need to have the same number of rows and columns The letters r g b indicate the values for red green and blue for the individual checks in the pattern Example of a file for a user defined pattern with 8 rows and 8 cols This file defines a red and a green bar centered in a blue region The name of the file might be P1000 883 00255 00255 00255 25500 02550 00255 00255 00255 00255 00255 00255 25500 02550 00255 00255 00255 00255 00255 00255 25500 02550 00255 00255 00255 00255 00255 00255 25500 02550 00255 00255 00255 00255 00255 00255 25500 02550 00255 00255 00255 00255 00255 00255 25500 02550 00255 00255 00255 00255 00255 00255 25500 02550 00255 00255 00255 00255 00255 00255 25500 02550 00255 00255 00255 Example of a file for a user defined pattern with 8 rows and 2 cols This file also defines a red and a green bar but does not have the blue region The name of the file might be P2000 823 25500 02550 25500 02550 25500 02550 25500 02550 25500 02550 25500 02550 25500 02550 25500 02550 RETURN VALUE GLvex will return the signal BATCH_DONE 241 when it completes this action Page 206 EXAMPLE int num int objects 5 int patterns 5 int sizes 5 int contrasts 5 int setup int i num 5 for i 0 i lt num i objects i i 1 patterns i i 10 sizes i 4 contrasts i 1 return
72. or up and down When the cursor displays the left right arrows you can move the Y axis by pressing the left mouse button and dragging the mouse left or right When the cursor displays the up down arrows you can move the X axis by pressing the left button and dragging the mouse up or down To set criteria for a neuron first select a neuron by clicking with the left mouse button on one of the three neuron buttons The button will become highlighted All subsequent boxes will belong to this neuron Next click with the left mouse button on the cluster button E Finally click with the left mouse button in the display A box will be drawn at the site of the mouse cursor The color of the box will match the color of the neuron To set more boxes for this neuron just click on the box button and then in the display To set criteria for another neuron click on one of the other neuron buttons and then proceed to set boxes If you click on a neuron button that is already highlighted that neuron will be deselected and you will not be able to set boxes until you select another neuron All of the criteria for a neuron do not have to be defined in one set of axis parameters You can for example set some criteria for the purple neuron with the display plotting Peak Latency versus Peak amplitude then switch the display to plot Spike Width versus Peak to Peak amplitude and set some more criteria for the purple neuron You can move resize and delete boxes as wit
73. port all the bits in the port will be changed to match value Definitions for DIO_IDs are kept in the header rex hdr cnf h and in various local headers in rex sset This system enhances portability of Spot files among different laboratories To use a Spot file in a laboratory where devices are connected to different interfaces or bits one only has to change the DIO_ID definitions not the Spot files For further information see the header file rex hdr device h RETURN VALUE Returns 0 EXAMPLE dio_on LED1 This example turns on LED1 dio _off LEDI This example turns off LED1 dio_onoff LED2 LED 1 This example turns on LED2 and turns off LED1 SEE ALSO rex hdr device h rex hdr cnf h FILE rex act dout c rex int dio c Page 42 Digital to Analog Controls da_cntrl da_cntrl_1 da_cntrl_2 Pda_cntrl Pda_cntrl_1 Pda_cntrl_2 control d a converter SYNOPSIS da_cntri_1 long da long s long snum Pda_cntrl_1 long da long s long snum da_cntrl_2 long da0 long s0 long snumo0 long da1 long s1 long snum1 Pda_cntrl_2 long da0 long s0 long snumo long da1 long s1 long snum2 da da0 da1 d a converter number s S0 s1 source connected to d a converter output snum snum0 snum1 source number specifier Note following function cannot be called as an action da_cntrl int cnt DA_CNTRL_ARG ap not an action typedef struct int da_cntrl_num int da_cntrl_src int da_cntrl_src_num DA_CNTRL_A
74. position of window 0 is controlled by ramp generator number 0 wd_src_pos 0 WD_DA 0 WD_DA 1 The x position of window 0 is controlled by d a 0 the y position is controlled by d a 1 wd_src_pos 0 WD_JOY_X 0 WD_JOY_Y 0 The position of window number 0 is controlled by the joystick SEE ALSO wd_center wd_cntrl wd_cursor wd_disp wd_pos wd_siz FILE rex act wd_set c Page 70 Obsolete Actions Beginning with Rex 7 1 you can have multiple running line and eye window displays The properties of each display can be set independently of the others This new functionality makes several actions relating to these displays obsolete These actions are maintained in the actions library so that old spot files will compile however these actions have no effect They simply return a 0 rl trig The running line displays are now triggered by the running line level Each display can be set to run in either triggered or continuous mode The trigger level of each display can be set independently rl erase The running line displays can only be erased be iconifying the display window rl_stop Because there may be multiple running line displays they can not be stopped from the Spot file wd_disp The display options for each window display are set using toggle buttons in the bottom part of the display window wd_cursor Each window display can show all eight eye windows Each eye window is represented by a rectangle The choic
75. produce translation at 10 degrees sec 100 rex units sec upward and away from the viewer Each check will be displayed for 10 video fields and then turned off and moved to a new location All checks will move in the specified direction Ot 0 90 10 2000050 Page 158 This command will produce a counter clockwise rotation of 20 degrees sec coupled with translation away from the viewer at 10 degrees sec The checks will remain on as long as the movement continues Half of the checks will move in the specified manner and half will move in random directions In the Ov command the letters in brackets stand for the number of the object in which to make the movie and the length of the movie in frames You can get an explanation of the parameters by typing Ov lt return gt to get a help message similar to the following o object with flow movie number of frames in movie The number of frames defines the maximum length of the movie but you can show it for shorter periods if you want Before creating a movie in any object you must define a flow field pattern for that object and you must define the way in which the checks in the flow field will move You may also define an occluding mask Example commands Ov 1 300 This command will create a flow field movie in object 1 that can be run for up to 300 frames In the Os command the letters in brackets stand for the object containing the flow field movie and the starting frame of the movie Y
76. rectangle 1 degree below and to the left of the center of the screen and makes the clipping rectangle for the active object 15 degrees wide and 10 degrees tall cfull This command makes the clipping rectangle for the active object span the entire screen clear This command completely clears the screen and sets all object switches to OFF This command is useful for cleaning up garbage left by improperly sequenced switch or move commands D Debug flag This command sets the debug condition If you type D lt return gt you will get a help message similar to the following D 0 1 set Debug state to 0 NO 1 YES Example commands D1 This command will turn the rex debugging flag on When the debugging flag is on GLvex will print to the console window every command and parameter that it receives from rex and it will print each signal that it sends to rex To use this command effectively you should use the w command see below to reduce the size of the GLvex display window so you can see the console window Also if you set the console window screen buffer size to 200 to 300 lines you will be able to run your paradigm for several trials then be able to use the scroll bar on the console window to view the debugging output d Rex scaling This command sets up the rex scaling factor If you type d lt return gt you will get a help message similar to the following d d w set screen distance pattern width in millimeters The lette
77. roll pitch yaw span coher to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 226 PvexShowFlowMovie shows a number of flow field movie SYNOPSIS PvexShowFlowMovie int nObjects int startFrame int lastFrame int objList nObjects number of flow field objects startFrame number of the frame on which to start the movie lastFrame number of the last frame to display objList array of flow field object numbers DESCRIPTION This action shows flow field movies The length of the movie is lastFrame startFrame The movies in all objects must start and end on the same frame number You must call PvexDrawFlow PvexNewFlow and PvexMakeFlowMovie before calling this action RETURN VALUE If the digital sync is enabled GLvex will return the signal FLOW_RAMP_START 236 when the checks begin to move and the signal FLOW RAMP STOP 235 when the checks stop moving If the video sync is enabled the sync object will flash white when the checks begin to move and again when the checks stop moving EXAMPLE int num 4 int start 10 last 50 int objects 4 1 2 3 4 A state do PvexShowFlowMovie amp num amp start amp last objects to run on 0 tst_rx_new run to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 227 PvexStartFlowRamp starts flow fields and ramps together SYNOPSIS PvexStartFlowRamp int nFlows int flwList int nRamps int rmpList int objList nFlows number
78. sty 0 for i 0 i lt 4 i vexbuf index flbuf i vexbuf index ob2 I first object number flbuf float2byte stx 1 for i 0 i lt 4 i vexbuf index flbuf i flbuf float2byte sty 1 for i 0 i lt 4 i vexbuf index flbuf i to_vex index If the digital sync is enabled GLvex will return the signal SHIFTED 240 at the beginning of the first video field in which the objects are shifted The rex video sync square will not flash for this command The float2byte function is defined in GLvex_com c Page 261 REPORT_LOCATION This is a non batchable command that reports the screen location of a specified object This command has a single parameter the number of the object whose location is desired The purpose of this command is to allow rex to find the location of a GLvex object to use for positioning an eye movement window Example set of actions it Action that gets object location from VEX I short act 1 object_location short index index 0 vexbuf index REPORT_LOCATION vexbuf index act to_vex index return 0 JE Action that moves target window to GLvex object location targ_wnd void unsigned char msg unsigned char code msg vex_message get the last message from vex if msg I if msg is not null code vex_code msg get the return code from the message if code OBJECT_LOCATION vex_location msg
79. table to start its gray scale can be 0 to 255 lengthList number of gray levels in each objectis gray scale can be 1 to 255 DESCRIPTION This action sets up a gray scale in the objectis color lookup tables The sum of the start and length parameters cannot exceed 255 The luminance range of the gray scale is always 0 to 255 The size of the steps between luminances is determined by the length of the gray scale This command is used to initialize a gray scale for continuous tone stimuli RETURN VALUE Glvex will return the signal BATCH DONE 241 after completing this action EXAMPLE int num int objList 1 5 int startList 15 int lengthList 15 int setup int i for i 0 i lt 15 i objList i i 3 startList i 32 i 2 lengthList i 64 return 0 lo prev do setup to state state do PvexSetObjectGrayScale amp num objList startList lengthList to nextstate on 0 tst_rx_new FILES rex act vexActions c Page 176 PvexSetLutEntryClr sets the color of the specified entry in each objectis color look up table SYNOPSIS PvexSetLutEntryCir int nEntries int entryList int rList int gList int bList nEntries number of entries to set can be 1 to 255 entryList array of look up table indices to set can be 0 to 255 rList array of red values can be 0 to 255 gList array of green values can be 0 to 255 bList array of blue values can be 0 to 255 DESCRIPTION This
80. than 0 then the display will draw over several triggers before refreshing If the refresh mod is manual then the display will be refreshed when ever you press the Refresh button on the menu bar Storage mode example Lets suppose you would like to see the track of a subjectis saccade In the state in your spot file that you give the prompt to make the saccade set the running line level to a unique value say 50 Then in the state that your paradigm reaches when the subject completes the saccade change the running line level to something else say 49 In the Window Display Options dialog set the Refresh Trigger toggle to Triggered mode and set the Level to 50 Now the display will draw data only Page 94 during the saccade and without refreshing so that the display will show the entire track of the saccade If the refresh mode is Auto and the Interval is 0 then the display will be refreshed prior to each saccade If the nterval is 5 then the display will draw 5 saccades before being refreshing so you will see the tracks of 5 saccades If the refresh mode is Manual the display will keep drawing saccades one on top of the next until you click the Refresh button in the menu bar Running Line Display You launch the running line display by selecting the Running Line item from the Displays menu in the Process Switching tool bar The toggle buttons in the bottom panel control which channels are displayed The color of the toggle when set corr
81. the ID code in the spot files is to keep the data from different int processes separated in the data file Placing the data file and data saving functions in the process switching tool bar makes them independent of int processes Int Process Tool bar When you compile a spot file you create an int or interrupt process This process controls the specifics of your experiment When you select an int process to run Rex displays a tool bar to the right of the process switching tool bar The base name of the spot file used to create the int process is displayed in the tool bar window frame in this case tstramp The buttons in the menu bar allow you to Page 80 bring up dialogs that display the various system and user menus The buttons in the control panel below the menu bar implement basic experiment controls tstramp Controls States Usr Menus Eye Win Analog Sig Sac Detect Bits Reset Controls Menu Clicking on the Controls menu button will display a menu with the following items Controls Process Controls Ramp Controls Ramps Summary Dto A Controls Dto A Summary Mem Array Controls Mem Array Summary Smi Controls Selecting one of the Controls items will bring up a dialog box that has a collection of widgets that allow you to change values Selecting one of the Summary items will bring up a dialog box that displays the current values but is not editable The Ramp Controls dialog is shown below The default Ramp
82. the X coordinate of the fixation point location and the second four of which are the four bytes of the Y coordinate of the fixation point location The X and Y coordinates are in REX units 1 e tenths of a degree REX and GLvex have the same screen coordinate system i e 0 0 is the center of the screen negative X values are to the monkey s left and negative Y values are down Example action float fpx 0 0 value may be set in Rex state variables menu float fpy 0 0 value may be set in Rex state variables menu fix_pos void unsigned short index short i char flbuf index 0 vexbuf index SET_FP_LOCATION flbuf float2byte fpx convert floating point X value to chars for i 0 i lt 4 i vexbuf index flbuf i flbuf float2byte fpy convert floating point Y value to chars for i 0 i lt 4 i vexbuf index flbuf i F other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not The float2byte function is defined in GLvex_com c Page 258 STIM_LOCATION This is a batchable command that sets the position of an object on the screen The X and Y coordinates of the object locations must be floating point values The first parameter is the number of objects to locate Each object requires nine parameters The first parameter i
83. the trigger level and continue to the end of the Page 95 display and then stop To enable another sweep click on the Reset button in the menu bar When the Running Line 30 y Options Reset WM horiz eye _ vert eye _fother eye other eyeY horiz_mirm Triggering M Continuous Level vert_mirroi_ horiz_eye _ horiz_eye _ rline _Sunits Display J Repeat 0 display is in continuous mode the Repeat One Shot button has no effect Running line display options Clicking the Options button in the menu bar will display a dialog that allows you to set various parameters of the display The Gain toggle buttons set the overall vertical scale 204 8 102 4 O 51 2 O 25 6 O 12 8 O 6 4 Running Line Parameters Running Line Bar Offset High Channel 0 Restart clock to affect changes Channel List Channel 1 Channel 2 Channel 3 Channel 4 Channel 5 Channel 6 Title horiz_eye Atten a High Offset i of the display in degrees Higher numbers represent lower gain The rate slider sets the time base of the display The Running Line Bar Offset slider sets the base location of the running line trace in the display Page 96 To set the parameters of the eight analog channels select a channel from the Channel List The signal number is shown in the Sig numerical field You can set this to any of the signals you have defined T
84. the values were not updated If you had variables that tracked the subjectis performance such as percent correct or number of trials completed you had to repeatedly bring up the menu or type the command to see the new values for these variables Rex 7 0 provides a mechanism to continuously display the values of variables This mechanism is to list the variables in an array of structures of type RTVAR The name of the RTVAR array must be rtvars For example RTVAR rtvars number of trials amp nTrials trials remaining amp trialsRemaining blocks completed amp nBlocks total trials amp totalTrials number correct amp correctTrials percent correct amp percentCorrect NS Y The RTVAR structure has the following format Rt name is a character string that identifies the variable in the dialog Table 4 RTVAR Structure This name may have imbedded spaces Rt_var is the address of the variable to be displayed Real time variables Member Name Example must be of type int You can display up to 64 variables in char rt_ name number of trials the dialog Z Rex updates the display with the values of the variables int rt_var amp nTrials every second for as long as the dialog is displayed As with the arrays of VLIST MENU and USER_FUNC structures the last entry in the rtvars array must be NS Failure to end the rtvars definition with an NS line will cause Rex to cras
85. then the help message must be defined using a null string For example char hm_sv_vl MENU structure The reason that submenus are no longer needed is that you are not limited to using just the default menu You may define as many menus as you wish The menus will be displayed in a pull down list This makes accessing menus easier than using chains of submenus The list of menus to display is defined in an array of structures of type MENU and must be named umenus For example MENU umenus state_vars amp state_vl NP NP 0 NP hm_sv_vi separator NP ramp_list amp ramp_vl NP ral_maf ME_BEF ral_agf hm_ramp separator NP eye_winds amp eyewnds_vl NP ral_maf ME_BEF ral_agf hm_eyewnds eye_offsets amp eyeoffs_vl NP ral_maf ME_BEF ral_agf hm_eyeoffs NS The MENU structure has the following format Me_name is the character string that will be displayed in the pull Table 2 MENU structure down menu list This character string may not have any imbedded spaces Member Name Example Me _vlpis a pointer to the array of VLIST structures that define the variables to be accessed from this menu Me _basep is a value that may be added to the address of each VLIST me_vlp amp ramp_ vl variable in this menu s VLIST structures array Me _accf is the address of the menu access function This char me _ name ramp list unsigned NP function can b
86. timer countdown an integer random factor can also be specified Upon entering a state this long time is loaded into a counter which is then decremented each interrupt States may contain multiple escapes of mixed types Each escape is evaluated in turn at interrupt time transition occurs on the first escape found true The Rex state processor is small and designed for fast execution It uses a linked list to efficiently test escapes State actions are not performed directly but are accomplished by calls to functions The action is therefore the address of a function that is called by the state processor when the state is entered Up to ten arguments can be passed to the function The arguments can be constants of type long or pointers to global variables Many standard actions are available in a system library or users may write their own An example of a commonly used action is dio_on BIT This action sets a bit specified by the device id BIT in the digital output interface word without disturbing other bits already set N ME ME ME NE ON A provision is made to store a record of state transitions and the time of the transition on disk This is done by specifying an integer event code contained either in the state or returned by an action When a state transition occurs this code is entered into the event buffer If the action for that state returns an event code it overrides the one stored in the state and is entered instead A state in Rex the
87. to click the Prior and Next buttons to display each page select a file name for that page then save the file The tig files can be printed on a postscript printer or can be converted to postscript by the ptig program Page 102 REX Version Release Notes Arthur V Hays and John W McClurkin REX 7 6 1 Nov 2002 This release includes support for the new QNX Momentics version of the Mex the LSRis multiunit spike sorting program This support includes reading spike occurrence from Mex and sending Mex time stamps REX 7 5 1 Sep 2002 This release allows users to control the GLvex stimulus display program through the Rex eye window display process The eye window display has a new dialog that allows users to input the name of the machine running GLvex so that a socket can be established While the mouse cursor is in the Rex eye window users can enter GLvex keyboard commands and can use the mouse to control the position of GLvex stimuli A new version of GLvex 7 0 was written to accept mouse and keyboard commands from the Rex eye window process REX 7 4 29 Mar 2002 This release allows users to define computed analog signals These signals are vergence conjugate eye movements and gaze The signals are computed as the source signals are acquired and can be saved to disk along with other analog signals This makes it possible to govern subject behavior with these computed signals as well as with acquired analog signals REX 7 3 20 Au
88. to go through grdd brdd or trdd fix them by running the file rex4_3patcher on irisf If you just type rex4_3patcher it will give a usage message of course Report problems to me Lance 11 24 1 4 2 FIX A bug was found in the PC to PC messaging code that resulted in receive checksum errors being reported on Type 1 messages when both Type 1 and Type 2 messages were being used To fix this bug add a single line of code to rex int pcmsg c pe Compare checksums switch p gt pcm_msg_type case PCM_TYPEO rxerr pcm_msg_process TYPEO has cksum goto rx_reset case PCM_TYPE1 Page 105 ifdef PCM_DEBUG puts rx_type1_ck endif p gt pcm_rx_calcksum amp Oxff p gt pcm_rx_cksum amp Oxff ADD THIS LINE HERE F fall through case PCM_TYPE2 2 4 3 FIX The code that saves the contents of the digital input word is currently after the code that looks to check for units This means that the times for units are offset by msec To fix this problem look in int int c and make sure that the section titled Digital input processing is just before instead of after the section titled Collect units data If this is not the case edit int c and move it Thanks to Barry Richmond for finding this 3 4 3 F IX A problem has existed with the variable ras_wakeup_ecode in the dsplay menu When a root was read back in this variable would often be set to 0 The fix for this is to add a single line of code t
89. value Note the pointer version of this function can be called as an action Pda_set int cnt DA_SET_ARG ap ADDITIONAL HEADERS REQUIRED None DESCRIPTION The da_set_1 and da_set_2 actions cause the specified value to be output to the d a converter da_set_1 can be called to output to a single converter da_set_2 can be called to output two values to two different converters In the case of the da_set_2 action both converters will be updated as close together in time as possible with no interrupts permitted between the first and second converter The function da_set can be used to update more than two d a converters The d a s will be updated as close together in time as possible with no intervening interrupts allowed da_set is not an action however and it cannot be called as an action from a state because its arguments are not of type long It must be called from subroutines in the Spot file This function takes the following arguments cnt number of DA_SET_ARG structs passed as arguments DA_SET_ARG pointer to array of structs containing d a converter number and output value Note that there would normally be no reason to use the da_set function instead of the da_set_1 and da_set_2 actions unless one wanted to update more than two d a s as simultaneously as possible The da_set_1 and da_set_2 actions are wrapper functions that repackage the arguments and call da_set RETURN VALUE Returns 0 EXAMPLE da_set_1 0 100 Output value 100
90. values in states that test the transmission lines In particular you should not write paradigms that exit from states before the communication conditions have been met This can cause problems You may find that not giving the time variable a value causes your paradigm to hang This is a bug in your spot file which you should try to fix rather than ignore Page 146 Ethernet communications The second method is to use an ethernet card and the subroutines in pcsSockets To use this method you must use the sockets version of Rex and you should have the QNX TCP IP Developer s toolkit installed on your computer Ethernet communications are more easily implemented in your spot files and have a broader bandwidth than do parallel I O communications However ethernet communications are subject to network fluctuations especially if you connect the GLvex and Rex machines using a network with a lot of other machines Depending on your situation you may be better off using a 3 or 4 port mini hub to isolate your experimental machines from the rest of the network Also ethernet communications do not guarantee millisecond precision in synchronizing communications between the GLvex and rex machines so the use of the video sync object is more important To use ethernet communications connect your GLvex and rex machines to your network then try to ping each machine from the other using their names For example From the rex machine execute ping vex_machine_n
91. yellow and blue checks etc In monochromatic stimuli the foreground and background checks can each have any of 256 shades of gray In poly chromatic stimuli the foreground and background checks can each have any of 16 777 216 colors Walsh patterns Haar patterns random check patterns circles flow fields okn gratings and annuli are all two toned stimuli User defined patterns may be two toned Examples of how to define a two toned user pattern are given below Continuous tone stimuli may have up to 256 different gray levels or any number of colors simultaneously The calibration pattern is a continuous tone pattern and users may define continuous tone patterns Examples of how to define a continuous toned user pattern are given below Calibration pattern When you first start GLvex it will display a calibration pattern on the screen This calibration pattern is 40 checks high and 40 checks wide The pattern is a hollow white square that is bisected by horizontal vertical and diagonal white bars The horizontal and vertical bars contain sets of 16 gray shades The center of the pattern has a black spot that indicates the 0 0 coordinate of the display The width of the square in video pixels is printed across the pattern This pattern can be used to determine whether your monitor has any barrel or pincushion distortion and whether the horizontal and vertical scales are the same The gray shades give you a standard that you can use to tweak the c
92. 0 A prev do setup to state state do PvexDrawRgbUserPattern amp num objects patterns sizes contrasts to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 207 PvexDrawTifflmage draws a tiff image in an object SYNOPSIS PvexDrawTifflmage int nObjects int objList int patList nObjects number of objects in which to draw images objList array of object numbers patList array of pattern numbers DESCRIPTION This action allows you to draw a TIFF image in an object The image is taken from a file named Inumber tif where number is the image number you are going to use for that image For example 1100 tif is a valid tiff image file name I chose to have file names start with I because they contain images not patterns The reason for requiring the tif extension is so that other windows programs can recognize the file as a TIFF file Though TIFF image files may contain multiple images currently GLvex will only draw the first image in the file Further GLvex does not support image compression The images in the TIFF files should be in RGBA format RETURN VALUE GLvex will return the signal BATCH_DONE 241 when it completes this action EXAMPLE int num int objects 16 int patterns 16 int setup int i num 16 for i 0 i lt 16 i objects i i 1 patterns i i 100 return 0 A prev do setup to state state do PvexDrawTiffImage amp num objects pat
93. 0 90 25 0 0 50 50 40 40 0 0 30 30 RA_CENPT E_D90 200 180 30 0 0 50 50 40 40 0 0 40 40 RA_CENPT E_D180 200 135 35 0 0 50 50 40 40 0 0 20 20 RA_CENPT E_D135 200 270 40 0 0 50 50 40 40 0 0 10 10 RA_CENPT E_D270 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 RA_LIST rlp amp list0 0 int rxwind 0 rywind 0 int roxwind 0 roywind 0 int fxwd 100 fywd 100 int foxwd 50 foywd 50 int do_two_ramps 1 int r0_xda 0 r0_yda 1 r1_xda 2 r1_yda 3 int clear_all 0 int tst_single 0 single_step 0 RL rl_sav int nTrials int trialsRemaining 16 int nBlocks 0 int correctTrials 0 int errorTrials 0 Page 24 int totalTrials 0 int percentCorrect 0 int nextramp long flag if flag rlp gt len 1 rlp amp listO 0 nBlocks nTrials 0 trialsRemaining 16 else nTrials totalTrials trialsRemaining ra_new RAMPO rlp gt len rlp gt ang rlp gt vel rlp gt xoff rlp gt yoff rlp gt ecode rlp gt type if do_two_ramps ra_new RAMP1 rlp gt len rlp gt ang 180 360 rlp gt vel rlp gt xoff rlp gt yoff rlp gt ecode rlp gt type rxwind rlp gt xwind rywind rlp gt ywind roxwind rlp gt oxwind roywind rlp gt oywind off_eye rlp gt eyehoff rlp gt eyevoff off_oeye rlp gt oeyehoff rlp gt oeyevoff rlp return rlp gt e
94. 5a hoc tet eR theese heehee an Ce 259 STIM FROM FIX POINT rod areon 260 SHIFT LOC TI ON aot dado 261 REPORT LOCATION iar ae a ia EAEE 262 SEI ACTIVE OBIECT Git an yl el Gal AA Oe 264 SET FP SZE olay eer a r O NN 265 CHIP RECT E A E 266 CLIP RECT SET FROM a 267 FUL CLIP RECTI E A pa osc tere st EE 268 DRAW WALSH PATTERN n on anaoa raroa 269 DRAW HAAR PATTERN ds dado 270 DRAW RANDOM PATTERN ss 271 DRAW ANNULUS nananana aeeoea O 272 DRAW B R Stand doa rot A A 273 DRAW FLOW PATTERN nooo 274 MASK PLOW madra AA A 275 DRAW USER PATTERN ononon 276 DRAW RGB USER PATTERN 0cceeeeeeeeeueeeeeees 278 DRAW TIFF IMAGE ds 280 Page viil DRAW ORIN PATTERN a 281 LOAD PATTERN 05 bit Bt bi tied os bail bach Ada tdi bade es 282 COPY OBJECT sin cit eae ace ha Foe ii Become A 283 NEW RAMP vico DE EA ene Ee oR Tay ke aoe 284 NEW _RAMP FROM FP 0 00 c eee eee e ee teen ete a 285 LOAD RAMPA A E O EA met cates fe 286 NN AAA arrn 287 TO RAMP START id iii ee de tie da eae 288 STAR TARAMP ee Sec hb a Sota ep a a a a yee toh Ree ee S 289 RESET RAMPS a RA A gale le We ag eRe es 290 NEW FLOW ici eee a bd tle Sao ated EEEE REO A 291 START FEO Wisin a Ue 292 TIME SEL OW raid A a a A hile aod Sel 293 MAKE FLOW _MOVIE 0 00 cece rr 294 TO FLOW MOVIE START ii A PAST Pose pode 295 SHOW FLOW MOVIE orsay iaa pe n FROON INAN AAN AEN AERA EAN 296 START FLOW RAMP oe reret eiet nan a O a cette a 297 STOP FLOW RA
95. A ES 104 REX 4 30 4 April LIA A occ Adena ee A 104 REX 4 56 24 NOV 93 das Uae eae ae ah oC ae eRe CREO eRe ERS 105 REXAZ NO Oya car eect oe elie ee ela Dae E A 106 REX 1B 1S NOV 92 25 oy ule E ERA E yawns pares 107 REXA LO ta o a a 107 REX AO Step A E NO 107 Current DUES Aso sados orita td 109 REX SALIA A a te a 109 REX PO Us S Taone A E 109 The following enhancements were made to REX 3 o ooooooooooooo o 111 REX 3 527 May 80ra IS A len 112 REX 34 30 NOV 84 a BEG aE Rae R eld Bae WA 112 REX 3330 Oti GA es naa o e a a R EEE EE nea aa na nn EEA 112 Bugs fixed in this version 0 eect eee eet as 113 Bugs reported in this version 0 2 0 0 cece eee cece eee eens 114 Page iv Current bugs of Release Ti A Sees 115 REX Internal Calibrations 117 REX Internal Calibrations 0 ccc ec cee eee eee ene 117 A D Full Scale Range Calibrations 6 0 00 0 e secu eee eees 118 Configuring PC Systems for Running REX 119 REX Software Configuration 0 000s 119 REX Hardware Configuration 00 cece eee ene 119 PC aay A A Es a aaa 119 Real time Interface Cards 2 0 0 eee ec eet ee eens 120 D A Cards a led 120 Digital TO ita ia ea aden aaa Stand hs 121 Counter Timer Cada 121 Device Addresses Vectors Jumpers o oooooooooomommoo o 121 EISA Configuration for HP Vectra obvious settings not listed 124 Analogics DAS 12 50s cota ad 124 Computer Boards CIO DDA06
96. A_TIMEDONE 8 ramp RAMPO ra_rampflag fpoff code FPOFFCD do dio_ off LED1 rl 35 to stoff stoff code STOFFCD do dio_off BACKLT to closew closew do awind CLOSE_W to wdback wdback do set_wsiz 0 I flag false for fixation sizes to rewon rewon do dio_on BEEP time 35 to rewoff rewoff do dio_off BEEP to stopramp stopramp do rampstop 1 stop ramp move to 0 0 rl 20 to correct correct do correctTrial to first error abort trial do awind CANCEL_W to reset reset code ERR1CD do reset_s 1 to wrong wrong Page 33 do errorTrial to first abort list fpoff stoff rewoff stopramp wdback closew Ti rampt_set status ON begin ramptw to timeramp on RA_TIMESTART 8 ramp RAMPO ra_rampflag timeramp The escape time for this state is computed by ramptset action each time it is called to ramptw on RA_TIMESTART amp ramp RAMPO ra_rampflag to ramptd ramptd code RTDONECD do ramptd RAMPO this action will set RA_TIMEDONE bit to ramptw Ramp timing state set Works together with ra_compute_time action r Marks test set marks_set status ON begin mfirst to msecond msecond do newmark time 3000 to mthird mthird do newstring to mfirst Page 34 REX Actions Library Actions are C callable subroutines executed by the state set processor Each state can contain one action The action is executed when the state is entered In rex versions 7
97. Actions c Page 218 Actions That Control OKN Stimuli PvexStartOkn starts a number OKN gratings drifting SYNOPSIS PvexStartOkn int nObjects int objList nObjects number of objects to start objList array of object numbers DESCRIPTION This action starts OKN gratings drifting You must have defined the OKN gratings prior to calling this action RETURN VALUE If the digital sync is enabled GLvex will return the signal FLOW RAMP START 236 when the gratings start If the video sync is enabled the sync object will flash white when the gratings start EXAMPLE int num int object direction speed width height barwidth int setup num 1 object 1 direction 180 speed 10 width 100 height 100 barwidth 10 return 0 A prev do setup to state state do PvexDrawOknGrating amp num amp object amp direction amp speed amp width amp height amp barwidth to nextstate on 0 tst_rx_new nextstate do PvexStartOkn amp num amp object to next on 0 tst_rx_new FILE rex act vexActions c Page 219 PvexStopOkn stops all OKN gratings SYNOPSIS PvexStopOkn void DESCRIPTION This action stops all OKN gratings that are drifting You must have previously defined OKN stimuli and called PvexStartOkn before calling this action RETURN VALUE If the digital sync is enabled GLvex will return the signal FLOW RAMP STOP 235 when the gratings stop If the video sync is enabled the sy
98. AllocPassiveSocket subnet port wd_disp D_W_EYE_X wd_src_pos WINDO WD_DIRPOS 0 WD_DIRPOS 0 wd_src_check WINDO WD_SIGNAL 0 WD_SIGNAL 1 wd_src_pos WIND1 WD_DIRPOS 0 WD_DIRPOS 0 wd_src_check WIND1 WD_SIGNAL 0 WD_SIGNAL 1 wd_center CU_CENTER wd_cntrl WINDO WD_ON wd_cntrl WIND1 WD_ON return 0 VLIST state_vi fixWndSiz amp wndsiz fix_x_ctr 8wndxctr fic y_ctr amp wndyctr targWndsiz amp targsiz NS char hm_sv_vl MENU umenus state_vars amp state_vl NS void f_setTargs int xpos int ypos mfTargX xpos mfTargY ypos return USER_FUNC ufuncsT setTargets amp f_setTargs d d RTVAR rtvars blocks completed amp blockcount NP NP NP NP NP trials completed amp totalTrials block trials left amp trialCounter tot correct tris amp correctTrials tot error tris amp errorTrials tot prent right amp percentCorrect NP NP NP NP NP 25 prent right amp memSacTrialList 0 percent 50 prent right amp memSacTrialList 1 percent Page 318 Sooo ME_DEC ME_DEC ME_DEC ME_DEC NP hm_sv_vl id 300 100 prent right amp memSacTrialList 2 percent 200 prent right amp memSacTrialList 3 percent 400 prent right amp memSacTrialList 4 percent 800 prent right amp memSa
99. By default Rex plots both spike rasters and spike density functions in each plot To disable either type of plot deselect the Raster or Density toggle button You can display up to 10 units per plot Rex draws each unit in a different color List the units you want to display in the Units text field After each unitis number enter a lt return gt You can display the time of occurrence of one other ecode in each plot For example a plot might contain data aligned on the time of occurrence of a saccade target You can display the time of occurrence of the saccade by having your paradigm drop and ecode when the saccade Page 100 starts and entering that ecode in the Mark Ecode numerical field Enter the symbol you want Rex to use Y Dx New Page Label Rows 1 Font Duplex v Complex v Compiex iaie Size 15 Columns 1 Left 0 10 Bottom 0 90 Class Units Mark Start 250 msec from alignment code set 1 o a Display tor 500 l msec xi a Ecode 0 vi Mark Max Rate 500 sp sec A a Symbol Sigma 3 00 vi m Tic Interval 100 msec W Raster Mark F Y Axis T Alignment Line Size JT Density 10 aj Number Axes Int v Float A aj Font Dup v Comp v Comp Size 5 y Plot Label defaut X Label as Font Dup v Comp v Comp Size 10 Y Label yo yo Left 0 10 Bottom 0 90 Font Dup v Comp v Comp Size 10 gt z3 in plotting this ecode in the Mark Symbol field The defaul
100. CH_DONE 241 when it completes this action EXAMPLE int num int objects 5 int patterns 5 int sizes 5 int contrasts 5 int setup int i num 5 for i 0 i lt num i objects i i 1 patterns i i 10 sizes i 4 contrasts i 1 return 0 A prev do setup to state state do PvexDrawUserPattern amp num objects patterns sizes contrasts to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 205 PvexDrawRgbUserPattern draws an rgb pattern defined in useris template file SYNOPSIS PvexDrawRgbUserPattern int nObjects int objList int pList int sList int cList nObjects number of objects in which to draw objList array of object numbers pList array of pattern numbers sList array of pattern check sizes in screen pixels cList array of contrasts for the patterns can be 1 or 1 DESCRIPTION This action allows you to define an RGB pattern in a template file The name of the template file must be Pnumber where number is the number of the pattern For example the file P10 holds the template for pattern number 10 The format of the template file is rc3 rgbrgbrgb rgb rgb rgb rgbrgbrgb rgb rgb rgb rgbrgbrgb rgb rgb rgb rgbrgbrgb rgb rgb rgb rgbrgbrgb rgb rgb rgb rgbrgbrgb rgb rgb rgb The letters r and c indicate the number of rows and columns in the pattern The number 3 indicates that each pixel is defined by 3 values r g and b This number can
101. Doff Switch digital sync off Object number 1 is now active The letter n in brackets stands for the object to be made active It must be a valid object number Example command s2 This command makes object 2 active and breaks any master slave linkages created with the m command t Timing commands These commands affect the timing of the stimuli If you type t lt return gt you will get the following help message t n turn active object on for n fields t 01 mn 02 p object 1 for m fields n gap object 2 for p fields Example command t45 This command will display the active object for 45 video fields t 130 30 2 30 This command will display object 1 for 30 fields wait 30 fields then display object 2 for 30 fields W Video sync size By default the size of the video sync object is 64 pixels wide and 64 pixels high However for low resolution screens such as 640 X 480 this may be too large This command sets the size of the video sync object If you type W lt return gt you will get the following help message Ws w h set video sync size to width w height h The letter w in brackets stands for the width of the video sync square in pixels The letter h in brackets stands for the height of the video sync square in pixels Example command Ws 32 32 This command will set the size of the video sync square to 32 pixels wide and 32 pixels high w Set window size Normally GLvex runs in a full screen window However there are t
102. DrawBar int nObjs int oList int anglList int widList int lenList int cntrList nObjs number of objects to draw in oList array of object numbers anglList array of the orientations of the bars in degrees can be 0 to 180 widList array of the widths of the bars in 10ths of a degree lenList array of the lengths of the bars in 10ths of a degree cntrList array of the contrasts of the bars in 10ths of a degree can be 1 or 1 DESCRIPTION This action draws rectangular stimuli in objects The width and length parameters are in 10ths of a degree of visual angle If the contrast is 1 the bar will be drawn in the objectis foreground color If the contrast is 1 the bar will be drawn in the objectis background color RETURN VALUE GLvex will return the signal BATCH DONE 241 when it completes this action EXAMPLE int num int objects 8 int angles 8 int widths 8 int lengths 8 int contrasts 8 int setup int i num 8 for i 0 i lt num i objects i i 1 angles i i 22 widths i 2 lengths i 10 contrasts i 1 return 0 A prev do setup to state state do PvexDrawBar amp num objects angles widths lengths contrasts to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 200 PvexDrawFlowField sets initial check locations in flow field patterns SYNPOSIS PvexDrawFlowField int nObjects int objList int widthList int heightList int nearList i
103. EX LEBO la Files Settings EA IE Launching To start Mex type mex in a terminal window After about 10 seconds the Mex tool bar will appear in the upper left corner of the screen If you have saved a root file from a previous run you can start Mex by typing mex r rootfile Mex will start with the configuration specified in the root file Untitled HH Toolbar in one desk Operation Mode Clock Source o Internal External Clock Clock Number of Electrodes 5V 1 Electrode 5V Input Range 2 Electrodes Q 1V 1V O 4 Electrodes EHF Unit Length msec The first time you run Mex you must configure its operation Click on the Settings button in the Mex menu bar This will bring up the settings dialog box Your options are as follows Page 324 Settings Toolbar in one desk By default the Mex tool bar is placed on only one of the nine Photon desktops Clicking on this toggle button will cause the tool bar to be placed on all desktops This option is useful if you spread your displays out over several desktops Operation Mode By default Mex runs in Rex mode but it can operate a stand alone waveform classification program In Rex mode Mex will run with a one kilohertz temporal resolution It will toggle bits on the digital I O corresponding to how it classifies input waveforms and it will use two bits from each of the first two ports on the digital I O card for sequence information It will use the
104. GLvex requesting fewer objects Press any key to exit Page 305 VEX REX Parallel I O Communication Errors It is possible for the parallel I O communications between the rex and GLvex PC s to get out of sync If this happens your paradigm will hang or the stimulus display will become erratic In either event stop the rex paradigm by setting the PSTOP switch to on hit the lt return gt key on the GLvex PC to halt any messages to rex type r s on the rex PC to restart the state list and finally set the PSTOP switch to off to resume the paradigm If your paradigm still does not run check to see if the GLvex PC is hung by typing lt return gt GLvex should print a help message If not quit GLvex If GLvex is not hung kill and reload the offending rex process In the worst case you will have to quit rex and GLvex There are four general ways that rex to GLvex communications can get out of sync First if you end the rex clock to stop a paradigm or you reset the state list after rex has sent a command to GLvex but before GLvex has sent its response signal you may de synchronize the communications To avoid this ALWAYS stop paradigms using the PSTOP switch This should guarantee that all communications have been resolved At this point you can end the clock begin the clock reset the state list or open or close files Second including states that call actions which communicate with GLvex in the rex abort list Rex will attempt to execute t
105. Guide to Conducting Experiments in the LSR Rex Mex and GLvex Arthur V Hays Lance M Optican Barry J Richmond John W McClurkin Laboratory of Sensorimotor Research National Eye Institute National Institutes of Health Rex At a Glance 1 Data ACUISTA A ti la 1 Data File Ronit a ed ad e ee do 1 Laboratory Control ia E A O da 1 Displays LAS A A A a A 1 MS AS a A o de 1 PO 10 PC Communications dl ee oy ok hee a eared ee ad Ba te ee 2 Multi Unit SOferses wpe ead ew dG eee aaa Pew ba Save Rates Sas 2 Rex Structure and Operating System Environment 2 PV VANDI rd ds Sik ete e ote eet Si 2 REX A Unix Based Multiple Process System for Real Time Data Acquisition and Control 3 POUR A a ceed ee ee Se Aaa ae ake SoA 3 Rex Str ct re A ds rl aha 3 Previous Design Approach voen ei oi s E E E eect EES 3 New Approa h siene ineen Hee eA a e a ae a e e iS 4 Rex Processes anoa 6 Bde AA A aa ake Deke ares ae A A ae 4 Daiana A non Manat Hie k eae da 4 BLOC SWIC Stee Nose Roe ao tance ote eset at tase Bath Ses is or De te At 4 SAD ii Rats idee teed Oey Meet a eae el ea phere EO ees 5 NN 5 Running Line Display 0 ccc teeta 5 Window Display 20 tb 5 Raster Display ui ded Soe dd EA a 5 Laboratory COMES ad Ee Socata de Mie on eh BAM ed cado dE 6 State Concepts e nce drea e etea A 6 State Set Specification Language 00 c cece cece ence ne eees 7 Runtime Considerations 00 0 ccc cette tenes
106. Location in 10ths of a degree DESCRIPTION This action retrieves any of the signals returned by GLvex and places them in the variable code If the signal was OBJECT LOCATION 233 then this action places the X coordinate of the object in the variable x and the Y coordinate of the object in the variable y NOTE This action should only be called from a state which is entered because GLvex returned a signal RETURN VALUE returns 0 EXAMPLE int code int x y A laststate do some action that sends commands to GLvex to state on 0 tst_rx_new state do PvexMessage amp code amp x amp y to codestate on FLOW_RAMP_CHANGE code to endstate on FLOW_RAMP_STOP code to tarwnd on OBJECT_LOCATION code codestate endstate tarwnd FILE rex act vexActions c Page 192 PvexSetActiveObject sets GLvexis active object SYNOPSIS PvexSetActiveObject int object object number of the object to make active DESCRIPTION This action has the same effect as the s keyboard command RETURN VALUE Glvex will return the signal BATCH DONE 241 after completing this action EXAMPLE int active 2 A state PvexSetActiveObject amp active to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 193 Actions That Draw Stimuli PvexClipRectSet PvexClipRectFromFixPoint sets a clipping rectangle to limit the extent that an object is visible SYNOPSIS PvexClipRectSet int nObjs int oList int wList int hL
107. Lvex command line arguments r name name of the rex machine p n number of port on which to connect socket default 9999 n n n n n IP address of the ethernet card to use default NULL o n set number of objects Hz n set video vertical refresh rate v 0 1 disable enable rex video sync d 0 1 disable enable rex digital sync e 0 1 each object whole screen erase Sx n X coordinate of the video sync object Sy n Y coordinate of the video sync object Sw n width of the video sync object in pixels Sh n height of the video sync object in pixels s n distance between viewer and screen mm w n width of calibration pattern mm You must enter values for both s and w to set scaling Press any key to exit Note the argument identifier Hz etc must be separated from the parameter by a space The default video refresh rate is 60 Hz By default both the video sync and digital sync are enabled have values of 1 By default the erase method is whole screen has a value of 1 By default the video sync object is located in the upper left corner of the screen and is 64 X 64 pixels in size Therefore you do not need to enter values for these arguments unless you need something different Since the distance between the viewer and the screen and the width of the calibration pattern will probably be the same for all of your experiments you can start GLvex without entering values for screen distance and pattern wi
108. MP oo A Uae ee OA 298 START OR Nooo id eee We RSD ERS TON 299 SHOW MOVE CLIP di aid te bee hued 300 STOR MOVIE o Ai Date guia teed tii 301 SET TRIGGERS siii a ace a Wadena daa 302 ERRORS AND WARNINGS 000 000s ccc eee e teen eee 303 Memory Management Errors 0 0 0 cece cee eee nee 304 Object Memory errors ci as 305 VEX REX Parallel I O Communication ErTOTS o oooooooooooooo o 306 Argument Errors ni cani 308 Memory Management Warnings 0000s eee eee cette 309 Pattern Specification WamingS 0 0 cece cee eee eee eee ee 310 Flow Field Transforms 0 0 cece cece eee eens 311 Contrast Specifications 6s c2 ceccwen lA ade 312 Color Luminance Specification Warnings 0 0 00 eee eee eee eee 313 Sample Spot File Demonstrating Socket Communication 313 MEX User s Manual 323 A E DO NO 323 THEORY Of Operation aaa ath eae wd abe Mees 323 Configuring Mek 3 2 oon oo awe AR A AAA E i 324 Selvin gs MA te oe ee hi hh ed de eto che Ral ae tae ld 325 Toolbar cic Sash bd oe a a 327 ROS ondo PA E a 328 A A ee a a E ivan eos ene a a Sear eA 329 Displaying Dita e e e bei he See a oe 329 Page ix The Oscilloscope Display 329 The Time Amplitude Display 331 The Cluster Display 333 Combining Time Amplitude and Cluster Classification 335 The Waveform Display 335 Recording From Multiple Electrodes 336 The Signals Display 336 Saving Data content pets Met epee ae Re a 337
109. ON 243 is sent when the second list of objects is turned on SECOND_ OFF 242 is sent when the second list of objects is turned off If the video sync is enabled the rex video sync square will flash white when the first list of objects is turned on at the beginning of the gap if any when the second list of objects is turned on and when the second list of objects is off EXAMPLE int i n1 frst 5 frstFids gap n2 scnd 5 scndFlds int setup n1 n2 5 frstFlds 2 scndFlds 30 gap 0 for i 0 i lt 5 i frst i i 1 scnd i i 10 return 0 A prev do setup to state state do PvexSequenceStim amp n1 frst amp frstFids amp gap amp n2 scnd amp scndFlds to first on 0 tst_rx_new if digital sync is enabled to first on PHOTO_CELL amp drinput if video sync is enabled first to second on 0 tst_rx_new if digital sync is enabled to second on PHOTO_CELL amp drinput if video sync is enabled second to nextstate FILE rex act vexActions c Page 187 Actions That Position Stimuli PvexSetFixLocation sets the location of the fixation point object SYNOPSIS PvexSetFixLocation float x float y x the x coordinate of the fixation point in 10ths of a degree y the y coordinate of the fixation point in 10ths of a degree DESCRIPTION This action sets the location of the fixation point object RETURN VALUE Glvex will return the signal BATCH DONE 241 after com
110. Qty 1 Grayhill 7ORCK24 HL 24 Module I O rack 2 2 Grayhill 70 ODCS5 DC output module 30 3 Grayhill 70 IDC5 DC input module 8 4 Grayhill 70 0AC5 AC output module 4 5 Grayhill 70 0AC5A5 AC output module NC 2 6 Grayhill 70 IAC5 AC input module 2 7 Grayhill 70 ODC5A DC output module 200V 2 8 Opto 22 ODCS5R Dry contact output module normally open 8 9 Opto 22 Input Switch Standard size input test switch 2 10 Opto 22 Output Switch Standard size output test switch 2 11 Gordos ODC5ML FET DC output module 2 12 Bud PA 1106 MG 10 5 Rack panel metallic grey 2 13 Panduit E1x2LG6 Wiring duct 6 length 1 14 Panduit WR2 C20 Wire Retainer 100 pckg 1 15 Beau 71114 7233 14 50 Terminal block 10 16 Beau 77014 50 Terminal block 10 NOTE Each rack handles 24 bits output or input Adjust quantities accordingly Quantities below are good estimate for one lab For digital inputs that are logic levels you don t need a DC input module The 1 O rack must be mounted on the Bud panel so it can be screwed into a 19 rack cabinet You will need 50 pin flat cables to connect the rack to the card in the pc For QNX NOTE As of Oct 92 QNX Software has a promotion for University users You can buy QNX for an enormous savings Contact QNX Software DIRECTLY at 613 591 0931 Florida Datamation 4720 NW Boca Roton Blvd Suite 101 D Boca Roton FL 33431 800 642 5938 Attn David Schimmel Page 135 Order the latest release of QNX Watc
111. REEN method is more robust The default method is EACH OBJECT Once the erase method is set it will remain in effect until changed so you only need to call this command once This variable can be set using the e command line argument to GLvex The WHOLE SCREEN and EACH OBJECT constants are defined in GLcommand h RETURN VALUE Glvex will return the signal BATCH DONE 241 after completing this action EXAMPLE int method WHOLE_SCREEN A state do PvexEraseMethod amp method to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 167 PvexVideoSync switch the video sync signal SYNOPSIS PvexVideoSync int sync sync switch determining whether GLvex will use a video syncing signal can be 0 or 1 DESCRIPTION PvexVideoSync allows you to turn on or off GLvexis video syncing object When the video sync is enabled GLvex will draw a small black square in the upper left corner of the screen This square will flash white for 1 video field when synchronization is needed The video sync is enabled by default Once the video sync is enabled it will remain enabled until disabled so you only need to call this action once This variable can be set using the v command line argument to GLvex RETURN VALUE Glvex will return the signal BATCH DONE 241 after completing this action EXAMPLE int sync 1 A state do PvexVideoSync amp sync to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 168 PvexDigital
112. RG da_cntrl_num d a converter number da_cntrl_src source connected to d a converter output da_src_num source number specifier Note the pointer version of this function can be called as an action Pda_cntrl int cnt DA_CNTRL_ARG ap ADDITIONAL HEADERS REQUIRED None DESCRIPTION The da cntrl_1 Pda cntrl_1 da cntrl 2 and Pda cntrl_2 actions control the operation of the d a converter da_cntrl_1 and Pda_cntrl_1 can be called to control a single converter da cntrl_2 and Pda_cntrl_2 can be called to control two different converters In the case of the da cntrl_2 and Pda_cntrl_2 actions the operation of both converters will be changed as close together in time as possible with no interrupts permitted between the first and second converter The da _cntrl_1 da_cntrl_2 actions take the following arguments danum d a converter number src source to which the d a converter is connected This source supplies the output of the d a The source can be any of the following DA_STBY d a is in standby mode and is not connected to a source When in this mode the output of the d a can still be changed however by calling the da_set_1 da_set_2 actions DA_RAMP_X source is the X component of the internal ramp generator src_num specifies the ramp generator number DA_RAMP_ Y source is the Y component of the internal ramp generator src_num specifies the ramp generator number DA_JOY_X source is the X component of the joystick
