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PILATUS User Manual

1. 32 YJECTRIS Next Generation X Ray Detectors 9 1 2 Make a new Bad Pixel Mask from an Uniform Illumination If you expose the detector with a flat field you can use this image to create a new mask with TVX by defining upper and lower limits Pixels in the detector that are either dead too noisy or behave in a non desirable manner can be masked out If you have now an image called e g img_01 tif with an average count see boxall in 12 2 for the statistical analysis of e g 1000 counts in the image directory p2_det images you can use the following command in TVX to get a mask image In TVX mkmask img_01 tif goodpixel_mask tif 600 1400 This will give you a file called goodpixel_mask tif with O where the pixel values are outside the mentioned boundaries of 60 and 140 of the mean value of the provided image img_01 tif To obtain the appropriate format for Camserver please invert the image In TVX move badpixel_mask tif 1 goodpixel_mask tif This created badpixel_mask tif should then be copied to config calibration Mask Please make a backup copy of the old mask 9 2 Flag the Module Gaps Only for Multi Module Detectors On multi module detectors the gaps between the modules can be filled either with O or with 1 Which number will be filled in is controlled by the Camserver command called GapFill see Camserver command at section 1 During startup with the runivx script GapFill is set to 1 This causes the gaps to
2. Exposures per frame set to nn MxXsettings Mxparameters text none Set crystallographic parameters reported in the image header mxsettings parm_name value parm_name value Possible Wavelength Energy_range Detector_distance Detector_Voffset Beam_xy Beam_x Beam y Flux Filter_transmission Start_angle Angle_increment Detector_2theta Polarization Alpha Kappa Phi Phi_increment Chi Chi_increment Omega Omega_increment Oscillation_axis N_oscillations Start_position Position_increment Shutter_time CBF_template_file Not settable with mx_settings but provided to templates from detector settings Timestamp Exposure_period Exposure_time Count_cutoff Compression_type X_dimension Y_dimension 15 None set or current settings 55 YECTRIS Next Generation X Ray Detectors SetThreshold Threshold Set gain and threshold 15 Setting the threshold parameters pathname of file text none This allows setting the threshold energy in eV with following method Without argument once setthreshold gain threshold set Settings xxx gain If parameters are omitted the current settings are shown threshold xxxx eV vcmp Gain is highG midG lowG x xxx V Trim file If gain is omitted the previous setting is retained path to trim file abc bin setthreshold 0 turns off invalidates the current remembered settings however nothing is transmitted
3. The air inlets and outlets for the detector fan should not be blocked The detector system should have enough space for proper ventilation Operating the detector outside the specified ambient conditions could damage the system The detector is not specified to withstand direct beam at a synchrotron Such exposure will damage the exposed pixels Place the protective cover on the detector when it is not in use Opening the detector or the power supply housing without explicit instructions from DECTRIS will void the warranty The Linux operating system on the DETECTOR SERVER has a customized Kernel to improve data throughput DO NOT UPDATE THE OPERATING SYSTEM OR THE KERNEL DO NOT TOUCH THE ENTRANCE WINDOW OF THE DETECTOR YJECTRIS Next Generation X Ray Detectors 4 System Description 4 1 Overview A PILATUS detector system consists of the following components see also Figure 1 e Detector e Detector server with a customized Linux operating system the data acquisition tool Camserver and the data analysis tool TVX e Power supply where applicable e Connecting cables Pilatus detector GigaStar data cable Detector server Figure 1 Overview of the PILATUS detector system setup Monitor or laptop are not included 4 2 Hardware DECTRIS X ray detector systems operate in single photon counting mode and are based on the newly developed CMOS hybrid pixel technology The main difference with respect to existing detectors is