113. Spot Language Specification Spot file sections The Spot translator takes as input a specification file termed a spot file with suffix d Each Spot specification file is divided into two sections separated by the delimiter 25 The first section is Page 11 composed of include files actions and other pre initialized subroutines user defined menus user defined functions and user defined real time variables Actions may also be placed in user libraries however placing actions specific to individual paradigms in the paradigm s Spot file is usually much more convenient Between the first and second sections a delimiter is placed The second section contains the Spot state set specification for the paradigm The state set chains of the paradigm are declared here The Spot translator produces a C source file with the suffix d c appended to the Spot file name Include files The following headers are included automatically in the C source produced by Spot include lt stdio h gt include lt sys types h gt include hdr sys h include hdr cnf h include hdr proc h include hdr buf h include hdr menu h include hdr state h include hdr ecode h include hdr device h include hdr cdsp h include hdr idsp h include hdr int h Since these headers are automatically added by Spot they should not be included again in the d Spot file User defined actions Rex include
114. Sync switch the digital sync signal SYNOPSIS PvexDigitalSync int sync sync switch determining whether GLvex will use a digital syncing signal can be 0 or 1 DESCRIPTION PvexDigitalSync allows you to turn on or off GLvexis digital syncing signal When the digital sync is enabled GLvex will return a signal via ethernet or pcmsg at the beginning of the first video field where synchronization is needed The digital sync is enabled by default Once the digital sync is enabled it will remain enabled until disabled so you only need to call this action once This variable can be set using the d command line argument to GLvex RETURN VALUE Glvex will return the signal BATCH DONE 241 after completing this action EXAMPLE int sync 1 A state do PvexDigitalSync amp sync to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 169 PvexSetRexScale set the scale factors to allow tangent correction in the placement of objects on the screen SYNOPSIS PvexSetRexScale int distance int width distance distance from the subject to the screen in millimeters width width of the initial calibration pattern in millimeters DESCRIPTION PvexSetRexScale allows you to set the parameters necessary for GLvex to compute locations on the viewing screen in degrees of visual angle Once the scale is set it will remain in effect until reset so you only need to call this action once The distance variable can be set using the s comma
115. TION This action allows you to define a pattern in a template file The name of the template file must be Pnumber where number is the number of the pattern For example the file P10 holds the template for pattern number 10 The format of the template file is rc nnn nnn nnn nnn nnn nnn nnn nnn nnn nnn nnn nnn The letters r and c indicate the number of rows and columns in the pattern The maximum number of rows or columns is 255 The pattern may be rectangular i e you do not need to have the same number of rows and columns The letter n indicate the values for the individual checks in the pattern If equals 1 the object s foreground color will be used in that check If n equals 1 the object s background color will be used in that check If n equals 0 the screen s background color will be used in that check If n equals 2 255 lookup table entries will be use in that check Example of a file for a user defined pattern with 8 rows and 8 cols This file defines a white and a black bar centered in a gray region The name of the file might be P1 88 0001 1000 0001 1000 0001 1000 0001 1000 0001 1000 0001 1000 0001 1000 0001 1000 Example of a file for a user defined pattern with 8 rows and 2 cols This file also defines a white and a black bar but does not have the gray region The name of the file might be P2 82 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Page 204 RETURN VALUE GLvex will return the signal BAT
116. TURN VALUE Glvex will return the signal BATCH DONE 241 after completing this action EXAMPLE int nObjects int objList 32 red 32 green 32 blue 32 alpha 32 int setup int i j nObjects 32 for i 0 i lt 15 i objList i i red i 255 green i 0 blue i 0 alpha i 0 for i 16 i lt nObjects i objList i i red i 0 green i 255 blue i 0 alphali 0 return 0 A prev do action to state state do PvexSetColorMask amp nObjects objList red green blue alpha to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 179 Actions That Switch Stimuli PvexAllOff switch off all objects and the fixation point SYNOPSIS PvexAllOff void DESCRIPTION This action switches all objects and the fixation point off Its purpose is to quickly and simply clear the screen RETURN VALUE If the digital sync is enabled Glvex will return the signal ABORT_TRIAL 255 at the beginning of the first clear video field In this case you should escape to the next state when the tst_rx_new function returns 0 indicating receipt of a signal from GLvex If the video sync is enabled the sync square will flash white for the first field in which all objects are off EXAMPLE A state do PvexAllOff to nextstate on 0 tst_rx_new if digital sync to nextstate on PHOTO_CELL amp drinput if video sync FILE rex vexActions c Page 180 PvexSwitchF
117. The disk can be partitioned so that DOS and QNX have separate segments One can then boot either DOS or QNX Under QNX one can read write the DOS segment Under DOS however one cannot see the QNX segment REX Hardware Configuration PC The preferred PC for REX is a 486 33 or faster machine with EISA or PCI bus The machine should have 4 or 5 available ISA slots for real time devices These slots would be allocated as follows a d card d a card digital i o card and one or two free I recommend only buying a system that is known to run QNX one can call QNX and ask whether they know if QNX runs on a machine under consideration This recommendation is due to the fact that the QNX operating system runs in protected mode It exercises the hardware more vigorously than DOS Note that devices that require DOS drivers f3will not work fl under QNX Sometimes a device will emulate another e g a SCSI controller will emulate an Adaptec when used with a supplied driver This driver however is written for DOS DOS drivers cannot be used under QNX This is a very important point to remember when considering purchasing devices to run under QNX If the device depends on any supplied software written for DOS it will not work under QNX REX will run in only 4MB but I recommend 16MB The disk should be at least 400MB This is to contain both a QNX partition and a DOS partition The disk should be a SCSI disk see below QNX supports the Adaptec controller
118. X mY location on screen Current locations object 1 x 100 y 100 object 2 x 100 y 100 The letter n in brackets stands for the horizontal position and the letter m in brackets stands for the vertical position of the object in rex units The center of the screen is location 0 0 Negative X values will place the object in the left half of the screen and negative Y values will place the object in the bottom half of the screen Example command x 50 50 This command will position the active object 5 degrees below and to the left of the screen center Z Set the size of all objects This command sets the sizes of the pattern checks in all objects If you type Z lt return gt you will get a help message similar to the following Z n set size of pattern checks in all objects to n pixels The letter n in brackets stands for the height and width of each pattern check in video pixels Example command Z4 This command will set the pattern check size of all objects to 4 video pixels by 4 video pixels Zz Set the size of active object This command sets the size of the pattern checks in the active object If you type z lt return gt you will get a help message similar to the following z n set size of pattern checks in active object to n pixels The letter n in brackets stands for the height and width of each pattern check in video pixels Example command z2 This command will set the pattern check size of the active object to 2 vid
119. _b gt rl rl_sav i_b gt d_flags amp D_RL_SINGLE return 0 y Declaration of statelist menu VLIST state_vi clear_all_da amp clear_all NP do_clear_vaf ME_AFT ME_DEC do_two_ramps amp do_two_ramps NP NP 0 ME_DEC ramp0_xda amp r0_xda NP NP 0 ME_DEC ramp0_yda amp r0_yda NP NP 0 ME_DEC ramp1_xda amp r1_xda NP NP 0 ME_DEC ramp1_yda amp r1_yda NP NP 0 ME_DEC fix_xwind amp fxwd NP NP 0 ME_DEC fix_ywind amp fywd NP NP 0 ME_DEC fix_oxwind amp foxwd NP NP 0 ME_DEC fix_oywind amp foywd NP NP 0 ME_DEC test_user_msg amp tst_user NP NP 0 ME_DEC test_single_trace amp tst_single NP setup_single_vaf ME_AFT ME_DEC NS char hm_sv_vl Page 28 do_two_ramps n 0 one ramp active n 1 two ramps active int ral_agf int call_cnt MENU mp char astr if call_cnt gt 16 Done Return null to terminate writing of root for this menu astr 0 else itoa_RL call_cnt d astr amp astr P_ISLEN return 0 int ral_maf int flag MENU mp char astr ME_RECUR rp RA_LIST rlp int rampnum if astr 10 rampnum 0 else rampnum atoi astr if rampnum lt 0 rampnum gt 16 return 1 rip amp listO rampnum mp gt me_basep unsign rlp return 0 It Declaration of ramp list menu VLIST ramp_vi length
120. _new if digital sync to nextstate on PHOTO_CELL amp drinput if video sync FILE rex act vexActions c Page 184 PvexSetStimSwitch sets the switches a number of objects to on or off SYNOPSIS PvexSwitchStim int nObjects int objList int swtchList nObjects number of objects to switch objList array of object numbers swtchList array of switch values can be OBJ_OFF or OBJ_ON DESCRIPTION This action allows you to set the switches of a number of objects to on or off You can set some of the switches on and some off simultaneously This action does not actually switch the objects The objects will be switched by the next action that changes the display The purpose of this action is to switch objects on or off while a ramp flow field or movie is running For example you would use this command if you wanted to blink a pursuit target off and on while it is moving RETURN VALUE If the digital sync is enabled GLvex will return the signal FLOW_RAMP_CHANGE 234 if you call this action while a ramp is running in the first video field in which the switch is executed If the video sync is enabled the sync object will flash white in the first video field in which the switch is executed If you call this action when no ramp flow field or movie is running GLvex will return the signal BATCH DONE 241 after completing the action EXAMPLE int num int objArray 16 int swtchArray 16 int setup int i num 16 for i 0 i
121. a lt return gt 0004 150 PAGE UP 150 PAGE DOWN 151 UP ARROW 151 DOWN ARROW 151 LEFT ARROW 151 RIGHT ARROW 151 Keyboard commands terminated by a lt return gt 20 00 0000 0008 151 b Set screen background color 151 c Absolute clipping rectangle Clear 151 D Debug flag 152 d Rex scaling 152 e Set erase method 152 F Fixation point properties 153 f Switch fixation point set video frame rate 153 H h Help message 155 k Start stop okn stimulus 155 L Look up table color 155 I Foreground and background luminance 155 M Start a movie clip 156 m Link two objects on mouse 156 0 Flow fields 157 o Foreground and background colors 159 P Copy pattern 160 p Draw pattern 160 q Quit 162 r Absolute ramps 162 S Switch all objects 163 s Switch set active object set sync 164 t Timing commands 164 W Video sync size 164 w Set window size 164 X Video Sync X and Y coordinates 165 x Absolute X and Y coordinates 165 Z Set the size of all objects 165 z Set the size of active object 165 REX ACTIONS 1 E a gd SNS 166 Actions That Duplicate Command Line Arguments 04 167 PvexEraseMethod 167 PvexVideoSync 168 PvexDigitalSync 169 PvexSetRexScale 170 Actions That Set Luminance and Color oooooooooooooorommmoo 171 PvexSetBackLum 171 PvexSetFixColors 172 PvexSetStimLuminances 173 PvexSetStimColors 174 PvexSetGr
122. accepted saccade The global variables h_sacsize and v_sacsize contain the size of the most recently accepted saccade RETURN VALUE Returns 0 EXAMPLE sd_set 1 Saccade detector is turned on FILE rex act sd_set c Page 66 Eye Window Controls wd_cntrl turn window on off SYNOPSIS wd_cntrl long wdnum long flag wdnum window number flag control flag ADDITIONAL HEADERS REQUIRED None DESCRIPTION The wd_cntrl action turns the specified eye window on off flag can be the following WD _ OFF turn window off WD_ON turn window on Turning an eye window on causes Rex to set corresponding bits in the global variable eyeflag depending on whether the eye is inside or outside the window Separate tests are made for vertical and horizontal position Tuning an eye window off prevents Rex from testing eye position against that window RETURN VALUE Returns 0 EXAMPLE wd_cntrl 0 WD_ON Turn window number 0 on SEE ALSO wd_center wd_src_check pos wd_cursor wd_disp wd_pos wd_siz FILE rex act wd_set c Page 67 wd_pos set eye window position SYNOPSIS wd_pos long wdnum long xpos long ypos wdnum window number xpos ypos x and y position of window in tenths of degree ADDITIONAL HEADERS REQUIRED None DESCRIPTION wd_pos specifies the position of the designated window RETURN VALUE Returns 0 EXAMPLE wd_pos 0 100 200 Set window number 0 to position 10 20 degrees SEE ALSO wd _center
123. ack Nelson for finding this REX 3 4 30 Nov 84 Release 3 4 contains support for the Unibus Data Translation a d converter No old bugs fixed or new ones reported REX 3 3 30 Oct 84 Release 3 3 includes changes to makefiles and bug fixes of Release 3 2 The makefiles were changed so that paradigms could be recompiled from a local subset of the int source that is likely to be different per investigator while sharing a single copy of the majority of the REX source This is useful when multiple users share a single machine and when integrating new releases REX since code that is specific per user is kept separately from the shared source Page 112 Bugs fixed in this version 1 3 2 FIX Afile Efile overflow errors now reported 2 3 2 FIX String compare function bug resolved by changing improper uses of match to stremp 6 3 2 FIX Control B problem resolved by not calling dumpe under certain conditions from dumperr in scribe dumpe was flooding screen with output because of errors due to Efile pointers not being valid since clock had never been started Now dumperr will not call dumpe unless in addition to other constraints Efile keeping is also enabled Page 113 Bugs reported in this version 7 3 3 When a command is given to read a rootfile that doesn t exist an error is reported However system status is not returned to full quiescent state rootflag still shows that a rootfile is being read If at this time
124. ade active it remains active until changed All subsequent keyboard commands such as drawing switching moving or sizing will affect only that object There are two forms of keyboard commands single stroke commands which are not terminated by a lt return gt and single or multi stroke commands which are terminated with a lt return gt Keyboard commands not terminated by a lt return gt These keys may be tapped once for a single execution of the command or they may be pressed and held for repeated execution of the command Vex will not be able to keep up with repeat execution so the action will continue for a while after you have released the key Also you will get input buffer overflow errors if you hold the key down too long PAGE UP For Walsh Haar user and TIFF stimuli this key decreases the stimulus number by one For example if Walsh pattern 2 is drawn in the active object pressing the PAGE UP key will draw Walsh pattern 1 in the active object Similarly if the user pattern defined in file P102 is drawn in the active object pressing the PAGE UP key will draw the user pattern defined in file p101 in the active object If the TIFF pattern defined in file I102 tif is drawn in the active object pressing the PAGE UP key will draw the TIFF pattern defined in the file 1101 tif For bar stimuli this key changes the orientation of the bar by 10 degrees For annulus and circle stimuli this key reduces the outer radius by
125. again and send the signal FLOW_RAMP_ CHANGE at the beginning of the first video field in which the ramps start moving if the digital sync is enabled If the video sync is enabled the rex video sync square will flash white for the field in which the ramps start again You can leave the flow fields running across multiple trials while using the RESET RAMPS command to restart the ramps at the beginning of each trial In this way you can use the flow fields as an adapting stimulus Page 297 STOP_FLOW_RAMP This is a non batchable command that stops all ramps flow fields and OKN gratings It requires no parameters Example action stop unsigned short index index 0 vexbuf index STOP_FLOW_RAMP to_vex index return 0 If the digital sync is enabled GLvex will return the signal FLOW_RAMP_STOP 235 at the beginning of the first video field after the ramps stop Otherwise GLvex will not return any signal after this command If the video sync is enabled the rex video sync square will flash white for the first field after the ramps have stopped Page 298 START_OKN This is a non batchable command that starts the bars moving in square wave OKN gratings The first parameter is the number of objects to start Each object requires one parameter the object number You must define an OKN grating in an object before calling this function Example action startOkn unsigned short index int i index 0
126. aining two objects continue in motion Objects GLvex draws all stimuli in logical objects The objects may be switched on or off for static displays or they may be placed on ramps for moving displays Presenting stimuli using GLvex is somewhat like presenting pictures using an overhead projector Using an overhead can be broken into three steps you first draw a picture or write some text on a sheet of acetate you then place the acetate on the projector platen and slide it into the correct position and finally you turn the overhead projector on All three of these steps are independent That is the projector does not have to be turned on to draw a picture on a sheet of acetate or to position the acetate A GLvex object is analogous to a sheet of acetate GLvex drawing operations are analogous to drawing on the acetate GLvex positioning operations are analogous to sliding the acetate around on the projector platen and GLvex switching operations are analogous to switching the projector on or off Moving an object on a GLvex ramp is analogous to sliding the acetate around on the projector platen while the projector is on The three steps in displaying a stimulus in GLvex take different amounts of time just as they do in using overhead projectors Drawing a stimulus in an object can take a fair amount of time depending on the complexity of the stimulus several seconds for a large random check pattern Positioning an object on the screen is fairly fas
127. ame From the GLvex machine execute ping rex_machine_name Don t use the IP addresses because the ethernet communications protocol implemented in rex only uses names not IP addresses Your systems must pass this test or the ethernet communications won t work To use ethernet communications you must set the flags that will compile the sockets code Edit the rex hdr cnf h file and make sure that it contains the line define PCS_ SOCKET PC to PC messaging code with sockets The rex int directory should contain the files pesVexSocket c and pcsVexSocket o Once you have your rex and GLvex machines communicating you can turn to your spot files In each spot file you must define a restart function The beginning of the first chain of states should look something like A id 100 restart rinitf main_set status ON begin first In this example rinitf is the name of the restart function You can call it anything you want This function is called whenever you start a paradigm using the r p command reset the states using the r s menu command or return to a paradigm using the c p command Beginning with Rex 7 6 the restart function should look something like rinitf void char host Isr sgia name of the GLvex machine as defined in etc hosts pcsConnectVex host open a udp socket to the GLvex machine wd_disp D_W_EYE_X other functions in rinitf When you launch GLvex you should set the name of your rex ma
128. amp RA_LIST NP gt len NP NP ME_GB ME_DEC angle amp RA_LIST NP gt ang NP NP ME_GB ME_DEC velocity amp RA_LIST NP gt vel NP NP ME_GB ME_DEC xoff amp RA_LIST NP gt xoff NP NP ME_GB ME_DEC yoff amp RA_LIST NP gt yoff NP NP ME_GB ME_DEC type amp RA_LIST NP gt type NP NP ME_GB ME_DEC ecode amp RA_LIST NP gt ecode NP NP ME_GB ME_DEC NS y char hm_ramp_vi lig Declaration of eye windows menu VLIST eyewnds_vi xwind amp RA_LIST NP gt xwind NP NP ME_GB ME_DEC ywind amp RA_LIST NP gt ywind NP NP ME_GB ME_DEC oxwind amp RA_LIST NP gt oxwind NP NP ME_GB ME_DEC oywind amp RA_LIST NP gt oywind NP NP ME_GB ME_DEC Page 29 NS char hm_eyewnds_vi it Declaration of offsets menu VLIST eyeoffs_vi eyehoff amp RA_LIST NP gt eyehoff NP NP ME_GB ME_DEC eyevoff amp RA_LIST NP gt eyevoff NP NP ME_GB ME_DEC oeyehoff amp RA_LIST NP gt oeyehoff NP NP ME_GB ME_DEC oeyevoff amp RA_LIST NP gt oeyevoff NP NP ME_GB ME_DEC NS char hm_eyeoffs_vl E User supplied menu table MENU umenus state_vars amp state_vl NP NP 0 NP hm_sv_vi separator NP ramp_list amp ramp_vl NP ral_maf ME_BEF ral_agf hm_ramp_vl separator
129. amp Summary El E gl a Ramp Anchor Length Angle Velocity X Off Ecode Phi Dev Phi On Phi Off 0 CENPT NO25MS CENPT NO25MS CENPT NO25MS States Menu Clicking on the States menu button will display a menu with the following items Usr Menus Show All States Show Timed States Selecting either of these menu items will display a dialog that allows you to set parameters in your state set definitions The difference between the two items is that the Show All States dialog Page 82 presents all of the states in your paradigm whereas the Show Timed States dialog presents only those states which have a time or rand value State List P Ti Random Ti y pausel Running Line Value O Abs Rel pause2 go First Argument Dec Hex selramp Second Argument Dec Hex stramp openw Third Argument Dec Hex fpon eyeon stimon wdchange The states in your paradigm are listed in the State List tree The states in each chain are listed in their own branch of the tree Individual chains can be opened or closed by clicking on the or symbol to the left of the chain name To view or change the parameters of a particular state click on its name in the State List tree The top panel of the dialog contains widgets that allow you to change the preset and random times for this state and to set the running line level for this state The Abs and Rel buttons indicate whether the running line level in
130. an the times specified This is due to the way REX manipulates and stores data from the in memory circular buffers Default values are 100 msec for both pre time and post time RETURN VALUE Returns 0 EXAMPLE pre_post 100 100 Ppre_post amp preTime amp postTime Set the pre time and post time to at least 100 milliseconds Set the pre time and post time to at least the values contained in the variables preTime and postTime SEE ALSO awind uw_set FILE rex act awind c Page 40 uw_set control latched unit data storage window SYNOPSIS uw_set long ctlflag ctlflag See below ADDITIONAL HEADERS REQUIRED None DESCRIPTION uw_set controls the latched unit storage window ctlflag may be one of the following 1 open the unit window 0 close the analog window By default ctlflag is 1 This command will have no effect if LATCHED_UNITS is not defined in cnf h RETURN VALUE Returns the following event codes UWOPENCD If request is to open window UWCLOSECD If request is to close window EXAMPLE uw_set 1 This command will open the latched unit window from the current time SEE ALSO awind pre_post FILE rex act uw_set c Page 41 Digital Output Controls dio_on dio_off dio_onoff dio_out Pdio_on Pdio_off Pdio_onoff Pdio_out control digital outputs SYNOPSIS dio_on DIO_ID id dio_off DIO_ID id dio_onoff DIO_ID id_on DIO_ID id_off dio_out DIO_ID id long value DIO_ID Device id specifying devi
131. ands in the list regardless of whether digital synchronization is enabled or not Page 295 SHOW_FLOW_MOVIE This is a non batchable command that displays flow field movies The first parameter is the number of movies to show The second parameter is the starting frame of the movies The third parameter is the last frame to show Each movie requires one parameter the number of the object containing the movie Each movie must start on the same frame and end on the same frame The movies must have been defined prior to calling this function The number of frames to show can be less than the number of frames defined Example action i this action displays a single flow field movie of 60 frames beginning with frame 30 and ending with frame 90 int obi 1 int start 30 int end 90 start_movie short index index 0 vexbuf index SHOW_FLOW_MOVIE vexbuf index 1 number of flow movies vexbuf index start first frame of the movie vexbuf index end F last frame of the movie vexbuf index obi number of the object containing the movie to_vex index return 0 If the digital sync is enabled GLvex will return two signals from this command The signal MOVIE_START 239 is sent at the beginning of the video field in which the ramp starts moving and the signal MOVIE_STOP 238 is sent at the beginning of the first video field after the ramp stops moving Otherwise GLvex will not return
132. ape condition performs a bitwise and between the CONSTANT and the integer variable If the CONSTANT is preceded by a transition occurs if the result of the test is true If the CONSTANT is preceded by a transition occurs if the result of the test if false This test Page 21 then will result in a transition for the case when any of the bits set in the CONSTANT are also set in the variable For the case transition results only when all of the bits set in the CONSTANT are also not set in the variable Note that the or sign is required in this condition r Transition on Comparison Test gt lt This escape condition performs a comparison between the CONSTANT and the integer variable If the CONSTANT is greater than gt less than lt or equal to the integer variable transition occurs The sign is optional If it is not present the CONSTANT is assumed to be positive Transition on Query This escape condition first performs a comparison between the CONSTANT and the integer variable then decrements the integer variable If the integer variable is less than or equal to the CONSTANT transition occurs Transition on Return Value of Function This escape condition first calls the function whose name or address is specified by function name or address The integer return value from this function is then compared to CONSTANT If they are equal transition occurs Error Handling Abort List When an er
133. arameters of the array with int After initializing the array resources ma_cntrl calls ma_reset to set initial parameters RETURN VALUE Returns 0 EXAMPLE int array 500 int scale 800 int rate 5 int repeat 1 double ang_inc ang_inc 2 M_PI 500 for i 0 i lt 500 i array i sin i ang_inc scale ma_cntrl 0 array 500 rate repeat This example establishes an array of 500 initializes the elements of the array with a sinusoid and registers the array with int SEE ALSO ma start ma_stop ma_reset FILE rex act ma_set c Page 58 ma_reset Pma_reset reset previously registered memory array resources to their initial state SYNOPSIS ma_reset int num Pma_reset int num num number of the memory array ADDITIONAL HEADERS REQUIRED None DESCRIPTION If you wish to output a memory array on a number of trials you do not need to define and register for each trial Rather you may define and register the array once then merely call ma_reset before each trial to reset the array resources to their initial states This is particularly useful if computation of the array values is fairly time consuming RETURN VALUE None EXAMPLE ma _reset 0 This command resets the resources of a previously registered array so that it can be played out again SEE ALSO ma _cntrl ma_start ma_stop FILE rex act ma_set c Page 59 ma_start Pma_ start start outputting a memory array to the
134. are made to a paradigm BUT the root for the old version is read than any new default initializations may be lost This can easily happen for many times a paradigm is actually run by invoking a root file that in turn reads another initialization root file For example a state may be changed in the spot file so that it now calls an action where previously it did not When the old root file is read all arguments to the action will be set to zero for the state previously did not call an action This occurs because the state even though its function has been modified still has the same name states are accessed by name when roots are read Likewise defaults of menu variables may be lost if an old root is read Problems caused by reading old roots can be very subtle If mysterious problems are encountered the safest course is to manually begin the new process to ensure that no roots are read If symptoms are different when process is run a new root can be written out and compared to old root to determine differences Roots take longer and longer to read Remember that when a new root is written and a root file of the same name currently exists the new root is APPENDED to the existing root file Thus a root file may get longer and longer but still work properly for the end of the root file will have the current values Data Keeping Windows Data is saved in REX by opening and closing windows Windows have an associated pre time and post time The
135. array These variables must be globals and they must be of type int number of trials trials remaining blocks completed total trials number correct The fields in Real time Variables dialog are not editable They are for display only The dialog updates the values of the variables every second as long as the dialog is open The Time field show the number of minutes and seconds that the Rex clock has been running since the dialog was opened The Reset button will set the Time values and the values of all of the variables to 0 Eye Win Clicking on the Eye Win menu button will display a menu with the following items Analog Sig Eye Window Controls Eye Offset Controls Eye Window Summary Eye Window Controls Selecting the Eye Window Controls item from the Eye Win menu will display a dialog that allows you to change the parameters of the electronic windows that Rex uses to monitor eye position The frequency with which Rex compares a signal to the eye window is governed by the Eye Win Check Rate The fields in the Actual panel show the current state of the window To override values select the window you want to modify from the list at the left Enable the dialog for that window by clicking the Dialog button so that the indicator turns green and the text reads i Dialog Enabledi If neither the On or Off toggles in the Window panel are set then the window is under control of the spot file Clicking the On toggle will force Rex to
136. artFlow 224 PvexTimeFlow 225 PvexShiftFlow 226 PvexShowFlowMovie 227 PvexStartFlowRamp 228 PvexStopFlowRamp 229 Actions That Control Object Movies 0 00 ccc eect eee es 230 PvexShowMovieClip 230 PvexStopMovie 231 Actions That Set Arbitrary Trigger Points 0 c cece eee eee 232 PvexSetTriggers 232 REXSCOMMANDS marrara sat buenas pe ew ae as EES 233 SET ERASE METHOD E 234 Page vii ENABLE REX VIDEO SYNC veceri yie a tE eee eee 235 DISABLE REX VIDEOS YNGs 14562 alias dal ea ag 236 ENABLE REX DIGITAL SYNC 000eeeccccceneevscceeees 237 DISABLE REX VIDEO SING ira eros 238 SET REX SCALE ape o e ae ase rca 239 SENBACK UM oct a E dote 240 SET FP C1 Jak pean NO aT WU OO Tg Ot aT Ure UE 241 SET EP AAA 242 SET STIM UUMINANCES e ore aaraa 243 SET STIM COLORS te ech cere alee SS A eat ed a ls 244 SET GRAY SCALE ie a ise eel canes cilia EE tne Ss 245 SET OBJECT GRAY SCALE cg aa 246 SET LUT ENTRY CER ue aint a ag e ade Dated 247 SET OBJECT LUT ENTRY Rda 248 PM SOB ARPO A E E 249 SWITCH FIX POINT oreo sons ik oat te Sings pleat tpi 250 DIM EIX PONE nt a a a thas ay Mearns a iat 251 PRELOAD STIM onoonoae oeaan rora 252 SWAP BUFFERS pocion iar are E E E T 253 SWITCH STN A See e a cat 254 SET STM SWITCH easiest eS lew oR tn ett raran ranen 255 TUM SS CIM cts ees cae ets ag hea RN Neate a 256 SEOUE NCEE Mi rd bite Scie act alas 257 SET FPE o AAA veut e he ces ayt Pel 258 SEIM LOCATION sn 6 0
137. asts of the patterns in each object can be 1 or 1 DESCRIPTION This action draws patterns based on Haar functions in objects Haar patterns are 16 rows by 16 columns The individual checks in the patterns can be either white black or transparent depending on the Haar function number White checks are drawn in the objectis foreground color black checks are drawn in the objectis background color transparent checks are drawn in the screenis background color The size parameter sets the sizes of the individual checks That means that the smallest Haar pattern can be 16 pixels high and 16 pixel wide Specifying a contrast of 1 yields a contrast reversed version of a pattern specified with a contrast of 1 RETURN VALUE GLvex will return the signal BATCH DONE 241 when it completes this action EXAMPLE int num int objects 16 int haar 16 0 17 34 51 68 85 102 119 136 153 170 187 204 221 238 255 int size 16 int contrast 16 int setup int i num 16 for i 0 i lt num i object i 1 1 size i 4 contrast i 1 return 0 A prev do setup to state state do PvexDrawHaar amp num objects walsh size contrast to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 197 PvexDrawRandom draws patterns of random checks in a number of objects SYNOPSIS PvexDrawRandom int nObj int oList int cList int rList int sList int pList nObj number of
138. ates that vl_basep is the address of the value that should be added to vl_add The ME_GB bit indicates that the menu contains a global pointer me_basep that must be added to vl_add The ME _IGB bit indicates that the menu global pointer is the address of the value that must be added to vl_add Vl type is a flag that indicates the variable type Valid types are ME_ACHAR ME OCT ME_DEC ME_HEX ME_LOCT ME_LDEC ME_LHEX and ME_STR Me_achar indicates that the variable is a single ascii character Me_oct indicates that the variable is on octal value Me_dec indicates that the variable is a decimal value Me_hex indicates that the variable is a hexidecimal value Me_loct indicates that the variable is a long octal value Me_ldec indicates that the variable is a long decimal value Me_lhex indicates that the variable is a long hexidecimal value Me_str indicates that the variable is a string The last entry in any VLIST structure array must be NS on a line by itself NS stands for null string and marks the end of the variable list Note failure to end the VLIST definition with an NS line will cause REX to crash when it attempts to display the menu If you only use the default state_vars menu then you must also define a help message The name of the help message must be 2m_sv_v For example char hm_sv_vl do_two_ramps n 0 one ramp active n Page 14 1 two ramps active If you donit want to define a help message
139. ation protocol All of these actions return a value of 0 However GLvex will return various digital signals after completing the required action If the video sync is enabled GLvex will flash the sync object white on the first video field in which the action is completed for those actions requiring precise timing Note The only escapes you should use from states that call these actions are when the function tst_rx_new returns 0 or when a photo cell is triggered by the video sync object With Rex 7 2 you can continue to use the older Rex commands described below and you can write some actions that use the Rex commands while defining other states that use the Rex actions If you have an earlier version of Rex you must use the Rex commands describe below Page 166 Actions That Duplicate Command Line Arguments PvexEraseMethod set the erase method to be either whole screen or individual objects SYNOPYSIS PvexEraseMethod int method method erase method can be WHOLE_SCREEN or EACH_OBJECT DESCRIPTION PvexEraseMethod allows you to set whether GLvex turns off stimuli by clearing the whole screen or by erasing individual stimuli If method equals WHOLE_SCREEN the whole screen will be erased If method is EACH OBJECT then GLvex will erase objects by drawing a rectangle the color of the background over them If method is WHOLE SCREEN then GLvex will erase objects by clearing the entire screen The EACH OBJECT method is faster but the WHOLE SC
140. attern 101 contrast 1 object 3 function c radius 40 contrast 1 object 4 function r resolution 120 percent white 10 Page 160 The letter immediately following p stands for the function of the pattern The letter n in brackets following the pw ph pt and pu commands stands for the pattern number The letter s in brackets following the ph pr pu and pw commands stands for the size of the pattern checks The letter c in brackets following the pw ph pu and pa commands stands for the contrast normal or reverse of the pattern The contrast value can be either 1 for normal contrast or 1 for reverse contrast The letter p in brackets following the pr command stands for the percentage of white checks in the random pattern The letters in brackets following the pr command stands for the number of rows and the letter c in brackets following the pr command stands for the number of columns in the random check pattern The letter o in brackets following pa stands for the outer radius of the annulus and the letter i in brackets following pa stands for the inner radius of the annulus If the value for i is 0 then the pattern will be a filled circle The letter a in brackets following the pk command stands for the direction of drift This value must be 0 90 180 or 270 The letter s in brackets following the pk command stands for the speed of drift in degrees second The letter w in brackets following the pk command stands for the width of the grati
141. awList array of angular velocities around the Y axis only valid for 3 D flow fields spanList array of check life spans in video fields coherList array of percentages of coherent checks DESCRIPTION This action is similar to PvexNewFlow except that it shifts the direction of movement of the checks in a flow field while the checks are moving Checks can move in a linear direction or in a rotational direction Linear and rotational movement can be combined If the checks are given a non zero life span they will move as directed by the translation matrix for the given number of video fields then they will turn off This gives a scintillating appearance to the flow field The percentage of coherent checks governs the number of checks that will move in the direction specified by the translation matrix Non coherent checks will move in random directions RETURN VALUE GLvex will return the signal FLOW_RAMP_ CHANGE 234 on the first video field in which the checks have changed direction If the video sync is enabled the sync object will flash white when the checks change direction EXAMPLE int num 4 int objects 4 1 2 3 4 int xy 4 0 90 180 270 int z 4 0 45 45 90 y int vel 4 10 15 20 25 int roll 4 0 0 0 0 int pitch 4 0 0 0 0 int yaw 4 0 0 0 0 y int span 4 0 5 0 5 int coher 4 100 75 50 25 A state do PvexShiftFlow amp num objects xy z vel
142. ay electrode 1 You can instantiate as many copies of each of the four display described above as you have electrodes That is if you have set Mex to record from two electrodes you can have two copies of the oscilloscope display two copies of the time and amplitude display etc Mex will not allow the multiple copies of the displays to show input from the same electrode That is if you set Mex to record from four electrodes and you have two copies of the oscilloscope display each copy must show the input from a different electrode When you click on the electrode button in the menu bar of one of the oscilloscope displays you will find that the choices corresponding to that displayis electrode and the other displayis electrode will be inactive You will be able to shift that display only to one of the undisplayed electrodes This prevents you from setting conflicting criteria for an electrode The Signals Display The four displays described above all show the input from a single electrode and all require that the input cross threshold defined by amplitude and slope Thus if the input from an electrode drops markedly in amplitude or goes completely flat these displays will not show anything Mex has a fifth Page 336 type of display that shows the a of all electrodes Y regardless of amplitude This is aa the signals display This display is refreshed every 16 milliseconds On each cycle it shows all of the data from all electrodes acquired
143. ayScale 175 PvexSetObjectGrayScale 176 PvexSetLutEntryClr 177 PvexSetObjectLutEntryClr 178 PvexSetColorMask 179 Actions That Switch Stimuli 180 PvexAllOff 180 Page vi PvexSwitchFix 181 PvexDimFix 182 PvexPreloadStim PvexSwapBuffers 183 PvexSwitchStim 184 PvexSetStimSwitch 185 PvexTimeStim 186 PvexSequenceStim 187 Actions That Position Stimuli 0 0 0 0 eee 188 PvexSetFixLocation 188 PvexStimLocation PvexStimFromFixPoint 189 PvexShiftLocation 190 PvexReportLocation 191 PvexMessage 192 PvexSetActiveObject 193 Actions That Draw Stimuli 0 0 or 194 PvexClipRectSet PvexClipRectFromFixPoint 194 PvexClearClipRect 195 PvexDrawWalsh 196 PvexDrawHaar 197 PvexDrawRandom 198 PvexDrawAnnulus 199 PvexDrawBar 200 PvexDrawFlowField 201 PvexDrawEllipticalFlowField 202 PvexMaskFlowField 203 PvexDrawUserPattern 204 PvexDrawRgbUserPattern 206 PvexDrawTiffImage 208 PvexDrawOknGrating 209 PvexLoadPatterns 210 PvexLoadPointArray 211 PvexCopyObject 212 rex act vexActions c 212 PvexRotateObject 213 Actions That Control Ramps 0 000s ect eeeeeeeteees 214 PvexNewRamp PvexNewRampFromFixPoint 214 PvexLoadRamp 215 PvexToRampStart 216 PvexStartRamp 217 PvexResetRamps 218 Actions That Control OKN Stimuli 2 02 0 0 cee eee eee 219 PvexStartOkn 219 PvexStopOkn 220 Actions That Control Flow FieldS o ooooooooooommomoo 221 PvexNewFlow 221 PvexMakeFlowMovie 222 PvexToFlowMovieStart 223 PvexSt
144. because QNX does not restart output to slow ttys after interruption by a signal the pdp11 version of Unix did this Note that input from the keyboard is not affected One can stop the clock to see intact printout on the screen While the clock is on one must know the line number of the variable being changed This problem is not easily solved and requires porting a public domain version of the standard I O library 2 4 0 When REX is exited an error message is printed concerning null pointer assignment detected This is benign REX 3 11 Jul 88 Release 3 11 adds support for two eyes and changes to the window display The primary eye channel is now displayed on the window display as an X the other eye channel is displayed as an O The two channels are simply called the eye and other eye There are two windows as well which can be different sizes Offsets can now be applied to the eye channel signals These offsets are in effect for all on line operations on the eye signals such as the window check saccade detection displays etc The offsets are not applied to the values stored in the A file however The offset mechanism is useful when sampling two eyes at various depths The applied offset is changed to compensate for varying angles between the eyes thus keeping the displays and window check accurate The following actions have been added wd_osiz wd_pos wd_ctl off eye and off oeye The action wd_set has been r
145. bel reads i Checking Windowsi In this state Rex will set or clear bits in the eyeflag variable depending on whether a given signal is inside or outside of the electronic window To force Rex to ignore the windows click on the button The indicator will turn red and the label will read i Ignoring Windowsi In this state Rex will report that all signals are always inside their windows Page 90 Debug Older versions of Rex provided a mechanism for debugging spot files If you set the pausel 0 pause2 0 li i i closew wdback 0 stopramp 0 Co cet eal cea ETC PTC a EA debug states variable in the control _param menu to 1 as the state processor entered each state it would print the name of the state With Rex 7 0 this debugging information is provided in a dialog Click on the Debug button to display the dialog When debugging is enabled the button s indicator turns green and label reads i Debug Oni When debugging is disabled the button s indicator turns red and the label reads i Debug Offi The dialog contains a button for each state The state button are grouped together by chains If the name of the state is preceded by a 1 T the stateis time variable is non zero As the state processor enters each state it toggles the color of state s button between yellow and blue It also prints the time that it entered the state in the button If you toggle the Reset States button the color of all Page 91
146. bjArray i i 1 swtchArray i OBJ_ON return 0 o prev do setup to state state do PvexPreloadStim amp num objArray swtchArray to nextstate on 0 tst_rx_new onState do PvexSwapBuffers to newstate on 0 tst_rx_new if digital sync to nextstate on PHOTO_CELL amp drinput if video sync FILE rex act vexActions c Page 183 PvexSwitchStim switches a number of objects on or off SYNOPSIS PvexSwitchStim int nObjects int objList int swtchList nObjects number of objects to switch objList array of object numbers swtchList array of switch values can be OBJ_OFF or OBJ_ON DESCRIPTION This action allows you to switch a number of objects on or off You can switch some of the objects on and some off simultaneously RETURN VALUE If the digital sync is enabled GLvex will return the signal LIST_ON 249 if the first objectis switch is on or LIST_OFF 248 if the first objectis switch is off in the first video field in which the switch is executed If the video sync is enabled the sync object will flash white in the first video field in which the switch is executed EXAMPLE int num int objArray 16 int swtchArray 16 int setup int i num 16 for i 0 i lt num i objArray i i 1 if i 2 swtchArray i OBJ_ON else swtchArray i OBJ_OFF return 0 A prev do setup to state state do PvexSwitchStim amp num objArray swtchArray to nextstate on 0 tst_rx
147. bjects SYNOPSIS PvexDrawAnnulus int nObjects int objList int outerList int innerList int cntrstList nObjects number of objects to draw in objList array of object numbers outerList array of the outer radii of the annuli in 10ths of a degree may be 2 to 255 innlerList array of the inner radii of the annuli in 10ths of a degree may be 0 to 255 cntrstList array of the contrasts of the annuli may be 1 or 1 DESCRIPTION This action draws circular and annular stimuli in objects The inner an outer radii are in 10ths of a degree of visual angle If the inner radius is 0 GLvex will draw a filled circle If the contrast is 1 the annulus will be drawn in the objectis foreground color If the contrast is 1 the annulus will be drawn in the objectis background color The center of the annulus is transparent To get a center surround annulus requires two objects RETURN VALUE GLvex will return the signal BATCH_DONE 241 when it completes this action EXAMPLE i use two objects to create an annulus with a black center and a white surround the two objects must be given the same location coordinates I int num 2 int objects 2 1 2 int outer 2 10 5 int inner 2 5 0 int contrast 2 1 1 A state doPvexDrawAnnulus amp num objects outer inner contrast to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 199 PvexDrawBar draws rectangular stimuli in objects SYNOPSIS Pvex
148. ble table RTVAR rtvars number of trials amp nTrials Page 31 trials remaining amp trialsRemaining blocks completed amp nBlocks total trials amp totalTrials number correct amp correctTrials number wrong amp errorTrials percent correct amp percentCorrect NS A id 700 restart rinitf main_set status ON begin first code STARTCD time 1500 to pause pause to pause2 on PSTOP amp softswitch to go on PSTOP amp softswitch pause2 code PAUSECD to go on PSTOP amp softswitch go code ENABLECD rl 0 to selramp selramp do nextramp 0 F select next ramp to stramp stramp Start the next ramp Pass name of device on mirror so that it can be turned off at end of ramp if it has not already been turned off explicity by an action I do rampstart LED1 rl 15 to openw openw do awind OPEN_W to fpon on RA_STARTED amp ramp RAMP0 ra_rampflag fpon code FPONCD do dio_on LED1 rl 5 time 250 to eyeon eyeon rl 40 time 250 to error on EYEALL amp eyeflag start checking for eye to stimon Page 32 stimon code STIMCD do dio_on BACKLT to error on EYEALL amp eyeflag to wdchange wdchange do set_wsiz 1 flag true for ramp sizes rl 50 to setpres setpres Compute time until ramp is completed Args to ramptset action are a preset and random do ramptset RAMPO 80 20 to error on EYEALL 8 eyeflag to fpoff on R
149. but allows users to move flow fields with the mouse while the flow field is running This may be useful for mapping movement sensitive neurons The user may choose EACH_OBJECT which erases individual objects or checks This method achieves the fastest performance GLvex runs in RGBA mode rather than color lookup table mode To maintain backwards compatibility GLvex maintains its own 256 byte color lookup tables one for each object Users may specify user objects using either RGB values or color lookup table values There is no limit to the number of objects you can have in GLvex other than system memory GLvex 7 0 adds support for accepting keyboard and mouse commands from the eye window process of Rex 7 5 Subtractions The following Rex commands have been eliminated from vex 3 1 JOYSTICK LOCATION PATTERN CHECK SIZE DRAW_POLYGON and REX DRIVE RAMP The command SHIFT LOCATION can be substituted for the commands JOYSTICK LOCATION or REX DRIVE _ RAMP The size of checks in stimulus patterns must be specified when the pattern is specified so the command PATTERN CHECK SIZE is redundant The command DRAW POLYGON Page 140 was never implemented in earlier versions of GLvex so it has been deleted This command may be implemented in a later version of GLvex Starting GLvex You start GLvex from a WinNT console window GLvex has several command line arguments To get a list of arguments type GLvex h You will get the following help message G
150. by entering them into a circular event buffer If events are being saved scribe writes the data to the disk whenever a high water mark is reached The circular buffer is large enough to make many events available to the running line window and raster display processes During a neurophysiological experiment the most common event is the single unit action potential or spike These can occur with average firing rates as low as 1 per second or as high as 1000 per second It is essential that some representation of them be available on line The raster display process provides an on line version of the standard unit raster built out of the incore event buffer Page 7 Analog Buffer During the experiments run with Rex many analog signals must be sampled and saved Collection of analog data is greatly complicated by several factors For example the time from which to begin saving may precede the actual time when recognition of the need to save occurs e g one may wish to save eye position from 100 milliseconds before the beginning of an eye movement Also the number of samples collected during the run may be greater than the storage capacity of the disk The approach taken in Rex is to collect the data continuously in rotating buffers and only store data according to requests in the state set A very large buffer is used to hold the analog samples and when the buffer is full the load pointer wraps around to the beginning of the buffer The user
151. by the ramps can contain any kind of image or pattern You must use the actions described above to define the ramps before calling this action RETURN VALUE GLvex will return the signal BATCH DONE 241 when it completes this action EXAMPLE int num int objList 5 int rampList 5 int setup int i num 5 for i 0 i lt num i objList i i 1 rampList i i 1 return 0 A prev do setup to state state do PvexToRampStart amp num objList rampList to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 216 PvexStartRamp starts a number of ramps moving SYNOPSIS PvexStartRamp int nRamps int rmpList int objList int cycleList nRamps number of ramps to start rmpList array of ramp numbers objList array of object numbers to place on ramps cycleList array of ramp cycle types DESCRIPTION This action starts ramps moving You must use the actions described above to define the ramps before calling this action The cycle types can be RA_ONCE 0 which causes the ramp to run once RA_OSCIL 1 which causes the ramp to go back and forth and RA_LOOP 2 which causes the ramp to run over and over RETURN VALUE If the digital sync is enabled GLvex will return the signal FLOW RAMP START 236 when the ramps start moving the signal FLOW_RAMP_ STOP 235 when the ramps stop moving and the signal FLOW_RAMP_ CHANGE 234 at each step specified by the PvexSetTriggers action see
152. c First if you end the rex clock to stop a paradigm or you reset the state list after rex has sent a command to GLvex but before GLvex has sent its response signal you may de synchronize the communications To avoid this ALWAYS stop paradigms using the PSTOP switch before ending the rex clock or using the r s command This should guarantee that all communications have been resolved At this point you can end the clock begin the clock reset the state list or open and close files i Second including states that call actions which communicate with GLvex in the rex abort list Rex will attempt to execute these actions without testing the transmission bits or acknowledging signals from GLvex This will cause problems Monkey subject errors must be handled explicitly in the following manner Example state loop F other states in your paradigm to vstwts vstwts to vexst on 0 tst_tx_rdy test if transmission is ready vexst do vex_time vex command that will take a while to error on WD0_XY 8 eyeflag to vexack on 0 tst_rx_new escape when signal is received vexack code ECODE do pcm_ack 0 I acknowledge signal from vex time 100 rand 100 to othst othst F other states in your paradigm error code ERR1CD do reset_s 1 but don t include vex states in abort list Page 149 to alloff on 0 tst_tx_rdy alloff do off_all turn off all stimuli and fixation point to offack o
153. c begin flow field in active object and Ramp r with Object o cycle 0 1 2 In the Op command the letters in brackets stand for the parameters of the flow field You can get an explanation of the parameters by typing Op lt return gt to get a help message similar to the following w width of flow field h height of flow field n distance to near plane f distance to far plane p tenths percent coverage lt 255 s check size Current values for object 0 width 640 height 480 near 500 far 2000 tenths percent 50 The values for the near and far planes determine whether the flow field is two or three dimensional If the values for the near and far planes are equal the flow field will be two dimensional If the values for the near plane are less than the far plane the flow field will be three dimensional For three dimensional flow fields if the value for the near plane is much smaller than the values for the height or width you will get wide angle distortion during yaw or pitch movements If the value for the near plane is much larger than the values for the height or width you will get telephoto distortion during yaw or pitch movements Example commands Op 640 480 1 1 50 4 This command will set up a two dimensional flow field 640 rex units wide 480 rex units high with 5 of its area covered by checks and the checks will be 4 pixels square Op 1000 700 1000 3000 10 4 This command will set up a three dimensional
154. cTrialList 5 percent 1600 prent right amp memSacTrialList 6 percent 25 prent right amp memSacTrialList 7 percent 50 prent right amp memSacTrialList 8 percent 100 prent right amp memSacTrialList 9 percent 200 prent right amp memSacTrialList 1 0 percent 400 prent right amp memSacTrialList 1 1 percent 800 prent right 8 memSacTrialList 12 percent 1600 prent right amp memSacTrialList 13 percent E 0 restart rinitf main stat ON begin first to disabl disabl to enable on PSTOP amp softswitch paradigm enabled enable code ENABLECD rl 0 to pcktarg pcktarg do pick_ramp_direction to fpncmd on 0 tst_rx_new fpncemd do on_fix to awnopn on 0 tst_rx_new awnopn code FPONCD do awind OPEN_W rl 10 to waitfix waitfix do ctr_wnd time 1000 to fixtim on WDO_XY amp eyeflag to error fixtim time 400 rand 400 rl 20 to error on WD0_XY 8 eyeflag to setrmp setrmp do to_ramp_start to tgncmd on 0 tst_rx_new tgncmd Page 319 Page 320 fpfcmd strtramp rampon flshoncmd timefish floffcmd ramprun waitsac waittarg correct rewon do pursuitOn to fpfcmd on 0 tst_rx_new do off_fix rl 30 to strtramp on 0 tst_rx_new do start_ramp to rampon on 0 tst_rx_new do vex_gate 1 rl 40 to flshoncmd to waitsac on RAMP_DONE amp rampFlag do flash_on to timefls
155. capacity of machines such as the pdp11 which have a larger physical memory space than virtual address space For example the pdp11 73 has a memory capacity of 4MB and a virtual address space of 64KB text 64KB data Rex is written in C a structured high level language C has separate compilation provides full access to hardware and is very efficient C is easily interfaced to assembly language Rex Processes A typical Rex system is composed of five or more processes The most common processes are described below Data The data process is a null process that declares the common in core data area and launches the procSwitch process It is executed before other Rex processes and remains in memory at all times Since the data process is the first process executed it is named Rex ProcSwitch The procSwitch process supervises the launching of all other processes and the opening and closing of files ProcSwitch displays a small tool bar containing pull down menus and toggle buttons that provide user input ProcSwitch maintains a table of all currently established Rex processes and their status Page 4 Scribe The scribe process writes and maintains data files on disk When a Rex process desires that data be saved on disk it sends a message to scribe telling it what the data is and where it is located It is scribe s responsibility to write the data into the proper file in the correct format For example the int process might sample data fr
156. ce port and bit s to turn on or off see below Pdio_on DIO_ID id Pdio_off DIO_ID id Pdio_onoff DIO_ID id_on DIO_ID id_off Pdio_out DIO_ID id long value DIO_ID address of the device id specifying device port and bits to turn on or off see below ADDITIONAL HEADERS REQUIRED None DESCRIPTION dio_on dio_off dio_onoff and dio_out control digital output devices The output device port and bit s to turn on or off are specified by the DIO_ID This id is defined by using the macro Dio _id For example suppose an LED is connected to bit 3 on port 2 of the Industrial Computer Source PCDIO board One would define a DIO_ID as follows define LED1 Dio_id PCDIO_DIO 2 0x4 One could then turn this LED on by using the dio_on action dio on LED1 To use the pointer version of this action define a DIO_ID and assign it to a variable as follows define LED1 Dio_id PCDIO_DIO 2 0x4 long led led LED1 Pdio_on amp led The dio_off and Pdio_off actions turn the specified bits off The dio_onoff and Pdio_onoff actions take two id arguments the first id is turned on the second is turned off The actions dio_on Pdio_on dio_off Pdio_off dio_onoff and Pdio_onoff keep a software state of the digital output port Setting or clearing bits does not affect the state of other bits previously set in the same port The actions dio _out and Pdio out do NOT keep a software state The contents of value are directly copied to the
157. ce of the RA RAMP TIME struct with the computed preset and random times These values are then inserted into the time and random fields of a state this state is usually in a separate chain from the main paradigm When this state transitions the action ramptd is called to set the RA_TIMEDONE bit to terminate the ramp An example of the use of these functions is in the test paradigm rex sset tstramp d RETURN VALUE Returns 0 EXAMPLE ramptd RAMP0 Sets the RA_TIMEDONE bit in ramp 0 SEE ALSO ira_phistart ra_phiend ra_start ra_stop ra_tostart FILE rex act ramp_act c Page 52 ra_tostart Pra_tostart move mirrors to starting position of ramp SYNOPSIS ra_tostart long rnum Pra_tostart long rnum rnum ramp number ADDITIONAL HEADERS REQUIRED None DESCRIPTION ra_tostart moves the mirrors to the starting position of the specified ramp This action is not necessary in general since ra_start moves the mirrors to the starting position as part of initiating a ramp However for some paradigms such as fixation ramp away it is necessary to hold the mirrors at the starting position for some time before the ramp begins Note that if the 25 msec acceleration time is enabled the mirrors will move to a position before the specified start of the ramp RETURN VALUE Returns 0 EXAMPLE ra_tostart 0 This action moves the mirrors to the starting position of ramp number 0 SEE ALSO ra_new ra_phistart ra_phiend ra_start
158. ch laboratory In addition larger machines may exist for off line tasks such as data analysis data archiving program development etc Previous Design Approach In a previous approach to developing software for this environment a single large program performed all the functions of data acquisition control and display generation To conserve space the machines ran under a small operating system with real time capability RT 11 Coding was done in assembly language for efficiency and access to hardware registers As more laboratories with different needs used this program it became larger and more complex Modularity broke down as different programmers modified it This single program was difficult to debug maintain and modify Capabilities not needed in one experiment were removed when memory space was critical and other capabilities Page 3 were added A feature of one version was often difficult to transfer to another because of buried differences Debugging problems were more difficult since the operating system did not run the program under the protection of memory management Stacks could overflow without being caught and the operating system itself could be corrupted New Approach The multiple process structure of Rex solves many of these problems With inexpensive solid state memories the laboratory computers can be configured with enough memory to run a larger and more sophisticated operating system such as Unix A process in Unix
159. chine on the command line using the r flag described above Page 147 GLvex exe r Isr labvex o 5 other arguments This argument tells GLvex to accept commands only from the machine Isr labvex Synchronizing ethernet communications The ethernet communications protocol between rex and GLvex are not as complicated as the parallel I O protocol You need not test to see if the transmission line is clear and you do not need to acknowledge responses from GLvex Therefore the set of states described for the parallel I O communications protocol can be reduced to the following Example GLvex ethernet communication state set F other states in your paradigm to vexst escape to the vex state vexst I a state that sends a message to vex do vex_call do action which sends a message to vex to nxtst on 0 tst_rx_new escape when GLvex signal received nxtst code ECODE to indicate the start of a display change time 100 rand 100 to othst othst means other states othst F other states in your paradigm Note The only escapes you should use from states that call these actions are when the function tst_rx_new returns 0 or when a photo cell is triggered by the video sync object Synchronizing stimuli GLvex sends a signal at the beginning of the first video field when the display needed to synchronized to the data collection 1 e when a stimulus was turned on or a ramp started Your spot file can drop
160. cilloscope menu bar The icon in the button will change to ON when Mex enters antidromic mode In doing collision experiments you will probably want to manipulate both the display interval and the antidromic latency until you have a display of the triggering waveform the shock artifact and the presence or absence of an induced waveform Once you begin saving data for a collision experiment the display interval scroll bar will become inactive because collision data file can contain waveforms of a single length If you decide that you really need a different display interval you will have to stop saving antidromic data and open a new file before saving data at the new interval Of course the antidromic latency scroll bar remains active Page 330 The Time Amplitude Display The time amplitude display shows the waveforms that satisfy the threshold conditions set in the Time Amplitude Based Discrimination oscilloscope display This display shows the half millisecond of the waveform that occurred before the trigger crossing and 1 2 3 or 4 milliseconds of the waveform after the trigger crossing The interval is set by the Unit Length item in the Settings dialog box not by the display interval slider in the oscilloscope display Therefore you can set the oscilloscope to show a long interval of data but still see the details of the waveform around the time of the trigger crossing The purpose is to allow you to place boxes through which a wa
161. clipy i low byte of height other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not The hibyte and lobyte functions are defined in GLvex_com c Page 267 FULL_CLIP_RECT This is a batchable command that resets the clipping rectangles of objects to the full screen The first parameter is the number of objects Each object has one parameter the object number Example action rF This action restores the clipping rectangles of 4 objects to full screen restore_clip void unsigned short index short i index 0 vexbuf index FULL_CLIP_RECT vexbuf index 4 number of objects for i 0 i lt 4 i vexbuf index i 1 object number F other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not Page 268 DRAW_WALSH_PATTERN This is a batchable command that draws a Walsh pattern in an object The first parameter is the number of objects to draw in Each object requires four parameters the object number the pattern number the pattern check size and the contrast The pattern numbers can range from 0 to 255 The contrast can be either 1 for normal contrast patterns or 1 for r
162. code int rampstart long LED ra_start RAMPO 1 LED if do_two_ramps ra_start RAMP1 1 LED return 0 int rampstop void ra_stop RAMPO if do_two_ramps ra_stop RAMP1 clear_all_da return 0 Page 25 int ramptset long rnum long preset long rand RA_RAMP_TIME ra_time ra_time ra_compute_time rnum preset rand if ra_time ra_ramp_time_preset 1 set_times timeramp long ra_time ra_ramp_time_preset long ra_time ra_ramp_time_random ramp rnum ra_rampflag RA_TIMESTART return 0 int set_wsiz long flag if flag wd_siz WINDO rxwind rywind wd_siz WIND1 roxwind roywind else wd_siz WINDO fxwd fywd wd_siz WIND1 foxwd foywd return 0 int correctTrial score YES correctTrials if totalTrials percentCorrect 100 correctTrials totalTrials return 0 int errorTrial score NO errorTrials if totalTrials percentCorrect 100 correctTrials totalTrials return 0 void rinitf void Initializations da_cntrl_2 r0_xda DA RAMP_X RAMPO r0_yda DA_RAMP_Y RAMPO first ramp da_cntrl_2 r1_xda DA_RAMP_X RAMP1 r1_yda DA_RAMP_Y RAMP I second ramp da_cursor r0_xda r0_yda CU_DA_ONE da cursors da_cursor r1_xda r1_yda CU_DA_TWO clear_all_da wd_disp D_W_ALLCUR amp D_W_JOY all cursors but joystick Page 26 wd_src_pos WINDO WD_DA r0_xda WD_DA r0_yda
163. completed etc In older versions of Rex to view such variables experimenters had to place them in menus and then display the menus using keyboard commands These menus could not be updated while being displayed so to see new values experimenters had to dismiss then re display the menu With the graphical user interface we are able to construct dialogs that display and automatically update any variables the experimenter needs The new features of Rex have rendered some old features obsolete The following is a list of changes in the behavior of Rex Page 77 Root files With Rex 7 0 only the int process uses the old Rex root files Because experimenters can bring up multiple eye window and running line displays we have disabled the running line and eye window entries in the root file We plan to provide an alternate root system for these displays Because of the increased functionality and the possibility of having multiple raster displays the raster display root is now separate from the main root file Verbs and nouns Because the verb noun syntax of Rex commands has been replaced by button clicks the root file system no longer supports verb noun strings Process Switching Tool bar When you start Rex you are greeted by a short tool bar as shown here Use the controls in this tool bar to launch all other Rex applications Files Displays CntrkB Keep Data Clicking on the Files button will display a menu with the following
164. consists of a program memory image register values status of open files etc Unix is a timesharing system and schedules run time among processes that reside in memory or are swapped out to secondary storage Processes are executed under the full protection of memory management stack faults are caught a process has access only to its own address space and execution of sensitive instructions such as halt or reset is prohibited Each process interacts with other processes only through inter process communication protocols The major functions of Rex exist as individual Unix processes The boundaries thus imposed enforce some degree of modularity in Rex Of course any process can still be poorly constructed internally However there is a i firewall between it and the rest of the system Its interactions are better defined than if it were a section or overlay in a single large program sharing the same address space and registers The multiple process structure facilitates maintenance and the development of new functions Rex systems may run different processes for various applications yet still include the same processes for functions such as keyboard handling and file writing When changes are made to processes each Rex system needs only to run the new versions to be updated When debugging each process has its own address space and can be traced separately Multiple processes also provide a way for large systems to effectively utilize the full memory
165. cting the addition of a selection set You can use the scroll bar to view your selection sets When you create a new selection set all of the parameters of the previous set are copied to the new set so you donit have to enter everything For example you might have one set of Any Of codes to group your data but you might want to align it in several different ways Define the first set of selection criteria click New then just change the Align Code in second set Or you might want to view the data from correct and incorrect trials separately Define the first set of selection criteria and use a reward code in the All Of list click New then delete the reward code from the A Of list and enter it in the None Of list Rex will use two parameters to group your data the number of the selection set and the ecodes in the Any Of list Page Layout To define how Rex is to lay out the raster plots click on the Rasters button in the menu bar and select the Build Raster Specs item This dialog is divided into thirds The top part of the dialog contains fields to define page wide parameters of your plots The middle part of the dialog contains a set of buttons that allow you to select individual plots The bottom of the dialog contains fields to enter the parameters for individual plots To set up you raster specification first decide how many rows and columns of plots you want per page and enter these values in the Rows and Columns numerical fields The ap
166. d color to rgb b n set Background luminance level to n Current background 128 128 128 The letters r g b in brackets stand for the values of red green and blue to use for the screen background The values for r g and b each can range from 0 to 255 The letter n in brackets stands for the gray level to use for the screen background These values can range from 0 to 255 Example commands b12800 This command sets the screen background to a medium red b 128 This command sets the screen background to a medium gray c Absolute clipping rectangle Clear These commands set the clipping rectangle of the active object and clear the screen If you type c lt return gt you will get a help message similar to the following clear clear the screen cfull set Clipping rectangle to FULL screen cr x y w h set Clipping rectangle to location x y width w height h Page 151 The letter w in brackets stands for the width of the clipping rectangle in rex units tenths of a degree The letter A in brackets stands for the height of the clipping rectangle in rex units The letter x in brackets stands for the X coordinate of the center of the clipping rectangle in rex units The letter y in brackets stands for the Y coordinate of the center of the clipping rectangle in rex units The word full in brackets stands for setting the clipping rectangle to the full screen Example commands cr 10 10 150 100 This command places the center of the clipping
167. d of the ramp In the rs command the letters in brackets stand for the number of the ramp to run and the object to put on it You can get an explanation of the parameters by typing rs lt return gt to get a help message similar to the following r number of ramp to run o object to put on the ramp c type of ramp cycle c 0 ramp runs once c 1 oscillation ramp goes back and forth c 2 loop ramp runs over and over Each ramp must have been previously computed with the re command Example commands rs 110 This command will place object 1 on ramp 1 and start ramp 1 moving The ramp will run once You can start two ramps simultaneously with the command rs 110220 This command will place object 1 on ramp 1 object 2 on ramp 2 and start both ramps moving Both ramps will run once S Switch all objects These commands switch all objects on or off If you type S lt return gt you will get the following help message Ston Switch all objects on Stoff Switch all objects off Page 163 s Switch set active object set sync These commands switch the active object on or off enable or disable the sync signals and change the active object If you type s lt return gt you will get a help message similar to the following s n make object n active release slave ston Switch active object on stoff Switch active object off syncVon Switch video sync on syncVoff Switch video sync off syncDon Switch digital sync on synd
168. d signals when the shift is complete SYNOPSIS PvexShiftLocation int nObjects int objList float xList float yList nObjects number of objects to position objList array of object numbers xList array of the x coordinates of the objects in 10ths of a degree yList array of the y coordinates of the objects in 10ths of a degree DESCRIPTION This action sets the locations of a number of objects and signals the beginning of the first video field in which the object positions have changed This action is useful if you want to move a GLvex object with a Rex ramp or if you want to move objects with a joystick connected to one of Rexis A D ports RETURN VALUE If the digital sync is enabled GLvex will return the signal SHIFTED 240 at the beginning of the first video field in which the objects are shifted The rex video sync square will not flash for this command EXAMPLE int num int objectArray 4 float xArray 100 00 100 00 100 00 100 00 float yArray 100 00 100 00 100 00 100 00 int setup int i num 4 for i 0 i lt num i objectArray i i 1 return 0 A prev do setup to state state do PvexShiftLocation amp num objectArray xArray yArray to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 190 PvexReportLocation asks GLvex to report the location of the indicated object SYNOPSIS PvexReportLocation int object object number of the object wh
169. d we are just using the digital inputs for units The counter timer should permit unit resolutions of 10 microseconds vs current 1 2 milliseconds You should not to buy this card at present since it is not being used Device Addresses Vectors Jumpers The following is a list of the addresses vectors and DMA assignments we use at NIH Note that these can be changed The files rex hdr cnf h rex hdr device h and rex int cnf c contain the configuration information Table 1 Vectra Configuration for QNX and REX Interrupts 0 System Timer 1 Keyboard 2 Cascaded interrupts 8 15 8 CMOS Real time clock not used by QNX 9 Unused 10 COM3 VT100 serial port Page 121 Table 1 Vectra Configuration for QNX and REX Interrupts 11 Adaptec 1740 12 Vectra internal mouse port 13 Coprocessor 14 IDE disk if enabled 15 Unused 3 SMC 8013 and or Archive 1 4 tape adapter 4 COM1 modem 5 a d converter 6 Floppy 7 LPT1 Interrupt priorities are established by QNX at boot time by assigning one of the levels to be the highest The priority then decreases from the assigned level for each succeeding interrupt number Note that interrupt 2 is really the cascaded input from interrupts 8 15 QNX by default assigns interrupt 3 to be highest This results in a priority order from highest to lowest of 3 4 5 6 7 0 1 8 9 10 11 12 13
170. dex SET_STIM_SWITCH set stimulus switches vexbuf index 2 number of objects to set for i 0 i lt 2 i vexbuf index i 5 object numbers 5 and 6 if i vexbuf index OBJ_ON set object 5 switch on else vexbuf index OBJ_OFF and object 6 switch off vexbuf index RESET_RAMPS to_vex index return 0 If the digital sync is enabled GLvex will return the signal FLOW_RAMP_ CHANGE 234 at the beginning of the first video field in which the ramp is reset Otherwise GLvex will not return any signal after this command If the video sync is enabled the rex video sync square will flash white for the first field in which the ramp is reset Page 290 NEW_FLOW This is a batchable command that defines the translation matrix for flow fields The first parameter is the number of objects Each object requires 15 parameters the object number the hi and lo bytes of the angle of movement in 2 D the hi and lo bytes of the angle of movement in 3 D the hi and lo bytes of the velocity the hi and lo bytes of the rotation about the Z axis roll the hi and lo bytes of the rotation about the X axis pitch the hi and lo bytes of the rotation about the Y axis yaw the life span of the checks and the percentage of coherent checks If the value for life span is 0 then the checks will be displayed constantly If the value for life span is greater than 3 then each check will be
171. display with rex It does not require any parameters When the digital sync is enabled GLvex will return a signal via pcmsg at the beginning of the first video field where synchronization is needed The digital sync is enabled by default Once the digital sync is enabled it will remain enabled until disabled so you only need to call this command once Example action setup unsigned short index index 0 other batchable commands vexbuf index ENABLE_REX_DIGITAL_SYNC other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not Page 237 DISABLE_REX_VIDEO_SYNC This is a batchable command that disables the digital sync for synchronizing the display with rex It does not require any parameters The digital sync is enabled by default Once the digital sync is disabled it will remain disabled until enabled so you only need to call this command once Example action setup unsigned short index index 0 other batchable commands vexbuf index DISABLE_REX_DIGITAL_SYNC other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not Page 238 SET_REX SCALE This is a batchable command that sets the scalin
172. displayed for the specified number of fields as it moves then moved to a new location and be redrawn again for the specified number of fields This gives the flow field a scintillating appearance If the value for coherence is less than 100 then some of the checks will move in quasi random directions Example action F Set up a sliding expanding flow field in one object and a contracting field in a second object short xy 180 0 short z 45 90 short ob 1 2 short vel 10 F velocity of checks in degrees sec short span 10 number of video field each check is displayed short coher 50 percentage of checks that move in the specified direction make_transform short index i roll pitch yaw index 0 roll pitch yaw 0 vexbuf index NEW_FLOW vexbuf index 2 number of objects for i 0 i lt 2 i vexbuf index ob i object number vexbuf index hibyte xy i high byte of translation in 2 D vexbuf index lobyte xy i low byte of translation in 2 D vexbuf index hibyte z i high byte of translation in depth vexbuf index lobyte z i low byte of translation in depth vexbuf index hibyte vel high byte of translation in depth vexbuf index lobyte vel low byte of translation in depth vexbuf index hibyte roll high byte of roll rate vexbuf index lobyte roll low by
173. displaying buttons for all the states grouped by chain As each state is entered the color of its button is toggled between yellow and blue and the time the state was entered is printed on the button Debugging messages can be printed by using the routines dprintf dputchar dputs and rxerr If one of these routines is called from the interrupt level or when the variable doutput_inmem in the control param menu is non zero the results are not printed on the console They are instead stored in a rotating buffer in memory This buffer can be printed by issuing the command int print debug The variable doutput_rotate determines whether the memory buffer rotates when filled if non zero the buffer rotates if zero the buffer freezes when filled and does not accept further input The buffer is initialized with a as the first character If the variable doutput_tofile is non zero the contents of the buffer are also printed to a file in tmp when the int print_debug command is issued For more information about these debugging routines see the comments in the source files sys rlib dprintf c and sys rlib dputs c Example An example of a complete spot file with multiple chains of states follows it Rex ramp test paradigm I include lt stdlib h gt include hdr ramp h include Idev_tst h include Icode_tst h define RAMPO 0 ramps and windows used in paradigm define RAMP1 1 define WINDO 0 define WIND1 1 defi
174. dth make the measurements then add those values to the command line arguments the next time you start With the exception of the number of objects argument all of the other arguments can also be set with keyboard commands or with rex commands If you do not enter a value for the number of objects you will get the following prompt Enter number of objects GLvex will then wait until you enter a value To make entering these command line arguments easier you can create a shortcut to GLvex and enter the arguments on the command line of the shortcut Then all you need to do is double click the shortcut symbol to launch GLvex with the desired arguments Click the right mouse button on the desktop and select New Shortcut In the Create Shortcut window select Browse and traverse the drives and folders to where you installed GLvex exe Select GLvex exe and click open Enter the command line arguments you want in the Command line window after the program name Click Next and enter a name for the short cut Click Finish Now whenever you launch GLvex from this shortcut the command line arguments you entered will be applied Included in the distribution is an icon for GLvex GLvex ico To set the icon for the short cut click on the short cut with the right mouse button select the Shortcut tab click on Change Icon select the Browse button enter the GLvex directory in the path and select the GLvex icon Page 141 To make debugging easier set the w
175. e connection will work in a Photon terminal window on the Mex machine run the command ping rex_machine and in a Photon terminal window on the Rex machine run the command ping mex machine These Page 325 commands should result in a number of lines of output showing the IP address of the target machine and ttypO sh ping Ilsr labrtp PING lsr 64 bytes 64 butes 64 bytes labrtp Isrnet nei nih gov 18 1 8 229 56 data bytes from 10 1 8 229 icmp_seq 8 tt1 255 time 0 ms from 18 1 8 229 icmp_seq 1 tt1 255 time 6 ms from 18 1 8 229 icmp_seq 2 tt1 255 time 8 ms lsr labrtp Isrnet nei nih gov ping statistics 3 packets transmitted 3 packets received By packet loss round trip min aug max 6 6 76 ms 4 the time it took to receive each packet If ping seems to hang then your host machine cannot resolve the IP address of your target machine You will need to examine the host file or DNS name resolution to find the problem Type control C in the terminal window to stop ping To use Mex with Rex you also need to establish a socket from the Rex side You do this in your spot files just as you do for GLvex In each spot file you must define a restart function The beginning of the first chain of states should look something like id 100 restart rinitf main_set status ON begin first In this example rinitf is the name of the restart function You can call it anything you want This functi
176. e corrupted REX 4 3 24 Nov 93 Release 4 3 adds a new field to the sample header that specifies the delay of the anti aliasing filter on the a d inputs A subsystem for PC to PC communication has been added This subsystem implements an 8 bit wide full duplex point to point link between the REX PC and other PCs Each link requires a dedicated 24 bit parallel I O chip the Intel 8255 The link is designed so that the interface boards containing the 8255 chip can be cabled together directly pin for pin without external glue logic or cable re mapping The link protocol is designed to be independent of timing differences between the PCs The programming interface presents a messaging model to the user Messages include checksums Please see rex hdr pcmsg h and rex int pcmsg c for further info about this subsystem REX 4 3 conversion a temporary fix to the rextools has been made that knows about the upgraded data files in version 4 3 of REX It is installed on irisf Since this is a temporary fix there is an extra printout to stderr that announces whether your files are in old or new format If you have any data files that were collected under the version of 4 2 that included the delay variable those files will not work correctly they are really 4 3 version data files I made a perl script to convert A and E files from 4 2 to 4 3 ONLY FOR THOSE FILES If you run it on good 4 2 files you will ruin them So if and only if your 4 2 files fail
177. e corrupted REX 4 3c 4 April 1994 This is a version of REX 4 3b ported from QNX 4 0 1 to QNX 4 2 You must use the latest update of 4 2 available from QNX s BBS system It may run on the version from your diskettes but I Page 104 don t guarantee it Note that QNX is on the net now qnx com however they don t have anonymous ftp up yet So you must download updates from the BBS or call them for diskettes When you install your QNX 4 2 kernel specify that you want the 32 bit version However REX is still running in 16 bit mode except for spot This version has some advantages menus print out without missing characters reading roots is very fast Note that the way the screen is switched from text to graph mode is different under 4 2 If you used to use the program greset located in rex sys matrox it will no longer work properly and should not be used The file config tar contains my configuration files You will need to make a new kernel to run Rex The file boot go is a shell file to make the new kernel and install it This must be done after downloading any updates as well This new kernel build file assumes that your a d is on interrupt number 5 If not edit boot build aha32 1 and change the flag to Proc for the interrupt level of your a d PLEASE NOTE With this release one must change the unit latch circuit Please see the new circuit in Chapter 9 of the REX manual If you don t make the change your unit data will b
178. e of which eye windows to display is made using toggle buttons in the bottom part of the display window wd_center The cursor that is the center of the screen can be set in each window display independently Page 71 Page 72 When Things Don t Work in REX Arthur V Hays Revised 10 September 92 When and what to recompile There are two levels of making REX The first is when modifications have been made ONLY to the spot file the d file of a paradigm or to the source of the int process In this case only the int process needs to be recompiled This is done by changing directory to rex sset and typing the command make sf whatever The second level is when changes have been made to the source of other parts of the REX system In this case the entire REX system may need to be recompiled To do this change directory to rex sset and type command make complete No return value specified from actions An action must always specify a return value either 0 or an ecode to be loaded into the Efile Where is the moving display Symptom the clock is begun the status says the clock is on but there is no moving display Possible remedy make sure the running line stop switch is not on Paradigm not behaving or operating properly times arguments to actions incorrect menu variables mysteriously changed nothing corresponds to initialized values The REX root file mechanism is very powerful but must be used carefully If changes
179. e source object the number of the destination object the hi and lo bytes of the percentage of horizontal scaling of the copied object and the hi and lo bytes of the percentage of the vertical scaling of the copied object The purpose of this command is to draw identical random check patterns or identical flow field patterns in multiple objects however it will copy any pattern from one object to another with the exception of TIFF images NOTE If you want to create a series of copies each of a different size then start with the same source object each time For example if you want to scale the pattern in object 1 by 125 and by 150 you should copy object 1 to object 2 with 125 scaling and then copy object 1 to object 3 with 150 scaling If you copy object 1 to object 2 with 125 scaling then copy object 2 to object 3 with 125 scaling object 3 will be 125 of the size of object 1 not object 2 i e object 3 will be the same size as object 2 not 25 larger Example action draw random pattern in one object copy into second object and shrink width by 10 short vres 100 short hres 200 short size 5 short prent 20 short ob1 1 short ob2 2 short xs 90 short ys 100 copy will be 90 as wide as and same height as source binoc void unsigned short index index 0 draw random pattern in one object vexbuf index DRAW_RANDOM_PATTERN vexbuf index 1 number of objects vexbuf index
180. e the ALL_OFF function to abort ramps or flow fields the normal ramp and flow field completion signals will not be sent The off all action shown above is defined in GLvex_com c Page 249 SWITCH_FIX_POINT This is a non batchable command that switches the fixation point on or off It requires one parameter the switch value The switch values are 0 for OFF and 1 for ON Example actions rF This action will switch the fixation point on on_fix void unsigned short index index 0 vexbuf index SWITCH_FIX_POINT vexbuf index OBJ_ON GLcommand h define OBJ_ON 1 to_vex index return 0 If the digital sync is enabled GLvex will return the signal FIX_ON 254 at the beginning of the video field in which the fixation point is switched on Otherwise GLvex will not return any signal after this command If the video sync is enabled the rex video sync square will flash white for the first field in which the fixation point is switch on pe This action will switch the fixation point off off_fix void unsigned short index index 0 vexbuf index SWITCH_FIX_POINT vexbuf index OBJ_OFF GLcommand h define OBJ_OFF 0 to_vex index return 0 If the digital sync is enabled GLvex will return the signal FIX_OFF 253 at the beginning of the video field in which the fixation point is switched off Otherwise GLvex will not return any signal after this command If enabled the rex video tr
181. e used to set the me_basep in cases where the menu me_basep displays elements of an array of structures int me_accf ral maf Me _flagis a flag variable that consists of the oried combination of any of the following bits ME_BEF ME_AFT The ME_BEF bit int me_flag ME_BEF indicates that the menu access function should be called before accessing the menu variables The ME_AFT bit indicates that the oe ral_alg function should be called afi ing th me_rtagen menu access function should be called after accessing the menu aa variables char me help hm ramp Me _rtagen is the address of a the root argument generation function If the menu requires arguments for example if it accesses the members of an array of structures this function will generate the array indices when writing root files Me help is a pointer to this menu s help message Rex 7 0 and later allow special menu entries marked by the me_name separator The me_vlp member of these entries must be null NP The remaining MENU structure members may be left undefined If you do define the remaining members of a separator MENU structure they must be defined to be 0 Rex will put a separator line in the user menus pull down menu where ever there is a separator entry Page 15 As with the arrays of VLIST structures the last entry in the umenus array must be NS Failure to end the umenus definition with an NS line will cause Rex to crash when it attempts to displa
182. e will start The value of this parameter can range from 0 to 255 The second parameter is the number of bytes in the gray scale The value of this parameter can range from to 255 The sum of the start and length parameters cannot exceed 255 The luminance range of the gray scale is always 0 to 255 The size of the steps between luminances is determined by the length of the gray scale This command is used to initialize a gray scale for continuous tone stimuli Example action It This action sets up a 128 byte gray scale starting at lookup table index 64 gray void unsigned short index index 0 vexbuf index SET_GRAY_SCALE vexbuf index 64 F start of gray scale vexbuf index 128 F length of gray scale other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not Page 245 SET_OBJECT_GRAY SCALE This is a batchable command that sets up a gray scale in the specified object s color lookup table The first parameter is the number of objects to set Each object requires three parameters The first parameter is the object number The second parameter is the index of the lookup table where the gray scale will start The value of this parameter can range from 0 to 255 The third parameter is the number of bytes in the gray scale The value of this paramet
183. e window and running line the both display is available Also color is implemented in the displays The raster display has been changed to fully occupy a 640 by 480 VGA resolution screen The running line display can now be customized and split into different vertical sections The traces can be triggered from the Spot file and a new mode has been added that prevents erasing of the previous trace to simulate a storage scope An example of this type of running line control is in the tstramp Spot file A software switch has been added for the PSTOP RLSTOP etc bits These bits used to have to be controlled by external switches To use the software switch change the paradigm to look for PSTOP in the variable softswitch instead of drinput Then the noun softswitch can be used from the keyboard to set and clear bits such as PSTOP Some minor changes to Spot were made The first state of a chain cannot contain an action Also up to 10 escapes are now supported This version also contains interface code to the MEX multi unit analyzer A bug exists in the running line code By default 8 running line channels are initialized They are set to display various signal numbers 0 3 8 and 9 If one changes the default signal list so that any of these signals are no longer valid then the running line display will complain The solution is to change the running line menus so that they donit reference a non active signal REX 5 0 8 April 94 This rel
184. ease includes new programming interfaces for controlling the d a converters signal windows and ramps The interfaces have been made more general and REX now supports multiple d a converters signal windows 8 by default and ramps 10 by default simultaneously These changes require paradigm modifications to include new actions Please see the sample paradigm at the end of the Spot manual This release only runs under QNX 4 2 the 32 bit version of QNX However REX is still compiled to run 16 bit except for spot spot has been modified to permit a max of six arguments to actions Some new variables have been added to the control_param menu Please see the description of this menu in Chapter 6 Also two new verbs were added to the tty noun map tty and unmap tty These verbs permit the VGA screen to be returned to text mode while REX is running One could then use telnet or an editor in the background without affecting REX The d a converters can now be driven by pre computed waveforms stored in memory The ramp is still generated at run time as before but other waveforms can now be used by pre computing them and storing them into memory buffers This feature will be more usable when REX is ported to 32 bit mode and the length of memory buffers is not restricted PLEASE NOTE With this release one must change the unit latch circuit Please see the new circuit in Chapter 9 of the REX manual If you don t make the change your unit data will b
185. ecision Number of Electrodes With the PCI DAS4020 12 A D board Mex can record from up to 4 electrodes There is no default number you must select one of these values or Mex will not work If you want to record from 3 electrodes select the 4 electrode option and ground one of the inputs You should select only the number of electrodes you are using so that Mex can sample your signals with the greatest precision Unit Length This item allows you to select the length of a neuronis waveform The default is 1 millisecond You can set this to 1 2 3 or 4 milliseconds after the threshold crossing Mex begins classifying a waveform only after it has obtained the complete waveform The classification routine takes between 3 and 10 microseconds Thus if you set the unit length to 1 millisecond Mex will toggle the bit signifying acceptance of the waveform 1 003 to 1 010 milliseconds after threshold crossing If you set the unit length to 4 milliseconds Mex cannot toggle the bit signifying waveform acceptance until 4 003 to 4 010 milliseconds after threshold crossing Therefore you should set this value to be as small as possible while still capturing the significant details of the neuronal waveform Toolbar After you have entered the settings for Mex you will be able to bring up its various displays and start data collection These actions are controlled by the large buttons below the menu bar in the Mex tool bar If you hover the mouse cursor over a
186. ected electrode satisfies the trigger conditions Mex starts a timer to count down a delay that you specify and begins displaying data for an interval that you specify The minimum stimulation delay from trigger crossing is 300 microseconds and Page 323 the maximum delay interval is 500 milliseconds Once the timer count down is complete Mex sets a bit in the digital I O for 100 microseconds This bit should be connected to the trigger input of stimulator Mex continues to display data for the interval you selected By setting the display interval longer than the stimulation delay you can see both the shock artifact and whether the shock evoked an action potential If you save antidromic data to disk Mex will save data beginning one half millisecond before the trigger and continue for the interval you specify Mex does not classify waveforms during antidromic collision tests it only looks for trigger criteria Configuring Mex Calibration AFter rebooting your computer and before running Mex you must run the calibration program for the Measurement Computing PCI DAS4020 12 A D board If you have installed the executable files in the default location usr local bin in a terminal window type cal4020 This program will generate a large amount of output which you can ignore After it exits the A D board will be ready to function You donit need to run the calibration each time you start Mex It is necessary only after rebooting the computer M
187. ed in two files The E file contains data which can be described as epochs The A file contains all other data including information about the experimental run that created the data The E file also indexes the A file Both files contain redundant information so that a complete loss of either file does not preclude access to the other file and that partial losses from one file can be bridged over The E file has a fixed record length structure while the A file has a variable record length structure Both files begin with a one block header The Unix system dynamically allocates file space pre determination of file length is unnecessary Rex Header Block A 512 byte header block is written for both files when they are created The first word of the header block is a size in bytes In the E file this is the size of the fixed record length in the A file it is the size of a fixed length header associated with each variable length record The next item in the header block is the file name used to create the files Then follows the version number for the Rex system that created the file These two items are stored as null terminated ASCII strings making them readable without a special program The rest of the header block is available for other information Page 8 E file Format After the header block the E file consists of an arbitrary number of records each four words long The structure of each record is identical The first word is a sequence
188. ed on the specified preset and random percentages The ra_compute_time version of this function can not be specified as an action because it returns a structure of type RA RAMP TIME rather than an int It must be called from an action The Pra_compute_time version of this function can be specified as an action because it returns the RA RAMP TIME structure in the fourth argument typedef struct long ra_ramp_time_preset long ra_ramp_time_random RA_RAMP_TIME rnum ramp number presetper preset percentage randper random percentage RETURN VALUE The ra_compute_time function returns a structure of type RA RAMP TIME The Pra_compute_time action returns 0 EXAMPLE ra_time ra_compute_time rnum preset rand Pra_compute_time amp rnum amp preset amp rand amp ra_time SEE ALSO ira_phistart ra_phiend ra_start ra_stop ra_tostart FILE rex act ramp_act c Page 51 ramptd Pramptd This function sets the RA_TIMEDONE flag for the current ramp This function is an action and is used in conjunction with ra_compute_time or Pra_compute_time SYNOPSIS ramptd long rnum Pramptd long rnum The ra_compute_time function computes the time remaining until the ramp completes based on the specified percentages Suppose one wanted to stop a ramp after 70 of the duration plus an added random 10 The ra_compute_time function would be called with arguments of 70 for presetper and 10 for randper The function would return an instan
189. ed to cause a crash when run in kernel mode These errors are now caught and recovered from In addition the restriction that all variables used in the lower level of the interrupt routine be initialized is no longer needed In fact there is now no difference between the first and third sections of the Spot file Variables and code can be placed in either section and variables do not have to the initialized in either section Page 109 Therefore there is no longer any need to run the shell file prt_bs in the run directory to check paradigms for uninitialized variables 4 There is now only one kernel for both REX and using the Ethernet One does not have to reboot another kernel to use the Ethernet Page 110 The following enhancements were made to REX 1 Support for more than 80 states was added The statelist menu now can be advanced to the next page of states by typing gt to the prompt after the menu is entered The previous page is accessed by lt Alternatively the nth page can be directly accessed by typing set statelist n where n is the desired page For example s s 1 enters the first page The upper limit on states is probably between 150 and 200 depending on how much other code is in the Spot file 2 Information concerning errors which occur in the interrupt routine and are caught and recovered by the kernel is stored in the error file In addition when an error occurs the clock is stopped and all files closed
190. eft mouse button in the scroll bar trough or on the arrow buttons to the left or right of the slider The minimum display interval is 1 millisecond the maximum is 500 milliseconds The scroll bar on the right controls the gains of Mex s displays You can set the gain by moving the mouse cursor over the scroll bar slider pressing the left mouse button and moving the mouse up or down or by clicking the left mouse button in the scroll bar trough or on the arrow buttons above or below the slider Increasing the display gain may be helpful in discriminating low amplitude waveforms Note this scroll bar affects only the displays not the internal data The scroll bar on the top controls the latency between threshold crossing and stimulation for antidromic collision experiments You can set the latency by moving the mouse cursor over the scroll bar slider pressing the left mouse button and moving the mouse left or right A vertical red line and a value will appear indicating the latency in milliseconds The value and line will disappear as soon as you release the left mouse button If you want to the latency value and line to remain on the display set the latency by clicking the left mouse button in the scroll bar trough or on the arrow buttons to the left or right of the slider The minimum latency is 300 microseconds after the threshold the maximum is the display interval To start the antidromic stimulation click on the antidromic toggle in the os
191. emoved The following menus have been added or changed wind mir has been split into windows and mirror Menu offsets_eye has been added Menus control param and dsplay have been changed A number of default display configurations have also been added to the raster display Displays from 1 to 16 rasters are now available REX 3 10 Jun 87 Release 3 10 has been converted to run under the new real time 11 73 kernel that utilizes 22 bit addressing A number of advantages result 1 All REX processes are now compiled split 1 D This yields much more room for paradigms and more complicated raster displays 2 The Unix kernel utilizes full 22 bit addressing Multiple loaded paradigms now reside in memory instead of being swapped out This makes changing processes almost instantaneous A bug was present in the old kernel that caused intermittent system crashes most often when changing processes or escaping to the shell This condition no longer arises given the much larger memory available One should no longer need to follow such precautionary steps as ending the clock or explicitly stopping or killing the current process before executing a change process command One can also escape to the shell at any time even with the clock on without fear of a crash 3 The interrupt part of REX now runs in the 11 73 s supervisor mode instead of kernel mode as before Such errors in the interrupt routine as segmentation violations stack overflows etc us
192. end long rnum rnum ramp number ADDITIONAL HEADERS REQUIRED None DESCRIPTION ra_phiend Ends phi blinking The variables ramp rnum ra_phidevice ramp rnum ra pontime and ramp rnum ra_pofftime must have been previously initialized RETURN VALUE Returns 0 EXAMPLE ra_phiend 0 End phi blinking on ramp number 0 SEE ALSO ra_new ra_phistart ra_start ra_tostart FILE rex act ramp_act c Page 57 Memory Array Controls Rex allows users to define up to 16 arrays of arbitrary values that can be used to control the d a converters This allows greater flexibility than the simple linear arrays provided by the ramp generator ma_cntrl Pma_cntrl Control memory array resources SYNOPSIS ma_cntrl int num int map int count int rate int repeat Pma_cntrl int num int map int count int rate int repeat num number of the memory array map pointer to memory array data count number of points in memory array data rate number of milliseconds to wait before sending next element repeat number of times to repeat memory array ADDITIONAL HEADERS REQUIRED none DESCRIPTION ma_cntrl registers a user defined array with the int process Once registered the contents of the memory array may be output to a d a converter by linking the array to the port using the da_cntrl commands above To use ma_cntrl you first allocate space for the array then assign values to the array elements You then call ma_cntrl to register the p
193. eo pixels by 2 video pixels Page 165 REX ACTIONS Rex 7 2 introduces a new control protocol You can now send commands to GLvex using a set of actions All of the actions take points to global variables as arguments The reason for this change is to provide an interface that is more simple and robust The earlier command protocol required you to load values into a char buffer then call a function to send the buffer to Rex You had to break int and float variables into byte arrays by hand Getting the order of the bytes wrong resulted in nonsensical displays Also filling out the buffer required a lot of coding which was both tedious and error prone With the actions control protocol you assign values to global array elements then call the action with the arrays as arguments The action takes care of assembling the buffer for GLvex One disadvantage of the actions control protocol is that all of the new vex actions are non batchable That is only one vex action can be called per state You cannot write an action that calls a series of vex actions If you try only the last action will be executed This means that your paradigms will have more states However you will have to write fewer actions so your spot files will be shorter All spot files using Rex actions must include the header file GLcommand h and either the header file pcsSocket h or the header file pcemsg h depending on whether you are using the ethernet or parallel I O communic
194. er can range from to 255 The sum of the start and length parameters cannot exceed 255 The luminance range of the gray scale is always 0 to 255 The size of the steps between luminances is determined by the length of the gray scale This command is used to initialize a gray scale for continuous tone stimuli Example action DE This action sets up a 128 byte gray scale starting at lookup table index 64 in objects 5 and 10 list 5 10 gray void unsigned short index int i index 0 vexbuf index SET_OBJECT_GRAY_SCALE vexbuf index 2 number of objects to set for i 0 i lt 2 i vexbuf index list i I list of object numbers vexbuf index 64 F start of gray scale vexbuf index 128 F length of gray scale other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not Page 246 SET_LUT_ENTRY_CLR This a batchable command that sets the colors in a variable number of color lookup table entries for all objects The first parameter is the number of lookup table entries to set Each lookup table entry requires four parameters the table index and the values for the red green and blue guns for that index These parameters can range from 0 to 255 Example action E This action loads counter phase red and g