4. w created lt modifications Fole get startup gl honerdet p2 det inages inage_00000 tif Filling image from home det p2_det images image_00000 tiF Setting BY Ms yos ee to integer 0x11f 0 699 x Set B15 M7 var Setting Be M A vis voltage to integer 0x320 1 150 ge THread _ none det p2_det images image_00001 tiF Channel 0 Temperature 37 2C Rel Humidity 18 4 Filling image from imgmode p 4 home det p2_det it f image_00001 tif t fillpix Ox9d367 Le i ree eee 9 imgonly home det p2_det images image_00000 tif cam imgmode x a file used for trim file calculation in multi bank detectors imgonly home det p2_det images image_00001 tif 4 nb gt 1 get trim_gls t g ti ff ginamode x ul Figure 7 Startup screen after executing runtvx example for a 100k detector 14 YJECTRIS Next Generation X Ray Detectors e The command runtvx is a shell script which starts the programs Camserver yellow window on the left side of figure 9 and TVX yellow window on the right side of figure 9 as well as manages all log files e During startup the detector sets several parameters in the startup scripts details in 6 1 Once two images green and blue appear on the screen the detector is ready to operate In Figure 7 only one blue is visible since it is above the other green one Both terminals
5. A major function of Camserver is to accept socket connections from a high level controller e g TVX which can provide high level services to this or other cameras The interface is a simple text based message passing system Images the ultimate product of a working area X ray detector do not pass thruogh the socket interface but are written to a configurable location e g a NFS mount where any program can access them 12 YECTRIS Next Generation X Ray Detectors 4 3 3 Description of the File Structure and Configuration Files on the Pilatus Detector Server In the default setup all data necessary for the use of the PILATUS detector system is in the directory nome det p2_ det Directory Sub Directory Desorption SSCS config Configuration aaa C fema pontons ofthe camera albraions eataton A eaoratondetais including Maskties C fema sesona O OO oO ma beam programs _ Program code fr TVX and Camsener eons beauty WX graphs corest mass for stata analyisin WX docs ocureniation of Wx and Camsenver Important configuration files are listed in the followings table The directory is given relative to the default path p2_det Fie fryser 13 YECTRIS Next Generation X Ray Detectors 5 Quick Start Guide Before you turn on the system make sure you have read this manual the technical specification and set up the detector accordingly e Turn on the detector server e Log in procedure Us
6. define 1 ldmc maskimg basepath correct cal ibrate_mask tif ie 1 Is an example tdefine 1 pasteBn scan fbase is ni for j istj lt Listni j mkimage fbase _ Tesi 32 for i 03i lt 4si paste fbase i 1 j fbase _ j 0 G x 0 y 0 Intensity 100 setting B m venez voltage to Integer Uxllr VEST Set B15_M7_vcmp3 0 7000 Setting B _M _VCHP3 voltage to integer 0x11f 0 699V Set B15_H7_vcmp4 0 Setting BY Ms _VCHP4 voltage to integer 0x11f 0 699 Set B15 M7 vemps 0 7000 Setting BY Mt _VCHPS voltage to integer Ox1if 0 699V Set B15_H7_vemp6 0 7000 Setting B _M _VCHPG voltage to integer 0x11f 0 699V Set B15_H7_vemp 0 7000 Setting B MY VCHP7 voltage to integer 0x11f 70 699V Set B15_H7_vcmp 0 7000 Setting BY_M _VCHPS voltage to integer 0x11f 0 699V Set B15_M7_vcmp9 0 7000 Setting B _M _VCHP9 voltage to integer 0x11f 0 699V Set B15 M7_vcmpl0 0 7000 Setting BY _N _VCHP10 voltage to integers 0x11f 0 699V Set B15_H7_vcmpl1 0 7000 Setting BY M YCMPIL voltage to integer 0x11f 70 699V Set B15_H7_vompl2 0 7000 Setting BY H VCHP12 voltage to integer Oxiif 0 699 Set B15_H7_vompl3 0 7000 Setting BY MH VCHP13 voltage to integer Oxiif 0 699V Set B15_H7_vcmpi4 0 7000 Setting Be A YEHPL4 voltage to integer Oxl1F 70 698 Set B15_H7_vcmpl5 0 700 1 purpose user variable definitions and commands
7. li 7 1 Main Commands Set the exposure time 10 to 10 sec Exposure filename Make an exposure with the exposure time and exposure period predefined with the command ExpTime and ExpPeriod respectively The format of the file is determined from the supplied extension The file is stored relative to the path defined by the imgpath unless an absolute path is given ExtTrigger fname Start exposure with defined variables after receiving an external trigger and store images fname ExtMTrigger fname Start multiple exposures with defined variables after receiving multiple external triggers and store images fname see section 7 3 3 ExtEnable fname Start exposure defined by external signal and store images in fname help Type this in the TVX window for a discussion of how exposurenaming exposure series are named Re initialize the detector control board We recommend that full command names are used for clarity 19 YECTRIS Next Generation X Ray Detectors 7 1 1 Variables The following variables can be viewed just by typing them all times are in seconds Variable Description Nimages N Query or set the number of images in a sequence ExpTime time Query or set the exposure time ExpPeriod time Query or set the exposure period for serial exposures The exposure period must be at least 2 3 ms longer than the exposure time imgpath path Query or set the default imgpath Delay time