195. er of objects in second list for i 0 i lt n_in_scnd i vexbuf index scnd_Ist i object number vexbuf index fld3 number of fields to present second list to_vex index If the digital sync is enabled GLvex will return three or four signals from this command depending on whether there is a gap between presentations of the two lists of objects The signal FIRST_ON 245 is sent at the beginning of the video field in which the first list of objects is turned on The signal FIRST_OFF 244 is sent at the beginning of the first video field of the gap if any The signal SECOND_ON 243 is sent at the beginning of the video field in which the second list of objects is turned on The signal SECOND_ OFF 242 is sent at the beginning of the video field in which the second list of objects is turned off Otherwise GLvex will not return any signal after this command If the video sync is enabled the rex video sync square will flash white for the first field in which the first list of objects is turned on for the first field of the gap if any for the first field in which the second list of objects is turned on and for the first field in which the second list of objects is off Page 257 SET_FP_LOCATION This is a batchable command that sets the position of the fixation point on the screen The X and Y coordinates must be floating point values It requires eight parameters the first four of which are the four bytes of
196. es irer es ane ated Ta ae a a eS 74 Debugging Aids sins AA AAA AAA A AAA A 74 Endless abona 74 Arguments to actions are not passed correctly o ooooooooo 74 REX Graphical User Interface 77 TOCAN A A A A A A A EGE 77 Process Switching Tool bar 0 ii ea aad 78 O a apd atte Soe OR 78 Page iii Displays sates cee ies ieee ees ind eee Lae ates alts 80 EntrllBi 0 Ad ile o AAs ne ale 80 Data A A te pee has Mgt eens Meet ees 80 Int Process Toolbar s inca as edhe th aie ba Sig 80 Controls Men uc kus eee petits a aii 81 States Menu usec se ciao a signe sate o tae eaten gine seh gai soa 82 User Menus E la eek GAS ate oy ea eee da ee ss 83 EJE With e e ad ee EE sO AR gs a de EE EE 85 Analog e ee he eh ee et 87 Sac Detect maree cose seeds ane dd Hee Soke Pee sed Moyea otra 89 BS alg deg tia EA E NA O E Madea eben ies 89 Control Panel isto eas seeing pte EN ied CMMs EOS ORE ERE 90 Dita Displays ares ah OS tne pale 92 Window Display i2 6 2 4 aaa 92 Running Line Display caie eta piant tn a a a T a aa i e 95 R ster Displayen nn na a E E dus E A owas 97 REX Version Release Notes 103 REX 7 6 LINO oer II E E EE eed A T ah ee ata 103 REX 7 3 1 Sepz2002 dios 103 REX 74 29 Mar 2002 6 5 tae na aada bea ae alae wa ae aoe ES 103 REX 7 320 Aug 200402 OS aces Oe iy eee e Diy eS 103 REX 72 Mar 200 Ls OS guste aie Bare E ee oie 103 REXTA SS Feb 200 lire oats rd das 103 REXIA Jan 95 4 gS A AA A ES A 104 REX S O S April caci n SERA GRY SAMI DOR
197. esponds to the color of its trace in the display The title of the toggle shows the signal carried in that channel The rline toggle determines whether the running line level is displayed The units toggle determines whether unit activity is displayed The width of the display and the display rate determine the length of the epoch of data displayed If you increase the width of the window or reduce the display rate you will see a longer period of data The Running Line display can operate in either continuous or triggered modes By default the display is in continuous mode To put the display in triggered mode click on the button labeled i Continuous Its indicator will change color to green and its label will change to i Triggered In triggered mode the display sweep will start when the running line level reaches the trigger level and continue to the end of the display Set the trigger level in the Level numerical field The trigger is a level trigger not an edge trigger In triggered mode the display has repeat and one shot modes Be default the display in repeat mode In this mode a new sweep will start after the previous sweep completes each time the running line level reaches the trigger level To put the display in one shot mode click on the button labeled i Repeati Its indicator will change color to green and its label will change to i One Shot In triggered one shot mode the display sweep will start when the running line level reaches
198. est the speed of your animations If you find that your animation runs slower than you specified you should increase the specified speed to compensate How much drawing can be done in each vertical refresh cycle depends on the graphics hardware Generally the more expensive the hardware the more it can draw in each vertical refresh cycle Of the machines I have tested I have found that the SGI 320 workstation provide the best animation performance for the price of Windows NT workstations If you need higher animation performance Dell Hewlett Packard and IBM among others offer high end graphics workstations using Intergraph graphics that may be better Further though I haven t done it yet it would not be difficult to port GLvex to unix and X windows so that it could be run on high end unix graphics workstations such as the SGI Octane series Stimuli Most GLvex static stimuli are sets of square checks that are laid out in a rectangular matrix to form the desired pattern The resolution of a pattern refers to the number of rows and columns of the check matrix Pattern checks are not the same as video pixels A video pixel is the smallest element that the graphics board can draw on the screen and depends on the hardware configuration A pattern check is the smallest element of a pattern and is a logical concept Each pattern check can be several video pixels high and wide The exceptions to this are bar annulus and circle stimuli and TIFF image
199. et to 0 If you try to compute a transform that produces movement in depth for a 2 D flow field you will get the following message compute_transform Warning no depth movement allowed in 2 D flow fields Setting trans v trans w trans p to 0 The transform will be computed but with the depth parameters set to 0 If you requested a transform with nothing but movement in depth then the flow field will not move when turned on Page 311 Contrast Specification In specifying patterns from the keyboard you must specify the contrast of the pattern normal or reverse even if it is a continuous tone pattern Failure to specify the contrast will result in the pattern being drawn with unpredictable luminances However GLvex will not print any warnings Page 312 Color Luminance Specification Warnings All color and luminance values can range only between 0 and 255 If you try to specify a color or luminance value outside this range you will get a warning similar to the following red value 256 out of range If you enter an illegal value from the keyboard no change will be made If you enter an illegal value from rex the object you are changing may take on an unpredictable color or luminance Sample Spot File Demonstrating Socket Communication include hdr ramp h include localEcodes h include memSac h include GLvex_com c include shuffle c define WINDO 0 define WIND1 1 define RAMP_DONE 1 define RAMP_ON 2 de
200. eturns 0 or when a photo cell is triggered by the video sync object All of the actions that can be done using the keyboard commands described above can also be done from rex using the proper sequences of the commands described below Page 233 SET_ERASE METHOD This is a batchable command that sets which erase method will be used This command requires 1 parameter which must be EACH OBJECT 0 or WHOLE SCREEN 1 If the parameter is EACH_ OBJECT then v3GLvex will erase objects by drawing a rectangle the color of the background over them If the parameter is WHOLE SCREEN then GLvex will erase objects by clearing the entire screen The EACH OBJECT method is faster but the WHOLE SCREEN method is more robust The default method is EACH OBJECT Once the erase method is set it will remain in effect until changed so you only need to call this command once Example action setup unsigned short index index 0 other batchable commands vexbuf index SET_ERASE_ METHOD vexbuf index WHOLE_SCREEN defined in GLcommand h other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not Page 234 ENABLE_REX_VIDEO_SYNC This is a batchable command that enables the video sync for synchronizing the display with rex It does not require any parameters When the video
201. everse contrast patterns Example action pp This action draws Walsh patterns in three objects short patterns 7 18 21 24 43 63 short ptrlst 6 0 y short ob 3 5 2 y short size 4 draw_walsh unsigned short index short i j static int rs_shift 10 static int tricntr 6 for i 0 i lt tricntr i ptrist i i shuffle tricntr rs_shift ptrist index 0 vexbuf index DRAW_WALSH_PATTERN vexbuf index 3 number of objects for i 0 i lt 3 i j ptrist i vexbuf index ob i object number vexbuf index patterns j pattern number vexbuf index size pattern check size vexbuf index 1 positive contrast other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not Page 269 DRAW_HAAR PATTERN This is a batchable command that draws a Haar pattern in an object The first parameter is the number of objects to draw in Each object requires four parameters the object number the pattern number the pattern check size and the contrast The pattern numbers can range from 0 to 255 The contrast can be either 1 for normal contrast patterns or 1 for reverse contrast patterns Example action J This action draws Walsh patterns in three objects
202. exTimeStim amp num objects amp fields to nextstate on 0 tst_rx_new if the digital sync is enabled to nextstate on PHOTO_CELL amp drinput if the video sync is enabled FILE rex act vexActions c Page 186 PvexSequenceStim presents a group of objects for one interval waits presents a second group of objects for another interval SYNOPSIS PvexSequenceStim int nFrstObj int firstList int firstFields int gapFields int nScndObj int secondList int secondFields nFrstObj number of objects in the first group firstList array of object numbers in the first group firstFields number of video fields to present first group of objects gapFields number of video fields to wait before presenting second group of objects may be 0 nScndObj number of objects in the second group secondList array of object numbers in the second group secondFields number of video fields to present second group of objects DESCRIPTION This action allows you to present one group of objects for up to 255 video fields wait for up to 255 video fields then present a second group of objects for up to 255 video fields RETURN VALUE If the digital sync is enabled GLvex will return three or four signals from this command depending on whether there is a gap between presentations of the two lists of objects FIRST _ON 245 is sent when the first list of objects is turned on FIRST OFF 244 is sent at the beginning of the gap if any SECOND_
203. example if a ramp were specified with a length of 10 degrees and the reference point in the middle the ramp would begin 10 degrees before the reference point and continue to 10 degrees after the reference point length is one half total length If however the reference point were the beginning the ramp would start at the reference point and continue for 20 degrees type must have one and only one of the following bits set RA_CENPT 02 reference point is the middle or center of ramp RA_BEGINPT 04 reference point is the beginning of ramp RA_ENDPT 010 reference point is the end of ramp In addition to the above flag bits another bit causes the mirrors to begin motion at a point before the actual start of the ramp This initial distance is calculated to provide 25 msec of acceleration time for the mirrors to reach a stable velocity before reaching the starting point of the ramp Therefore if a stimulus is illuminated at the starting point of the ramp the mirrors will already be at constant velocity RA _NO25MS 01 If set do not add acceleration distance to beginning of ramp Page 49 Note well that ra_new or Pra_new must be called before every ramp even if the parameters of the ramp haven t changed from the previous ramp For example if the same ramp is to be output over and over ra_new or Pra_new must be called between each one Variables controlling the ramp may be accessed from user written C code if needed However
204. exbuf index lobyte breakTwo lo byte of the step number on which to trigger other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not The hibyte and lobyte functions are defined in GLvex_com c ERRORS AND WARNINGS There are a number of conditions that will result in errors or warnings Errors are fatal and require that you exit GLvex and fix the problem Warnings are not fatal and GLvex will continue execution but you may not be able to access all of the functions or get the result you were expecting Page 303 Memory Management Errors During the initialization phase and when computing ramps and flow fields GLvex dynamically allocates the memory it needs on the host computer Failure to allocate memory for objects is fatal and will cause GLvex to quit Failure to allocate memory for ramps or flow fields is not fatal but if you attempt to run a ramp or flow field that could not be allocated you will get unpredictable results Page 304 Object memory errors GLvex allocates space for the object structures stimulus templates and flow field buffers in the host computer memory If there is not sufficient host memory for the requested number of objects you will get an error message similar to the following Unable to allocate memory for 25 objects Exit and invoke
205. exclusive non transferable license and right to use PC REX No right is granted for any use of PC REX by any third party RECIPIENT will be responsible for assuring that PC REX will not be released or sold to any other party without the prior written approval of LSR 3 RECIPIENT guarantees that PC REX and any modified versions thereof will not be P R ublished for profit or in any manner offered for sale to THE GOVERNMENT If PC EX is modified or enhanced using funds from THE GOVERNMENT THE GOVERNMENT owns the results whether PC REX is the basis of or incidental to a contract PC REX may be used in contracts with THE GOVERNMENT but no development charge may be made as part of its use 4 PC REX is provided as is without warranty Neither THE GOVERNMENT or LSR is liable or responsible for maintenance updating or correcting any errors in any materials provided In no event shall THE GOVERNMENT or LSR be liable for any loss or for any indirect special punitive exemplary incidental or consequential damages arising from use possession or performance of PC REX 5 RECIPIENT will own full rights to any data files databases or images created using PC REX Page 137 By signing here RECIPIENT signifies agreement to these terms and conditions of the PC REX distribution as detailed ab
206. f trials as a conditioning stimulus while running ramps on a per trial basis Vex 4 4 also allows users to load patterns from Rex Vex 4 5 adds circular motion to the ramp generator Also ramps can oscillate or run continuously GLvex is a port of Vex 4 5 to OpenGL and the Windows NT operating system I did this to eliminate the dependence on any particular graphics card and to eliminate the need for the Pharlap 286 Dos Extender GLvex is a 32 bit application We have found that in some LCD Projectors the video fields are not phase locked to the vertical sync pulse This means that the display cannot be synchronized to the data by software alone GLvex adds a video syncing object flashes when synchronization is necessary You can place this object anywhere on the screen This video sync can be disabled Included with this manual is the schematic for a photo diode trigger that we use in the LSR GLvex adds automatic correction for tangent error For calibration users now input the distance from the subject s eyes to the screen and the width of the initial calibration pattern both in millimeters instead of the number of Rex units per pixel GLvex adds the ability load ramps from Rex This allows users to have ramps that vary in velocity i e accelerating or decelerating ramps GLvex enables users to choose the object erase method The default WHOLE SCREEN is to simply clear the screen This method is slower particularly on low end graphics boards
207. f analog data the eye window display an oscilloscope like display of analog and unit data the running line display and a histogram raster display of unit data the raster display The X Y and oscilloscope displays could be superimposed but the raster display was separate To view raster data the other displays had to be disabled Because of the resolution of the display a maximum of 16 rasters or histograms could be displayed a serious limitation in conducting experiments with many conditions With the Photon window system we are able to use resolutions of up to 1280X1024 Also the Photon window manager maintains 9 virtual desktops allowing various data displays to be spread out while retaining ease of access By placing each display in its own window we are able to provide multiple X Y oscilloscope and raster displays Because of the higher resolution raster displays can have up to 64 plots By using spike density functions instead of histograms summary and trial by trial data can be superimposed Because we can provide multiple copies of each type of display experimenters can have both triggered and free running oscilloscope displays high and low gain X Y displays and multiple sets of rasters Better performance tracking Experimenters frequently need to monitor the progress of an experiment or subjectis performance This is done by continuously updating variables such as percent correct number of trials per block or number of trials
208. f the trial when time is not critical Then use the SWAP_BUFFERS command to actually display the objects NOTE This procedure makes the display and draw buffers different so you can t do anything to GLvex between the PRELOAD_STIM and the SWAP BUFFERS commands Also you may need to call the PRELOAD STIM command again after the SWAP_ BUFFERS command to synchronize the display and draw buffers Example actions E This action will preload object 3 on and object 4 off simultaneously preload_stim unsigned short index index 0 F other batchable commands vexbuf index PRELOAD_STIM vexbuf index 2 number of objects to load vexbuf index 3 I first object number vexbuf index OBJ_ON GLvex_com c define OBJ_ON 1 vexbuf index 4 second object number vexbuf index OBJ_OFF GLvex_com c define OBJ_OFF 0 F other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not Page 252 SWAP_BUFFERS This is a non batchable command that swaps the display and drawing buffers It requires no arguments Example action it This action will swap the display and draw buffers swap_buffers unsigned short index index 0 vexbuf index SWAP_BUFFERS to_vex index return 0 If the digital sync is enabled GLvex will re
209. file by selecting the Close Waveform File item from the Files menu The second save button toggles the saving of data during antidromic collision tests The DA button remains inactive until you have opened a file and have switched into antidromic mode While Mex is saving antidromic data to disk the button will display a waveform picture next to the floppy disk picture Also the clock button is inactive When you stop saving antidromic data Mex automatically closes the antidromic file Roots After you have entered the settings and launched and positioned the displays you can save this information to a file so that you can start Mex again with the same settings and display geometry Click on the Write Root entry in the Files menu to bring up the file selection dialog Enter the directory and Page 328 file name and click Save Once you have a root file you can have Mex read it a start up by entering the name of the file after the r command line argument mex r root or you can have Mex read a root after it has started by clicking on the Read Root entry in the Files menu and entering the name in the file selection dialog Running Mex Displaying Data The Oscilloscope Display The oscilloscope display has buttons in the menu bar at the top of the display allow you to select the electrode to display if you are Ai am eae electrodes set the weet slope draw a grid over the display and toggle antidromic activation If you hover the
210. fill the entire 240 element array You must use the data length element to read the waveform from the array The complete record is as follows define MEX_WAVE_LEN 240 typedef struct short int pTrig pointer to element of data at trigger ignore short int pDataTop pointer to last element of data ignore unsigned long tim F time of element at trigger crossing short int elc electrode number short int spk neuron number will be 1 if unclassified short int trglndx index of data element at trigger crossing short int valley minimum value of waveform short int valTim F time of minimum value relative to trigger short int peak maximum value of waveform short int peakTim time of maximum value relative to trigger short int height maximum minimum short int width time of maximum time of minimum short int dataLen number of elements of data occupied by waveform short int data MEX_WAVE_LEN the waveform data WAVEDATA Antidromic Data Mex saves data from antidromic collision tests to disk in binary format The format consists of variable length records containing an unsigned short integer holding the length of the record followed by a array of short integers containing the analog data To read the file first read a short integer from the file to get the length of the following array Then read the array of short integers Repeat until the file is empty Pa
211. fine TARG_SWITCH 4 define LOCATE 8 F begin user action block int rampFlag 0 int vexMessage 0 int mfTargX 0 int mfTargY 0 int rLength 150 int rSpeed 5 int trialCounter 1 int blockcount 0 number of blocks of trials int totalTrials 0 int correctTrials 0 int errorTrials 0 int percentCorrect 0 int currstim int targsiz 100 int pick_ramp_direction static int ptrist 2 NUM_STIM 0 static int rs_shift 10 int rDir int index int i char flbuf if trialCounter lt 0 trialCounter NUM_STIM for i 0 i lt trialCounter i ptrist i i shuffle ptrist to randomize stimulus conditions shuffle trialCounter rs_shift ptrist blockcount Page 313 currstim ptrist trialCounter 1 index to this condition totalTrials memSactTrialList currstim total F set the time of the target fixation point gap set_times rampon memSacList currstim delay 1 F set the location of the target window switch memSacList currstim direction case 1 rDir 0 break case 1 rDir 180 break define the ramp index 0 vexbuf index NEW_RAMP vexbuf index 1 number of ramps vexbuf index 1 ramp number vexbuf index hibyte rLength high byte of ramp length vexbuf index lobyte rLength low byte of ramp length vexbuf index hibyte rDir
212. five racks each rack holding 24 modules The racks are mounted on standard BUD aluminum panels See Figure 2 I O RACK LAYOUT Connect 5 from external power supply 50 pin Move fuse from top flat cable connector position to bottom ote ALO omen ERP Module Barrier Strip SS Panduit Wire Duct Notes 1 Mount single and double row barrier strips on 3 4 spacers 2 All positions on single row barrier strip are connected to 5v 3 Do not use computer s power supply to power 1 0 rack You must have an external 5v supply Connect this supply to connectors in upper right hand corner of board Then move fuse from top position to bottom position it just pulls out of pin sockets 4 Barrier strips have 14 positions Figure 2 I O Rack Layout Page 125 Also mounted on the BUD panel are two rows of terminal barrier strips The single row strip is wired to 5v The double row strip is not connected to power or ground These strips provide space to wire resistors and pots Port Z Output Port 1 Input Port Ce Input ALU UU UUs ANA Rack O Ports 0 3 port 3 is a control port Port 6 Output Port 5 Output Port 4 Output AU DDD AAC AAA AAA l Rack 1 Ports 4 7 port 7 is a control port Note Every fourth port on an 8255 programmable peripheral interface chip ls a control port Do not use this port to address VO modules Figure 3 Port Layout Each eight modules form a group called a port A
213. flow field Three dimensional flow fields are required for yaw pitch and zoom movements see PvexNewF low RETURN VALUE GLvex will return the signal BATCH DONE 241 when it completes this action EXAMPLE int num 1 int object 2 int rad 100 radius of 10 degrees diameter of 20 degrees int width 100 width equal to radius int height 100 F height equal to radius int near 500 int far 1500 int coverage 25 int size 4 A state do PvexDrawEllipticalFlowField 8 num amp object amp rad amp width amp height amp near amp far amp coverage amp size to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 202 PvexMaskFlowField masks part of a flow field SYNOPSIS PvexMaskFlowField int nObjects int oList int wList int hList int xList int yList nObjects number of objects to mask oList array of object numbers wList array of mask widths in 10ths of a degree hList array of mask heights in 10ths of a degree xList array of x coordinates of mask centers in 10ths of a degree yList array of y coordinates of mask centers in 10ths of a degree DESCRIPTION This action allows you mask part of a flow field stimulus The x and y parameters are position relative to the center of the flow field object If the width and height variables are both non zero the mask will be rectangular For a circular mask set the width variable to the desired radius of the mask in te
214. flow field 1000 rex units wide and 700 rex units high with 1 of its area covered by checks and the checks will be 4 pixels square The near plane will be 1000 rex units from the viewer and the far plane will be 3000 rex units from the viewer If the visual display subtends 1 centimeter degree of visual angle then the near plane will be 1 meter from the viewer and the far plane will be 3 meters from the viewer In the Om command the letters in brackets stand for the dimensions and location of an occluding mask over the flow field You can get an explanation of the parameters by typing Om lt return gt to get a help message similar to the following w width of mask h height of mask Page 157 X x coordinate of mask in object y y coordinate of mask in object Current values for object 0 width 100 height 100 x 100 y 0 Example commands Om 200 200 100 0 This command will create an occluding mask in a flow field that is 200 rex units wide and high and centered 100 rex units to the left of the center of the object In the Of command the letters in brackets stand for the parameters defining the way in which the checks in the flow field will move You can get an explanation of the parameters by typing Ot lt return gt to get a help message similar to the following x angle of 2 D translation in degrees 0 to 360 z angle of 3 D translation in degrees 90 to 90 v translation velocity in degrees sec r rate
215. from the Spot file to determine if a source is within the bounds of a window The wd _src_pos and wd_src_check actions specify the x and y components of the source that governs the window position and the source for the window to check Possible sources for both are WD_DIRPOS The source is a position specified by the wd_pos action src_num is ignored WD_RAMP_X source is the X component of the internal ramp generator src_num specifies the ramp generator number WD_RAMP Y source is the Y component of the internal ramp generator src_num specifies the ramp generator number WD _JOY_X source is the X component of the joystick src_num is ignored WD_JOY_Y source is the Y component of the joystick src_num is ignored WD_DA source is the current output of the d a converter src_num specifies the d a converter number WD_SIGNAL source is a signal src_num specifies the signal number WD_MEM source is an internal memory array src_num specifies the internal memory array number RETURN VALUE Returns 0 EXAMPLE wd_src_check 0 WD_SIGNAL 0 WD_SIGNAL 1 If the horizontal eye is signal 0 and the vertical eye is signal 1 this action will set the source for window number 0 to check to eye position The following examples then specify various sources for the x y position of the window wd_src_pos 0 WD_DIRPOS 0 WD_DIRPOS 0 The position of window 0 is controlled by the wd_pos action wd_src_pos 0 WD_RAMP_X 0 WD_RAMP Y 0 The
216. g 2001 This release includes support for PCI bus A D cards REX 7 2 1 Mar 2001 This release allows actions to have pointers as arguments as well as long integers This allows actions defined in states to have variable arguments and it allows actions to return values that can be used in the spot file The rex actions library includes versions of each action that take pointers as arguments facilitating the declaration of actions in states The rex actions library also includes a set of 60 actions for controlling the GLvex stimulus display program These actions cut down the amount of code you have to write and reduce the potential for error when using GLvex This release also allows the code declaration in a state to have a pointer as well as a constant That is this release allows the declaration code amp code in a state as well as the declarations code 1100 or code FPONCD REX 7 1 5 Feb 2001 This release is built using the Photon window system to provide a graphical user interface This new interface provides multiple eye window running line and raster displays The eye window display has a storage mode that allows you to see the full path of eye movements The raster display allows multiple pages with up to 64 plots per page The command line menu and verb noun interfaces have been replaced with graphical dialogs Page 103 REX 5 4 1 Jan 95 This release includes work done on the REX window displays A new display combining both th
217. g factors This command requires four parameters The first two parameters are the hi and lo bytes of the distance between the viewer and the screen in millimeters The last two parameters are the hi and lo bytes of the with of the calibration pattern in millimeters Example action short screenDistance 572 distance between viewer and screen short patternWidth 900 width of initial calibration pattern set_scale void unsigned short index index 0 F other batchable commands vexbuf index SET_REX_SCALE vexbuf index hibyte screenDistance vexbuf index lobyte screenDistance vexbuf index hibyte patternWidth vexbuf index lobyte patternWidth other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not The hibyte and lobyte functions are defined in GLvex_com c Page 239 SET_BACK_LUM This is a batchable command that sets the luminance or color of the screen background It requires three parameters the values for the red green and blue guns These parameters can range from 0 to 255 Example action pe This action will set the background to a specified color bgrnd_cir long r long g long b unsigned short index index 0 vexbuf index SET_BACK_LUM vexbuf index r vexbuf index g vexbuf index
218. gbrgb rgb rgb rgb rgbrgbrgb rgb rgb rgb rgbrgbrgb rgb rgb rgb The letters r and c indicate the number of rows and columns in the pattern The number 3 indicates that each pixel is defined by 3 values r g and b This number can only be 3 The maximum number of rows or columns is 255 The pattern may be rectangular i e you do not need to have the same number of rows and columns The letters r g b indicate the values for red green and blue for the individual checks in the pattern Example of a file for a user defined pattern with 8 rows and 8 cols This file defines a red and a green bar centered in a blue region The name of the file might be P1000 883 00255 00255 00255 25500 02550 00255 00255 00255 00255 00255 00255 25500 02550 00255 00255 00255 00255 00255 00255 25500 02550 00255 00255 00255 00255 00255 00255 25500 02550 00255 00255 00255 00255 00255 00255 25500 02550 00255 00255 00255 00255 00255 00255 25500 02550 00255 00255 00 255 00255 00255 00255 25500 02550 00255 00255 00255 00255 00255 00255 25500 02550 00255 00255 00255 Example of a file for a user defined pattern with 8 rows and 2 cols This file also defines a red and a green bar but does not have the blue region The name of the file might be P2000 823 25500 02550 25500 02550 25500 02550 25500 02550 25500 02550 25500 02550 25500 02550 25500 02550 Example action E This action draws user defined patterns in three objects Page 278 gi short patterns
219. ge 338
220. h yaw span coher to movie on 0 tst_rx_new movie do PvexMakeFlowMovie amp num amp nFrames objects to moviestart on 0 tst_rx_new moviestart do PvexToFlowMovieStart amp num amp startFrame objects to nextframe on 0 tst_rx_new FILE rex act vexActions c Page 223 PvexStartFlow starts the flow fields in a number of objects SYNOPSIS PvexStartFlow int nObjects int objList nObjects number of flow field objects objList array of flow field object numbers DESCRIPTION This actions starts the checks in the specified flow field objects moving according to the objects translation matrices You must have called the PvexDrawFlowField and PvexNewFlow actions before calling this action RETURN VALUE If the digital sync is enabled GLvex will return the signal FLOW_RAMP_START 236 when the checks begin to move If the video sync is enabled the sync object will flash white when the checks begin to move EXAMPLE int num 4 int objects 4 1 2 3 4 state do PvexStartFlow amp num objects to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 224 PvexTimeFlow runs the flow fields in a number of objects for a given number of video fields SYNOPSIS PvexTimeFlow int nObjects int fields int objList nObjects number of flow field objects fields number of video fields to show flow field objList array of flow field object numbers DESCRIPTION This actions starts the checks in
221. h is half the total length in tenths of a degree Angle is the polar angle of the ramp with 0 degrees defining motion from the monkey s left to right Velocity is in degrees second Offset is a cartesian point in tenths of a degree Spot files that use ramps must include the rex hdr ramp h header file Type defines the reference point of the ramp RA_CENPT 02 reference point is the center of the ramp RA_BEGINPT 04 reference point is the beginning of the ramp RA_ENDPT 08 reference point is the end of the ramp RA_CLKWISE 16 computes a clockwise circular ramp RA_CCLKWISE 32 computes a counter clockwise circular ramp Action defines what happens to the object on the ramp after the ramp stops OFF AFTER RAMP 0 object turns off after the end of the ramp ON AFTER RAMP 1 object stays on after the end of the ramp Example action This action defines a ramp short length 200 short direction 15 short speed 20 short rfx 100 short rfy 20 make_ramp void unsigned short index index 0 vexbuf index NEW_RAMP_FROM_FP vexbuf index 1 number of ramps vexbuf index 1 ramp number vexbuf index hibyte length 1 high byte of ramp length vexbuf index lobyte length 1 low byte of ramp length vexbuf index hibyte direction 1 high byte of ramp direction vexbuf index lobyte direction 1 low byte of ramp direction vexbuf index hibyte speed 1
222. h on TARG_SWITCH 8 vexMessage to waitsac on RAMP_DONE amp rampFlag code TARGONCD do resetSwitch rl 50 time 100 to waitsac on RAMP_DONE amp rampFlag to floffemd do flash_off to ramprun on TARG_SWITCH amp vexMessage to waitsac on RAMP_DONE amp rampFlag code TARGOFFCD do resetSwitch rl 40 to waitsac on RAMP_DONE amp rampFlag code FPOFFCD time 100 rl 60 to waittarg on WD0_XY amp eyeflag to error code SACSTARTCD time 100 to correct on WD1_XY amp eyeflag to error code REWCD do goodTrial to rewon do dio_on REW rl 35 time 50 to rewoff rewoff error last abort J do dio_off REW to last code ERRCD do badTrial time 1000 rl 25 to last do awind CLOSE_W rl 15 to first rewoff last move eye win to follow ramp object move_win status ON begin mfirst halt qrywts qryvex tstmsg stgwnd wait to halt to qrywts on PSTOP amp softswitch to qryvex on RAMP_ON amp rampFlag do object_location to tstmsg on 0 tst_rx_new do tstVexMsg to stgwnd on LOCATE amp vexMessage to wait do targ_wnd to tstmsg on 0 tst_rx_new to wait time 50 to tstmsg on 0 tst_rx_new to halt on RAMP_DONE amp rampFlag to qryvex Page 321 Page 322 MEX User s Manual John W McClurkin Ph D Laboratory of Sensorimotor Research National Eye Institute National Institutes of Health Overview Mex is a
223. h the time and amplitude display For Mex to classify a waveform as belong to a neuron the parameters of that waveform must fall within all of the ranges that you have specified for that neuron Mex will draw the points for waveforms that meet your criteria for a neuron in that neuron s color Mex draws points for waveforms that don t meet criteria for any neurons in white If you have set up boxes for several neurons Mex prioritizes classification first purple then green then blue For example if the parameters of a waveform fall within the ranges you set for purple neurons and for green neurons Mex will classify the waveform as belonging to the purple neuron When you set criteria for a neuron a hollow box defining the range of parameters of those criteria is drawn in the display A small filled box is also drawn in the upper left part of the display The Page 334 purpose of this box is to allow you to rapidly switch the display among the parameters and axis positions you have chosen For example if you set some criteria while plotting Peak Latency versus Peak Amplitude and other criteria while plotting Valley Latency versus Valley click on an icon box with the left mouse button will switch the display to plot the parameters and position the axes as they were when you set the criteria represented by that icon This allows you to rapidly switch among the parameter sets you want to use without having to use the Axis Parameters dialog B
224. h when it attempts to display the real time variables dialog Comments Comments are allowed anywhere and unlike comments in the C compiler they may be nested They are stripped out of the output file State set declaration The beginning of the state set declaration is marked by the delimiter Following the delimiter each paradigm must start with the keyword ident or id followed by the paradigm number which is displayed on the screen at run time This is not optional and Spot will give an error if it is Page 19 not included Optionally the keyword restart followed by the name of an initialization subroutine may follow A id 300 restart rinitf declaration of state set chains A Spot file may have multiple independent chains of states which are executed asynchronously Each of the asynchronous chains must start with a name followed by an open curly brace The entire chain must then be terminated by a close curly brace After the opening curly brace the next statement must be status or stat followed by ON or OFF to indicate whether the chain is on or off at start or restart time For example chainA status ON state declarations States Each state begins with its name followed by a colon e g fpon The initial state in each chain must be indicated by preceding it with the keyword begin An example of the first state in a chain begin fpon code FPONCD rl 30 time 2000 rand 1000 to stimo
225. he Title field displays the signalis title This is not an editable field You can reduce the gain of the signal with the Atten slider High attenuation represents low gain The Offset slider sets the base location of the channelis signal Raster Display You launch the raster display by selecting the Raster Display item from the Displays menu in the Process Switching tool bar The raster display can show up to 64 plots per page The number of pages is v 3D x File Classes Rasters Stat Stop Re init Prior Next 106142 1m TPT i ry e mira to 1d Ea al i mn i mt iis i mimes ii j i HOHE a Mi IN 1041 tu 1 EU nmw UM EE OT O prosa smmm n l mom mijan a limited only by your RAM and virtual memory The plots can show combined rasters an spike density functions shown or rasters or spike density functions alone Each plot can show the data from up to 10 neurons The plot can also show the time of occurrence of one other event in the trial the red and green marks in the plots on the left above Configuration To use the raster display you must first tell Rex how you want to organize your data and how you want to lay out each raster page Data organization To tell Rex how to organize your data click on the Classes button in the menu bar and select the Build Select Specs item from the menu here This brings up the Ecode Selection Set Page 97 dialog The top panel contains two numerical fields for enter
226. he ramps to_vex index return 0 If the digital sync is enabled GLvex will return the signal FLOW_RAMP_ START at the beginning of the first video field in which the flow fields and ramps start moving If the video sync is enabled the rex video sync square will flash white for the field in which the flow fields and ramps start The display will continue until the RA_ONCE ramps have completed During this period GLvex will run all of the ramps but will display only those objects that you have switched ON If the digital sync is enabled GLvex will then return the signal FLOW_RAMP CHANGE at the beginning of the first video field after the ramp objects have turned stopped If the video sync is enabled the rex video square will flash white for the field in which the ramps stop At this point the flow fields will still be running You have a couple of choices now You can stop the flow fields and get out of this loop entirely by switching off the flow fields using the STOP_FLOW_ RAMP command see below If you do this GLvex will send the signal FLOW_RAMP_ STOP at the beginning of the video field after the flow field stops moving if the digital sync is enabled If the video sync is enabled the rex video sync square will flash white for the field in which the flow fields stop moving Alternately you can send the command RESET RAMPS see below GLvex will place the ramp objects at the beginnings of their respective ramps start all ramps running
227. he total length in tenths of a degree Angle is the polar angle of the ramp with 0 degrees defining motion from the monkey s left to right Velocity is in degrees second Reference point is a cartesian point in tenths of a degree For circular ramps the length is the radius of the circle and angle is the starting point of the object on the rim of the circle Spot files that use ramps must include the rex hdr ramp h header file Type defines the reference point of the ramp RA_CENPT 02 reference point is the center of the ramp RA_BEGINPT 04 reference point is the beginning of the ramp RA_ENDPT 08 reference point is the end of the ramp RA _CLKWISE 16 computes a clockwise circular ramp centered on reference point RA CCLKWISE 32 computes a counter clockwise circular ramp centered on reference point Action defines what happens to the object on the ramp after the ramp stops OFF AFTER RAMP 0 object turns off after the end of the ramp ON AFTER RAMP 1 object stays on after the end of the ramp Example action This action defines a ramp short length 200 short direction 15 short speed 20 short rfx 100 short rfy 10 make_ramp void unsigned short index index 0 vexbuf index NEW_RAMP vexbuf index 1 number of ramps vexbuf index 1 ramp number vexbuf index hibyte length 1 high byte of ramp length vexbuf index lobyte length I low byte of ramp length
228. heck size other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not The hibyte and lobyte functions are defined in GLvex_com c Page 274 MASK FLOW This is a batchable command that defines an area within a flow field where checks will not be drawn The first parameter is the number of objects in which to mask flow fields Each object requires 13 parameters The first parameter is the object number The next four parameters are the hi and lo bytes of the width of the mask and the hi and lo bytes of the height of the mask The next four parameters are the four bytes of the X coordinate of the mask in the flow field The last four parameters are the four bytes of the Y coordinate of the mask in the flow field The width height X and Y coordinates are all in rex units i e tenth of a degree of visual angle The X and Y coordinates are relative to the center of the object Negative X values are in the left half of the object and negative Y values are in the lower half of the object A flow field pattern must be specified for an object before a flow field mask can be specified for the object The width and height of the mask should not exceed the width and height of the flow field Example action T This action sets up a mask in a flow field pattern in 1 object s
229. her eye signal Selecting the Eye Offset Controls item from the Eye Win menu will display a dialog that allows you the change the offset parameters Eye Offset Parameters O Dialog Disabled Eye Offsets Override Menu Eye Horiz Off Override Menu Eye Vert Off Override F Menu Other Eye Horiz Off Override Menu Other Eye Vert Off Override Offsets are in tenths of a degree Page 86 Eye Window Summary Selecting the Eye Window Summary item from the Eye Win menu will display a summary of the parameters of all of the eye windows you have defined XPos YPos Width Height XPosNam XPos YPosNam YPos XChkNam XChk YChkNam YChk Pm eye ee ee fae Analog Sig Clicking on the Analog Sig menu button will display a menu with the following items Analog Signal Controls Analog Signal Summary Analog Signal Controls Selecting the Analog Signal Controls item from the Analog Sig menu will display a dialog that allows you to control the parameters of the analog signals saved by Rex Select the Signal Properties Signal 0 a d del Signal List ald channel 1 008 eta seconds Signal Type off Dad QO mem computed eyeh oeyeh otherh addh joyh O eyev oeyev otherv addv joyv QO d a0 Q d a1 Q d a2 Q d a3 memory source Q ramp0X Q ramp0Y Q ramp1X O ramp 1 Y Qwd0X Qwd0Y Qwd1X Qwd1Y a d variable OQ vergh Q vergy Q cycloph Q cyclopy computed signal O gazeh Qgazev Qogazeh Q ogazev
230. hese actions without testing the transmission bits or acknowledging signals from GLvex This will cause problems Monkey subject errors must be handled explicitly in the following manner Page 306 Example state loop vstwts vexst vexack othst error alloff offack abort F other states in your paradigm to vstwts to vexst on 0 tst_tx_rdy test if transmission is ready do vex_time vex command that will take a while to error on WDO_XY 8 eyeflag to vexack on 0 tst_rx_new escape when signal is received code ECODE do pcm_ack 0 I acknowledge signal from vex time 100 rand 100 to othst F other states in your paradigm code ERR1CD do reset_s 1 but don t include vex states in abort list to alloff on 0 tst_tx_rdy do off_all action that turns off all stimuli and fixation point to offack on 0 tst_rx_new do pcm_ack 0 time 5000 time out to disabl offrew no vex communications in these clwind two states Third the monkey can make an error that causes an escape from a state such as vexst in the example above that is expecting a signal from GLvex just as GLvex is about to send the signal In the above example if the actions to handle monkey errors do not send the abort command off_all before GLvex sends the signal at the end of the vex_time action you may have an extra unacknowledged signal from GLvex This situation should occur i
231. high byte of ramp direction vexbuf index lobyte rDir low byte of ramp direction vexbuf index hibyte rSpeed high byte of ramp speed vexbuf index lobyte rSpeed low byte of ramp speed vexbuf index hibyte 0 high byte of X offset vexbuf index lobyte 0 low byte of X offset vexbuf index hibyte 0 high byte of Y offset vexbuf index lobyte 0 low byte of Y offset vexbuf index RA_CENPT I reference is center of ramp vexbuf index OBJ_OFF I object switches off at end of ramp F set the location of the saccade target vexbuf index STIM_LOCATION vexbuf index 1 number of objects vexbuf index 2 object number flbuf float2byte mfTargX for i 0 i lt 4 i vexbuf index flbuf i flbuf float2byte mfTargY for i 0 i lt 4 i vexbuf index flbuf i to_vex index wd_pos WIND1 mfTargX mfTargY return memSacList currstim ecode int to_ramp_start Page 314 int index index 0 vexbuf index TO_RAMP_START vexbuf index 1 number of objects vexbuf index 1 object number vexbuf index 1 ramp number to_vex index return 0 int wndxctr 0 int wndyctr 0 int wndsiz 5 ctr_wnd wd_pos WINDO wndxctr wndyctr wd_siz WINDO wndsiz wndsiz wd_siz WIND1 targsiz targsiz return 0 int pursuitOn
232. hort wide 200 short tall 200 short obi 2 short x 20 0 short y 20 0 mask_flow unsigned short index int i index 0 vexbuf index MASK_FLOW vexbuf index 1 number of objects vexbuf index obi object number vexbuf index hibyte wide high byte of mask width vexbuf index lobyte wide low byte of mask width vexbuf index hibyte tall high byte of mask height vexbuf index lobyte tall low byte of mask height flbuf float2byte x for j 0 j lt 4 j vexbuf index flbuf j flbuf float2byte y for j 0 j lt 4 j vexbuf index flbuf j other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not The hibyte and lobyte functions are defined in GLvex_com c Page 275 DRAW_USER_PATTERN This is a batchable command that draws a user defined pattern in an object The pattern is defined in a file named Pnumber where number is the pattern number you are going to use for that pattern The first parameter is the number of objects to draw in Each object requires five parameters the object number the high byte of the pattern number the low byte of the pattern number the pattern check size and the contrast The pattern numbers can range from 0 to 65536 The contras
233. i object number to put on ramp vexbuf index RA_ONCE run each ramp once to_vex index return 0 If the digital sync is enabled GLvex will return the signal FLOW RAMP START 236 at the beginning of the video field in which the ramp starts moving and the signal FLOW_RAMP_ STOP 235 at the beginning of the first video field after the ramp stops moving Also GLvex will return the signal FLOW_RAMP_ CHANGE 234 at each step specified in the SET_TRIGGERS command see below If the digital sync is not enabled GLvex will not return any digital signal in this command If the video sync is enabled the rex video sync square will flash white for the first field in which the ramps are running and for the first field after the ramps have stopped Also the rex video sync square will flash white for one field at each step specified in the SET_TRIGGERS command see below Page 289 RESET_RAMPS This is a non batchable commands that resets ramps that were set to run only once This is ramps with a cycle type of RA ONCE The purpose of this command is to allow users to restart an RA ONCE ramp that is running in conjunction with a flow field or with RA LOOP or RA_OSCIL ramps It requires no parameters This command can be used in conjunction with the SET STIM_ SWITCH command see above to change which objects will be displayed when the ramps restart Example action reset_ramp unsigned short index index 0 vexbuf in
234. iate condition recognized in either hardware or software occurs a transition or escape to another state takes place When a new state is entered after an escape has occurred two useful things happen First a function called an action may be called Actions are usually written in the C language and must be compatible with C calling conventions The action may be passed up to sixteen arguments These arguments can be either long integers or pointers to variables Second an event code composed of an integer number and a long integer time of occurrence can be placed into the event buffer The user selects the event code Standard event codes generally come from some include file while specific codes for the particular experiment may be placed directly in the paradigm specification If the user wishes a code may be returned by the action which will placed in the event buffer instead For example if the action was setting some variables from a table it might return a code that indicates which table entry was selected A state also contains the variables time a long integer and random a short integer When a state is entered a countdown timer is initialized to the time variable if it is non negative plus a portion of the random variable The random variable is divided into quarters with 0 1 4 1 2 3 4 or the whole added to the timer Note if the time variable is negative the countdown timer is not re initialized when the state is entered
235. ich signals are displayed The color of the toggle when set corresponds to the color of its cursor in the display window Display E El O a Options Refresh Eye Other Eye 30 30 Offset Horiz Vert Offset Horiz 0 Vert 40 41 0 30 7 20 5 10 2 10 2 20 5 30 7 41 0 center _ o eye C joy stick DA 1 _ eye C additional DA 0 C vergence Window 0 C Window 2 C Window 4 C Window 6 O Grid Window 1 C Window 3 C Window 5 C Window 7 Window display options Clicking the Options button in the menu bar will display a menu with the Options Options Connect Vex following items Beginning with version 7 5 you can control GLvex 7 0 through the eye window display Clicking on the Connect Vex item will bring up a dialog in which you enter the name of the Page 93 Vex machine Once you have connected to vex the eye window display will have a blue text line at the Untitled bottom You can enter GLvex keyboard commands whenever the mouse cursor is inside the eye window display area Entering incomplete commands causes a help message to be printed in the eye window display area You can position and flash GLvex stimuli when the mouse cursor is inside the eye window display area The scales on the bottom and left of the eye window display area indicate the position of the GLvex stimuli You can also display a grid that allows more accurate placement of the GLvex stimuli Clicking on the Options item will bri
236. ich the flow fields start and again for the first field in which the flow fields stop Page 293 MAKE FLOW MOVIE This a batchable command that creates the successive frames of flow field movies and places them in memory for subsequent playback The first parameter is number of objects that will contain the movies The second parameter is the number of frames in the movies One parameter is required for each of the movie objects the object number Before using this command you must call DRAW_FLOW_PATTERN and NEW_FLOW for each of the objects that hold flow movies Example action i This action defines flow field movies 500 frames long based on flow fields defined for objects 2 and 3 short mobi 1 short fobi 2 3 y short wide 600 short tall 400 short near 600 short far 1500 short cov 20 F 50 of flow field area will be covered by checks short size 4 size of the flow field checks short xy 180 270 IF xy direction of the flow fields short z 45 1 z depth angle of the flow field short vel 100 velocity of checks in 1 10ths degree sec short span 0 F life span of the checks continuous short coher 100 coherence of motion short nframes 500 number of frames flow_movie short index i roll pitch yaw DRAW_FLOW_PATTERN and NEW_FLOW have already been called for objects 2 and 3 index 0 vexbuf index MAKE_FLOW_MOVIE
237. ifth display button launches Mexis raw signal display Mex plots the value of its inputs in this display regardless of trigger conditions If you lose the signal in the oscilloscope or waveform displays you can still see something in the signals display Even if there is no signal on an input Mex will still plot a flat line for that input Saving Data The last two button in the tool bar toggle Mexis data saving functions If you want to save neuronal waveforms for offline sorting or antidromic data for later display you must first open a data file Select the Spike Waveforms or Antidromic Waveforms entry from the Files menu and enter the name of the file in the dialog box Until you open a file and start the clock the neuronal and antidromic data save buttons are inactive SPIKE WAVEFORM FILE Oct 03 16 22 Oct 30 09 55 May 22 10 19 Oct 30 09 55 gt EJ cal4020 Oct 21 07 30 gt EJ das4020_chain Oct 18 09 21 gt E data Oct 18 15 15 File Name a The first save button toggles the saving of neuron waveforms Click the button to toggle BEA saving While Mex is saving neuron waveforms to disk the button will display a waveform picture next to the floppy disk picture Also the clock button is inactive while saving data If you want to stop the Mex clock you must first stop saving data You can start and stop the saving of waveforms whenever you like while the data file is open When you are finished stop saving and close the waveform
238. igger will flash white for the first field in which the fixation point is switch off The on_fix and off fix actions shown above are defined in GLvex_com c Page 250 DIM_FIX_POINT This is a non batchable command that dims to fixation point to a preset level It does not require any parameters Example action dim_fix void unsigned short index index 0 vexbuf index DIM_FIX_POINT to_vex index return 0 If the digital sync is enabled GLvex will return the signal FIX_DIM 252 at the beginning of the video field in which the fixation is dimmed Otherwise GLvex will not return any signal after this command If enabled the rex video trigger will flash white for the first field in which the fixation point is switch dimmed The dim_fix action shown above is defined in GLvex_com c Page 251 PRELOAD_STIM This is a batchable command that loads a variable number of objects into the drawing buffer The first parameter is the number of objects to load Each object requires two parameters the object number and the switch value The switch values are 0 for OFF and 1 for ON This command is meant to be used with the SWAP BUFFERS command see below to achieve short latency switching of complex displays Typically you use the various DRAW_ commands to draw stimuli in your objects the STIM_ LOCATION command to position the objects and the PRELOAD_STIM command to load the objects into the drawing buffer during a part o
239. igital sync to nextstate on PHOTO_CELL amp drinput if video sync FILE rex act vexActions c Page 182 PvexPreloadStim PvexSwapBuffers load a set of objects into the drawing page but donit display them yet SYNOPSIS PvexPreloadStim int nObjects int objList int swtchList nObjects number of objects to load objList array of object numbers switchList array of switch values can be OBJ_OFF or OBJ_ON PvexSwapBuffers void DESCRIPTION Normally GLvex switches objects on or off by placing them in its draw buffer then doing a buffer swap to display the objects If you have a lot of objects or large objects it may take GLvex several video frames to get the draw buffer set up These two actions allow you to have GLvex place the objects into its draw buffer when time is not critical then to swap the buffers when a short latency is needed RETURN VALUE Glvex will return the signal LIST _ON 249 if the first object in the list is to be switched on or LIST_OFF 248 if the first object in the list is to be switch off after completing the PvexPreloadStim action If the digital sync is enabled GLvex will return the signal BUFFER _ SWAP 232 at the beginning of the first video field after the buffer swap If the video sync is enabled the sync object will flash white in the first video field after the buffer swap EXAMPLE int num objArray 15 swtchArray 15 int setup int i num 15 for i 0 i lt num i o
240. ill not be able to plot that condition by itself Also trials that include the super set code as an ecode may not be aligned properly in the data plot If a trial contains more than one of the ecodes in the list it will be included more than once in the plot each time with a different alignment To compare data from different trials you must align the data on events in the trials Rex can use three methods to align data The default method is to align the data using the time of the Any Of ecodes in the trials If you want to align data on an ecode that is not in the Any Of list enter the ecode on the Align Code line in the middle panel of the ecode selection window Each trial in the set must contain this ecode If a trial doesnit contain the align code the data from that trial will be aligned on the time of the Any Of ecode If you want to align the data at a given time before or after an alignment ecode or analog record mark enter the time in milliseconds on the Align Offset line If you enter a negative number Rex will align the data the specified number of milliseconds before the alignment mark If you enter a positive number Rex will align the data the specified number of milliseconds after the alignment mark You can define multiple ecode selection sets To define a new set click on the New button in the middle panel of the dialog The label will change to reflect the new selection set number and the scroll bar at the right will shorten refle
241. ill not put the correct value for c in arg3 Paradigms written for the pdp11 version of REX must be changed so that all action arguments are declared as longs Page 75 Page 76 REX Graphical User Interface John W McClurkin Ph D Laboratory of Sensorimotor Research National Eye Institute National Institutes of Health Introduction Beginning with release 7 0 we have fully ported Rex to QNXis Photon window system Use of the window system allowed us to not only present better displays of data but to also provide a graphical user interface The reasons for doing this are as follows i Better self documentation Older versions of Rex used a command line interface in which the experimenter interacted with the program through a series of screen menus and a set of commands verbs and nouns Efficient use of this interface required experimenters to memorize the keystrokes needed to bring up the menus and the rather terse verb noun combinations needed to execute commands i e ik Bi to beginning saving event and analog data With the graphical user interface all menus are available from menu buttons and all commands are executed by clicking on buttons that are displayed in the interface Better data displays The data displays of older versions of Rex were limited to VGA 640X480 resolution This limited the resolution of the data that could be displayed Older versions of Rex had three types of data display an X Y display o
242. image in the file Further GLvex does not support image compression The images in the TIFF files should be in RGBA format The first parameter is the number of objects to draw in Each object requires three parameters the object number the high byte of the image number and the low byte of the image number The image numbers can range from 0 to 65536 Example action it This action draws a TIFF image in three objects short patterns 1001 1002 1003 1004 1005 1006 y short ptrist 6 0 y short ob 3 5 2 draw_tiff unsigned short index short i j static int rs_shift 10 static int tricntr 6 for i 0 i lt tricntr i ptrist i i shuffle tricntr rs_shift ptrist index 0 vexbuf index DRAW_TIFF_IMAGE vexbuf index 3 number of objects for i 0 i lt 3 i j ptrist i vexbuf index obli object number vexbuf index hibyte patterns j high byte of pattern number vexbuf index lobyte patterns j low of pattern number other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not Page 280 DRAW_OKN_ PATTERN This is a batchable command that creates either a horizontal or a vertical square wave pattern that can be used as an optokinetic nystagmus stimulus The first pa
243. imes when you might want to reduce the size of the window For example to see the console window during debugging If you type w lt return gt you will get the following help message ws w h set Window size to width w height h The letter w in brackets stands for the width of the GLvex window The letter h in brackets stands for the height of the GLvex window Example commands ws 800 600 Page 164 This command will set the size of the window that GLvex runs in to 800 pixels wide and 600 pixels high NOTE Once you have changed the size of the GLvex window you cannot go back to a full screen window To go back to full screen mode you will need to restart GLvex X Video Sync X and Y coordinates By default GLvex places the video sync object in the upper left corner of the screen This command allows you place the object anywhere you like if you type X lt return gt you will get the following help message X n m set video sync location to nX mY The letter n in brackets stands for the X coordinate of the sync object The letter m in brackets stands for the Y coordinate of the sync object Example command X 0 240 This command places the sync object at the left edge of the screen 240 pixels from the bottom x Absolute X and Y coordinates This command moves the active object to an absolute position on the screen If you type x lt return gt you will get a help message similar to the following X n m move active object to n
244. in which the objects are switched Page 254 SET_STIM_SWITCH This is a batchable command that sets the switches of a variable number of objects but does not implement the switch Switch implementation will be done by the next non batchable command that is executed The first parameter is the number of object switches to set Each object requires two parameters the object number and the switch value Switch values can be ON 1 or OFF 0 The purpose of this command is to turn an object on in the field in which the ramp carrying it begins to move You can also turn an object on at some time after its ramp begins to move This allows you some independence between switching objects and starting ramps but still allows synchronization Example action E This action sets the switches of objects 1 2 8 3 to ON set_switch unsigned short index index 0 surround switch vexbuf index SET_STIM_SWITCH vexbuf index 3 number of objects to switch vexbuf index 1 object number vexbuf index OBJ_ON switch value center switch vexbuf index 2 object number vexbuf index OBJ_ON switch value square switch vexbuf index 3 object number vexbuf index OBJ_ON switch value F other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digi
245. index hibyte stepsOne hi byte of steps in first ramp vexbuf index lobyte stepsOne I lo byte of steps in first ramp for i 0 i lt stepsOne i flbuf float2byte rampOne i x for j 0 j lt 4 j vexbuf index flbuf j flbuf float2byte rampOne i y for j 0 j lt 4 j vexbuf index flbuf j vexbuf index 2 second ramp number vexbuf index OBJ_ON object stays on after end of ramp vexbuf index hibyte stepsTwo hi byte of the number of steps in second ramp vexbuf index lobyte stepsTwo lo byte of the number of steps in second ramp for i 0 i lt stepsTwo i flbuf float2byte rampTwo i x for j 0 j lt 4 j vexbuf index flbuf j flbuf float2byte rampTwoli y for j 0 j lt 4 j vexbuf index flbuf j vexbuf index SET_TRIGGERS vexbuf index 2 number of trigger sets vexbuf index 1 first ramp from which the triggers will come vexbuf index 1 number of triggers in this set vexbuf index hibyte breakOne hi byte of the step number on which to trigger vexbuf index lobyte breakOne lo byte of the step number on which to trigger vexbuf index 2 second ramp from which the triggers will come vexbuf index 1 number of triggers in this set vexbuf index hibyte breakTwo hi byte of the step number on which to trigger v
246. individual checks in the patterns can be either white or black depending on the Walsh function number White checks are drawn in the objectis foreground color black checks are drawn in the objectis background color The size parameter sets the sizes of the individual checks That means that the smallest Walsh pattern can be 16 pixels high and 16 pixel wide Specifying a contrast of 1 yields a contrast reversed version of a pattern specified with a contrast of 1 RETURN VALUE GLvex will return the signal BATCH DONE 241 when it completes this action EXAMPLE int num int objects 16 int walsh 16 0 17 34 51 68 85 102 119 136 153 170 187 204 221 238 255 int size 16 int contrast 16 int setup int i num 16 for i 0 i lt num i object i 1 1 size i 4 contrast i 1 return 0 prev do setup to state state do PvexDrawWalsh 8num objects walsh size contrast to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 196 PvexDrawHaar draws patterns based on Haar functions in a number of objects SYNOPSIS PvexDrawHaar int nObjects int objList int patList int sizList int cntrstList nObjects number of objects to draw in objList array of object numbers patList array of Haar function numbers on which to base patterns can be 0 to 255 sizList array of sizes of the pattern checks in screen pixels can be 1 to 255 cntrstList array of the contr
247. indow size of the console or shortcut to 80 columns and 25 lines but set the screen buffer size to 80 columns and 200 to 300 lines This way you can set the debug flag run you paradigm for a trial or two then use the scroll bar on the console window to scan the debugging output Normally GLvex runs as a full screen application This means that the window decorations border title bar are not shown If you set the WinNT task bar option to Auto hide then there will be no windows decorations at all This also means that the console from which you started GLvex will be covered GLvex does have a pseudo console that appears in the upper left corner of the screen to echo keyboard commands and display help messages but this is not sufficient for debugging output Therefore you can set the window size to be smaller than the screen resolution so you can see debugging output in the WinNT console window Once you have reduced the window size you cannot go back to full screen mode even if you try to set the window size to the screen resolution The window decorations will always be visible To go back to full screen mode you will need to quit and restart GLvex Coordinate System The screen coordinate system used by GLvex is the same as that used by rex That is the center of the screen has a coordinate of 0x Oy Negative x values are in the left half of the screen and negative y values are in the lower half of the screen The basic unit of position i
248. ines of C code comments not included Rex takes advantage of many Unix features to provide a real time laboratory system that is easy to use The Spot language and the make utility allow the user to easily create new Rex modules to meet his experimental needs Hence the investigator has more time to spend on the design of the experiment and the analysis of the data References Unix is a trademark of the Bell Telephone Laboratories RT 11 pdp11 and DEC are trademarks of Digital Equipment Corporation QNX is a trademark of Quantum Software Systems Ltd 175 Terrence Matthews Crescent Kanata Ontario K2M 1W8 613 591 0931 Ritchie D M and Thompson K The Unix Timesharing System Bell System Technical Journal Vol 57 1978 pp 1905 1929 Kernighan B W and Ritchie D M The C Programming Language Prentice Hall New Jersey 1978 Snapper A G and Inglis G B SKED Software System Manual 3 Rev D State Systems Inc Kalamazoo MI Lesk M E and Schmidt E Lex A Lexical Analyzer Generator Unix Programmer s Manual Seventh Edition 1979 Bell Telephone Laboratories New Jersey Johnson S C Yacc Yet Another Compiler Compiler ibid Feldman S I Make A program for Maintaining Computer Programs ibid Page 10 SPOT State Process Translator for REX Barry J Richmond Arthur V Hays Lance M Optican John W McClurkin Introduction The REX real time laboratory control and data acquisition system has bee
249. ing ke This command stops all OKN drifting gratings L Look up table color This command sets the color of a color lookup table entry for the active object In GLvex each object has its own color lookup table If you type L lt return gt you will get a help message similar to the following L n get current values for lookup table entry n L n r set color lookup table entry n to colorrrr L n r g b set color lookup table entry n to colors r g b The letter n in brackets stands for the number of the color lookup table It can range from 0 to 255 The letters r g b in brackets stand for the values of red green and blue to place in the color lookup table entry They also can range from 0 to 255 Example command L 4 255 0 255 This command sets places a magenta color in the active object s lookup entry 4 I Foreground and background luminance This command sets the luminances of the foreground and background checks of two tone stimuli in the active object If you type lt return gt you will get a help message similar to the following n m set Luminances of foreground background checks of active object to n m Current luminances of active object are 255 0 The letter n in brackets stands for the luminance of the foreground checks and the letter m in brackets stands for the luminance of the background checks These values can range from 0 to 255 Example commands 1255 0 Page 155 This command sets the foreground and backgrou
250. ing a brief description of that buttonis function Page 335 Waveforms that Mex did not classify as belonging to any neuron are drawn in white Waveforms that satisfy your criteria for the purple green or blue neurons are drawn in the corresponding color Further the different types of waveforms are drawn separately The unclassified waveforms are all drawn in the upper left quadrant of the display Waveforms belonging to the purple neuron are drawn in the upper right those belonging to the green neuron are drawn in the lower left and those belonging to the blue neuron are drawn in the lower right Drawing the four different classes of waveforms in different parts of the display makes it easier for you to judge the variability in the shapes of the waveforms that match your criteria for the neuron types If you save waveforms to disk for later classification this display shows exactly what is being saved Recording From Multiple Electrodes Each of the four displays described above has a button in its menu bar to select which electrode to display If you set several of the displays to show the input from a particular electrode the inputs of those displays will be locked together That is if you have the oscilloscope display the time and amplitude display and the waveform display showing the input from electrode 0 and you change the waveform display to show electrode 1 the oscilloscope and time and amplitude displays will also change to displ
251. ing the start code and the pre time The y Start Code 1001 Pre Time Ecode Selection Set 1 Align Code 0 Align Offset 0 None Of Any Of Beg End 3000 2001 2007 2014 2021 2028 2035 default value for the start code is 1001 You don t need to change this unless you use a different trial start code Enter the amount of analog pre time that you use in the pre time numerical field There are three text fields in the bottom panel labeled 411 Of None Of and Any Of Beg Ena The 4 1 Of column is for listing the ecodes that each trial must contain to be accepted for plotting in the raster display Enter each of these icorrecti ecodes followed by a lt return gt You can enter as many ecodes as you want Remember to end each entry with a carriage return If you want to delete an entry you must remember to use a lt return gt after deleting the entry An alternative to making a list of ecodes that each trial must contain is to make a list of ecodes that each trial must not contain to be accepted for plotting You list these ierrori ecodes in the None Of column As with the 4 Of column press lt return gt after entering each ecode It is not necessary to use both the All of and the None Of lists In fact it is not necessary to use either the 4 Of or the None Of columns If you leave both of these columns blank Rex will plot all of the trials in your data file looking for Any Of ecodes The Any Of ecodes tell Rex how to organ
252. input When a new int process is launched its tool bar appears adjacent to the procSwitch tool bar The lower level subroutine is divided into functionally discrete sections making it simple to modify Rex provides a method for users to easily create new int processes see next section During an experiment many int processes may be executed by Rex the experimental paradigm can be changed quickly by switching to a different int process Running Line Display The running line display process provides the functions of a digital oscilloscope It can display analog data neuronal units and a timing bar The time base of the display varies from 30 Hz to 1000 Hz It has free running and triggered modes In triggered mode it has repeat and one shot modes Rex supports multiple running displays Window Display The window display process provides an X Y display of analog data It has immediate and storage modes In storage mode the screen refresh rate can be set to any interval between 16 and 1024 milliseconds or the screen refresh can be triggered In triggered storage mode users can vary the number of draws between refresh cycles Rex supports multiple window displays Raster Display The raster display provides T Y plots of unit data The data are grouped according to experimental condition for each plot Unit data can be displayed as spike rasters or as spike density functions The raster display can have multiple pages each containing up to 64 pl
253. int targ_wnd void wd_pos WINDO vx vy I set position from globals vx vy wd_siz WINDO wndsiz wndsiz set window size wd_cntrl WINDO WD_ON F turn window on return 0 int flash_on Page 316 int index index 0 vexbuf index SET_STIM_SWITCH vexbuf index 1 number of objects vexbuf index 2 object number vexbuf index OBJ_ON turn object on to_vex index return 0 int flash_off int index index 0 vexbuf index SET_STIM_SWITCH vexbuf index 1 number of objects vexbuf index 2 object number vexbuf index OBJ_OFF turn object on to_vex index return 0 int goodTrial correctTrials memSactTrialList currstim good if totalTrials percentCorrect correctTrials 100 totalTrials if memSacTrialList currstim total memSactTrialList currstim percent memSacTrialList currstim good 100 memSacTrialList currstim total return 0 int badTrial rinitf errorTrials memSactTrialList currstim bad if totalTrials percentCorrect correctTrials 100 totalTrials if memSacTrialList currstim total memSactTrialList currstim percent memSacTrialList currstim good 100 memSactTrialList currstim total return 0 Page 317 char port GLVEX_PORT_STR char host Isr sgia char subnet 0 pcsSetPeerAddr host port pcs
254. ion EXAMPLE int obj nPoints size pointArray 2048 int setup int nRows nCols i j k l int width 1280 int height 1024 nRows nCols 32 nPoints 2048 size 4 1 0 for i 0 i lt nRows i for j 0 j lt nRows j pointArray I getRand width X coordinate pointArray I getRand height Y coordinate return 0 A prev do setup to state state do PvexLoadPointArray amp obj amp nPoints amp size pointArray to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 211 PvexCopyObject copies the pattern in one object to another object SYNOPSIS PvexCopyObject int source int destination int xscale int yscale source number of the source object destination number of the destination object xscale percentage to scale copy width 100 means no scaling yscale percentage to scale copy height 100 means no scaling DESCRIPTION This action allows you make duplicates of random check and flow field patterns The copied patterns can be stretched or shrunk in either width or height The scaling is not cumulative That is if you copy a pattern from object 1 to object 2 with 125 scaling then copy object 2 to object 3 also with 125 scaling object 3 will be 125 larger than object 1 not 125 larger than object 2 RETURN VALUE GLvex will return the signal BATCH _DONE 241 when it completes this action EXAMPLE int num 1 int source 1
255. ion is defined in GLvex_com c Page 260 SHIFT_LOCATION This is a non batchable command that sets the position of an object on the screen The X and Y coordinates must be floating point values The first parameter is the number of objects to locate Each object requires nine parameters The first parameter is the object number The next four parameters are the four bytes of the X coordinate of the object location The last four parameters are the four bytes of the Y coordinate of the object location The X and Y coordinates are in REX units i e tenths of a degree REX and GLvex have the same screen coordinate system 1 e 0 0 is the center of the screen negative X values are to the monkey s left and negative Y values are down This command is identical to STIM_ LOCATION except that it returns a signal at the beginning of the first video field in which the objects are shifted The purpose of this command is to allow Rex ramps to control GLvex objects Example action J This action will shift two objects float stx 100 100 y float sty 100 100 short ob1 1 short ob2 2 stm_pos void return 0 unsigned short index int i char flbuf index 0 vexbuf index SHIFT_LOCATION vexbuf index 2 number of objects to position vexbuf index ob1 I first object number flbuf float2byte stx 0 for i 0 i lt 4 i vexbuf index flbuf i flbuf float2byte
256. ion point off fpdim dim the Fixation point fr n set frame rate to n Hz Example commands fpdim This command dims the fixation point fr 100 This command tells GLvex that the frame rate of your monitor is 100 Hz GLvex uses the frame rate to calculate how big to make each step of a ramp or how far to move each check in a flow field on each screen refresh Note Low end graphics boards may not be able to produce smooth animation such Page 153 as ramps or flow fields at high frame rates You may get a better looking display by setting the frame rate lower than you are actually using Page 154 H h Help message This command prints out the following help message Single key stoke commands are h print this message arrow keys move active object Page Up Page down decrement increment stimulus number Commands requiring arguments start with the letters b c D d e F f L I M m O o P p q r S s t wx Z zZ Type the first letter of the command for a help message and current values This command is not case sensitive k Start stop okn stimulus This command starts or stops an OKN drifting square wave grating if you type k lt return gt you will get a help message similar to the following kb 0 start OKN movement in object o ke stop OKN movement The letter o in brackets stands for the number of the object containing the OKN grating Examples command kb 2 This command starts an OKN grating in object 2 drift
257. is command is to allow you to draw exact copies of random check or flow field patterns in several objects but it will copy any pattern The reason that this command is needed is that if you execute the draw random pattern function separately for each object the patterns would have the same statistical properties but the positions of the white and black checks would be different p Draw pattern These commands draw patterns in the active object Currently GLvex will draw patterns based on one of 8 functions Walsh functions Haar functions User defined templates User defined RGB templates Random functions Annuli Bars and Tiff images To draw a filled circle specify an annulus with an inner radius of 0 If you type p lt return gt you will get a help message similar to the following pa o i c draw Annulus with outer radius o inner radius i contrast c pb a w h c draw a bar with angle a width w height h contrast c ph n c s draw Haar pattern n with contrast c size s pk as w h t draw translation OKN stimulus angle a speed s w X h size bar width t pr p r c s draw Random pattern with p white r X c checks size s pt n draw a TIFF image from the file In tif pu n c s draw User pattern from the file Pn with contrast c size s pu n s draw user RGB pattern from the file Pn size s pw n c s draw Walsh pattern n with contrast c size s Current patterns object 1 function w pattern 1 contrast 1 object 2 function u p
258. is a batchable command that sets the foreground and background colors of one and two tone stimuli The first parameter is the number of objects to set Each object requires seven parameters the object number the levels of red green and blue for the foreground pixels and the levels of red green and blue for the background pixels The levels of each color can range from 0 to 255 Example action i This action will set the foreground and background colors of an object I short fgr 255 short fgg 128 short fgb 0 short bgr 0 short bgg 0 short bgb 255 stim_clr void unsigned short index index 0 vexbuf index SET_STIM_COLORS vexbuf index 1 number of objects vexbuf index 2 object number vexbuf index fgr foreground red vexbuf index fgg foreground green vexbuf index fgb foreground blue vexbuf index bgr background red vexbuf index bgg F background green vexbuf index bgb background blue F other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not Page 244 SET_GRAY SCALE This is a batchable command that sets up a gray scale in all objects color lookup tables It requires two parameters The first parameter is the index of the lookup table where the gray scal
259. is is a non batchable command that stops flow field and object movies It does not require any parameters This command allows you to stop an object movie that is in a continuous loop or to stop object or flow field movies before their designated number of cycles or frames have completed Example action pp this action stops all running movies gi stop_movie short index index 0 vexbuf index STOP_MOVIE to_vex index return 0 If the digital sync is enabled GLvex will return MOVIE STOP 233 at the beginning of the first video field after the movie has stopped Otherwise GLvex will not return any signal after this command If the video sync is enabled the rex video sync square will flash white for the first field after the movie stops This command has no effect and GLvex will not return any signals if the command is issued outside the context of the SHOW _FLOW_MOVIE or SHOW_MOVIE_ CLIP commands Page 301 SET_TRIGGERS This is a batchable command that allows you to tell GLvex that you want a trigger to be sent when a ramp reaches a specified step or an object movie reaches a specified frame You can specify up to 10 triggers for each ramp or object movie The first parameter is the number of trigger sets to define Each trigger set requires two parameters the ramp number or object movie number from which you want triggers and the number of triggers in you want in that ramp or object movie Each trigger requires two
260. is is because the red brick will not pass a pulse smaller than 12usec in width This would require a timing loop in REX that would be processor speed dependent To avoid this timing problem the red brick is bypassed A jumper is inserted instead of the brick This jumper connects the reset pulse directly to the digital I O card Page 127 R external Current limiting resistor use if necessary depending on value of R internal R internal orbs Odd Numbered Terminals gt Even Numbered Terminals NY O DC Input Module White Unit pulse hi Power 14 Gnd 7 Do not install a red brick in Oo this output module position Insert an 18 ga jumper capaci acres nine sirio capacitor across pins 7 gnd wire as shown and 14 5 of 7474 chip T o is a decoupling capacitor Place a 1uF ceramic disc 18 Ga jumper wire O Unit Latch Circuit Figure 6 Unit Latch Circuit The following circuits show various ways to drive LEDs Figure 7 shows a single LED with a fixed current limiting resistor This resistor could also be replaced with a pot to vary the brightness Note the 10k shunt resistor A DC output module has a small amount of leakage current in the off state typically 10 30 micro amps This current though small is still sufficient to illuminate an LED in a dark Page 128 room The resistor shunts this current around the LED preventing the LED from becoming forward biased when the I O module is off
261. is the character string that will identify the variable in the Table 1 VLIST Structure menu This character string may not have any imbedded spaces VI_add is the address of the variable itself This variable must be a Member name Example global char yl name clear all VI_basep is an amount that may be added to the variable pointer For E da simple global variables vl_basep should be NP null pointer If vl_add is a pointer to the first element of an array vl_basep might be the offset void vl add amp clear_al into the array for this variable l V1_accf is the address of a function to be called when the variable is changed Variable access functions are useful for checking the range of Anr N DE a variable or doing some type of initialization If you do not need a Sep variable access function the vl_accf member of the structure should int clearVaf be NP vl_accf Vl flag is a flag variable that consist of the oried combination of any of the following bits ME BEF ME AFT ME LB ME ILB ME GB char vl flag MECART ME_IGB The ME BFF bit indicates that the variable access function char vl_type ME DEC vl_acef should be called before changing the value of the menu variable The ME_AFT bit indicates that the variable access function should be called after changing the value of the menu variable The ME LB bit indicates that the value of vl_basep should be added directly to vl_add The ME_ILB bit indic
262. ist gList and bList arrays must be at least as large as the product of the number of objects and the number of entries RETURN VALUE Glvex will return the signal BATCH DONE 241 after completing this action EXAMPLE int nObjects nEntries int objList 32 entryList 1024 red 1024 green 1024 blue 1024 int setup prev state int i int j nObjects 32 nEntries 32 for i 0 i lt nObjects i objList i i for j 0 j lt nEntries j entryist j i red j i 8 green j i 4 blue j 127 return 0 do action to state do PvexSetObjectLutEntryClr amp nObjects objList amp nEntries entryList red green blue to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 178 PvexSetColorMask sets the red green blue and alpha channel flags of a list of objects SYNOPSIS PvexSetColorMask int nObjects int objList int redList int greenList int blueList int alphaList nObjects number of objects to set objList list of the number of the objects to set redList list of flags controling the objectsi red masks should be0 or 255 greenList list of flags controlling the objectsi green masks should be 0 or 255 blueList list of flags controlling the objectsi blue masks should be 0 or 255 alphaList list of flags controlling the objectsi alpha masks should be 0 or 255 DESCRIPTION This action allows you to set which color planes the object will be drawn in RE
263. ist int xList int yList PvexClipRectFromFixPoint int nObs int oList int wList int hList int xList int yList nObjs number of objects for which clipping rectangles are needed oList array of object numbers wList array of clipping rectangle widths in 10ths of a degree hList array of clipping rectangle heights in 10ths of a degree xList array of the X coordinates of the clipping rectangles in 10ths of a degree yList array of the Y coordinates of the clipping rectangles in 10ths of a degree DESCRIPTION These actions set clipping rectangles for a number of objects The clipping rectangle of each object is independent of the clipping rectangles of other objects You can use clipping rectangles to achieve optic flow by moving a large object behind a smaller clipping rectangle Another use is to display small parts of a complex image PvexClipRectSet sets the location of the clipping rectangles in absolute screen coordinates PvexClipRectFromFixPoint sets the location of the clipping rectangles relative to the fixation point RETURN VALUE Glvex will return the signal BATCH DONE 241 after completing this action EXAMPLE int num objArray 4 widthArray 4 heightArray 4 xArray 4 yArray 4 int setup int i num 4 for i 0 i lt num i objArray i i 1 widthArray i 50 heightArray i 50 if i lt 2 xArray i 50 else xArray i 50 if i 3 yArray i 50 else yArray i 50 return 0
264. items Files Displays Cnti Processes Root Files Open Data File Close Data File Selecting the Process Root Files or Open Data File items will bring up a file browser dialog similar to that shown below except for the action buttons at the bottom The file selection tool displays the contents of the directory specified in the Directory text field Changing the entry in the Directory text field or clicking on a directory folder in the file list display causes the directory to be copied to the File Name text field However if you just open a directory by clicking on the sign to the right of the folder the directory name is not copied to the File Name text field Sorry that just the way this Photon widget works If you select a file by clicking on its name in the file list display the name is appended to the string in the File Name text field Alternately you can specify a file by typing its name in the File Page 78 Name text field You then do something with the file by clicking on one of the action buttons at the bottom of the dialog Run Directory sa home nih JWM develop rtp PCl rex7 6 run Oct 23 16 29 stFlow ict c g StstFl Oct 30 07 37 rocSwitc ict g procSwitch Oct 23 16 45 rex Oct 23 16 44 tstram ct J C p Oct 28 08 27 File Name With the Process dialog clicking on the Run action button will load the int process you selected put it in the run state and display an int process tool bar shown bel
265. ius is 0 then GLvex will draw a filled circle The contrast can be either for normal contrast annuli or 1 for reverse contrast annuli Example action e This action draws an annulus in an object short outer 45 short inner 10 short obi 1 short size 4 draw_annulus unsigned short index index 0 vexbuf index DRAW_ANNULUS vexbuf index 1 number of objects vexbuf index obi object number vexbuf index outer outer radius vexbuf index inner inner radius can be 0 vexbuf index 1 I positive contrast other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not Page 272 DRAW_BAR This is a batchable command that draws a bar in an object The first parameter is the number of objects to draw in Each object requires 5 parameters the object number the orientation of the bar the width of the bar length of the bar and the contrast of the bar The contrast can be either for a normal contrast bar or 1 for a reverse contrast bar A normal contrast bar is drawn in the object s foreground color and a reverse contrast bar is drawn in the object s background color Example action p This action draws an oriented bar in an object I short angle 15 short width 5 short
266. ix switches the fixation point on or off SYNOPSIS PvexSwitchFix int switch switch whether the fixation point turns on or off can be OBJ_OFF or OBJ_ON DESCRIPTION This action allows you to switch the fixation point on or off if the value of switch is OBJ_ OFF the fixation point will be switched off If the value is OBJ_ON the fixation point will be switched on RETURN VALUE If the digital sync is enabled Glvex will return the signal FIX_ON 254 or FIX_OFF 253 at the beginning of the first video field in which the fixation point is switched If the video sync is enabled the sync square will flash white for the first field in which the fixation point is switched EXAMPLE int switch OBJ_ON A state do PvexSwitchFix amp switch to nextstate on 0 tst_rx_new if digital sync to nextstate on PHOTO_CELL amp drinput if video sync FILE rex act vexActions c Page 181 PvexDimFix dim the fixation point SYNOPSIS PvexDimFix void DESCRIPTION This action allows you to dim the fixation point object to the color or luminance previously defined RETURN VALUE If the digital sync is enabled Glvex will return the signal FIX_DIM 252 at the beginning of the first video field in which the fixation point is dimmed If the video sync is enabled the sync square will flash white for the first field in which the fixation point is dimmed EXAMPLE A state do PvexDimFix to nextstate on 0 tst_rx_new if d
267. ize your data for plotting Rex searches each trial that passes the 411 Of or None Of tests for the ecodes in the Any Of list Rex will group all trials that contain the same Any Of ecode will together If a trial contains several Any Of ecodes Rex will place it into multiple groups You can plot your data by individual stimulus conditions or you can create super sets of conditions To specify individual stimulus conditions enter a single ecode or a range of ecodes on a line in the Any Of list You specify ecode ranges by listing the first and last ecodes of the range on the line separated by a dash For example the second line in the illustration above causes Rex to create a class for each ecode from 2001 to 2036 inclusively To specify a super set of conditions enter a number to identify the super set followed by a list of the ecodes you want included in the set For example the Page 98 third line in the illustration above causes Rex to create the super set 3000 consisting of trials containing the ecodes 2001 2007 2014 2021 2028 and 2035 Rex will align the data from the 6 types of trials on the time of the ecode in the list or on the time of the Align Code see below NOTE WELL The super set code 3000 must be a number that you do not use as an ecode in your spot file Further each of the ecodes in the list must occur only once in the trial If the super set code is an ecode that you use to identify a stimulus condition then you w
268. j int red green blue red 255 green 0 blue 0 index 0 vexbuf index SET_OBJECT_LUT_ENTR_CLR vexbuf index 2 number of objects to set for i 0 i lt 2 i vexbuf index list i object number vexbuf index 64 number of table entries to set for this object for j 0 j lt 64 j vexbuf index j 64 I table index vexbuf index red red value vexbuf index green F green value vexbuf index blue blue value red 4 decrement red green 4 increment green other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not Page 248 ALL_OFF This is a non batchable command that turns off the fixation point and all stimuli by clearing both drawing pages and stops all ramps and flow fields It does not require any parameters Example action off_all void unsigned short index index 0 vexbuf index ALL_OFF to_vex index return 0 If the digital sync is enabled GLvex will return the signal ABORT _TRIAL 255 at the beginning of the first clear video field Otherwise GLvex will not return any signal after this command If the video sync is enabled the rex video sync square will flash white for the first field in which the objects are off If you us
269. jects amp nFrames amp interval amp cycles to runstate on 0 tst_rx_new runstate to stopstate on 0 tst_rx_new FILE rex act vexActions c Page 230 PvexStopMovie stops all flow field movies and movie clips SYNOPSIS PvexStopMovie void DESCRIPTION This action allows you to halt flow field movies and movie clips in the event that an error has occurred RETURN VALUE If the digital sync is enabled GLvex will return the signal FLOW RAMP STOP 235 if you have been showing a flow field movie or the signal MOVIE_STOP if you have been showing a movie clip after all movement has stopped If the video sync is enabled the sync object will flash white after all movement has stopped EXAMPLE A state do PvexStopMovie to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 231 Actions That Set Arbitrary Trigger Points PvexSetTriggers sets a list of steps at which to send a trigger SYNOPSIS PvexSetTriggers int nTrigs int rmpList int trigList int frameList nTrigs number of trigger lists rmpList array of the numbers of the ramps or movie clips in which to place triggers trigList array of the number of triggers in each trigger list frameList array of the step numbers of each ramp or frame numbers of each movie clip to trigger DESCRIPTION When you define ramps using PvexLoadRamp or setup movie clips using PvexShowMovieClip you may way to introduce discontinuities into the display For example y
270. k locations in circular or elliptical flow field patterns SYNPOSIS PvexDrawFlowField int nObjects int objList int radList int widthList int heightList int nearList int farList int covList int sizList nObjects number of objects in which to draw flow fields objList array of object numbers radList array of flow field radii in 10ths of a degree widthList array of percentages of the radius for the width heightList array of percentages of the radius for the height nearList array of near clipping planes in 10ths of a degree farList array of far clipping planes in 10ths of a degree covList array of 10ths of a percent of field covered by checks can be 1 to 255 sizList array of check sizes DESCRIPTION This action specifies the initial positions of the checks in flow field stimuli in a number of objects The radius is the radius of the flow field in tenths of a degree The width and height are the percentages of the radius to use in setting the width and height of the flow field If width and height are 100 the flow field will be a circle with its radius defined by the radius variable If the width and height are different the flow field will be elliptical The near and far parameters are the distances to the near and far clipping planes of the flow field If the near and far parameters are the same you will get a two dimensional flow field If the near parameter is smaller than the far parameter you will get a three dimensional
271. kept for compatibility In this release Spot has been modified so that it only accepts files that have two sections a C code section and a Spot language section To modify existing Spot files simply move the entire third section after the double percent into the first section Then delete the last double percent that marked the beginning of the third section The rex Ihdr directory has been deleted All header files that pertain to the general REX source are now in rex hdr Header files that pertain to each individual laboratory such as files that declare local ecodes or local device ids are now kept in rex sset See the chapter Installing REX for an overview of important configuration headers and their locations REX 4 0 Step 92 Release 4 0 is the first release of the PC version of REX This version is a port of REX 3 11 REX 4 0 runs on the QNX operating system Incore space for the event buffer and analog buffer were increased given the PC s larger address space QNX currently runs in 16 bit protected mode When a later release supports 32 bit mode the only limit on the buffers will be memory size Page 107 The C compiler under QNX is ANSI C ANSI C is more stringent in error checking than the compiler on the pdp11 Existing paradigms will generate many errors the first time they are compiled and will have to be converted to ANSI C Page 108 Current bugs 1 4 0 Output to dumb tty has gaps when clock is on This is
272. length 200 short contrast 1 draw_bar unsigned short index index 0 vexbuf index DRAW_BAR vexbuf index 1 number of objects vexbuf index 5 this object number vexbuf index angle orientation of the bar 0 180 degrees vexbuf index width width of the bar in rex units vexbuf index length 1 length of the bar in rex units vexbuf index contrast a normal contrast bar other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not Page 273 DRAW_FLOW_PATTERN This is a batchable command that specifies the initial positions of checks for a flow field The first parameter is the number of objects in which to draw flow fields Each object requires 11 parameters the object number the hi and lo bytes of the width of the flow field the hi and lo bytes of the height of the flow field the hi and lo bytes of the distance to the near plane the hi and lo bytes of the distance to the far plane the coverage of the flow field and the check size The width and height are in rex units 1 e tenths of a degree of visual angle You specify the distances to the near and far planes in rex units but these parameters are converted internally from degrees of visual angle to the equivalent linear distance If the far
273. ll four directions is a move cursor With this cursor you can move a box without changing its size by pressing the left mouse button and dragging the mouse The cursor with arrows pointing left and right is the horizontal resize cursor With this cursor you can change the width of the box by pressing with the left mouse button and dragging the mouse left or right The cursor with arrows pointing up and down is the vertical resize cursor With this cursor you can change the height of the box by pressing with the left mouse button and dragging the mouse up or down The cursor with arrows pointing diagonally is the combination horizontal vertical resize cursor With this cursor you can change the width and the height of the box by pressing with the left mouse button and dragging the mouse left right up or down To obtain the resize cursors position the mouse cursor just inside the box To obtain the move cursor position the mouse cursor in the middle of the box or at one edge If you have a very thin box you might not be able to obtain a resize cursor by placing the mouse cursor in the middle of the box In this case you will have to move the box by bringing the mouse cursor to one edge To delete a box move the mouse cursor over the box and click the right mouse button The mouse cursor will change to a blocked cursor circle with a line through it and a dialog will pop up asking if you want to delete the box Click the Delete button in the dialog with
274. ll value type variables REX 4 2 9 Nov 93 Release 4 2 incorporates a new A file format and signal specification menus It is now possible to specify sampling rates for each a d channel independently from a menu Global memory variables can also be stored to the A file The new A file format is incompatible with the old however Page 106 REX 4 1b 18 Nov 92 Release 4 1b is an minor release which fixes some bugs in the d a converter code It also adds the code for resetting the unit latch A new command f3bit has been added This permits output bits on the default digital I O device to be turned on off easily from the keyboard for testing purposes The header rex hdr lab h has been folded into rex hdr cnf h Support for a joystick was added to the action wd_ctl and mr_set Joystick support currently is enabled by a define in rex hdr cnf h A new system of naming major and minor releases has been established Major releases will be designated by numerics e g version 4 2 Minor releases will be designated by lower case letters e g version 4 2c Current version levels are displayed by the command type proc The default address for the d a card has been changed from 0x210 to 0x180 This is because some of the ICS d a card addresses can only be set modulo 0x20 not 0x10 If you originally installed your d a card at 0x210 you will either need to change it to 0x180 or modify rex hdr cnf h to reflect the old address All non syste
275. low fields in which checks move in a two or three dimensional space You can place stimuli on ramps such that the stimulus moves across the screen You can define square wave gratings in which the bars drift horizontally or vertically You can set up sequences of stimuli to be displayed as a movie In computing the animation sequences GLvex assumes that all drawing will be completed in one vertical refresh cycle of the video system However if your animation involves a lot of drawing the graphics hardware may not be able to draw everything in one vertical refresh cycle When this occurs your animation will be much slower than you specified For example the drawing requires between 1 and 2 vertical refresh cycles your animation Page 142 will run at half the speed you specified Further if the drawing requires exactly vertical refresh cycle the movement will likely be jerky GLvex has no way of knowing how much time the drawing is taking so it has no way of adjusting the animation to deliver the speed you specified Therefore you should manually time your animation sequences You do not need precision timing to do this because the speed drops so much as the drawing timing increases first to half speed then to third speed then to quarter speed etc It is possible to test this by setting up an animation sequence to take say two seconds and then counting one mississippi two mississippi as the sequence runs One way or another you should t
276. ly be no reason to use the da_cntrl function instead of the da_cntrl_1 and da_cntrl_2 actions unless one wanted to control more than two d a s as simultaneously as possible The da_cntrl_1 and da_cntrl_2 actions are wrapper functions that repackage the arguments and call da_cntrl RETURN VALUE Returns 0 EXAMPLES da_cntrl_2 0 DA_RAMP_X 0 1 DA_RAMP Y 0 Connect d a number 0 to the X component of ramp generator 0 and d a number 1 to the Y component of ramp generator 0 da_cntrl_1 4 DA_SIGNAL 0 Connect d a number 4 to signal number 0 DA_CNTRL_ARG da arg struct 0 DA_RAMP_X 0 1 DA_RAMP Y 0 2 DA RAMP X l 3 DA_ RAMP Y 1 da_cntrl 4 amp da_arg_sruct Connect d a numbers 0 and 1 to ramp generator 0 and connect d a numbers 2 and 3 to ramp generator 1 SEE ALSO da_cursor da_mode da_offset da_set_1 2 FILE rex act da_cntrl c Page 44 da_set da _set_1 da_set_2 Pda _ set Pda_set_1 Pda set 2 output value to d a converter SYNOPSIS da_set_1 long num long val da_set_2 long numo long val0 long danum1 long value Pda_set_1 long num long val da_set_2 long numo long val0 long num1 long value num d a converter number val output value Note following function cannot be called as an action da_set int cnt DA_SET_ARG ap not an action typedef struct int da_set_num int da_set_val DA_SET_ARG da_set_num d a converter number da_set_val output
277. m cards to work I suggest purchasing the 8013 Real time Interface Cards A D Cards Two a d cards are recommended for PC REX One is an inexpensive 12 bit low end card the other a 16 bit card The low cost unit is the Analogics DAS 12 50 500 It will sample 8 channels at 1K Hz with 12 bit resolution It cannot be used to sample any faster I also evaluated 16 bit a d converters I tested the ADAC 5508SHR the Analogics LSDAS16 and the National Instruments ATMIO16 X The disappointing fact is that one doesn t really get 16 bits with the current generation of products When the input is grounded the output of the converter ranges over 4 5 counts A 16 bit converter has 4 more bits than a 12 bit and this equals 16 additional counts Therefore one gets only about 2 3 of this extra resolution 5 counts of noise 16 possible counts Statistically the situation is better given some processing or averaging The standard deviation is only 0 5 0 7 counts Whether you should use a 16 bit converter depends on your application If you are looking at slow velocities processing the signal such as software differentiation etc the extra resolution may be very helpful I quantitatively tested the ADAC and National Instruments I did not like the way the Analogics did software calibration and sent it back before I did these latest tests The National card was cleaner see results below It is more expensive 2k vs 1 3k however it has a lot more featu
278. m ecodes have been removed from rex hdr ecode h This is most of the codes greater than 1000 Please place paradigm specific ecodes in headers in rex sset and include these headers in your Spot file The intent is to keep most of the user specific code in the sset directory REX 4 1 Oct 92 Release 4 1 adds the programming interface for digital 1 O devices This addition necessitated changing the arguments to actions from ints to long ints Because of this change existing actions need to be modified so that their arguments are explicitly declared as longs This is a minor change but f8 ALL existing user written actions must be modified to run properly See section 11 of Chapter 4 When Things Don t Work for a more detailed information and examples Changes were also made to the menu handler code for accessing state variables Arguments to actions are now printed in hex and base 10 A hex number can be entered from the keyboard by prefacing it with 0x In general the PC world thinks in hex as opposed to octal for pdp11s A knowledge of the hex digits will be very useful for the PC version of REX Some modifications have been made to Spot An escape test has been added that will call a function and transition to the next state based on the return value of the function The Spot document has been updated and the section on escape tests has been expanded The need for three sections in Spot files disappeared in REX 3 10 however they were
279. mbers DESCRIPTION This action allows you to pre compute the movement of checks in a flow field for later display This action is useful if you want to display exactly the same sequence of check movements on successive trials You must call PvexDrawFlowField and PvexNewFlow to define flow field stimuli and setup the translation matrices before calling this action RETURN VALUE GLvex will return the signal BATCH _DONE 241 when it completes this action EXAMPLE int num 4 int nFrames 100 int objects 4 2 3 4 5 int widths 4 100 100 100 100 int heights 100 100 100 100 int nears 4 500 500 500 500 int fars 4 1500 1500 1500 1500 int coverages 4 25 25 25 25 int sizes 4 4 4 4 4 int xy 4 0 90 180 270 int z 4 0 45 45 90 y int vel 4 10 15 20 25 int roll 4 0 0 0 0 y int pitch 4 0 0 0 0 int yaw 4 0 0 0 0 int span 4 0 5 0 5 int coher 4 100 75 50 25 A state do PvexDrawFlowField amp num objects widths heights nears fars coverages sizes to trans on 0 tst_rx_new trans do PvexNewFlow 8num objects xy z vel roll pitch yaw span coher to movie on 0 tst_rx_new movie do PvexMakeFlowMovie amp num amp nFrames objects to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 222 PvexToFlowMovieStart shows the starting frame of a flow field m