8. lossless compressed format The cbf and edf headers are pure text and therefor human readable The tif headers are encoded so only the comment section is human readable e The img file contains only the uncompressed data e The edf file starts with the header according to the ESRF data format followed by the uncompressed data e The tif file contains the standard TIF header including a Pilatus section followed by the uncompressed data The Pilatus section contains at least the following items example o Silicon sensor thickness 0 000320 m Exposure_time 1 0000000 s Exposure_period 1 00230000 s Tau 199 1e 09 s Count_cutoff 1280469 counts Threshold_setting 5900 eV Gain_setting mid gain vrf 0 200 N_excluded_pixels 4 Excluded pixels badpix_mask tif Flat_field nil Trim file p100k0273_T5900_vrf_m0p20 bin o i Image path home det p2_det images This list can be extended with several items described in section 10 The TIF header is of a fixed length of 4096 bytes so it is possible to make a file reader by stripping off the header and reading the row major block of data O O 0 0 0 0 0 0 0 0 e The cbf format is the only compressed image format and is recommended in situations where I O bandwidth may be limited The byte offset compression algorithm usually reduces the file size to a quater of the tif image The initial header data this time a cbf header is followed by a Pilatus
9. Client for Camserver Compile with gcc o cam_client cam_client c DECTRIS Ltd Neuenhoferstrasse 107 CH 5400 Baden www dectris com NER ES ERE CEASA ESTERS TERRA RENTS AAAS KEE eee Re ee tee eae ee include lt stdio h gt include lt netdb h gt include lt signal h gt include lt unistd h gt include lt string h gt define BUFSIZE 1024 int main Change to required IP or hostname char server 64 localhost II Change to required port int port 41234 char buffer BUFSIZE int s struct sockaddr ins addr fd set rfd Open socket descriptor s socket PF_INET SOCK_STREAM 0 Resolve hostname and try to connect to server struct hostent hostent gethostbyname server s_addr sin_family PF_INET s_addr sin_port htons unsigned short port s_addr sin_addr struct in_addr hostent gt h_addr Connect to socket if connect s struct sockaddr amp s_addr sizeof s_addr lt 0 return printf n Command line socket interface for camserver n n printf Type exit to quit n 62 YJECTRIS Next Generation X Ray Detectors Main loop processing user input and socket input while 1 printf cam_client gt fflush STDIN_FILENO Wait for data either from terminal stdin or from socket FD_ZERO amp rfd FD SET s amp rfd FD _SET STDIN_FILENO amp rfd if select int s 1 amp rfd NULL NULL NULL 1 break Dat
10. Convert S D type Change the image data type S source image D destination image Type Char Short Int Float define DEFINE name instruction1 instruction2 Defines user symbol name and value E g define tpict zpict move imt im3 defines symbol tpict as a comination of zpict and the built in move instruction CapturelM filename Capture the default image to filename captures a displayed image and its zoom as a ppm portable pixmap file including coloration and contrast adjustments CaptureGR filename Capture the default graph to filename Captures a displayed graph and its zoom as a ppm portable pixmap file connect ip address Connect the socket connection from TVX to the Camserver at ip_address The IP is not necessary if TVX is running on the same computer Disconnect the socket connection from TVX to Camserver E g so that a beamline operating system like EPICS can take control over the Camserver 39 YECTRIS Next Generation X Ray Detectors 12 1 Description of the Image Display The TVX command disp allows display of images It contains several options to adjust the contrast and the min max values Moreover it is possible to display the image in different color schemes This image display will automatically show up after you execute the expose macro in TVX filemenu editmenu imagemenu helpmenu 3 Sliders for color range Selection tool i i and contrast af Actual pos