280. mmand will open the analog window from the current time minus the w_pre time SEE ALSO pre_post uw_set FILE rex act awind c Page 39 pre_post Ppre_post set pre time and post time of analog window SYNOPSIS pre_post long pre_time long post_time Ppre_post long pre_time long post_time pre_time post_time times in units of msec pre_time post_time are pointers to long variables containing the pre and post times ADDITIONAL HEADERS REQUIRED None DESCRIPTION pre_post sets times associated with the manipulation of the analog window The pre time is the time previous to the window open request that analog data saving is begun The post time is the time after the window close request that analog data continues to be saved If a window open request comes shortly after the previous close request it may be possible that the previous post time and current pre time will cause window overlap In this case the full contents of both windows is still saved and there will be duplication of stored data on disk This guarantees that data records will always be the full size requested Note well a possible trouble area if an open request is given during the post time the request is ignored Only one window can be processed at a time open requests are not stacked Please also note that pre times and post times are guaranteed to be at least as long as specified Most likely however the actual pre time and post time will be somewhat longer th
281. mple of a file for a user defined RGB pattern with 3 rows and 8 cols This file defines a horizontal red bar flanked by two green bars The name of the file might be P2000 383 0255002550 02550 02550 02550 02550 02550 02550 25500 25500 25500 25500 25500 25500 25500 25500 02550 02550 02550 02550 02550 02550 02550 02550 Example of a file for a user defined pattern with 8 rows and 8 cols This pattern will have 8 vertical strips of different gray levels if you set up a gray scale ranging from 128 to 184 The name of the file might be P100 88 128 136 144 152 160 168 176 184 128 136 144 152 160 168 176 184 128 136 144 152 160 168 176 184 128 136 144 152 160 168 176 184 128 136 144 152 160 168 176 184 128 136 144 152 160 168 176 184 128 136 144 152 160 168 176 184 128 136 144 152 160 168 176 184 mat 5 q Quit This commands quits GLvex These commands are not case sensitive If you type q lt return gt you will get the following help message qv quit Vex r Absolute ramps The command rc computes the absolute location of ramps and the command rs starts ramps If you type r lt return gt you will get the following help message rc n len ang vel xoff yoff type action Compute a ramp rs r o c Start Ramp r with Object o continuation c 0 1 2 rstop stop all ramps reset reset ramps Page 162 In the rc command the letters in brackets stand for the parameters of the ramp You can get an explanation of the parameters by typi
282. mptom can write a root but then not read it back in Menu variable names cannot have embedded spaces Spaces are parsed as argument delimiters To simulate a space use an underscore If a menu variable name does have an embedded space everything will seem to work fine until a root is read The part of the variable name after the space will be interpreted as the value for the variable The space serves to delimit the name of the variable from its value Debugging Aids Some debugging aids exist These will allow printing of debugging messages See the section in the Spot manual titled General Considerations for more info on these aids Endless abort loop Don t place a state that contains the action reset_s in the abort list You will create an endless loop The action reset_s causes the abort list to be executed Arguments to actions are not passed correctly Arguments to actions are always long integers Therefore the arguments to actions must be declared as long integers For example the following action has three arguments and is correctly written do_something long a long b long c int arg3 arg3 c conversion to int done automatically by C compiler However the next action shown below will not work because the C compiler is not informed that the arguments are longs The C compiler will assume they are ints and not pick them up properly Page 74 do_something a b c int arg3 arg3 c F this w
283. n An example of a subsequent state in a chain stimon code STIMCD do dio_on LED2 rl 50 time 500 to stimoff If there is an event code to be put into the event buffer when the state is entered it must be next The event code is specified using keyword code for example code 1101 or code FPONCD Beginning with Rex7 2 you can specify the event code with a pointer to a global variable as well as with a constant value This allows you to drop trial specific event codes with out having to call an action For example code amp trialCode Actions running line levels and times follow in any order with the following restriction time and random must be adjoining in either order Running line The running line is used both to indicate state transitions in the running line display and to trigger the running line and eye window displays The running line level is displayed on the REX moving display as a continuous line at different positions on the screen Its keyword specifier is rl Running line levels are absolute when not preceded by a or and relative when they are preceded by a or Page 20 Actions Actions are C callable subroutines One action is allowed per state and is called immediately when the state is entered Note that the initial state of a chain cannot contain an action An action is identified by the keyword do Beginning with Rex7 2 actions may have up to ten arguments The arguments may be either long integers or poi
284. n Aborting input loop you probably have not loaded the correct number of arguments into the buffer If the values that GLvex prints out are vastly different from what you think they should be you probably have not loaded the bytes of integer or floating point values in the correct order Page 308 Memory Management Warnings When you compute a new ramp GLvex dynamically allocates space for the X and Y buffers that hold the sequence of object positions defined by the ramp If you run out of host memory GLvex will print the following a warning similar to the following compute_ramp Warning unable to malloc space for ramp 10 Execution will continue but the ramp will not be computed If you attempt to start the ramp you will get unpredictable results If you have this problem try recomputing an old ramp If in recomputing an old ramp you get a warning similar to compute_ramp Warning unable to realloc space for ramp 10 you will probably have to quit GLvex to free up memory I don t know how many ramps can be defined simultaneously It will depend on the lengths and speeds of the ramps The shorter and faster the ramp the more that can be defined simultaneously When you compute a new flow field GLvex dynamically allocates a floating point buffer to hold the 3 D homogeneous coordinates of the points in the flow field and two integer buffers to hold the 2 D projects of the points in the flow field If you run out of host memory GLvex will
285. n the menu global base pointer me_basep is given the value of amp ramp the instance of the RMP_PAR structure being accessed by this menu This example assumes that ramp is a globally defined variable The next example shows a snippet of code for a menu that access members of an array of structures typedef struct int len int ang int vel int xoff int yoff Page 16 int type int ecode RMP_PAR RMP_PAR rampList 16 int r_agf int call_cnt MENU mp char astr if call_cnt gt 16 astr 10 else itoa_RL call_cnt d astr amp astr P_ISLEN return 0 int r_maf int flag MENU mp char astr ME_RECUR rp int rampnum if astr 0 rampnum 0 else rampnum atoi astr if rampnum lt 0 rampnum gt 16 return 1 mp gt me_basep unsign amp rampList rampnum return 0 VLIST ramp_vl length amp RMP_PAR NP gt len NP NP ME_GB ME_DEC angle amp RMP_PAR NP gt ang NP NP ME_GB ME_DEC velocity amp RMP_PAR NP gt vel NP NP ME_GB ME_DEC xoff amp RMP_PAR NP gt xoff NP NP ME_GB ME_DEC yoff amp RMP_PAR NP gt yoff NP NP ME_GB ME_DEC type amp RMP_PAR NP gt type NP NP ME_GB ME_DEC ecode amp RMP_PAR NP gt ecode NP NP ME_GB ME_DEC NS char hm_ramp_vi MENU umenus rampList amp ramp_vl NP r_maf ME_BEF r_agf hm_ramp_vi NS y This exam
286. n 0 tst_rx_new offack do pcm_ack 0 time 5000 time out to disabl abort offrew clwind Third the monkey can make an error that causes an escape from a state such as vexst in the example above that is expecting a signal from GLvex just as GLvex is about to send the signal In the above example if the actions to handle monkey errors do not send the abort command off_all before GLvex sends the signal at the end of the vex_time action you may have an extra unacknowledged signal from GLvex This situation should occur infrequently Fourth you are careless in testing the transmit and receive bits in your paradigm or you do not acknowledge signals from GLvex Study the example spot file at the end of this document carefully In particular don t hide the pem_ack 0 action in other actions to save on the number of states in your paradigm While this is legal it will make your paradigms harder to debug This type of error will cause frequent hang ups but may not occur on every trial In particular be suspicious if your paradigm runs properly only if some states need to have the time variable set to some minimum value KEYBOARD COMMANDS Unless otherwise indicated keyboard commands are case sensitive That is the command beginning with the letter x is different the command beginning with the letter X Most of the keyboard commands affect a single object A keyboard command is used to select which object is active Once an object has been m
287. n designed so control paradigms for specific experiments can be flexibly implemented During implementation the user s attention is largely directed to features that are unique for the experiment being designed This end is realized through implementation of a translator for a state set based control specification language Spot State PrOcessor Translator The Spot translator produces tables that are compiled by the C compiler These tables contain specifications that define states associated with each state are conditions escapes that govern transitions to other states When a new state is entered a user written subroutine termed an action can be called if its name is included in the specification of the new state Virtually no restrictions are placed upon the action It may touch hardware do calculations and set flags for later use process lists of stimuli etc The Spot translator makes the chain of states extremely easy to specify and edit Multiple independent state chains are permitted and executed in parallel Process Control REX process control is implemented using a logical structure which depends upon states actions and escapes This system is table driven executed by an interpreter that runs every millisecond The tables are difficult to construct by hand so a translatable language Spot has been implemented to make the creation of the tables transparent to the user Control routines are always in a current state When an appropr
288. n rex is one tenth of a degree Therefore in GLvex a rex unit is defined as one tenth of a degree of visual angle All position and window commands to GLvex will be in rex units if you set the scale factors properly However if you set the screen distance value to 0 then all position commands to GLvex will be in raw pixels Video Fields In raster displays drawing begins in the upper left corner of the screen and continues left to right top to bottom until the bottom right corner of the screen With the graphics board running at 60Hz this process is repeated 60 times a second To set the display rate and spatial resolution click on the Windows NT desktop with the right mouse button to bring up the Display Properties panel Select the refresh frequency and desktop area you want GLvex is able to determine the desktop area but not the refresh frequency Therefore you will need to enter the refresh frequency using the keyboard command described below In GLvex a video field is defined as the time it takes draw the screen once At 60Hz a video field is 16 67 milliseconds All stimuli in GLvex must be presented for some integer number of video fields Because modern video cards allow a range of vertical refresh rates I have included a keyboard command in GLvex to set the vertical refresh rate You will need to set this to get accurate flow field speeds and ramp movement speeds Animation GLvex allows several types of animation You can have f
289. nc object will flash white when the gratings stop EXAMPLE int num int object direction speed width height barwidth int setup num 1 object 1 direction 180 speed 10 width 100 height 100 barwidth 10 return 0 A prev do setup to state state do PvexDrawOknGrating amp num amp object amp direction amp speed amp width amp height amp barwidth to startstate on 0 tst_rx_new startstate do PvexStartOkn amp num amp object to runstate on 0 tst_rx_new runstate time 1000 to stopstate stopstate do PvexStopOkn to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 220 Actions That Control Flow Fields PvexNewFlow sets the translation matrices of a number of flow field objects SYNOPSIS PvexNewFlow int nObjects int objList int xyList int zList int velList int rollList int pitchList int yawList int spanList int coherList nObjects number of flow field objects objList array of object numbers xyList array of flow directions in the X Y plane zList array of flow directions along the Z axis only valid for 3 D flow fields velList array of linear velocities rollList array of angular velocities around the Z axis pitchList array of angular velocities around the X axis only valid for 3 D flow fields yawList array of angular velocities around the Y axis only valid for 3 D flow fields spanList array of check life spans in video fields c
290. nchronization signals do not need to be acknowledged In the LSR we feed the output of the photo diode into a latch that goes high when the video sync flashes white and stays high until reset by the rex Page 148 paradigm Further flashes have no effect Therefore to use only the video sync signals you are interested in you can send a reset command to the digital I O port dio_on just before you are expecting a critical sync signal This will clear any previously latched signals Parallel I O Communication errors This section is repeated in the ERRORS AND WARNINGS section It is possible for communications between the rex and GLvex PC s to get out of sync when you are using the pemsg protocol If this happens your paradigm will hang or the stimulus display will become erratic In either event stop the rex paradigm by setting the PSTOP switch to on hit the lt return gt key on the GLvex PC to halt any messages to rex type r s on the rex PC to restart the state list and finally set the PSTOP switch to off to resume the paradigm If your paradigm still does not run check to see if the GLvex PC is hung by typing lt return gt Vex should print a help message If not reboot the GLvex PC using the cntrl alt delete sequence If GLvex is not hung kill and reload the offending rex process In the worst case you will have to quit rex and reboot the GLvex PC There are four general ways that rex to GLvex communications can get out of syn
291. nd line argument to GLvex and the width variable can be set using the w command line argument to GLvex RETURN VALUE Glvex will return the signal BATCH DONE 241 after completing this action EXAMPLE int width 290 int distance 573 A state do PvexSetRexScale amp distance amp width to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 170 Actions That Set Luminance and Color PvexSetBackLum set the luminance or color of the screen background SYNOPSIS PvexSetBackLum int r int g int b r intensity of red in the background can be 0 to 255 g intensity of green in the background can be 0 to 255 b intensity of blue in the background can be 0 to 255 DESCRIPTION This is action sets the luminance or color of the screen background It requires three parameters the values for the red green and blue guns RETURN VALUE Glvex will return the signal BATCH DONE 241 after completing this action EXAMPLE set background to medium gray int red 127 int green 127 int blue 127 A state do PvexSetBackLum amp red amp green amp blue to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 171 PvexSetFixColors sets the colors of the fixation point when it is switched on or dimmed SYNOPSIS PvexSetFixColors int or int og int ob int dr int dg int db or intensity of red in fixation point when switched on can be 0 to 255 og intensity of green in fixati
292. nd moved to 200 200 and turned on again it might briefly appear at 0 0 before appearing at 200 200 This bug is do to a section of the window display being re interrupted during processing ONLY the display is wrong the actual window checking function is always accurate 5 3 2 srdd will not parse lc num 2c num arguments unless a preceding flag is present 6 3 2 Control B will produce erratic results if done if clock has never been begun Page 115 Page 116 REX Internal Calibrations REX Internal Calibrations Polarity Monkey View UP DOWN Page 117 A D Full Scale Range Calibrations Full scale range for A D input is selected by eye calib num in control menu Note that Rex performs most internal operations on the A D signals at a resolution of 40 steps degree 2 s complement representation cal eye calib num in control menu shift internal shift factor used for conversions FS Full Scale ST a d Steps Table 1 10 Bit A D cal shift 12 Bit A D cal shift 102 4 deg FS 10 ST deg 5 2 102 4 deg FS 40 ST deg 0 0 51 2 deg FS 20 ST deg 6 1 51 2 deg FS 80 ST deg 1 1 25 6 deg FS 40 ST deg 7 0 25 6 deg FS 160 ST deg 2 2 12 8 deg FS 80 ST deg 8 1 12 8 deg FS 320 ST deg 3 3 6 4 deg FS 160 ST deg 9 2 6 4 deg FS 640 ST deg 4 4 Convert to 40 ST deg by shifting right by shift Window Check lt
293. nd pixels of the active object to 255 and 0 respectively This command will have no effect if the active object has a continuous tone stimulus M Start a movie clip Commands beginning with M start movie clips If you type M lt return gt you will get a help message similar to the following Start a movie clip Mo f I i c start an Object movie Mf o n f I start flow field movie Ms stop movies You can get an explanation of the parameters in the Mo command by typing Mo lt return gt to get a help message similar to the following f first object in movie number of objects in the movie i number of video fields per movie frame c number of movie cycles The value for 1 cannot exceed the number of objects you created when you started Vex You can get an explanation of the parameters in the Mf command by typing Mf lt return gt to get a help message similar to the following o the first object with a flow field movie n the number of objects with movies f first frame of the movie last frame of movie The value for 1 cannot exceed the number of frames defined for the movie see below You can show a movie for shorter periods if you want Example commands Mf 1 2 100 300 This command will start movies at frame 100 of flow fields that were previously defined for objects 1 and 2 and will display them for 300 frames Mo 22055 This command will show an object movie using objects 2 through 20 Each object will be displayed
294. ndex SET_FP_DIM_CLR vexbuf index r vexbuf index g vexbuf index b other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not Page 242 SET_STIM_LUMINANCES This is a batchable command that sets the foreground and background luminances of one and two tone stimuli The first parameter is the number of objects to set Each object requires three parameters the object number the luminance of the foreground pixels and the luminance of the background pixels The luminance values can range from 0 to 255 Example action it This action will set the luminances of three objects to the same level I short fgl 255 short bgl 0 short num_stim 3 short list 2 3 4 stim_lum void unsigned short index short i index 0 vexbuf index SET_STIM_LUMINANCES vexbuf index num_stim number of objects for i 0 i lt num_stim i vexbuf index list i object number vexbuf index fgl foreground luminance vexbuf index bgl background luminance F other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not Page 243 SET_STIM COLORS This
295. ne EYEALL WDO_XY lt lt WINDO 2 WDO_XY lt lt WIND1 2 define EYEH_SIG 0 signal numbers for eyes define EYEV_SIG 1 define OEYEH_SIG 2 define OEYEV_SIG 3 typedef struct int len int ang int vel int xoff int yoff int xwind int ywind int oxwind int oywind int eyehoff int eyevoff Page 23 int oeyehoff int oeyevoff int type int ecode RA_LIST define E_DO 2000 ramp direction series define E_D45 2001 define E_D90 2002 define E_D135 2003 define E_D180 2004 define E_D225 2005 define E_D270 2006 define E_D315 2007 E Direction series for tracking I RA_LIST list0 200 315 5 0 0 50 50 40 40 40 40 0 0 RA_CENPT E_D315 200 90 10 0 0 50 50 40 40 20 20 0 0 RA_CENPT E_D90 200 225 15 0 0 50 50 40 40 10 10 0 0 RA_CENPT E_D225 200 0 20 0 0 50 50 40 40 30 30 0 0 RA_CENPT E_DO 200 180 25 0 0 50 50 40 40 40 40 0 0 RA_CENPT E_D180 200 45 30 0 0 50 50 40 40 20 20 0 0 RA_CENPT E_D45 200 270 35 0 0 50 50 40 40 10 10 0 0 RA_CENPT E_D270 200 135 40 0 0 50 50 40 40 30 30 0 0 RA_CENPT E_D135 200 0 5 0 0 50 50 40 40 20 40 0 0 RA_CENPT E_DO 200 315 10 0 0 50 50 40 40 0 0 40 40 RA_CENPT E_D315 200 45 15 0 0 50 50 40 40 0 0 20 20 RA_CENPT E_D45 200 225 20 0 0 50 50 40 40 0 0 10 10 RA_CENPT E_D225 20
296. nfrequently Fourth you are careless in testing the transmit and receive bits in your paradigm or you do not acknowledge signals from GLvex Study the example spot file at the end of this document carefully In particular don t hide the pem_ack 0 action in other actions to save on the number of states in your paradigm While this is legal it will make your paradigms harder to debug This type of error will cause frequent hang ups but may not occur on every trial In particular be suspicious if your paradigm runs properly only if some states need to have the time variable set to some minimum value Page 307 Argument Errors In sending a command to GLvex you load a buffer with a number that represents the command followed by more numbers that represent the parameters for the command GLvex parses this buffer by assuming that the first value represents a command GLvex treats a number of the following values as arguments for that command How many of the following values are treated as values depends on the command number Any given number can be treated as a command or as an argument depending on its context If you do not load the buffer correctly GLvex will not be able to parse the buffer correctly This results in unpredictable behavior If you are not getting the result you expect shrink the main window with the w s command then turn on debugging with the D 1 command If you get the message rexIn Command is an invalid command rexI
297. ng rc lt return gt to get a help message similar to the following n number of ramp to compute len half of the linear length tenths of a degree len radius of circular ramp tenths of a degree ang slope of linear ramp in degrees ang starting point of circular ramp vel velocity of ramp in degrees sec xoff yoff location of ramp reference point type type and reference point of ramp type 2 linear ramp centered on the reference point type 4 linear ramp beginning at the reference point type 8 linear ramp ending at the reference point type 16 Clock wise circular ramp centered on reference point type 32 Counter clock wise circular ramp centered on reference point action object switch after end of ramp action 1 leave object on after end of ramp action 0 turn object off after end of ramp Example commands rc 1 200 45 20 100 100 2 0 This command will compute ramp 1 with a length of 40 degrees a direction of 45 degrees a speed of 20 degrees second and a mid point that is 10 degrees to the right and 10 degrees below the center of the screen The object will be switch off after the end of the ramp rc 1 200 45 20 100 100 16 1 This command will compute a circular ramp with a radius of 40 degrees a starting location 45 degrees from the center a surface speed of 20 degrees second and a mid point that is 10 degrees to the right and 10 degrees below the center of the screen The object will be left on after the en
298. ng in tenths of a degree The letter h in brackets following the pk command stands for the height of the grating in tenths of a degree The letter in brackets following the pk command stands for the thickness of the bars in the grating in tenths of a degree Example commands pw 119 1 This command will draw a normal contrast version of Walsh pattern 119 an 8 X 8 checkerboard in the active object pu 101 1 This command will use the template found in the file p101 to draw a reverse contrast version of the user defined pattern pa 40 20 1 This command will draw a normal contrast annulus with an outer radius of 40 and an inner radius of 20 in the active object Valid pattern numbers for w and A functions range from 0 to 255 Valid pattern numbers for u and functions range from 0 to 65536 This means that files containing user defined templates can only have names ranging from PO to P65536 Files containing TIFF images can only have names ranging from 10 tif to 165536 tif To make user defined patterns you must provide GLvex with a template of the pattern you want The template can be a set of numbers indicating the color lookup table entries to use for each check or a set of 3 numbers indicating the R G and B values to use for each check This template is defined in an ascii file which must be placed in the directory from which you run GLvex The format of the lookup table template file is rc n n n n The letters r and c
299. ng up a dialog that allows you to set various parameters of the display The Window Scale toggle buttons control the overall extent of the display in degrees Higher Window Display Options O 204 8 102 4 51 2 Channel 0 Window Scale Restart clock to affect changes 0256 0128 O64 Cursors Signals Fast Slow Refresh Rate IT nash vigge P sima teei of numbers represent lower gain The Refresh Rate slider controls how often the display is refreshed when the Refresh Trigger is continuous At the fastest refresh rate the display is erased prior to every draw 16 milliseconds At slower refresh rates a number of draws occur before the display is refreshed This causes moving cursors to leave trails The display can be put in triggered mode by clicking on the Refresh Trigger toggle In this mode the indicator is green and the label reads i Triggeredi You set the trigger level with the Level numerical field In triggered mode data are drawn only when the running line level in the paradigm equals the level you set in the Level field When the display is refreshed is governed by the states of the Auto toggle and Interval field In auto refresh mode the toggle indicator is green and the label reads i Autof In manual refresh mode the toggle indicator is red and the label reads i Manual If the display is in auto refresh mode and the nterval is 0 then the display will be refreshed just prior to each trigger If the Interval is greater
300. nt farList int covList int sizList nObjects number of objects in which to draw flow fields objList array of object numbers widthList array of flow field widths in 10ths of a degree heightList array of flow field heights in 10ths of a degree nearList array of near clipping planes in 10ths of a degree farList array of far clipping planes in 10ths of a degree covList array of 10ths of a percent of field covered by checks can be 1 to 255 sizList array of check sizes DESCRIPTION This action specifies the initial positions of the checks in flow field stimuli in a number of objects The near and far parameters are the distances to the near and far clipping planes of the flow field If the near and far parameters are the same you will get a two dimensional flow field If the near parameter is smaller than the far parameter you will get a three dimensional flow field Three dimensional flow fields are required for yaw pitch and zoom movements see PvexNewFlow RETURN VALUE GLvex will return the signal BATCH_DONE 241 when it completes this action EXAMPLE int num 1 int object 2 int width 100 int height 100 int near 500 int far 1500 int coverage 25 int size 4 state do PvexDrawFlowField amp num amp object amp width 8 height amp near 8 far amp coverage amp size to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 201 PvexDrawEllipticalFlowField sets initial chec
301. nters to global variables NOTE If you write your own actions you must declare any arguments as longs or pointers so that they will be accessed properly by the C compiler Action arguments can be examined and changed through the REX menu system at run time All actions must return an integer value If the return value is non zero it is assumed to be an ecode and is loaded into the event buffer Note that only one ecode per state can be loaded into the event buffer An ecode returned by an action has priority over an ecode declared as part of the state using the code keyword and will be entered instead Escapes Escapes have the following format to nextstate on time to nextstate on CONSTANT 1 8 int_variable_name_or_address to nextstate on CONSTANT gt int_variable_name_or_address to nextstate on CONSTANT lt int_variable_name_or_address to nextstate on CONSTANT int_variable_name_or_address to nextstate on CONSTANT int_variable_name_or_address to nextstate on CONSTANT function_name_or_address The keyword that indicates an escape is to The next word is the name of a state to go to on transition Conditions for transition are specified after the keyword on A state may contain up to ten escapes Each escape is tested in sequence A transition occurs upon the first escape that tests true After an escape tests true transition occurs immediately the remaining escapes in the state are not evaluated The tes
302. nths of a degree and the height variable to 0 Circular masks are always centered in the flow field so if you select a circular mask the X and Y variables are ignored Note you must first draw a flow field in an object before setting the flow field mask for that object RETURN VALUE GLvex will return the signal BATCH DONE 241 when it completes this action EXAMPLE 1 rectangular mask int num 1 int object 2 int width 10 int height 10 int x 0 int y 0 A state do PvexMaskFlowField amp num amp object amp width amp height amp x amp y to nextstate on 0 tst_rx_new FILE rex act vexActions cEXAMPLE 2 circular mask int num 1 int object 2 int width 10 int height 0 int x 0 these variables will be ignored but must be defined int y 0 because the function requires 6 variables to be passed A state do PvexMaskFlowField amp num amp object amp width amp height amp x amp y to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 203 PvexDrawUserPattern draws a pattern defined in useris template file SYNOPSIS PvexDrawUserPattern int nObjects int objList int pList int sList int cList nObjects number of objects in which to draw objList array of object numbers pList array of pattern numbers sList array of pattern check sizes in screen pixels cList array of pattern contrasts can be 1 0 1 or between 2 and 255 DESCRIP
303. number 0 with settling pause turn off LED1 automatically when ramp completes SEE ALSO ra_new ra_phistart ra_phiend ra_stop ra_tostart FILE rex act ramp_act c Page 54 ra_stop Pra_stop stop ramp SYNOPSIS ra_stop long rnum Pra_stop long rnum rnum ramp number ADDITIONAL HEADERS REQUIRED None DESCRIPTION ra_stop terminates the specified ramp RETURN VALUE This action may return the following values RDONECD If ramp had not completed but was currently running when ra_stop was executed 0 If ramp had completed when ra_stop was executed EXAMPLE ra_stop 0 Stop ramp number 0 if currently running SEE ALSO ra_new ra_phistart ra_phiend ra_start ra_tostart FILE rex act ramp_act c Page 55 ra_phistart Pra_phistart start phi blinking on ramp SYNOPSIS ra_phistart long rnum Pra_phistart long rnum rnum ramp number ADDITIONAL HEADERS REQUIRED None DESCRIPTION ra_phistart switches the ramp device ramp rnum ra_device to the phi device ramp rnum ra_phidevice and starts phi blinking The variables ramp rnum ra_phidevice ramp rnum ra_pontime and ramp rnum ra_pofftime must have been previously initialized RETURN VALUE Returns 0 EXAMPLE ra_phistart 0 Start phi blinking on ramp number 0 SEE ALSO ra_new ra_phiend ra_start ra_tostart FILE rex act ramp_act c Page 56 ra_phiend Pra_phiend end phi blinking on ramp SYNOPSIS ra_phiend long rnum Pra_phi
304. number added by the scribe process The second word is the event code for this record If the code is a positive number it corresponds to an event that occurred at a time which is stored in the next two words as a long integer Time is kept as clock ticks and the clock rate is kept in a standard header stored in the A file If the code is negative the record is an index to a variable length record in the A file the next two words form a long integer that is the offset in bytes from the beginning of the A file to the record header A file Format After the header block the A file consists of an arbitrary number of variable length records Every record is written in the same format a ten word analog header followed by an arbitrary length data field The structure of the analog header is the same for every record The first two words are a long integer magic number The third word is an unsigned ordinal sequence number assigned by the scribe process The fourth word is the event code for this record the same as the event code in the E file record which indexes this A file record The next two words form a long integer containing the time of occurrence of the epoch associated with this record The following two words form a long integer available to the user The next word is an integer used to mark continuation records The last word is the length in bytes of the following data field Since Rex collects data in rotating buffers it is possible to s
305. numbers actList array of actions at ramp end can be ON_AFTER_RAMP or OFF_AFTER_RAMP stpList array of the number of steps of each ramp xLst array of the X coordinates of each step of each ramp yLst array of the Y coordinates of each step of each ramp DESCRIPTION This action allows you to specify arbitrary movements for objects RETURN VALUE GLvex will return the signal BATCH _DONE 241 when it completes this action EXAMPLE float Xarray 1024 Yarray 1024 int num 2 int ramps 2 1 2 int steps 2 256 768 int act 2 ON_AFTER_RAMP ON_AFTER_RAMP int setup define two horizontal ramps that increase speed int i j k end float x y k 0 for i 0 i lt num i if i 0 end 256 else end 768 x float end 2 y 0 0 for j 0 j lt end j Xarray k x Yarray k y if j lt end 2 x 1 0 else x 2 0 return 0 A prev do setup to state state do PvexLoadRamp amp num ramps act steps Xarray Yarray to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 215 PvexToRampStart places objects at the beginnings of their ramps SYNOPSIS PvexToRampStart int nObjects int objList int rampList nObjects number of objects objList array of object numbers rampList array of ramp numbers DESCRIPTION This action positions a number of objects at the beginnings of the ramps that will govern their movement The objects carried
306. o rex sys rlib access c E of odd num of args however pp must be checked for NP both before and after incrementing in for statement below for pp pbuf pp NP pp pp NP pp pp 1 far_ptr 0 ADD THIS LINE HERE vip mp gt me_vip if isdigit pbuf 0 line atoi pp else line sindex pp amp vlp gt vl_name sizeof VLIST Then you must recompile all of rex by running a make complete 3 4 3 FIX A bug in PC REX affects the setting of variables read in from root files If the variable is out of range it may be changed to something else For example the reset_s 1 action that is used in the spot file to cause the abort list to be executed requires a 1 argument When this argument is read in from a root file it is changed Then the actions in the abort list are no longer called I will be fixing this bug this week Until then a temp fix would be to edit your root and change the argument for the reset_s action from Oxffffffff to 1 The menu system will accept 1 but not Oxffffffff A good way to tell what is affected is to run rex and then run your process without calling in a root Write a root and then read it back in right away Then write a second root The first and second roots should be identical on a diff except for the line containing the date If there are differences then they are caused by this bug 4 4 3 FIX A bug in the menu system sometimes resulted in errors in inputting nu
307. obi object number vexbuf index hres horizontal pattern resolution vexbuf index vres vertical pattern resolution vexbuf index size size of pattern checks vexbuf index prent percentage of white checks copy and shrink random pattern from object 1 to object 2 vexbuf index COPY_OBJECT vexbuf index ob1 source object number vexbuf index ob2 I destination object number vexbuf index hibyte xs high byte of horizontal scaling vexbuf index lobyte xs low byte of horizontal scaling vexbuf index hibyte ys high byte of vertical scaling vexbuf index lobyte ys low byte of vertical scaling other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not The hibyte and lobyte functions are defined in GLvex_com c Page 283 NEW_RAMP This is a batchable command that defines a new ramp or redefines an old ramp The first parameter is the number of ramps to define Each ramp requires 13 parameters the ramp number the hi and lo bytes of the length the hi and lo bytes of the angle the hi and lo bytes of the velocity the hi and lo bytes of the X reference point the hi and lo bytes of the Y reference point the ramp type and the end action Length is half t
308. of check values you supply must equal the number of rows multiplied by the number of columns Example actions define MVLENGTH 20 define IMAGE_TOTAL 2 MVLENGTH define MAX_LOOKUP_NUMBER 100 struct grid_struct int obj int colorch static struct grid_struct grid IMAGE_TOTAL MAX_LOOKUP_NUMBER int rand_noise int flag1 if rand lt RAND_MAX 2 flag1 1 else flag1 1 return flag1 double rand double RAND_MAX 1 range grid_val int rand_perc i j int chksz 10 int fbd 50 unsigned short index 0 for i 0 i lt IMAGE_TOTAL i for j 0 j lt 100 j rand_perc float rand_noise fbd 100 0 grid i j colorch rand_perc vexbuf index LOAD_PATTERN vexbuf index i 1 object number vexbuf index i 1 stimulus number vexbuf index chksz check size vexbuf index 10 number of rows in stimulus vexbuf index 10 number of columns in stimulus for j 0 j lt 100 j the 100 values for the stimulus vexbuf index grid i j colorch other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not Page 282 COPY_OBJECT This is a batchable command that copies the stimulus in one object into a second object It requires 6 parameters the number of th
309. of ramp vexbuf index hibyte steps hi byte of number of ramp steps vexbuf index lobyte steps I lo byte of number of ramp steps for i 0 i lt steps i flbuf float2byte thisRamp i x for j 0 j lt 4 j vexbuf index flbuf j flbuf float2byte thisRampl i y for j 0 j lt 4 j vexbuf index flbuf j a other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not The hibyte and lobyte functions are defined in GLvex_com c The float2byte function is defined in GLvex_com c Page 287 TO_RAMP START This is a batchable command that moves objects to the beginnings of the ramps that will carry them Ramps must be defined before calling TO RAMP START The first parameter is the number of objects to position Each object has two parameters the number of the object and the number of the ramp that will carry it This command is necessary if you want to display a stationary object at the beginning of a ramp before starting the ramp Example action It This action will move an object that was turned on in a different part of the screen to the beginning of a ramp jump_and_run void unsigned short index index 0 vexbuf index TO_RAMP_START vexbuf index 1 number of objects to position vexbuf index
310. of rotation in degrees sec p rate of pitch in degrees sec w rate of yaw in degrees sec s life span of checks in fields c percent of checks coherent Current values for object 0 angle 45 depth 0 velocity 20 rotation 0 pitch 0 yaw 0 span 0 coherence 100 The x parameter is an angle that specifies the direction of movement in the X Y plane A value of 0 represents movement to the right and a value of 90 represents movement upwards The z parameter is an angle that specifies the direction of movement in depth A value of 90 represents movement away from the viewer a value of 0 represents no movement in depth and a value of 90 represents movement toward the viewer The v parameter represents the translational velocity of the checks in the direction specified by the compound X Y Z angle The X and Y velocity components are multiplied by the cosine of the z parameter so specifying z values of 90 or 90 will produce pure vergence movement no matter how you set the a parameter The s parameter defines the life span of checks in the flow field in numbers of video fields For a flickering display this parameter must have a value of 3 or greater Setting this parameter to 0 will produce a continuous flow field The c parameter defines the percentage of checks in the flow field that move as specified All other checks will move in random directions at random speeds Example command Ot 90 451000010100 This command will
311. oggle Pulse Set Reset Toggle Pulse _ Set Reset Toggle Pulse _ Set _ Reset Port 6 Port 5 Port 4 BEES E E EI CES EEE ESE EME E HEE SB Be 2 Toggle Pulse _ Set Reset Toggle Pulse Set Reset Toggle Pulse _ Set _ Reset represent the individual bits in a port Sets of toggles with white backgrounds represent bits in ports configured for input Sets of toggles with red backgrounds represent bits in ports configured for output Page 89 The sets of toggles below each port labeled Toggle Pulse Set and Reset configure the different modes of the dialog The dialog only displays panels corresponding to two Grayhill panels If you have more than two Grayhill panels you can display panels corresponding to those higher ports by incrementing the Starting Port Number value The actual value sent to each port is determined by the mode toggles If the Toggle mode is selected an output bit will be set as soon as the corresponding toggle is set and will remain set for as long as the toggle remains set If the Pu se mode is selected only one output bit can be set at a time The bitis toggle will be set only as long as you press the left mouse button Releasing the mouse button unsets the toggle and unsets the output bit If you unset all of the mode toggles then the port is in Set mode You can set or unset any of the bit toggles but nothing will be sent to the output port until you click on the Set
312. oherList array of percentages of coherent checks DESCRIPTION This action sets the direction of movement of the checks in a flow field Checks can move in a linear direction or in a rotational direction Linear and rotational movement can be combined If the checks are given a non zero life span they will move as directed by the translation matrix for the given number of video fields then they will turn off This gives a scintillating appearance to the flow field The percentage of coherent checks governs the number of checks that will move in the direction specified by the translation matrix Non coherent checks will move in random directions RETURN VALUE GLvex will return the signal BATCH DONE 241 when it completes this action EXAMPLE int num 4 int objects 4 1 2 3 4 int xy 4 0 90 180 270 int z 4 0 45 45 90 int vel 4 10 15 20 25 int roll 4 0 0 0 0 y int pitch 4 0 0 0 0 int yaw 4 0 0 0 0 int span 4 0 5 0 5 int coher 4 100 75 50 25 A state do PvexNewFlow 8num objects xy z vel roll pitch yaw span coher to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 221 PvexMakeFlowMovie makes a series of flow field frames SYNOPSIS PvexMakeFlowMovie int nObjects int nFrames int objList nObjects number of flow field objects nFrames number of frames in all movies objList array of flow field object nu
313. om C TCP IP Noise tests of Adac 5508SHR National ATMIO16 X Sampling rate all 8 channels scanned each millisecond For ADAC pacer clock is 33 3KHz for National 20KHz Data below is for channel 1 Every other point was saved so effective sample rate for data below is 500Hz Channel inputs 5 7 were open In front of A D input is a Burr Brown instrumentation amp with gain of 2 and a Freq Devices 6 pole Bessel filter with corner freq of 181Hz A D inputs were set to differential 10 10 volts gain of l Data was taken with input grounded labeled gnd and connected to one of our lab devices labeled coil This device was generating a DC level Histograms of output giving sample value and number of counts for that value adac_coil_h 8 total bins mean 1596 sd 1 0796 3 cnt 32 2 cnt 593 1 ent 4043 cnt 4618 cnt 4390 ent 1505 ent 120 cnt 2 adac_gnd_h 6 total bins mean 1 1754 sd 7511 1 cnt 182 cnt 2318 cnt 8209 cnt 4589 cnt 418 cnt 5 nix _coil h 6 total bins mean 9 5482 sd 9468 12 cnt 89 11 cnt 2634 10 ent 4818 9 cnt 5897 8 cnt 1766 7 cnt 99 nix_gnd_h 5 total bins mean 178 9268 sd 5319 181 cnt 11 180 cnt 1590 179 cnt 10993 178 cnt 2686 177 cnt 23 hh UN Ro hh O Page 136 Appendix B REX License Agreement REX for the PC is distributed under a license agreement This has been implemented to preserve the LSR s right
314. om an analog to digital converter and store it in a rotating buffer When a high water mark is reached it sends a message to scribe to write the data to disk Int Every experiment is unique and hence some part of Rex must be easily adaptable to the investigator s needs This is accomplished in Rex by devoting one process int to the experiment specific code The experiments currently running under Rex investigate the neurophysiology of the visual and eye movement systems Stimuli are presented to subjects according to a behavioral paradigm Analog signals are digitized and events such as pressing a bar or the firing of cells in the brain are recorded by the computer Since the control of the experiment and the collection of the data are dependent on the behavior of the subject in these applications a great deal of digital signal processing must be done in real time by Rex e g the onset of a rapid eye movement is detected by a digital filter In its present configuration Rex is interrupt driven from the real time clock which normally interrupts at a one kilohertz rate Other applications may have higher sampling rates when less processing is required The int process is divided into two parts an upper level one that handles the communication with the other Rex processes and the operator and a lower level one that responds to the interrupts The upper level part displays a tool bar containing pull down menus and toggle buttons to handle user
315. on is called whenever you start a paradigm using the r p command reset the states using the r s menu command or return to a paradigm using the c p command If you use both GLvex and Mex the restart function should look something like rinitf void char vexHost Isr labVex name of the GLvex machine as defined in etc hosts char mexHost Isr labMex name of Mex machine as defined in etc hosts pcsConnectMex host open a udp socket to the Mex machine pcsConnectVex host open a udp socket to the Vex machine wd_disp D_W_EYE_X other functions in rinitf If at another time you use this spot file without Mex you must remove the statement opening the socket to the Mex machine Otherwise you will get a stream of socket error messages when you run your spot file Clock Source By default the PCI DAS4020 12 A D board uses its internal 40 MHz clock to pace A D conversions However it can use an external clock signal For the time being you should leave this set to the default Internal Clock setting Page 326 Input Range The PCI DAS4020 12 A C board has two input ranges indicated by the two radio buttons The default is 5volts You should select the range that displays your signals at the greatest range without clipping If you select too small a range signals will be clipped and shape information will be lost If you select too large a range signals will not be represented with full 12 bit pr
316. on is to buy the Analogics screw terminal box 200 This box may also have an area to put RC anti aliasing filters Computer Boards CIO DDA06 CIO DAC08 CIO DAC16 These boards should be jumpered for address 0x180 I also jumper the boards to include a wait state The simultaneous update jumper should be on UPDATE XX for individual updates These boards have a 37 pin D connector The 2M37DSM termination board from Industrial Computer Source provides screw terminal connections for this connector This board can also be ordered from Newark The manufacturer is Augat RDI Industrial Computer Source PCDIO This board should be jumpered for address 0x280 See Figure 1 for other jumpers configuration information Jumpers set to 19 amp 23 50 pin flat cable connectors Pin 1 Pin 1 Pin 1 Pin 1 Pin 1 fs fe eles 5 EJ m 57 es 57 4 3 2 O oy UT I M ee lt vw vi N yi Y E 5 Address a a a a a 0x280 PCDIO Board Interrupt jumper set for no interrupts Figure 1 PCDIO Configuration Page 124 Digital VO Rack Panels and Circuits Digital I O is accomplished using I O rack systems These systems are composed of a PC board termed a rack and potted modules which plug into the PC board There are four general types of modules DC input DC output AC input AC output AC modules will switch 110v The Industrial Computer Source digital I O board will drive up to
317. on point when switched on can be 0 to 255 ob intensity of blue in fixation point when switched on can be 0 to 255 dr intensity of red in fixation point when dimmed can be 0 to 255 dg intensity of green in fixation point when dimmed can be 0 to 255 db intensity of blue in fixation point when dimmed can be 0 to 255 DESCRIPTION This function allows you to specify what the color or luminance of the fixation point will be when it is switched on and when it is dimmed RETURN VALUE Glvex will return the signal BATCH DONE 241 after completing this action EXAMPLE int onRed 255 int onGreen 0 int onBlue 0 int dimRed 0 int dimGreen 255 int dimBlue 0 state do PvexSetFixColors amp onRed amp onGreen amp onBlue amp dimRed amp dimGreen amp dimBlue to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 172 PvexSetStimLuminances sets the foreground and background luminances of one and two tone stimuli SYNOPSIS PvexSetStimLuminances int nObjects int objList int fgList int bgList nObjects number of objects to set objList array of object numbers to set fgList array of foreground luminances can be 0 to 255 bgList array of background luminances can be 0 to 255 DESCRIPTION This function allows you to specify the gray levels of the foreground and background checks of a number of objects RETURN VALUE Glvex will return the signal BATCH DONE 241 after completing this action
318. ontrast and brightness controls of your monitor to give you the best dynamic range This pattern is also essential for setting the Rex calibration To set Rex calibration you will need to measure the distance from the viewer to the screen in millimeters and the width of the calibration pattern in millimeters GLvex will use these values to calculate the number of video pixels per rex unit 1 10 of a degree and to correct for tangent error Flow fields Flow fields are drawn in rectangular objects which can be of any size up the to the limits of the screen Additionally a rectangular portion of the flow field can be masked out This mask can be located anywhere in the object Multiple flow fields may be displayed simultaneously For three dimensional flow fields the movement of the points are specified by 6 parameters movement along the X and Y axes sheer movement along the Z axis vergence rotation about the Z axis roll rotation about the Y axis yaw and rotation about the X axis pitch For two dimensional flow fields the parameters which produce movement in depth vergence yaw and pitch must be set to 0 or the program will hang The movement of points in the flow fields in the X Y plane are specified in rex units tenths of a degree of visual angle The movement of points in depth are in the linear equivalents of rex units That is if your display subtends 1 degree of visual angle per centimeter then movement of 10 degrees second
319. or a dimmable LED I O Module Rack Dimmable LED AN Note solder 18 ga solid wire to pot The stiffness of this wire will hold pot in place 10k resistor in parallel with LED is required to shunt leakage current from 1 0 module Figure 10 Dimmable LED Connections The a d input requires low pass filtering to prevent aliasing At NIH we use a custom built box that has an instrumentation amplifier and a six pole Frequency Devices active Bessel filter At the very minimum a single pole RC filter should be used Figure 11 shows the circuit for an RC filter for a differential input with a corner frequency of 241Hz R 10k In Hi is ERT C 033uF A D Differenti f Input Into O R 10k Corner Frequency 1 differential input filter f 241Hz 4 pi RC Figure 11 Single Pole RC Filter Page 132 Appendix A Example Orders Following are copies of the orders we used at NIH Industrial Computer Source 10180 Scripps Ranch Blvd San Diego CA 92131 1298 800 523 2320 FAX 619 271 9666 Attn Mark Thurman Table 4 Item Order Number Description Qty Price ea 1 DCC20 A 20 Channel 1 395 Counter Timer card 2 PCDIO120 P Digital I O 1 350 card 3 2M37DSM 37 pin ter 1 29 mination board NOTE Don t order the counter timer card at this time It is not currently used and may never be Computer Boards Inc 44 Wood Ave Mansfield MA 02048 508 261 1123
320. ort size 4 draw_user unsigned short index short i j static int rs_shift 10 static int tricntr 6 for i 0 i lt tricntr i ptrist i i shuffle tricntr rs_shift ptrist index 0 vexbuf index DRAW_USER_PATTERN vexbuf index 3 number of objects for i 0 i lt 3 i j ptrist i vexbuf index obli object number vexbuf index hibyte patterns j high byte of pattern number vexbuf index lobyte patterns j low of pattern number vexbuf index size pattern check size vexbuf index 1 positive contrast other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not Page 277 DRAW_RGB_USER_PATTERN This is a batchable command that draws a user defined RGB pattern in an object The pattern is defined in a file named Pnumber where number is the pattern number you are going to use for that pattern The first parameter is the number of objects to draw in Each object requires four parameters the object number the high byte of the pattern number the low byte of the pattern number and the pattern check size The pattern numbers can range from 0 to 65536 The format of the pattern template is rc3 rgbrgbrgb rgb rgb rgb rgbrgbrgb rgb rgb rgb rgbrgbrgb rgb rgb rgb rgbr
321. ose location you want DESCRIPTION This action together with PvexMessage described below allow you to query GLvex as to the location of objects The purpose of these two actions is to allow you to have Rex eye windows follow objects that are moving on GLvex ramps It is particularly important that the only escape you should use in a state that calls this action is when the function tst_rx_new returns 0 RETURN VALUE GLvex will return the signal OBJECT_LOCATION 233 plus the X and Y coordinates of the selected object Use the action PvexMessage to get the X and Y coordinates EXAMPLE int vexMessage int vexX vexY int trgsiz int obj 1 int targ_wnd void wd_pos WIND1 vexX vexY wd_siz WIND1 trgsiz trgsiz wd_cntrl WIND1 WD_ON return 0 A state do PvexReportLocation amp obj to tstmsg on 0 tst_rx_new no other escapes tstmsg do PvexMessage amp vexMessage amp vexX amp vexY to tarwnd on OBJECT_LOCATION vexMessage to otherstate do something else if the signal returned is not OBJECT_LOCATION tarwnd do targ_wnd to nextstate FILE rex act vexActions c Page 191 PvexMessage returns the signal number and possibly the location of an object SYNOPSIS PvexMessage int code int x int y code the signal returned by GLvex x the x coordinate of the object specified in a call to PvexReportLocation in 10ths of a degree y the y coordinate of the object specified in a call to PvexReport
322. other signals from the oeye signals The vergence gaze signals vgazeh vgazv are computed by subtracting the ogaze signals from the gaze signals The cyclopean gaze signals cgazeh cgasev are computed by summing the gaze and ogaze signals and dividing by 2 For computed signals the a d acquire rate and the signal store rate are taken from the source signals Analog Signal Summary Selecting the Analog Signal Summary item from the Analog Sig menu will display a summary of all of the signals that are on Signals Summary Sig Type Channel Cal Gain Delay Name Page 88 Sac Detect Clicking on the Sac Detect menu button will display a dialog that allows you to set up the parameters for Rexis saccade detector If neither the On or Off buttons are selected then the saccade Detector Horizontal Range Vertical Range Peak Velocity Start Velocity End Velocity Maximum Velocity Minimum Velocity Maximum Duration Minumum Duration Delay Time detector is under the control of your spot file Bits Clicking on the Bits menu button will display a dialog that allows you to set or clear various bits in the digital I O In this dialog the panels correspond to the Grayhill output panels Numbered toggles Toggle Digital Input Output Bits Set Clear Reset and Pulse Digital I O Bits VO Device ID Hexidecimal S Starting Port Number Port 1 Port 0 15 14 13 12 11 10 9 8 765 43 21 0 OESS SSe es OOOOOOOO DODODODO T
323. ots Data from up to 10 different units can be display in each plot Rex supports multiple raster displays Page 5 Laboratory Control To achieve useful control in the laboratory timing and sequencing of events in real time must occur precisely and efficiently State notation is a powerful tool for accomplishing this control The advantage of state notation is that it is simple and easy to learn yet able to implement even the most complex control sequences The process of reducing a control problem to state notation often helps clarify the problem and identify logical errors Rex incorporates a state set processor for laboratory control This processor is a part of the int process it is executed on interrupt from the clock currently every millisecond State Concepts State notation as implemented in Rex includes the following elements A state is the current condition or stage of a control sequence A state consists of the specification of a function to occur when the state is entered actions and the conditions that must be met for transition to occur to another state escapes Escapes to other states can happen in the following ways i Countdown of a timer to zero Bit pattern set in a flag word Bit pattern not set in a flag word True return from a function call Variable equal to a constant Variable less than a constant Variable greater than a constant Each state contains a long integer 32 bits to specify the time for escapes on
324. ou can get an explanation of the parameters by typing Os lt return gt to get the following help message o object for movie s starting frame of the movie Example command Os 2 50 This command will set the flow field in object 2 to movie frame 50 In the OB command the letters o and 02 in brackets stand for the lowest and highest priority objects in which you want to have moving flow fields The Ob command starts the flow field in the active object The Oe command stops the flow fields in all objects Example command OB 14 This command will start flow fields moving in objects 1 through 4 You can get an explanation of the parameters in the Or command by typing Or lt return gt to get the following help message r number of ramp to run with flow field o number of object to put on ramp c type of ramp cycle c 0 ramp runs once c 1 oscillation ramp goes back and forth c 2 loop ramp runs over and over Example command or150 This command will start the flow field in the active object and start ramp number 1 with object number 5 The ramp will run once o Foreground and background colors This command sets the colors of the foreground and background checks of two tone stimuli in the active object If you type o lt return gt you will get a help message similar to the following of r g b set cOlor of object foreground to r g b ob r g b set cOlor of object background to r g b Current values
325. ou may want the object on a ramp to change speed or direction or you may want one of the objects in a movie clip to have a different property color luminance size etc To have GLvex tell you when it displays the the discontinuity you need to tell it the ramp step number or movie frame of the discontinuity This action allows you to do that You may set a maximum of 10 trigger points in each ramp or movie clip RETURN VALUE GLvex will return the signal BATCH DONE 241 after completing this action During the display if the digital sync is enabled GLvex will return the signal FLOW_RAMP CHANGE 234 at each ramp step specified in the call or the signal MOVIE CHANGE 237 at each frame specified in the call If the video sync is enabled the sync object will flash white at each trigger point EXAMPLE int num 2 int ramps 2 1 2 int triggers 2 4 8 int frames 12 10 20 30 40 20 40 80 100 120 140 160 180 state do PvexSetTriggers amp num ramps triggers frames to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 232 REX COMMANDS To facilitate communication a number of actions and functions have been defined in a file named GLvex_com c This file should be included at the top of any spot file that communicates with GLvex In addition I have used defines to give provide names for the GLvex command values These defines are listed in a file named GLcommand h which is incl
326. ove RECIPIENT s Signature RECIPIENT s Printed Name Title Corporation Mailing Address City State Zip Code Country Phone FAX Date E mail Page 138 GLVEX User s Manual John W McClurkin Ph D Laboratory of Sensorimotor Research National Eye Institute National Institutes of Health Overview GLvex is a WindowsNT based program which displays a variety of visual stimuli on a video monitor Although it can be used as a stand alone program it was primarily designed to interface with the Rex real time data acquisition and control package GLvex requires a PC running Windows NT V4 0 or higher with at least 64 megabyte of RAM a graphics card that supports OpenGL version 1 1 and a mouse For communication with the machine running Rex you will need either an ethernet card or an Industrial Computer Source PCDIO 24 ISA parallel digital I O card If you are using the parallel I O card the port address of the card must be set to 0x280 I have tested GLvex with an STB Velocity 128 AGP graphics card an Intergraph Intense Pro 3D PCI graphics card an Elsa Gloria XL graphics card an Omnicomp 3DAEMON TWIN PCI graphics card and with SGI s 320 and 540 workstations While GLvex will run on OEM graphics cards as long as they support OpenGL animation performance is not as good as higher end boards such as the Intergraph and the Omnicomp The best performance is with the SGI workstations To use the pa
327. ovie SYNOPSIS PvexToFlowMovieStart int nObjects int startFrame int objList nObjects number of flow field objects startFrame the number of the movie frame to use as the start objList array of flow field object numbers DESCRIPTION This action allows you to show the starting frame of a flow field movie before starting the movie Thus when you show a flow field movie you do not need to start on the first frame You must call PvexDrawFlow PvexNewFlow and PvexMakeFlowMovie to define the flow field and the translation matrices and make the movie before calling this action RETURN VALUE GLvex will return the signal BATCH _DONE 241 when it completes this action EXAMPLE int num 4 int nFrames 100 int startFrame 25 int objects 4 2 3 4 5 int widths 4 100 100 100 100 int heights 100 100 100 100 int nears 4 500 500 500 500 int fars 4 1500 1500 1500 1500 int coverages 4 25 25 25 25 int sizes 4 4 4 4 4 int xy 4 0 90 180 270 int z 4 0 45 45 90 y int vel 4 10 15 20 25 int roll 4 0 0 0 0 int pitch 4 0 0 0 0 int yaw 4 0 0 0 0 int span 4 0 5 0 5 int coher 4 100 75 50 25 state do PvexDrawFlowField amp num objects widths heights nears fars coverages sizes to trans on 0 tst_rx_new trans do PvexNewFlow amp num objects xy z vel roll pitc
328. ow just to the right of the process switching tool bar This is equivalent to executing the command r p name in older versions of Rex Clicking on the Load action button will load the int process you selected but put it in a stopped state and iconify its tool bar This is equivalent to executing the command il p name in older versions of Rex If you already have an int process running and you click the Run action button with a new int process name Rex will stop the current running int process and iconify its tool bar load the new int process put it in the run state and display its tool bar This is equivalent to executing the command ic p name in older versions of Rex when you want to change to a new int process With the Root Files dialog clicking the Read action button will read in the root file you selected Note with Rex 7 0 and later you must have an int process in the run state before reading in a root file Clicking on the All Sys User System User or States action buttons will write out a root file with the name entered in the File Name text field A root file created with the A button will contain the current values of all menu items and all states A root file created with the Sys User button will contain the current values of all menu items but no states A root file created with the System button will contain only the current values of the system menus A root file created with the User button will contain only the current
329. parameter the number of the object to make active Example action it Action that sets the active object in VEX short act 1 set_active short index index 0 vexbuf index SET_ACTIVE_OBJECT vexbuf index act other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not Page 264 SET_FP_SIZE This is a batchable command that sets the size of the fixation point It requires one parameter which sets the radius of the fixation point in video pixels Example action JE This action sends the four GLvex commands that determine the properties and location of the fixation point as a single batch command I short fpsiz 4 value may be set in Rex state variables menu short fplum 128 value may be set in Rex state variables menu short fpdim 96 value may be set in Rex state variables menu float fpx 0 0 value may be set in Rex state variables menu float fpy 0 0 value may be set in Rex state variables menu set_fp unsigned short index int i char flbuf index 0 vexbuf index SET_FP_SIZE vexbuf index fpsiz vexbuf index SET_FP_ON_CLR vexbuf index fplum vexbuf index fplum vexbuf index fplum vexbuf index SET_FP_DIM_CLR vexbuf index fpdim vexbuf index
330. parameter determines whether the object on the ramp will be left on or turned off when the ramp stops Once specified GLvex can move objects according to the specifications If you are defining new ramps the ramp numbers must be sequential If you are redefining old ramps the ramp numbers need not be sequential Once defined a ramp remains defined until changed That is unlike the Rex action ra_new you do not have to call this action on every trial Call it once to define some ramps then reuse them as often as you like RETURN VALUE GLvex will return the signal BATCH _DONE 241 when it completes this action EXAMPLE int num 1 int ramp 1 int length 200 F half the length of the ramp in Rex units int direction 15 direction of travel in degrees int speed 20 I speed of 20 degrees sec int rx 100 X coordinate of reference point int ry 10 Y coordinate of reference point int type RA_CENPT 1 rx and ry define middle of ramp int act ON_AFTER_RAMP leave object on when ramp stops A state do PvexNewRamp amp num amp ramp amp length amp direction amp speed amp rx amp ry amp type amp act to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 214 PvexLoadRamp defines ramps from coordinates passed from Rex SYNOPSIS PvexLoadRamp int nRmp int rmpList int actList int stpList float xLst float yLst nRmp number of ramps rmpList array of ramp
331. parameters the hi and lo bytes of the ramp step or movie frame where you want the trigger Example action E This action sets up two user defined ramps then specifies that triggers be sent when the objects on the ramps change direction struct ramp float x float y struct ramp rampOne 300 struct ramp rampTwo 200 loadRamp unsigned short index short i j stepsOne stepsTwo short breakOne breakTwo rampOne 0 x 150 0 starting location of the first ramp rampOne 0 y 150 0 for i 1 i lt 150 i ramp goes to the right thisRamp i x thisRampli 1 x 2 0 thisRamp i y thisRampli 1 y for i lt 300 i ramp goes up thisRampli x thisRampli 1 x thisRamp i y thisRampli 1 y 2 0 rampTwo 0 x 100 0 I starting location of second ramp rampTwo 0 y 100 0 for i 1 i lt 100 i ramp goes up and to the right thisRampli x thisRampli 1 x 2 0 thisRampli y thisRampli 1 y 2 0 for i lt 200 i ramp goes down and to the right thisRampl i x thisRampli 1 x 2 0 thisRampli y thisRampli 1 y 2 0 stepsOne 300 stepsTwo 200 breakOne 150 breakTwo 100 index 0 vexbuf index LOAD_RAMP vexbuf index 2 number of ramps to load vexbuf index 1 F first ramp number Page 302 vexbuf index OBJ_ON l object stays on after end of ramp vexbuf
332. pcmsg communication protocol actions in your paradigm that communicate with GLvex should be called only when the transmission line is clear and your paradigm should be ready to handle signals returned from GLvex At the present time this synchronization must be done explicitly The best way to ensure proper synchronization is to embed actions that communicate with GLvex in a set of three states as follows Example GLvex parallel I O communication state set other states in your paradigm to vstwis vstwts means vex state wait to send vstwts to vexst on 0 tst_tx_rdy test if transmission is ready vexst a state that sends a message to vex do vex_call 1 do action which sends a message to vex to vexack on 0 tst_rx_new escape when vex signal is received vexack code ECODE to indicate the start of a display change do pem_ack 0 do action which acknowledges signal from vex time 100 rand 100 to othst othst means other states othst other states in your paradigm The escapes tst_tx_rdy and tst_rx_new are functions defined in vex_com c that test whether the transmission line is ready and whether a new message has been received respectively Beginning with Rex 7 2 the GLvex escape functions are defined in the vexActions c located in rex act In this example note that in the states vstwts and vexst the rex variables time and rand are not given values These variables should not be given
333. ples shows two functions the root argument generation function r_agf and the menu access function r_maf that are needed for menu access to arrays of structures The purpose of the root argument generation function is to convert an integer array index value into an ascii string to be written into a root file In the argument list for r_agf call_cnt is the element of the array mp is a pointer to the menu struct in this case amp umenus 0 and astr is a pointer to a string variable that holds the ascii representation of the index The purpose of the menu access function is to convert an ascii string into an integer array index and set a pointer to the appropriate array element In the argument list for r_maf mp is a pointer to the menu struct in this case amp umenus 0 and astr is a pointer to the string to be converted to an integer index The arguments flag and rp are required by the function protocol but are not used in this example Page 17 In the umenus definition the value of me_basep is set to null NP because me_basep is computed by the access function User defined functions In Rex actions are just functions but they are functions that are called by the state processor and are only called once when the processor enters a state Thus they will only be called when the Rex clock is running Rex 7 0 also provides a mechanism for calling functions independently of the state processor This mechanism is to list the functions in an
334. pleting this action EXAMPLE float fpx 0 0 float fpy 0 0 A state do PvexSetFixLocation amp fpx amp fpy to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 188 PvexStimLocation PvexStimFromFixPoint set the locations of a number of objects SYNOPSIS PvexStimLocation int nObjects int objList float xList float yList PvexStimFromFixPoint int nObjects int objList float xList float yList nObjects number of objects to position objList array of object numbers xList array of the x coordinates of the objects in 10ths of a degree yList array of the y coordinates of the objects in 10ths of a degree DESCRIPTION These actions set the locations of a number of objects PvexStimLocation sets the locations in absolute screen coordinates PvexStimFromFixPoint sets the locations relative to the location of the fixation point RETURN VALUE Glvex will return the signal BATCH DONE 241 after completing this action EXAMPLE int num int objectArray 4 float xArray 100 00 100 00 100 00 100 00 float yArray 100 00 100 00 100 00 100 00 int setup int i num 4 for i 0 i lt num i objectArray i i 1 return 0 prev do setup to state state do PvexStimLocation amp num objectArray xArray yArray to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 189 PvexShiftLocation sets the location of a number of objects an
335. point The first parameter is the number of objects to locate Each object requires nine parameters The first parameter is the object number The next four parameters are the four bytes of the X coordinate of the object location relative to the fixation point The last four parameters are the four bytes of the Y coordinate of the object location relative to the fixation point The X and Y coordinates are in REX units i e tenths of a degree For this command object coordinate 0 0 is the fixation point location which may not be the same as the center of the screen Negative X values are to the monkey s left of the fixation point and negative Y values are below the fixation point Example action J This action will position an object below and to the right of the fixation point float rlx 100 float rly 100 rel_pos void unsigned short index int i char flbuf index 0 vexbuf index STIM_FROM_FIX_POINT vexbuf index 1 number of objects to position vexbuf index 2 I first object number flbuf float2byte rlx for i 0 i lt 4 i vexbuf index flbuf i flbuf float2byte rly for i 0 i lt 4 i vexbuf index flbuf i other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not The float2byte funct
336. pre time is the time in msec before the window is opened that data keeping will Page 73 actually start The post time is the time after the window is closed that data will continue to be kept If a previous window overlaps a subsequent window e g the previous window s post time overlaps the subsequent window s pre time than the data in the overlapped section is stored twice on the disk both windows are completely written even though parts overlap Note however that only one window can be active at a time If a previous window has been closed BUT is still being written during the post time a subsequent window CANNOT be opened until the post time has expired The open request is ignored if given during the post time of a previous window however an open window ecode IS loaded into the Efile Also no error indication will occur Therefore one must be sure that a previous window s post time has elapsed before giving a subsequent open window request For situations where timings are close a flag can be tested in the state set to determine exactly when the post time has expired and the previous window is completed A state named init The spot compiler prepends s to the name of all states If a state is named init it will be become sinit This name conflicts with another symbol in an obscure way no error is reported however the paradigm will crash Therefore do not name a state init Menu variable names cannot have embedded spaces sy
337. print warnings similar to the following make_flow Warning unable to malloc space for object 10 hvec make_flow Warning unable to malloc space for object 10 pvec 0 make_flow Warning unable to malloc space for object 10 pvec 1 When you recompute an old flow field GLvex dynamically reallocates the 3 D homogeneous coordinates buffer and the two 2 D projection buffers If you run out of host memory GLvex will print warnings similar to the following make_flow Warning unable to realloc space for object 10 hvec make_flow Warning unable to realloc space for object 10 pvec 0 make_flow Warning unable to realloc space for object 10 pvec 1 Execution will continue but the flow field will not be computed The object s stimulus type will be set to NULL so that you won t be able to create masks movement transforms or to start the flow fields This is done to avoid unpredictable results To correct this problem you will probably have to quit GLvex to free up memory When you restart GLvex try defining smaller or less densely covered flow fields Page 309 Pattern Specification Warnings If you attempt to specify a pattern number greater than 255 say 256 you will get the following message 256 is an invalid number to specify pattern Pattern number must be between 0 and 255 A pattern will be drawn but only the low byte of the number will be used so you will get an unexpected result If you attempt to draw a random check pattern with a
338. program that allows you to classify in real time multiple neuronal waveforms from a micro electrode and to use neuronal waveforms as triggering events for antidromic collisions experiments Mex can save neuronal waveforms to disk for later classification Mex can also save data from antidromic collision experiments to disk for subsequent display Mex is designed either to interface with the Rex real time data acquisition and control program or to run in a stand alone mode for use with other data acquisition programs Mex runs under the QNX Momentics 6 2 real time platform operating system with the Photon microGUI Two cards a high speed analog to digital card for data input and a digital I O card for signaling the acceptance of waveforms Currently Mex supports only the Measurement Computing PCI DAS4020 12 12 bit high speed A D converter This board accepts inputs from up to 4 electrodes Mex supports the Kontron PCI DIO24 PCI DIO48 and PCI DIO120 digital I O boards To interface with Rex Mex also requires an ethernet card Theory of Operation Mex continuously samples the analog inputs at 2 mega samples per second If you use one electrode Mex samples that electrode at 2 MHz If you use 4 electrodes Mex samples each electrode at 500KHz For neuronal classification when the signal on any electrode satisfies trigger conditions Mex extracts a waveform from that input at a 5OKHz rate This waveform includes one half millisecond of data prior to
339. propriate number of buttons in the button panel will become active Enter the text of a page label if you like Below the label text field is a set of buttons that allow you to select the font for the label The choices correspond to normal bold and italic You specify the size of the label in the Size numerical field The size is in hundredths of an inch The Left and Bottom fields allow to specify the position of the page title on the page These values are in fractions of a page Specifying a Left position of 0 10 causes the page title to begin one tenth of the page width from the left edge Specifying a Bottom position of 0 90 causes the page title to begin one tenths of the page height up from the bottom edge Page 99 To specify a plot click on the appropriate cell in the cell panel The button will turn yellow and the current selection set and ecode will be displayed You specify the data to be plotted using widgets in the bottom left panel of the dialog You specify the scaling of the data using the widgets in the bottom right panel of the dialog Enter the selection set number and the ecode of the data for this plot in the Set and Ecode numerical fields Use the Sigma numerical field to specify the width of the Gaussian kernel used to build spike density functions The large the value for Sigma the smoother the spike density function If you enter a negative value for Sigma Rex will use an adaptive kernel in building spike density functions
340. ps PvexNewRamp PvexNewRampFromFixPoint computes parameters for a number of ramps SYNOPSIS PvexNewRamp int nRamps int rampList int lenList int dirList int velList int xList int yList int typeList int actList nRamps number of ramps to compute rampList array of ramp numbers ramp numbers must be sequential lenList array of lengths in 10ths of a degree length is half the length of the ramp dirList array of ramp directions in degrees velList array ramp velocities in degrees per second xList array of the X coordinates of ramp locations in 10ths of a degree yList array of the Y coordinates of ramp locations in 10ths of a degree typeList array of types of the ramps actList array of actions at ramp end can be ON_AFTER_RAMP or OFF_AFTER_RAMP DESCRIPTION This action allows you specify the parameters of a number of ramps The typeList parameters define the reference points of the ramps RA_CENPT 02 reference point is the center of the ramp RA_BEGINPT 04 reference point is beginning of the ramp RA ENDPT 08 reference point is end of the ramp RA CLK WISE 16 ramp is a clockwise circular ramp and the reference point is the center of the circle RA CCLKWISE 32 ramp is a counter clockwise circular ramp and the reference point is the center of the circle The reference point for PvexNewRamp is relative to the center of the screen The reference point for PvexNewRampFromFixPoint is relative to the fixation point The actList
341. put a mark on a signal channel running line trace SYNOPSIS sd_mark long channel long mark ADDITIONAL HEADERS REQUIRED None DESCRIPTION sd_mark puts a mark on a running line signal channel trace This is used by the saccade detector to mark the beginning and end of saccades but is also available to the user to place marks Each mark is composed of a varying number of dots situated vertically The maximum number of marks is defined by RL MARKMAX in the file idsp h RETURN VALUE Returns 0 EXAMPLE sd_mark 0 3 Place mark number 3 on the running line trace for channel 0 SEE ALSO rl_setbar rl_addbar rl_trig rl_stop rl_erase sd_mark FILE rex act sd_set c Page 65 Saccade Detector Controls sd_set saccade detector control SYNOPSIS sd_set long ctlflag ctlflag octal constant ADDITIONAL HEADERS REQUIRED None DESCRIPTION sd_ set controls the saccade detector If ctlflag is non zero the saccade detector is turned on If ctlflag is zero it is turned off The variable sacflags can be tested for the following values SF HOR 01 if this bit is set detector is following saccade on horizontal component if not set following saccade on vertical component SF ONSET 010 saccade start seen SF GOOD 020 saccade accepted The global variables h_sacinit and v_sacinit contain the initial position of a possible saccade The global variables h_sacend and v_sacend contain the final position of the most recently
342. quence numbers and magic numbers that can be used to verify file integrity Laboratory Control Rex includes a state set interpreter and language Spot for laboratory control Applications are programmed using Spot and associated C functions termed actions that are called from the state sets Users can also write custom actions in C The state set interpreter supports multiple independent state chains Timing resolution for the interpreter is 1msec Rex supports industry standard Opto 22 type I O modules for interfacing with devices in the laboratory These modules can interface with DC and AC voltages and provide optical isolation between the computer and the laboratory Displays Rex includes three displays The running line display is an oscilloscope simulation The window display is an X Y display suitable for showing eye position and eye position windows The raster display shows on line rasters and spike density functions This display is completely user customizes in terms of number of rasters histograms displayed size position triggers etc User Interface Users interact with Rex via a graphical interface consisting of pull down menus dialogs and toggle buttons Variables and parameters in Rex are contained in structures The contents of all structures can be saved in ascii to a file termed a root file Page 1 PC to PC Communication Rex provides two methods for PC to PC communication The first system pemsg is sui
343. r d in brackets stands for the distance from the viewer to the screen The letter w in brackets stands for the width of the initial calibration pattern Both values must be in millimeters Example command d 572 900 This command sets the screen distance to 572 millimeters and the pattern width to 900 millimeters e Set erase method GLvex allows two methods of erasing stimuli clearing the entire screen or erasing each individual object with rectangles the color of the screen background By default the erase method is set to clearing the entire screen Erasing each object is much faster than clearing the entire screen especially on low end graphics boards However using the entire screen method allows you to move and switch a running flow field with the mouse This could be useful in mapping the receptive fields of movement Page 152 sensitive neurons such as those found in area MT of the Macaque If you type e lt return gt you will get a help message similar to the following e 0 1 set erase method to 0 each object 1 whole screen The letters 0 in brackets stand for the erase method Example command e1 This command sets the erase method to clear the entire screen F Fixation point properties Commands beginning with F set the properties of the fixation point If you type F lt return gt you will get a help message similar to the following Fc n set Fixation luminanCe to n Fc r g b set Fixation Color to r g b Fm
344. ra_stop FILE rex act ramp_act c Page 53 ra_start Pra_start start ramp SYNOPSIS ra_start long rnum long ctlflag DIO_ID device Pra_start long rnum long ctlflag DIO_ID device rnum ramp number ctlflag constant device device specification recognized by dio_off ADDITIONAL HEADERS REQUIRED None DESCRIPTION ra_start initiates the ramp Following arguments may be specified rum ramp number ctlflag if non zero there will be a 40 msec pause after moving the mirrors to the starting point of the ramp before starting the ramp This allows the mirrors to settle after the jump to the starting position Note that this settling time is independent of the 25 msec acceleration time one does not affect the other either none or both can be specified device If non zero this argument is taken to be the device of the illumination stimulus on the mirrors When the ramp completes it is turned off A bit is set in ramp rnum ra_rampflag when the ramp actually begins the mirrors are directly over the starting position This takes into account settling pauses or the 25 msec acceleration time if enabled Therefore this bit can be tested to determine when an illumination stimulus should be turned on octal value of bit shown in parenthesis RA_STARTED 01 when this bit becomes set in ramp rnum ra_rampflag the mirrors are over the starting position of the ramp RETURN VALUE Returns 0 EXAMPLE ra _start 0 1 LED1 Start ramp
345. rallel I O card under windows NT V4 0 you must install Industrial Computer s PeekPoke drivers This are included in the file icspp zip in the distribution To install unzip the file and follow the installation instructions What s New Additions Vex 3 1 has the capability to display two and three dimensional flow fields The points in the flow fields are updated in real time so there is no limitation on the length of time that flow field stimuli can be presented Vex 3 6 adds the capability to vary the life spans of the checks in flow fields and the capability to vary the coherence of the movement of the checks in the flow fields Vex 3 6 has the capability to respond to queries from Rex about the locations of display objects and allows Rex to set the active object Vex 3 8 eliminates the need to switch overlapping objects on or off in a last on first off sequence Vex 4 0 changes the COPY OBJECT command to allow the copied object to be stretched horizontally or vertically Also the luminance or color of the copied object can now be set independently of the source object Vex 4 0 also adds a new command DRAW RECTANGLE RANDOM PATTERN DRAW RECTANGLE RANDOM PATTERN differs from DRAW RANDOM _ PATTERN in that the vertical and horizontal resolution of the pattern can be specified independently Vex 4 1 cleans up some bugs and improves the keyboard interface Vex 4 2 allows two objects to be moved in synchrony with the mouse Vex 4 3 adds mo
346. rameter is the number of objects to draw in Each object requires 11 parameters the object number the hi and lo bytes of the direction of movement the hi and lo bytes of the speed of movement the hi and lo bytes of the width of the pattern the hi and lo bytes of the height of the pattern and the hi and lo bytes of the width of the bars The direction of movement can only be 0 degrees 90 degrees 180 degrees and 270 degrees The height and width of the pattern and the width of the bars are in rex units i e tenths of a degree of visual angle The speed of movement is in degrees second Example action F This action sets up an OKN stimulus in object 2 draw_okn unsigned short index short direction short speed short width short height short thick direction 90 upwards movement speed 10 ten degrees second width 300 pattern is 30 degrees wide height 250 pattern is 25 degrees high thick 10 bars are 1 degree wide and 30 degrees long index 0 vexbuf index DRAW_OKN_PATTERN vexbuf index 1 number of objects to draw OKN stimuli in vexbuf index 2 object number vexbuf index hibyte direction high byte of the direction of movement vexbuf index lobyte direction low byte of the direction of movement vexbuf index hibyte speed high byte of the speed of movement vexbuf index lobyte speed low byte of the
347. reen ramps into the lookup table from index 64 to 127 rg_ramp unsigned short index int i int red green blue red 255 green 0 blue 0 index 0 vexbuf index SET_LUT_ENTR_CLR vexbuf index 64 for i 0 i lt 64 i vexbuf index i 64 vexbuf index red vexbuf index green vexbuf index blue red 4 green 4 to_vex index return 0 number of table entries to set table index red value F green value blue value decrement red increment green other batchable commands GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not Page 247 SET_OBJECT_LUT_ENTRY_CLR This a batchable command that sets the colors in a variable number of color lookup table entries for the specified object The first parameter is the number of objects to set Each object two parameters the object number and the number of entries to set Each lookup table entry requires four parameters the table index and the values for the red green and blue guns for that index These parameters can range from 0 to 255 Example action e This action loads counter phase red and green ramps into the lookup table from index 64 to 127 in objects 2 and 3 list 2 3 rg_ramp unsigned short index int i
348. refore is composed of Event code Action function address and up to ten long integer or global variable pointer arguments Long time to initialize timer for timed escapes Integer random factor for time Escapes e Page 6 State Set Specification Language A user specifies state sets by writing in a language called Spot State PrOcessor Translator The Spot compiler translates the language into the tables that drive the state processor The Spot compiler is implemented with the compiler writing tools of Unix Lex and Yacc Spot source files are divided into two sections The first section contains C source code and is passed through Spot untouched to the C compiler Functions for actions are placed in this section The second section is the state set specification The Spot source file is the primary user interface to the Rex system Contained in the file is the complete laboratory control specification for an experiment including the source for any specialized actions not found in the system library Usually when modifying or creating new Rex applications the user will only have to be concerned with this one file To further simplify the user interface the generation of the Rex int process as well as all Rex processes is under the control of make a Unix utility After the user edits the Spot source file he simply types the command make sf spotname where spotname is the name of the Spot source file This utility then perform
349. res including 16 bit dacs full auto calibration dual dma extensive on board buffering a channel gain list double the conversion rate etc My a d recommendations therefore are the Analogics DAS 12 50 for an entry level 12 bit converter at SOKHz throughput 500 and the National Instruments ATMIO16 X for 16 bit at 100KHz throughput 2000 I don t have a higher throughput 100 500KHz 12 bit converter programmed into REX but would suggest one of the National Instruments cards Note if you think you may have need in the future for anything more than just 8 channels at 1KHz you should buy the ATMIO16 X Some other cards are known to work under REX and are listed in the rex hdr cnf h file Included are the DT2821 which works fine and has excellent performance but is costly Note that the DT2801 cannot work under REX it cannot generate an interrupt If you have this widely used card you may be able to trade it up to a DT 2821 The Analogics and National Instruments cards are preferred for new purchases D A Cards REX supports d a cards with programmed I O transfers REX typically can update d as once per millisecond The recommended cards can be purchased with from 6 to 16 converters card Page 120 Digital I O For digital 1 O IO module systems are used These systems are composed of racks a rack in this terminology is a pc board not a floor standing cabinet and bricks that plug into the racks The bricks contain solid sta
350. resolution greater than 255 say 300 you will get the following message random check resolution 300 is too high setting resolution to 255 A random check pattern will be drawn with a resolution of 255 If you attempt to draw a flow field with more than 10 coverage say 15 you will get a message similar to the following make_flow tenth percent coverage 150 is too high setting coverage to 100 tenths percent A flow field will be draw with 10 coverage If you attempt to create a flow field mask that is larger than the flow field you will get the following message make_flow_mask Warning mask is larger that view field No mask will be draw in the flow field In specifying a user pattern say 101 if you don t have a file with the proper name in the working directory in this case P101 in you will get a message similar to the following Error make_user could not open file P101 If you attempt to define a user pattern with more than 255 rows or columns say 260 X 300 you will get a message similar to the following make_user rows 190 cols 70 make_user Error number of rows or columns must not be greater than 180 In these two cases GLvex will not draw any pattern and the stimulus in the object will be unchanged Page 310 Flow Field Transforms GLvex supports both two and three dimensional flow fields If you are using 2 D flow fields the three transform parameters which produce movement in depth vergence yaw pitch must be s
351. ror or special condition occurs during state set processing it is often necessary for certain actions to be executed to effect a reinitialization or resetting to known conditions for example turning off stimuli returning mirrors to center etc A special action exists to facilitate this named reset_s arg The state names containing the actions that should be executed on error are listed after the keyword abort list When the action reset_s arg is called the actions specified in the abort list will be executed in sequence If arg is 1 the usual case the abort list of all chains will be executed If arg is a positive number the abort list of only that chain will be executed Note the following distinctions between the abort list keyword and the restart keyword After the abort list keyword one places the name of states The actions of these states are called whenever the reset_s action is executed or during a reset statelist command Note however ecodes will not be entered into the event buffer from actions called in this manner from the abort list After the restart keyword one places a single C function name not a state name This function may in turn call actions or other C functions The function specified after the restart keyword will be executed the first time the clock is begun and afterwards whenever a reset statelist command is issued When the reset statelist command is issued the state processor does the following Calls rese
352. s Flow field stimuli are lists of points distributed at random in a two or three dimensional space The resolution parameter of static patterns has no meaning for flow fields so the size of the flow field stimulus is limited only by the size of the display screen Types of stimuli GLvex will display the following types of stimuli Walsh patterns with a resolution of 16 checks X 16 checks Haar patterns with a resolution of 16 checks X 16 checks User defined patterns with a resolution of up to 255 checks X 255 checks User defined patterns need not be square Random check patterns with a resolution of up to 255 checks X 255 checks Random check patterns need not be square Circular spots and annuli Oriented bar stimuli RGBA Tiff images A calibration pattern with a resolution of 40 checks X 40 checks Two and three dimensional flow fields Movies Square gratings to be used as optokinetic nystagmus stimuli Stimuli can be grouped into two classes two tone stimuli and continuous tone stimuli Two tone stimuli are those that have one set of checks that are one color or luminance and a second set of checks pis pio pS pd pS p pa Page 143 that are a second color or luminance These two colors or luminances are termed foreground colors and background colors Two tone stimuli may be monochromatic that is consist of white and black checks or they may be poly chromatic consisting of red and green checks or
353. s Selecting the Functions item from User Menus will display a dialog that lists your user defined functions This dialog is generated from the ufuncs array in your spot file Use the scroll bar on the right or resize the dialog window if necessary to view all of the functions To call a function just enter its arguments in the Function Arguments text field and type a carriage return Rex will parse text Function Name Function Arguments you entered according to the format string you provided in the ufuncs array and call the function If the Page 84 number of arguments you enter donit match the number of tokens in the format string Rex will post an error dialog and abort the call If you didnit provide a format string Rex will assign all of the characters up the first space to one character array and all of the rest of the characters to a second character array and call your function with two char arguments In this case it is up to your function to parse the arguments Note items that you have changed but are not yet set will have white lettering on a red background You must type a tab or a carriage return Enter or move the mouse cursor out of the dialog for the value or values to be set and the function called When the value becomes set the item will revert to black lettering on a white background Real time Variables Selecting the Real time Variables item from User Menus will display a dialog that lists the variables in your rtvars
354. s set a state s time and random entries SYNOPSIS set_times char name long time long rand Pset_times char name long time long rand name name of the state time value of the time entry random value of the rand entry ADDITIONAL HEADERS REQUIRED None DESCRIPTION set_times allows users to dynamically set the time and rand entries of a state If either the time or rand arguments are 1 the corresponding value is not changed RETURN VALUE Returns 0 EXAMPLE set_times timeramp thisTime thisRand Sets the time entry of the state timeramp to the value contained in the variable thisTime and sets the rand entry of the state timeramp to the value contained in the variable thisRand The values of thisTime and thisRand can be changed on a trial by trial basis FILE rex act stateTime c Page 37 getClockTime PgetClockTime get the current rex clock time Only the pointer version PgetClockTime of the function is an action SYNOPSIS getClockTime PgetClockTime long time ADDITIONAL HEADERS REQUIRED None DESCRIPTION getClockTime allows users to get the rex clock time RETURN VALUE getClockTime returns a long value that is the current rex clock time PgetClockTime long time loads the rex clock time into the variable pointed to by its argument and returns 0 EXAMPLE long time time getClockTime Gets the current rex clock time Note This function is not an action It can be called from an action to get
355. s a library of actions that can be called from states but this library will probably not be sufficient to build a complete experimental paradigm In particular if users want to present a number of conditions in a random sequence they will need to write an action that selects the experimental condition for each trial For example include memSac h table of conditions global variables int mfTargX 0 int mfTargY 0 int antiTargX 0 int antiTargY 0 int trialCounter 1 int totalTrials 0 int currstim int blockcount 0 int pick_targ_location static int ptrist 2 NUM_STIM 0 static int rs_shift 10 int targx int targy Page 12 F build list of conditions if trialCounter lt 0 trialCounter NUM_STIM for i 0 i lt trialCounter i ptrist i i shuffle trialCounter rs_shift ptrist blockcount currstim ptrist trialCounter 1 totalTrials memSactTrialList currstim total set the time of the target fixation point gap state set_times gap memSacList currstim delay 1 set the location of the target window switch memSacList currstim direction case 1 target in movement field targx mfTargX targy mfTargY break case 1 I target opposite movement field targx antiTargX targy antiTargY break F action to set eye window position wd_pos WIND1 targx targy return code to enter into E file
356. s all necessary compilations including Spot library searching and loading and yields a new int process Runtime Considerations At runtime the state set processor begins execution when the real time clock is started Some of the variables contained in a state can be changed at runtime A special pull down menu accessed from the int tool bar exists to do this The changeable variables are arguments to actions times and the event code Shared Data Structures The data process sets up a data space that is shared by all of the processes A process adjusts its memory map to reference the shared space This space contains the data buffers and the inter process communication area When an interrupt occurs the int process may collect data This data need not be saved on the disk but must be available for on line display by other processes Int keeps this data in two buffers in the shared space Data that can be described as an epoch e g a single unit s action potential or when the subject presses a bar are stored in the event buffer Any data that can not be described as an epoch e g eye position or target position are stored in the analog buffer The internal structures of the event and analog buffers are different and when the data are saved on the disk two separate files are used see below Event Buffer All event data can be identified by only two numbers an event code and a time of occurrence The int process records epochs
357. s eect wane gaa wand sae He LAS ee at e 36 TOS A A ot Rota see bers 36 set times Pset tS naene eein pts oe Bh gon ghee sE 37 getClockTime PgetClockTime 0 eee eens 38 Data Window Controls 0 0 0 0 ccc eee nen no 39 awind 39 pre post Pprexpost lt 2 nouae penn eee ENR tea Rake ats 40 A A wrath tensa etal hod an Ales aut E 41 Digital Output Controls 0c saad a want a e a baa wal 42 dio_on dio_off dio_onoff dio_out Pdio_on Pdio_off Pdio_onoff Pdio_out 42 Digital to Analog Controls 0 cee eens 43 da cntrl da_cntrl_1 da_cntrl_2 Pda cntrl Pda_cntrl_1 Pda _cntrl 2 43 da set da set_1 da_set_2 Pda set Pda set_1 Pda set 2 45 da_mode Pda mode 0 cece eet eees 46 da offset Pda offsets 2 2 2 0352 50 ht Oh Geb oe eR ee 47 da cursor Pda CUISINE See Se eS ee 48 Ramp Controls ee Ren O tee a ee ar en ie eee 49 fa NEW Pra neW sointi aoe RA a Las 49 ra compute time Pra compute time 0 0 cece eee eee 51 ramptd Pramptdi o a EA daa eee 52 ra tostarto Pra tostada ETA tae 53 ra start Pra statta cina ne aaa E Da 54 f Stop Prato eonen e a ara LEE ek Reals Cea ee 55 ta phustart Pra phistart a yeeros an A os Vs ie eee Ree 56 ra_phiend Pra_phiend 0 0 cece cece etn nee 57 Memory Array Controls o ns ety cama ede ohne ene A 58 Page il ma entrl Priascntr lest eee cate eee ate nena 58 ma reset Pina TeSet 3 0 nae daba NAA ae
358. s in that menu Use the scroll bar at right or resize the dialog window to see more of the menu items To change values you can either enter the values into the individual text fields or enter a series of index value pairs in the Batch Arguments text field For example entering 11 180 3 1001 in the Batch Arguments text field would set angle to 180 and xoff to 100 Rex will display an error dialog and abort if you enter an index that is out of range or donit enter the value member of the index value pair Note in either case items that you have changed but are not yet set will have white lettering on a red background You must type a tab or a carriage return Enter or move the mouse cursor out of the dialog for the value or values to be set When the value becomes set the item will revert to black lettering on a white background In this example the menu items are members of an array of structures named ramp_list The ramp_list length item has been changed but not set The Menu Number shows the index number of the array element whose values are displayed in the middle panel of the dialog When you change the Menu Number Rex will call the menu access function that you defined for this menu to get pointers to the new elements If the menu displays items that are not members of an array of structures Rex determines this by whether or not you defined a menu access function the Menu Number label and widget are inactive grayed out Function
359. s the object number The next four parameters are the four bytes of the X coordinate of the object location The last four parameters are the four bytes of the Y coordinate of the object location The X and Y coordinates are in REX units i e tenths of a degree REX and GLvex have the same screen coordinate system i e 0 0 is the center of the screen negative X values are to the monkey s left and negative Y values are down Example action it This action will position two objects one in the upper left quadrant and one in the lower left quadrant float stx 100 0 100 0 y float sty 100 0 100 0 y short ob 1 2 stm_pos void unsigned short index short i j char flbuf index 0 vexbuf index STIM_LOCATION vexbuf index 2 number of objects to position for i 0 i lt 2 i vexbuf index obli object number flbuf float2byte stx i for j 0 j lt 4 j vexbuf index flbuf j flbuf float2byte sty i for j 0 j lt 4 j vexbuf index flbuf j F other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not The float2byte function is defined in GLvex_com c Page 259 STIM_FROM_FIX_POINT This is a batchable command that determines the position of an object relative to the fixation
360. s to negotiate with any companies that may want to commercialize PC REX The intent is f3NOT f1 to restrict it s distribution in any way to researchers The source to REX is kept on machine Isr nei nih gov under usr ftp rex The distribution includes the REX source and the manual The REX source is encrypted The manual is not encrypted In order to get the REX source you must fax the completed license form below You will then be contacted and given the decryption password You can pick up the encrypted file via anonymous ftp Please fill out license form and return via FAX to 301 402 0511 My voice number is 301 496 7143 Statement of Terms and Conditions for Release of The PC REX Software System The Federal Government of the United States of America is hereinafter THE GOVERNMENT The Laboratory of Sensorimotor Research hereinafter LSR an agency of THE GOVERNMENT is the originator of the PC REX package The PC REX Package is a collection of computer programs data files and associated documentation which may be provided in either or both electronic and printed form hereinafter referred to as PC REX enter name of corporation or private individual requesting PC REX having an office at is hereinafter referred to as RECIPIENT 1 PC REX is an unpublished work that is not generally available to the public except through the terms of this limited distribution THE GOVERNMENT grants recipient a personal non
361. s very well Other SCSI controllers may be supported under QNX but call QNX before ordering to verify REX currently uses only VGA 640 480 resolution Any VGA adapter will work However in the future REX may use X Windows In this case greater resolution and screen size would be desirable Call QNX for a list of the currently supported adapters A 17 inch or greater screen would also be needed Page 119 REX also currently requires a dumb tty that can emulate the VT100 Please note that VT 100 emulation IS REQUIRED REX wont work with anything else This tty is connected to serial port 2 and runs the REX menu interface The VGA screen then takes the place of the old Matrox display Will REX run on less expensive PC configurations Perhaps but I haven t tested it I would imagine that an ISA bus would be fine however it is difficult to use more than 14MB of memory on an ISA bus machine The only EISA card we are currently using is the Adaptec 1740 1742 It is also available for ISA as the Adaptec 1540 1542 In the future the PCI bus will be more popular and the Adaptec and the graphics card may both be supported by QNX on this bus The disk type is very important The SCSI controller works by DMA Other types such as IDE and ESDI do not use DMA and require CPU cycles to move data This can lock out the CPU and interfere with real time processing QNX supports the Western Digital SMC 8013 ethernet card very well I have not been able to get the 3Co
362. se cursor over an icon a dialog will pop up giving a brief description of that parameter When you first bring up the cluster display the X axis parameter is the peak latency and the Y axis parameter is the peak amplitude To change the axis parameters click on the axis button Ea in Page 333 the cluster display menu bar This will bring up cluster axis parameter dialog Buttons representing the Cluster Axis Parameters X axis parameter Y axis parameter a Peak Latency AN Peak Latency ALA Valley Latency AA Valley Latency SEW Peak Amplitude WAN Peak Amplitude AA Valley Amplitude ALY Valley Amplitude A Peak To Peak AL Peak To Peak EE Spike width WLW Spike width current axis parameters will be drawn with dark backgrounds Select which parameter you want to plot on each axis by clicking with the left mouse button on that parameteris button in each axisis column Note Mex will not let you specify the same parameter for both axes For example if you wanted to plot the Peak Latency on the Y axis in the above example you would need to first specify the new parameter for the X axis before setting the Peak Latency for the Y axis You may find that for a given set of parameters all of the points are plotted in only one quadrant or only one half of the display To get better plotting precision you can move the position of the X and Y axes Move the mouse cursor over an axis and the cursor will change displaying arrows pointing left and right
363. set c Page 61 Running Line Controls rl_setbar set bar value on running line display SYNOPSIS rl_setbar long value value bar value ADDITIONAL HEADERS REQUIRED None DESCRIPTION rl_setbar sets the value of the bar line on the running line display RETURN VALUE Returns 0 EXAMPLE rl_setbar 10 Set the bar line value to 10 SEE ALSO rl_setbar rl_addbar rl_trig rl_stop rl_erase sd_mark FILE rex act rl_set c Page 62 rl_addbar add to the current bar value on running line display SYNOPSIS rl_addbar long value value amount to add to current bar value ADDITIONAL HEADERS REQUIRED None DESCRIPTION rl_addbar adds a value to the current value of the bar line on the running line display RETURN VALUE Returns 0 EXAMPLE rl_addbar 10 Subtract 10 from the current value of the bar line SEE ALSO rl_setbar rl_addbar rl_trig rl_stop rl_erase sd_mark FILE rex act rl_set c Page 63 rl_setspike put a spike dot on running line display SYNOPSIS rl_setspike long spike_num spike_num spike number ADDITIONAL HEADERS REQUIRED None DESCRIPTION rl_setspike puts a dot on the running line display signifying the occurrence of the designated spike RETURN VALUE Returns 0 EXAMPLE rl_setspike 0 Put a dot on the running line display for spike number 0 SEE ALSO rl_setbar rl_addbar rl_trig rl_stop rl_erase sd_mark FILE rex act rl_set c Page 64 sd_mark