11. Query or set the external trigger delay This is the time to wait after the external trigger before taking the first image The delay may not be greater than the exposure period nexptrame N Number of exposures per frame This is a so called multi exposure mode nexpframe sets the number of exposures before the detector is read out e g nexpframe 3 exposes the detector 3 times before reading out an image of the 3 combined exposures See point 7 3 5 for more details The usual way is to set all mentioned variables and then execute a command from the section above 7 2 Image formats Due to the high dynamic range of 20 bits 17048576 of the PILATUS detectors images are stored as 32 bit signed integers These images can be viewed and analyzed with TVX or other image viewers Many viewers do not support 32 bit TIFF files however these images may be read in IDL or MATLAB The default image file type for TVX is set in tvxrc however any file type can be specified explicitly Camserver has no default so the file type must be specified explicitly for each exposure TVX supports the following image formats Format Description LL O tif 32 bit TIFF files edf ESRF data format cbf Crystallographic binary format 20 YJECTRIS Next Generation X Ray Detectors raw data format no extension or raw data format misspelled Of these four image formats tif edf and img are uncompressed and cbf is the only
12. TVX and Camserver have their prompt indicated by an asterisk symbol e To operate the detector correctly you MUST TRIM THE DETECTOR according to the incoming X ray radiation We refer to trimming as the process of adjusting the settings voltages and trimbits of each pixel to the specified gain and energy for details see 8 This trimming can be done by the SetEnergy or the SetThreshold command These commands trim the detector to a uniform threshold across the detector surface The threshold should generally be set to 50 of the incoming X ray energy more details can be found in section 4 2 and 6 1 If you operate the detector every time at the same energy e g an X ray tube with Cu anode you can add such a command at the end of the startup glossary which gets executed during each start up sequence for details see 6 1 For example if you have a 8 048keV incoming beam type in the TVX window yellow window on the right side in Figure 7 the following command cam SetEnergy 8048 Details on this command can be found in section 8 For a finer control you can use the SetThreshold command see section 8 3 For more specific questions and detailed advice please contact DECTRIS Ltd for support Note that the SetEnergy command takes a relatively long time On a large multi module system it can take up to 2 minutes e The detector is now ready for operation e To take an image you can type expose 10 in the TVX window where 10 is
13. as compared to a threshold of 50 This decrease is continuous and almost linear until the threshold is 80 of the incoming energy The gain The adjustment of the threshold is limited by the detector electronics To be able to span a threshold range from 4 keV to 18 keV it is necessary to change the gain i e the amplification level of the detected signal There are three gains high mid and low gain implemented which all have a certain threshold range These ranges are overlapping for large energy ranges However lower gain settings should be preferred since they allow higher count rates and better count rate correction This is especially true if the count rate exceeds several 1075 counts s pixel The previously mentioned SetEnergy command 8 2 automatically calculates the threshold to 50 of the supplied incoming X ray energy and chooses the lowest gain for the desired threshold energy However for certain experiments it may be desired to stay at the same gain or just vary the threshold Then it is useful to use the SetThreshold command as described below 30 YECTRIS Next Generation X Ray Detectors SetThreshold gain SetThreshold set gain energy range and threshold threshold energy Usage SetThreshold gain threshold 1 if parameters are omitted the current settings are shown 2 gain is highG midG or lowG 3 if gain is omitted the previous setting is retained 4 threshold is in eV 5 this command build