364. short patterns 7 18 21 24 43 63 short ptrlst 6 0 short ob 3 5 2 short size 4 draw_haar unsigned short index short i j static int rs_shift 10 static int tricntr 6 for i 0 i lt tricntr i ptrist i i shuffle tricntr rs_shift ptrist index 0 vexbuf index DRAW_HAAR_PATTERN vexbuf index 3 number of objects for i 0 i lt 3 i j ptrist i vexbuf index ob i object number vexbuf index patterns j pattern number vexbuf index size pattern check size vexbuf index 1 positive contrast other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not Page 270 DRAW_RANDOM_PATTERN This is a batchable command that draws a rectangular random two dimensional matrix of white and black checks in an object The first parameter is the number of objects to draw in Each object requires five parameters the object number the horizontal resolution of the random pattern the vertical resolution of the random pattern the pattern check size and the percentage of checks to make white The horizontal and vertical resolution determines the number of rows and columns in the matrix and can range from 2 to 180 The white check percentage can range from
365. speed of movement vexbuf index hibyte width high byte of the width of stimulus vexbuf index lobyte width low byte of the width of stimulus vexbuf index hibyte height high byte of the height of stimulus vexbuf index lobyte height low byte of the height of stimulus vexbuf index hibyte thick high byte of the thickness of the bars vexbuf index lobyte thick low byte of the thickness of the bars other batchable commands to_vex index return 0 If you turn object 2 on after calling this action you will see a stationary horizontal square wave grating You must use the START_OKN command described below to start the bars moving GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not The hibyte and lobyte functions are defined in GLvex_com c Page 281 LOAD_PATTERN This is a batchable command that loads a user pattern from Rex The first parameter is the number of the object into which to load the pattern The second parameter is the stimulus number The third parameter is the size of the checks in the pattern The fourth parameter is the number of rows in the pattern The fifth parameter is the number of columns in the pattern The remaining parameters are the values to be loaded into the individual checks in the pattern from upper left to lower right The number
366. src_num is ignored DA_JOY_Y source is the Y component of the joystick src_num is ignored DA_WIND_X source is the X component of the position of the eye window src_num specifies the window number Page 43 DA_WIND_Y source is the Y component of the position of the eye window src_num specifies the window number DA_SIGNAL source is a signal src_num specifies the signal number DA_MEM source is an internal memory array src_num specifies the internal memory array number src_num source number specifier if needed The pointer versions of these actions take pointers to variables as arguments By default all d a converters are initialized to DA_STBY mode unless changed by calling this action The function da_cntrl can be used to control the operation of more than two d a converters The operation of the d a s will be changed as close together in time as possible with no intervening interrupts allowed da_cntrl is not an action however and it cannot be called as an action from a state because its arguments are not of type long However it can be called from user written C code subroutines in the Spot file This function takes the following arguments cnt number of DA CNTRL ARG structs passed as arguments DA_CNTRL_ARG pointer to array of structs containing d a converter number source and source number specifier The function Pda_cntrl is an action because its arguments are pointers to variables Note that there would normal
367. sync enabled the rex video sync square will flash white for the first field in which the flow fields start Page 292 TIME_FLOW This is a non batchable command that presents flow fields in a variable number of objects for a given number of video fields The first parameter is the number of objects to present Each object requires one parameter the object number The last parameter is the number of video fields to present the flow fields The number of fields can range from 1 to 255 Example action it This action will present flow fields in objects 3 and 4 simultaneously for 60 fields I short fields 60 value may be set in Rex state variables menu flow_time void unsigned short index index 0 vexbuf index TIME_FLOW vexbuf index 2 number of objects to present vexbuf index 3 I first object number vexbuf index 4 second object number vexbuf index fields number of video fields to_vex index return 0 If the digital sync is enabled GLvex will return two signals from this command The signal FLOW_RAMP _ START 232 is sent at the beginning of the video field in which the flow fields are turned on and the signal FLOW_RAMP_ STOP 231 is sent at the beginning of the first video field after the flow fields stop Otherwise GLvex will not return any signal after this command If the video sync is enabled the rex video sync square will flash white for the first field in wh
368. sync is enabled GLvex will draw a small black square in the upper left corner of the screen This square will flash white for 1 video field when synchronization is needed The video sync is enabled by default Once the video sync is enabled it will remain enabled until disabled so you only need to call this command once Example action setup unsigned short index index 0 other batchable commands vexbuf index ENABLE_REX_VIDEO_SYNC other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not Page 235 DISABLE_REX_VIDEO_SYNC This is a batchable command that disables the video sync for synchronizing the display with rex It does not require any parameters The video sync is enabled by default Once the video sync is disabled it will remain disabled until enabled so you only need to call this command once Example action setup unsigned short index index 0 other batchable commands vexbuf index DISABLE_REX_VIDEO_SYNC other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not Page 236 ENABLE_REX_DIGITAL_SYNC This is a batchable command that enables the digital sync for synchronizing the
369. t but switching an object on or off is the fastest operation By making the three steps in presenting stimuli independent GLvex allows you to group the time consuming steps of drawing and positioning into one action to be called at the beginning of the trial thus falling in the inter trial interval One of the properties of GLvex objects is priority Object 1 has the highest priority and objects with higher numbers have lower priorities The fixation point has the highest priority of all High priority objects always occlude lower priority objects This is different from previous versions of vex where object 1 had the lowest priority and higher number objects had higher priorities TIP If you want to move one object around on the screen while other objects are on performance will be best if you move the highest priority object Communications Users may communicate with GLvex directly through the keyboard from rex or with the mouse Objects can be moved on the screen or flashed on and off using the mouse To move the active object move the mouse while holding down the right mouse button Pressing the left mouse button will turn the active off This is different from previous versions of vex where pressing the left mouse button caused the object to reverse contrast Pressing the left mouse button will turn off all types of objects not just two toned objects as was the case with previous versions of vex You can change the active object using the
370. t xoff int yoff int ecode int type The ra_new routine can not be specified as an action in a state due to size of argument list Must be called from a C subroutine in the Spot file However the Pra_new routine can be specified as an action in a state rnum ramp number len tenths of degree angle degrees vel degrees per second xoff yoff tenths of degree ecode type See below ADDITIONAL HEADERS REQUIRED None DESCRIPTION ra_new specifies and computes parameters for a new ramp from the given arguments Ramps are specified in a combination of polar and rectangular coordinates as follows len one half total length of ramp in tenths of degree angle polar angle of ramp assuming 0 degrees is motion from monkey right to left in horizontal plane Higher angles proceed in clockwise direction 90 degrees is motion from monkey view bottom to top in vertical plane vel Velocity of ramp in degrees sec Range 1 to 1000 degs sec xoff yoff x and y offset of Cartesian reference point of ramp in tenths of degree Even though the ramp is primarily specified in polar coordinates its reference point may have a Cartesian offset See type below for explanation of the reference point ecode currently not used type flag used to specify type of ramp The ramp has a reference point that can be given a Cartesian offset This reference point can be considered to be the beginning middle or end of the ramp by setting the proper bit in type For
371. t can be either 1 for normal contrast patterns or 1 for reverse contrast patterns The format of the pattern template is rc nnn nnn nnn nnn nnn nnn nnn nnn nnn nnn nnn nnn The letters r and c indicate the number of rows and columns in the pattern The maximum number of rows or columns is 255 The pattern may be rectangular i e you do not need to have the same number of rows and columns The letter n indicate the values for the individual checks in the pattern If n equals 1 the object s foreground color will be used in that check If n equals 1 the object s background color will be used in that check If n equals 0 the screen s background color will be used in that check If n equals 2 255 lookup table entries will be use in that check Example of a file for a user defined pattern with 8 rows and 8 cols This file defines a white and a black bar centered in a gray region The name of the file might be p1 88 0001 1000 0001 1000 0001 1000 0001 1000 0001 1000 0001 1000 0001 1000 0001 1000 Example of a file for a user defined pattern with 8 rows and 2 cols This file also defines a white and a black bar but does not have the gray region The name of the file might be p2 82 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Page 276 Example action it This action draws user defined patterns in three objects short patterns 1 2 3 4 5 6 short ptrlst 6 0 y short ob 3 5 2 sh
372. t edge of the plot whereas the alignment line is drawn where ever time is 0 and the Y axis has tick marks numbering and a label whereas the alignment line is just a vertical line If you want Rex to number the axes click on the Number Axes button Choose the format of the numbers selecting either the nt or Float toggle buttons Choose the font of the numbers from the Font group toggle buttons and enter the size of the numbers in the Size field If you want labels on the X or Y axes enter the text in the X Label and Y Label fields Set the font of the labels by selecting one of the Font group toggles Set the size of the labels in the Size field When you select successive plots the parameters of the previous plot are copied to the new plot Therefore you donit have to set all of the parameters for each plot You just have to change the parameters that differ If you want another page of plots click on the New button at the top of the dialog The dialog title will change to reflect the page number and the scroll bar at the right will get shorter When you define a new page all of the parameters from the previous page are copied to the new page Therefore all you have to do is click each cell button and change just the parameters that are different for this page You can review each page using the scroll bar After you have defined the data organization and page layouts you can save the parameters in a root file Click on the File button in the men
373. t symbol is an hourglass Other symbols are circle diamond square or any alpha numeric symbol Set the size of the symbol in the Mark Size field The size is in hundredths of an inch If you enter a mark size of 0 Rex will automatically size the symbols to match the number of raster lines in the plot At the bottom of the input panel you can define a label for the plot If you enter default for the Plot Label Rex will use the values of Set and Ecode to build a plot label For example if the Set is 1 and the Ecode is 2000 the default plot label would be i 1 20007 Choose the font type by clicking on one of Page 101 the three Font buttons The size of the font is in hundredths of an inch Set the position of the label using the Left and Bottom fields These values are fractions of the plot width and height To set the scaling factors for the plot first enter a Start value This is the time in milliseconds from the alignment code that you want to start plotting data Enter the duration in milliseconds of the plot in the Display for field You set the vertical scaling of the plot using the Max Rate field This value is in spikes per second The Tic Interval field allows you to set the distance between tick marks on the X axis If you want a Y axis click on the Y Axis button If you want an alignment line click on the Alignment Line button The differences between the Y axis and the alignment line are that the Y axis is always drawn at the lef
374. t_s 1 which results in the abort list actions being executed Executes the function specified after the restart keyword Re initializes the state list chains to the first state Enters into the event buffer an ecode composed of the paradigm number specified after the id keyword or ed with the INIT MASK Lt ms ps ps General Considerations Numbers preceded by a zero are passed on to the C compiler as they are so they will be treated as octal White space is free so use it liberally to make your code clear to the users and yourself Error checking by Spot is miniscule If a syntax error is detected the line number at which it is recognized will be reported and Spot will terminate Line numbers reported by Spot refer to lines in the d Spot file Errors might also be reported later by the C compiler when the C source file generated by Spot the d c file is compiled In this case the error line numbers will refer to the d c file Corrections must be made however to the input to Spot the d file and not to the intermediate d c Page 22 file The user is responsible for seeing that escapes actually go to existing states The C compiler might catch this error but it is not guaranteed A few debugging aids exist at run time The running line display is often useful for debugging since its level is determined by values specified in the state declarations Clicking on the debug button in the int process tool bar brings up a dialog
375. table for real time pcmsg requires two interface boards that include the Intel 8255 parallel interface chip commonly found on digital I O boards pemsg is designed so that the two boards can be cabled together directly pin for pin without any external glue logic pcmsg provides an eight bit communications channel between the PCs This channel is full duplex information can travel in both ways simultaneously The handshaking protocol is designed to be independent of timing differences between the PCs The programming interface presents a messaging model messages are packaged and sent between the machines Messages include checksum The second method of communication is to use Ethernet with TCP IP sockets Multi Unit Sorters Rex communicates with the Mex multi unit sorter program via parallel interface using one 8255 parallel chip Rex will also communicate with the Spectrum Scientific MNAP system using counter timer boards Each board will accept up to 20 units from the MNAP system In order to accept more units the Rex PC must have available slots for more counter timer boards Rex Structure and Operating System Environment Rex is composed of multiple cooperating processes For example keyboard commands writing to disk raster display data acquisition are all handled by different processes This architecture originally designed to run on Unix is not easily ported to DOS Therefore the QNX real time operating system was chosen to s
376. tal synchronization is enabled or not Page 255 TIME_STIM This is a non batchable command that presents a variable number of objects for a given number of video fields The first parameter is the number of objects to present Each object requires one parameter the object number The last parameter is the number of fields to present the objects The number of fields can range from 1 to 255 Example action it This action will present objects 3 and 4 simultaneously for 60 fields short fields 60 value may be set in Rex state variables menu st_time void unsigned short index index 0 vexbuf index TIME_STIM vexbuf index 2 number of objects to present vexbuf index 3 I first object number vexbuf index 4 second object number vexbuf index fields number of video fields to_vex index return 0 If the digital sync is enabled GLvex will return two signals from this command The signal TIME_ON 247 is sent at the beginning of the video field in which the objects are turned on and the signal TIME_OFF 246 is sent at the beginning of the video field in which the objects are turned off Otherwise GLvex will not return any signal after this command If the video sync is enabled the rex video sync square will flash white for the first field in which the objects are switched on and again in the first field in which the objects are switched off Page 256 SEQUENCE_STIM
377. te of roll rate vexbuf index hibyte pitch high byte of pitch rate vexbuf index lobyte pitch low byte of pitch rate vexbuf index hibyte yaw high byte of yaw rate vexbuf index lobyte yaw low byte of yaw rate vexbuf index span F life span of checks vexbuf index coher coherence of checks other batchable commands to_vex index return 0 GLvex will return the signal BATCH_DONE 241 after completing all commands in the list regardless of whether digital synchronization is enabled or not The hibyte and lobyte functions are defined in GLvex_com c Page 291 START _FLOW This is a non batchable command that starts the flow fields in a variable number of objects The first parameter is the number of objects to turn on Each object requires one parameters the object number Example actions pp This action will switch on the flow fields in objects 3 and 5 simultaneously sw_flow unsigned short index index 0 vexbuf index START_FLOW vexbuf index 2 number of objects to switch vexbuf index 3 I first object number vexbuf index 5 second object number to_vex index return 0 If the digital sync is enabled GLvex will return the signal FLOW _RAMP_ START 232 at the beginning of the video field in which the flow fields start Otherwise GLvex will not return any signal after this command If the video
378. te relays or dry contact relays You use one brick per bit The racks are driven by a single digital I O card in the PC Note that you might not need all the different types of modules ordered here a NIH Some of these modules I wanted to have on hand incase of special applications If you have TTL level inputs an input module is not even needed TTL level inputs can wired directly into the digital I O card However when using the module the LED indicator on the rack will be used Note that DC input modules are not standardized across all vendors such as Grayhill Potter amp Brumfield Opto 22 Gordos Crydom Each companies DC input module has different timing specs and input impedances These specs are important when interfacing TTL or LSTTL gates The Grayhill module has a high input impedance 1 8k and can be driven easily by a TTL sinks 16ma or 74 series LSTTL sinks 8ma gate However it s switching times are somewhat slow 250usec on 400usec off I am currently looking at some other modules that have lower input impedances but faster switching times 50 microseconds on 100 microseconds off See circuit diagrams at end of this document for more info You will probably certainly need the DC output module and dry contact relay module If you want to switch AC loads by this system you should also get an AC output module Counter Timer Card For unit input we may use a counter timer card However it is currently not programmed into REX an
379. terns to nextstate on 0 tst_rx_new FILE rex act vexActions c Page 208 PvexDrawOknGrating draws an opto kinetic stimulus grating in a number of objects SYNOPSIS PvexDrawOknGrating int nObjects int objList int dirList int speedList int widList int heightList int barwidList nObjects number of objects in which to draw objList array of object numbers dirList array of grating drift directions can be 0 90 180 or 270 speedList array of drift rates in degrees sec widList array of grating widths in 10ths of a degree heightList array of grating heights in 10ths of a degree barwidList array of grating bar widths in 10ths of a degree DESCRIPTION This action draws one dimensional square wave gratings in objects to be used as opto kinetic stimuli The gratings may be horizontal or vertical the direction of drift may be left right up or down RETURN VALUE GLvex will return the signal BATCH _DONE 241 when it completes this action EXAMPLE int num int object direction speed width height barwidth int setup num 1 object 1 direction 180 speed 10 width 100 height 100 barwidth 10 return 0 A prev do setup to state state do PvexDrawOknGrating amp num amp object amp direction amp speed amp width amp height amp barwidth to nextstat on 0 tst_rx_new FILE rex act vexActions c Page 209 PvexLoadPatterns loads patterns defined in Rex into GLve
380. the addresses in device h are defined Page 111 The part of the matrox library that writes text strings on the screen has been replaced with a more efficient version written by Lance Optican The text part of the raster displays draws much faster REX 3 5 27 May 86 Release 3 5 integrates in support for ADAC devices written by Bill Newsome and Grant Tech devices written by Jack Nelson In addition the following bugs were discovered and or fixed 1 3 5 F IX Bug existed in computation of awtime in write to disk section of int c This is the time of the beginning of an analog record or the time of the beginning of a continuation record Problem only appeared if SAMP_P_ACQ and MS_P_ INT defined in Ihdr samp h were not equal Fix occurs in two places where awtime is computed This bug found independently by Jack Nelson and Reuben Gellman 2 3 5 FIX Bug in incrementing pointer ladr_3 in a d handlers in int c for versions that store more than two channels at a time in a buffer The old sequence was to use ladr_3 to store first sample and auto increment Then the second sample was stored At this point value bufinc_4 was added to ladr_3 to step it to next buffer However it would now be pointing one ahead of the proper location because it had previously been auto incremented This would result in the horizontal and vertical buffers being one sample out of sync with each other Fixed by adding bufinc 4 1 instead of bufinc 4 alone Thanks to J
381. the current clock time This can be useful for computing reaction times during an experiment PgetClockTime amp time Returns the current rex clock time in the variable time The variable must be of type long Note This function can be an action or it can be called from an action FILE rex act stateTime c Page 38 Data Window Controls Rex stores event and analog data in internal rotating buffers The data window controls determine how data is written from these internal buffers to files on disk awind control analog data storage window SYNOPSIS awind long ctlflag ctlflag See below ADDITIONAL HEADERS REQUIRED None DESCRIPTION awind controls the analog storage window ctlflag may be one of the following OPEN_W open analog window CLOSE_W close analog window CANCEL W cancel currently open analog window RETURN VALUE Returns the following event codes WOPENCD If request is to open window WCLOSECD If request is to close window WCANCELCD If request is to cancel window WERRCD If ctlflag is an illegal value Note that these codes are returned based on the value of ctlflag and DO NOT signify that the window command was successfully executed For example if an open request is made during the w_post time after the previous window has been closed the window will not be opened however the WOPENCD event code is entered into the event buffer signifying that the request was issued EXAMPLE awind OPEN_W This co
382. the left mouse button to delete the box The effect of deletion is instantaneous and cannot be undone For Mex to classify a waveform as belonging to a neuron the waveform must pass through all of the acceptance boxes and must not pass through any of the rejection boxes you have set for that neuron Mex will draw waveforms that meet your criteria for a neuron in that neuronis color Mex draws waveforms that donit meet criteria for any neurons in white If you have set up boxes for several neurons Mex prioritizes classification first purple then green then blue For example if a waveform passes through a set of purple acceptance boxes and a set of green acceptance boxes Mex will classify the waveform as belonging to the purple neuron The rejection boxes are specific to each neuron For example if a waveform passes through the purple acceptance boxes and through a purple rejection box Mex will reject that waveform as belonging to the purple neuron but it can still classify the waveform as belonging to either the green or blue neurons if the waveform passes through green or blue acceptance boxes By default Mex refreshes the display every 16 milliseconds At this rate you might have trouble setting criteria for neurons that fire infrequently MIEL y You can increase the interval between refreshes using the display refresh interval counter The refresh interval will increase by about one second for every increase by 16 in the counter In this e
383. the specified flow field objects moving according to the objectsi translation matrices and moves them for the given number of video fields You must have called the PvexDrawFlowField and PvexNewFlow actions before calling this action RETURN VALUE If the digital sync is enabled GLvex will return the signal FLOW RAMP START 236 when the checks begin to move and the signal FLOW RAMP STOP 235 when the checks stop moving If the video sync is enabled the sync object will flash white when the checks begin to move and again when the checks stop moving EXAMPLE int num 4 int frames 60 int objects 4 1 2 3 4 A state do PvexTimeFlow amp num amp frames objects to run on 0 tst_rx_new run to nexstate on 0 tst_rx_new FILE rex act vexActions c Page 225 PvexShiftFlow shifts the translation matrices of a number of flow field objects while the flow field is running SYNOPSIS PvexShiftFlow int nObjects int objList int xyList int zList int velList int rollList int pitchList int yawList int spanList int coherList nObjects number of flow field objects objList array of object numbers xyList array of flow directions in the X Y plane zList array of flow directions along the Z axis only valid for 3 D flow fields velList array of linear velocities rollList array of angular velocities around the Z axis pitchList array of angular velocities around the X axis only valid for 3 D flow fields y
384. the trigger and 1 2 3 or 4 milliseconds of data after the trigger If you want to save waveforms Mex writes these waveforms to disk together with the times in milliseconds of the trigger crossings If you are using Mex with Rex these times will be the Rex time stamps If you are using Mex in stand along mode these times will start with 0 Once Mex has acquired the waveform it can use two methods to classify it One method is time and amplitude This method uses two types of boxes acceptance boxes and rejection boxes Mex classifies the waveform as originating from a neuron if the waveform does pass through each of the acceptance boxes and does not pass through any of the rejection boxes that you set for that neuron The second method is parameter clusters Mex computes 6 parameters for each waveform waveform peak waveform valley time of peak relative to the trigger time of valley relative to trigger peak minus valley amplitude peak minus valley and width peak time minus valley time Mex classifies a waveform as originating from a neuron if these parameters of the waveform fall within the ranges you specify for that neuron Both methods may be used together If the waveform satisfies your criteria for the neuron Mex toggles a bit from in the digital I O When interfaced to Rex the bit remains set for 1 millisecond In stand alone mode the bit remains set for 250 microseconds For antidromic collision tests when the signal on the sel
385. this state was set to and absolute rl 10 or relative value rl 10 If both the Abs and Rel buttons are de selected then no running line level was specified for this state If you enter a running line level and click the Abs button the running line will be set to the level you entered in the numerical widget If you click the Re button the running line will be changed by the amount you entered in the numerical widget The middle panel of the dialog contains widgets that allow you to change the arguments of the action called in this state Use the Dec and Hex toggle buttons to view the argument as a decimal or hexidecimal value Use the scroll bar at the right to display the entire list of arguments The bottom panel of the dialog contains buttons that list the escapes for this state Currently the buttons are not functional we may add the ability to change the parameters of an escape or to add new escapes at run time Use the scroll bar at the right to display the entire list of escapes User Menus Clicking on the User Menus menu button will display a menu with the following items Usr Menus Functions ReabtimeVariables Eye Win Analog Sig state_vars ramp_list eye_winds eye_offsets Page 83 Menus gt Selecting the Menus gt pull right menu will display a list of the menus you defined in your spot file This list is generated from the umenus array Selecting a menu will display a dialog containing the variable
386. to d a converter number 0 da_set_2 0 100 1 100 Output value 100 to d ais 0 and 1 as close together in time as possible DA_SET_ARG da_arg_struct 0 100 1 100 2 100 3 100 da_set 4 amp da_arg_struct Output value 100 to first four d ais as close together in time as possible Cannot be called as an action SEE ALSO da cntrl_1 2 da_cursor da_mode da_offset FILE rex act da_set c Page 45 da_mode Pda_mode set d a converter offset output mode SYNOPSIS da_mode long danum long mode Pda_mode long danum long mode danum d a converter number mode offset output mode ADDITIONAL HEADERS REQUIRED None DESCRIPTION The da_mode action determines whether an offset will be applied to the output of the d a converter mode can be the following DA_DIRECT no offset is applied to d a output DA_OFFSET_CONN offset is applied to d a output for all connected sources all sources except DA_STBY DA_OFFSET_STBY offset is applied to d a output when source is DA_STBY Note that DA OFFSET CONN and DA_OFFSET_STBY can be specified together or each individually The applied offset is provided by the da_offset action Offset mode is useful to accomplish stabilization By default all d a converters are initialized to DA_ DIRECT mode unless changed by calling this action RETURN VALUE Returns 0 EXAMPLE da_mode 0 DA OFFSET CONN Set d a converter 0 to apply offset to each output value when source
387. tore arbitrarily long streams of data For practical reasons this stream is broken up into short data records that are stored on the disk When the data buffer pointer exceeds a high water mark the scribe process writes a partial data record into the A file Subsequent pieces of the data stream are then written as continuation records Each continuation record has the same format as all other A file records except for non zero continuation words in the headers Data File Consistency The Rex file formats incorporate redundant information to allow the consistency of files to be checked and some effort to be made at restoring damaged files Since data is often transferred from disk to disk or from disk to tape and back again it is necessary to check that blocks have not been lost or scrambled Both files are consistent if their sequence numbers are correct and if the analog records in the A file are correctly indexed by the E file If the E file becomes corrupted it is easily re synchronized by searching for a block boundary since the event record size evenly divides the physical block size If the A file becomes corrupted it may be re synchronized by searching for the magic number This number 1210832817L is four bytes long chosen to be unique by word or byte search and outside the range of 12 bit analog to digital converters The amount of data missing can be determined from the gap in the sequence numbers A utility program exists f3srdd fl
388. ts for transition in an escape all have the same form a constant CONSTANT is evaluated against a memory location int_variable_name_or_address or the integer return from a function call function_name_or_address The field int_variable_name_or_address can be either the name of a variable or the address of a variable Spot distinguishes between these two cases as follows If the name is a numeric constant or the first letter is upper case 1t is assumed to be the address of a variable Otherwise 1t is assumed to be the name of a variable Likewise the field function_name_or_address can either be the name of a function or the address of a function The same rules are applied as for variables to distinguish between the two Examples to nexstate on 01 amp goo goo is name of variable to nexstate on 01 amp 0x20 0x20 is memory address define FLAG 0x20 to nexstate on 01 amp FLAG FLAG is memory address The PC architecture as opposed to the pdp11 has separate memory and I O address spaces One is forced to use I O instructions to access I O ports The field int_variable_name_or_address is always in the memory address space There is no way to access the I O address space in an escape test Transition on Timer Countdown to Zero time This escape condition results in a transition when the timer ticks down to zero The last two words on time are assumed and are optional Transition On Bit Test amp This esc
389. turn the signal BUFFER SWAP 232 The signal is sent at the beginning of the video field in which the buffers are swapped Otherwise GLvex will not return any signal after this command If enabled the rex video trigger will turn white on the first field after the buffers are swapped Page 253 SWITCH_STIM This is a non batchable command that switches a variable number of objects on or off The first parameter is the number of objects to switch Each object requires two parameters the object number and the switch value The switch values are 0 for OFF and 1 for ON Example actions E This action will switch object 3 on and object 4 off simultaneously I sw_stim unsigned short index index 0 vexbuf index SWITCH_STIM vexbuf index 2 number of objects to switch vexbuf index 3 I first object number vexbuf index OBJ_ON GLvex_com c define OBJ_ON 1 vexbuf index 4 second object number vexbuf index OBJ_OFF GLvex_com c define OBJ_OFF 0 to_vex index return 0 If the digital sync is enabled GLvex will return the signal STIMULUS_ON 251 if the first object switch is on or the signal STIMULUS_OFF 240 if the first object switch is off The signal is sent at the beginning of the video field in which the objects are switched Otherwise GLvex will not return any signal after this command If enabled the rex video trigger will flash white for the first field
390. typical REX system requires a minimum of 16 input modules and 32 output modules See Figure 3 Page 126 Each I O module incorporates an opto isolator Following are suggested wiring diagrams for various input circuits Figure 4 shows a switch input REX requires at least two switch inputs one to start stop the paradigm the other to freeze the running line display 0 51 Optional current limiting resistor Not needed for SPST switch Odd Numbered Terminals Even Numbered Terminals DC Input Module r ito u switch Figure 4 Switch Input Circuit Logic outputs can also drive the I O module inputs Figure 5 shows an input driven by a TTL or LSTTL gate Note that an input module is not required An 18 ga wire can be inserted in the bottom two pins in place of an I O module However the LED will not function without the I O module Y 5v R extomi Current limiting resistor use if necessi extemal 4 depending on value of R internal R internal Ai Odd Numbered Terminals gt Even Numbered Terminals N DC Input Module White TTL 16ma sink or 74 series LSTTL 8ma sink Figure 5 TTL Input Circuit In the future REX may collect unit input either through a timer card or a multi unit analyzer Until that time a latch is required to catch the unit pulse This is constructed with a 7474 D type latch See figure 6 Note that the reset pulse is not passed through a red output brick Th
391. u bar and select the Write Root item from the menu This will bring up a file browser dialog that displays the contents of the root directory and provides a field to enter the root file name To use a previously defined raster display read in a raster root file by selecting the Read Root item from the File menu Displaying Rasters To display raster data start the Rex clock by clicking the Clock button in the int process tool bar and start the paradigm switching the PSTOP switch or clicking on the Paradigm button in the tool bar Next click the Start button in the raster display menu bar The raster display will collect data for two trials and then begin plotting rasters If you defined multiple pages of rasters you can display the different pages by clicking the Prior and Next buttons in the raster display menu bar To pause the raster display click the Stop button in the menu bar The display will ignore all data until you click the Start button again If you click the Re nit button in the menu bar the display will stop and erase all of the current data When you click Start the display will begin displaying new rasters Saving Rasters If you want to save a set of rasters click the Stop button to stop the display then select the Save Rasters item from the File menu This will bring up a file browser dialog that lets you enter the name of the raster file Rex will save the current page as a tig file If you have multiple pages of rasters you need
392. uded in GLvex_com c Both the GLvex_com c and the GLcommand h files should be placed in the rex sset directory A number of the GLvex commands are batchable that is several commands with their parameters can be loaded into vexbuf for a single transmission to GLvex These commands are batchable because GLvex will return one signal BATCH_DONE after executing all commands in vexbuf Other commands should not be batched because GLvex returns a signal after completing each of these commands Loading several non batchable commands into vexbuf at one time may cause communication problems between GLvex and Rex or may cause the time stamps in the rex E file to be inaccurate You may either load a single non batchable command and its parameters into vexbuf or load one non batchable command into vexbuf at the end of a series of batchable commands In either case GLvex will return the signal of the non batchable command Rex spot files control the behavior of GLvex by calling actions which first load command values and parameters into the vexbuf command buffer and then call the to_vex function Both vexbuf and to_vex are defined in GLvex_com c The following list describes the commands that can be executed from a rex spot file together with example actions In this list each section header consists of the defined name of the command Note The only escapes you should use from states that call these commands are when the function tst_rx_new r
393. upport Rex on the PC QNX provides a Unix foundation in a real time context with fast interrupt response and disk I O Availability Rex is available free of charge via executing a short license agreement the purpose of this agreement is to preserve the government s rights to Rex and restrict re distribution The Rex manual and a copy of the agreement can be obtained via anonymous ftp from Isr nei nih gov Page 2 REX A Unix Based Multiple Process System for Real Time Data Acquisition and Control A V Hays Jr B J Richmond L M Optican J W McClurkin National Eye Institute National Institute of Mental Health 9000 Rockville Pike Bethesda MD 20892 Introduction Rex Real time EXperimentation is a real time system that utilizes a multiple process structure to divide its functions among various cooperating processes A running Rex system includes the procSwitch process to control process interaction the scribe process to write data on disk an int process to respond to interrupts from clocks analog to digital converters etc a running line process that functions as a digital oscilloscope an window process to display analog data in an X Y coordinate system and a raster process to generate on line displays of unit activity A Rex system is not limited to these processes and may include others This modular architecture is flexible and easy to maintain Various applications may use the same procSwitch and scribe processes but different
394. value is greater than the near value the flow field will be three dimensional otherwise the flow field will be two dimensional The coverage of the flow field is the percentage of the area of the flow field you want covered by checks expresses in tenths of a percent Example action 1 This action sets up three dimensional flow fields in 2 objects short wide 640 200 short tall 480 200 short ob 2 3 short near 640 F near value is less than short far 2000 far value for 3 D flow field short cov 50 1 5 of flow field area will be covered by checks short size 4 draw_flow unsigned short index short i index 0 vexbuf index DRAW_FLOW_PATTERN vexbuf index 2 number of objects for i 0 i lt 2 i vexbuf index obli object number vexbuf index hibyte wide i high byte of flow field width vexbuf index lobyte wide i low byte of flow field width vexbuf index hibyte tall i high byte of flow field height vexbuf index lobyte tall i low byte of flow field height vexbuf index hibyte near high byte of near plane distance vexbuf index lobyte near low byte of near plane distance vexbuf index hibyte far high byte of far plane distance vexbuf index lobyte far low byte of far plane distance vexbuf index cov tenths percent coverage vexbuf index size I c
395. values of the user menus A root file created with the States button will contain only the current values of the process states With the Open Data File dialog the file list is shown as a convenience to indicate what data files you already have Rex will not reopen an existing data file so even if you select a file from the list you will have to modify its name in the File Name text widget before clicking on the Open action button You can also open a data file by entering its name in the File Name text field and hitting the return key On opening the new data file Rex will automatically close the dialog and will display the data file name in the tool bar window frame next to the label REX Rex does not display a dialog when you select the Close Data File item from the Files menu It just closes the data file and removes the file name from the tool bar window frame Page 79 Displays Clicking on the Displays button when the window is active will display a menu with the following items Displays Window Display Raster Display Running Line Display The Window Display is an X Y plot which displays the positions of the eye signals and eye windows The Raster Display shows unit activity as both spike rasters and spike density functions The Running Line display is an oscilloscope display that shows analog and unit data Prior to Rex 7 0 you could have only one copy of each display although the eye window display and the running line display
396. veform must pass to be classified as originating from a neuron The buttons in the menu bar allow you to select which electrode to display if you are recording from multiple electrodes to select which of 3 neurons purple green blue to define criteria for to set the type of box acceptance or rejection and to set the refresh interval If you hover the mouse cursor over a button a dialog will pop up giving a brief description of that buttonis function To set up criteria for a neuron first select a neuron by clicking with the left mouse button RAE on one of the three neuron buttons The button will become highlighted All subsequent boxes will belong to this neuron Next click with the left mouse button on one of the two box types acceptance or rejection Finally click with the left mouse button in the display A box will be drawn at the site of the mouse cursor The color of the box will match the color of the neuron To set more boxes for this neuron just click on the box type and then in the display To set criteria for another neuron click on one of the other neuron buttons and then proceed to set boxes If you click on a neuron button that is already highlighted that neuron will be deselected and you will not be able to set boxes until you select another neuron button Page 331 To position and resize boxes move the mouse cursor over the box The cursor will change into one of four types The cursor with arrows pointing in a
397. vexbuf index START_OKN vexbuf index 2 start OKN movement in two objects for i 0 i lt 2 i vexbuf index i 2 F objects 2 and 3 have OKN gratings to_vex index return 0 If the digital sync is enabled GLvex will return the signal FLOW_RAMP_ START 236 at the beginning of the first video field in which the bars are moving Otherwise GLvex will not return any signal after this command If the video sync is enabled the rex video sync square will flash white for the first field in which the bars are moving Page 299 SHOW_MOVE_CLIP This is a non batchable command that displays sequences of objects for a given number of video fields each It is assumed that you have loaded the appropriate patterns in the objects and positioned them on the screen before calling this function The first parameter is the number of clips to show All clips will be shown simultaneously Each clip requires one parameter the number of the first object in the clip Each of the clips must have the same number of objects and the objects must be sequential After entering the starting objects for each clip this command requires three more parameters These are the total number of frames in the movie the number of video fields to display each frame and the number of times to cycle through the movie If you set the number of cycles to 0 the movie will run in a continuous loop until you stop it with the STOP_MOVIE command see below
398. vies to the list of objects to display The movies can be either flow fields or sequences of objects The frames of the flow field movies are stored in extended memory using a simple Page 139 extended memory manager For this reason Vex 4 3 MUST be run under Dos 6 2 or higher If you want to run under Windows 95 you must use the pif file provided This pif file causes Windows 95 to reboot into dos only mode Vex 4 3 will not run in the default Windows 95 Dos shell Vex 4 3 also will not run under Windows NT Vex 4 3 also adds a ramp that erases the object that is being moved This allows small objects to be placed on a ramp and moved without needing clipping rectangles or erasing annuli to eliminate the trail left by the object as it moves However the maximum size of the object that can be placed on an erase ramp is smaller than that which can be placed on a standard ramp Vex 4 4 does away with the simple extended memory manager using instead the Pharlap 286 Dos extender This allows Vex 4 4 to run under the Windows 95 version of Dos To do this you must reboot the computer into Dos mode or use the pif file provided You cannot use a Dos shell under Windows 95 or Windows NT Vex 4 4 provides a flag to allow users state whether objects may overlap or not Setting this flag improves drawing performance when objects don t overlap Vex 4 4 also allows ramps and flow fields to be run at the same time The user can set a flow field running over a number o
399. which checks the data files and verifies their consistency Data File Portability Problems may arise when data files are moved to other computers In general data is not portable across machine architectures Differences may involve word size e g 16 bits on pdp11 32 bits on VAX byte ordering within words and bit ordering whether least significant bit is to left or right Because of alignment differences a structure used in a C program to access a data file on one machine may not access the same fields properly on another machine Page 9 One solution to this problem is to add to analysis programs multiple ways of accessing data files and multiple formats for each machine A much simpler solution however is to instead change the data file for each machine This permits a uniform access method and single data file structure for all architectures With this solution porting analysis programs to new machines does not require new data formats or changes to access methods A utility program exists to convert the Rex data files to a new format The identification of the current format of the data file is stored in the data file header block Information is not lost during conversion given the current format a data file can be again converted to any other format Discussion The prototype version of Rex was completed in March of 1981 and ran on the pdp11 processor The PC port of Rex was completed in Spring of 1992 Rex comprises about 8000 l
400. x SYNOPSIS PvexLoadPatterns int nObjects int objList int stimList int sizList int rowList int colList int checkList nObjects number of objects in which to draw objList array of object numbers stimList array of stimulus numbers dummy variable needed by GLvex sizList array of check sizes in screen pixels rowList array of numbers of rows of checks in pattern colList array of numbers of cols of checks in pattern checkList array of color lookup table indices for checks in pattern can be 0 to 255 DESCRIPTION This action is similar to PvexDrawUserPattern but you define the template in Rex The purpose of this action is to allow you to add visual noise to a pattern that changes from trial to trial The color or luminance of each check is determined by the value of the color lookup table element referenced by that checkis value You will need to set up gray scales or color lookup tables for each object The size of the checkList array must be at least as large as the sum of the products of the row values and the column values RETURN VALUE GLvex will return the signal BATCH _DONE 241 when it completes this action EXAMPLE int num int objArray 50 stimArray 50 sizArray 50 rows 50 cols 50 checks 5000 int setup int nRows nCols i j k l nRows nCols 10 num 50 1 0 for i 0 i lt num i objArray i i 1 stimArray i i 1 sizArray i 4 for j 0 j lt nRows j for
401. x act vexActions c Page 229 Actions That Control Object Movies PvexShowMovieClip displays a sequence of objects SYNOPSIS PvexShowMovieClip int nClips int objList int nFrames int interval int cycles nClips number of clips to show simultaneously objList array of the numbers of the first object in each movie clip nFrames number of objects in each movie interval number of video fields to display each frame of all clips cycles number of times to show the clips DESCRIPTION This action allows you to present an arbitrary number of objects in sequence Several groups of objects may be presented simultaneously If all of the objects in each group have the same position the effect is that of showing a movie You may also distribute the positions of the objects Each object is displayed for the same amount of time If you want more than one group of objects each group must consist of the same number of objects RETURN VALUE If the digital sync is enabled GLvex will return the signal MOVIE_START 239 when the first object in each clip is shown and the signal MOVIE _STOP 238 after the last object in each clip is shown If the video sync is enabled the sync object will flash white when the first object in each clip is shown and again after the last object in each clip is shown EXAMPLE int num 2 int objects 2 1 51 y int nFrames 50 int interval 5 int cycles 2 A state do PvexShowMovieClip amp num ob
402. xample Mex will refresh the display approximately every two seconds Page 332 The Cluster Display The cluster display plots pairs of various parameters in XY coordinates of waveforms that satisfy Cluster Analysis dond Me AN the threshold conditions set in the oscilloscope display These parameters are peak amplitude valley amplitude times of the peak and valley amplitudes relative to the threshold crossing the peak to peak amplitude peak minus valley and the width of the waveform time of peak minus time of valley The purpose is to allow you to place boxes through which a waveform must pass to be classified as originating from a neuron Each waveform is plotted as a point in a two dimensional space The position of the point along the X axis is governed by the value of that waveform s X axis parameter and the position of the point along the Y axis is governed by the value of that waveform s Y axis parameter The buttons in the menu bar allow you to select which electrode to display if you are recording from multiple electrodes to select which of 3 neurons purple green blue to define criteria for to set which parameters to plot on the X and Y axes to select a box and to set the refresh interval If you hover the mouse cursor over a button a dialog will pop up giving a brief description of that button s function The icons next to each axis indicate which parameter is being plotted on that axis If you hover the mou
403. y default Mex refreshes the display every 16 milliseconds At this rate you might have trouble setting criteria for neurons that fire infrequently MIEL y You can increase the interval between refreshes using the display refresh interval counter The refresh interval will increase by about one second for every increase by 16 in the counter In this example Mex will refresh the display approximately every two seconds Combining Time Amplitude and Cluster Classification If you wish you can classify waveforms using both time and amplitude and parameter range criteria Simply launch both a Time Amplitude display and a Cluster display Set criteria in both displays Mex will classify a waveform as belonging to a neuron if it meets all criteria in both displays and does not cross a time amplitude rejection box The only limitation is that for each electrode no more than 5 boxes may be used to define acceptance and rejection criteria for one neuron The Waveform Display The waveform display shows a summary of all of the waveforms that satisfy the trigger criteria set in the oscilloscope display and how Mex has classified those waveforms It doesn t matter which Waveforms display you use to set your neuronal criteria The buttons in the menu bar allow you to select which electrode to display if you are recording from multiple electrodes and to set the refresh interval If you hover the mouse cursor over a button a dialog will pop up giv
404. y the user menus pull down menu Rex will display the menus in the order they are listed in the umenus array This allows you to group menus as you like separating logical groups of menus with separator entries More menu examples The following code snippets illustrate how to use menus to access members of a structure and how to access members of an array of structures This example shows the menu access for a single instance of a structure typedef struct int len int ang int vel int xoff int yoff int type int ecode RMP_PAR RMP_PAR ramp VLIST ramp_vl length amp RMP_PAR NP gt len NP NP ME_GB ME_DEC angle amp RMP_PAR NP gt ang NP NP ME_GB ME_DEC velocity amp RMP_PAR NP gt vel NP NP ME_GB ME_DEC xoff amp RMP_PAR NP gt xoff NP NP ME_GB ME_DEC yoff amp RMP_PAR NP gt yoff NP NP ME_GB ME_DEC type RMP_PAR NP gt type NP NP ME_GB ME_DEC ecode amp RMP_PAR NP gt ecode NP NP ME_GB ME_DEC NS char hm_ramp_vl MENU umenus ramp_par amp ramp_vl amp ramp NP 0 NP hm_ramp_vi NS In this example the phrase amp RMP_PAR NP gt len in the ramp_vl definition indicates that this variable address is the address of the len member of a structure of type RMP_PAR The ME_BG notation indicates that a menu global base pointer must be added to this variable address In the umenus definitio

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