14. energy of 8 0keV T5p0 a threshold of 5 0keV and vrf_m0p2 means Vrf 0 2 V which is mid gain The last part can be vrf_m0p3 vrf_m0p2 and vrf_m0p15 which is low gain mid gain and high gain respectively LdFlatField The Camserver command LdFlatField will cause imagename Camserver to apply a specified flat field correction to every image taken The file is a floating point TIFF file with a mean value near 1 0 The command applies the flat field ONLY temporarily The information about the flat field file is lost once Camserver is restarted or a new threshold energy using the SetThreshold or the SetEnery command is set To automatically apply the flat field image please remove the signs in front of all lines which contain ffield in the file home det p2_det contig cam_data calibrations def This will cause the SetThreshold or the SetEnery command to apply the settings stored in calibration def file 35 YJECTRIS Next Generation X Ray Detectors 11 2 Creating a new Flat Field Image Intensity correction images can be created by the user To get an appropriate flat field from an homogeneous illumination one can calculate it manually or use a TVX command First set up a very uniform X ray illumination and verify that it is as flat as possible This can be very difficult but is critical to success e Load the required threshold settings e Record a picture with the desired statistics at least 107 counts per pi
15. faster than 30 Hz all trigger signals have to arrive approximately within 30 of the set ExpPeriod and ExpTime The required minimum time difference between ExpPeriod and ExpTime readout time is 2 28 ms see command ExpPeriod If the frame rate is less than 30 Hz and the readout time is more than 13 ms the trigger signals do not have to arrive within the mentioned 30 but the ExpTime and ExpPeriod still have to be defined similar to the shortest expected signal repetitions Use K transmitted over the socket connection to interrupt this state at the start 15 at the end 7 at start Starting externally multi triggered exposure s lt date amp time gt at the end full path name of last image 52 YECTRIS Next Generation X Ray Detectors ExtEnable file base name Make an exposure or an exposure series using an external gate atthe start 15 at start Starting externally file extension signal enabled exposure s lt date amp time gt Set timing parameters by the commands ExpTime and ExpPeriod before execution Each exposure is started when the atthe end 7 at the end full path name signal changes to high and is finished when the signal changes of last image to low again Individual exposures can be added within one readout image by specifying NExpFrame prior to execution see Multiple Exposure Mode 7 3 5 If the readout time i e the difference between ExpPeriod and ExpTime
16. is shorter than 13 ms and the ExpPeriod is shorter than 33 9 ms faster than 30 Hz all trigger signals have to arrive approximately within 30 of the set ExpPeriod and ExpTime The required minimum readout time is 2 28 ms see command ExpPeriod If the frame rate is less than 30 Hz and the readout time is more than 13 ms the trigger signals do not have to arrive within the mentioned 30 but the ExpTime and ExpPeriod still have to be defined similar to the shortest expected signal repetitions Use K transmitted over the socket connection to interrupt this state ExpTime Time s 1 0 Set the exposure time time lt 60days 15 Exposure time set to XXX Sec ExpPeriod Time s 1 05 Set the exposure period 15 Exposure period set to XXX SEC Time must be longer than exposure time readout time 2 28 ms The frame time is ExpPeriod NExpFrame 1 ExpTime Time lt 60 days YECTRIS Next Generation X Ray Detectors ImgPath Path nome det p2_det images Change the image path If the directory does not exist it will be created if it is possible to do so with write permission A path relative to the current path is accepted is accepted If imgpath test is given and the current directory named is test a new directory is NOT created If such a new directory is desired it may be specified by test test If imgpath test1 test2 is given and the current path is _ te
17. one det_spec gl loads detector specific parameters such as camera size and number of modules The second one user gl is used to enter user short cuts once you start to define your own ones The last one startup gl sets voltages on the actual X ray sensitive elements and carries out a test of the digital part and the analog part of each pixel The last two tests are done with the TVX definitions rbd read back detector and calibdet respectively The results are shown in a green digital test with 1000 counts loaded into the counter of each pixel and a blue analog test with 100 simulated pulses fed into each pixel image These two images show up automatically at the end of the startup procedure and verify the full functionality of the detector 6 2 From a Specific Environment In the previous section the stand alone operation is shown However often there is a need to integrate the detector in an existing environment The Pilatus detector can be easily integrated into any system To do this one has to send commands through a socket connection to Camserver Any client can connect to Camserver via a socket connection and issue plain text commands However only the first connection will get full control and can execute commands All following connections will only have read access The command syntax see section 7 over the socket is identical to the syntax to 16 YJECTRIS Next Generation X Ray Detectors be typed directly in the C
18. over the socket connection The exposure time and exposure period still have to be set to the approximate trigger structure If the exposure time is longer than the DMA timeout see above the polling method is enforced This causes that the read out time has to be set to more than 13 ms for the external enable and external multi trigger mode 7 3 2 External Trigger Mode The external trigger mode is exactly the same as an exposure except that an external pulse is used rather than the enter key on the keyboard External trigger mode is activated with the command ExtTrigger imagename tif where imagename tif is the name of the images you wish to be taken The first image name in a series will be imagename_00000 tif unless otherwise specified If Nimages gt 1 the image number will be incremented for each image in the series see footnote in section 1 for details Cli The settings that are necessary for external triggering are Nimages ExpTime ExpPeriod Delay optional After receiving a trigger on the positive edge the detector will wait a period of time defined by Delay take an exposure of length ExpTime readout the image and after a period defined by ExpPeriod will repeat the cycle for Nimages images A The image number is only incremented during the exposure series if you reissue the command ExtTrigger imagename tif the system will start writing images from imagename 00000 tif and overwri
19. section Exactly as in the tif format this section can be extended with additional items see section 10 Just before the actual compressed data there is additional information for the cbf format It should be mentioned that the full cbf header can be achieved through the commands described in section 10 More details to the cbf format can be found http www bernstein plus sons com software CBF 21 YJECTRIS Next Generation X Ray Detectors 7 3 External Triggering External triggering can be separated into three different modes e External Trigger triggers a predefined series of commands after the detector receives a positive edge e External Multitrigger triggers each exposure with an external pulse but times the exposures using the internal timer e External Enable gates the detector s images on the positive signal applied to the external enable input of the detector 7 3 1 Necessary Camserver Time Settings All exposure commands need to have set the ExpPeriod ExpTime and Nimages variables In some circumstances the times given can be approximate These values are used by the control program to determine the mode of operation of the system If the timing parameters are sufficiently relaxed the system uses a polling interface to watch for changes in state of the external enable signal and then responds appropriately This requires that the exposure time must be gt 33 9 ms 30 Hz and the dwell time betwe
20. that the X rays are directly YJECTRIS Next Generation X Ray Detectors transformed into electric charge Figure 2 and processed in the CMOS readout chips This new design has no dark current or readout noise a high dynamic range of 1 048 576 20 bits a read out time of less than 3 ms a frame rate of over 300 images s and an excellent point spread function of 1 pixel The quantum efficiency of the 0 32 mm thick silicon sensor is optimal for experiments in the energy range from 3 12 keV however the detectors can be used for energies of up to 30 keV or more The counting rate is greater than 2x10 s pixel enough to perform many experiments using the high flux of modern synchrotron light sources However the detector cannot withstand a direct synchrotron beam Single Photon Read Out Figure 2 Principle of direct detection A DECTRIS hybrid pixel detector is composed of a silicon sensor which is a two dimensional array of pn diodes processed in high resistivity silicon connected to an array of readout channels designed with advanced CMOS technology Figure 3 Each readout channel is connected to its corresponding detecting element through a microscopic indium ball with a typical diameter of 18 um This connection process is called bump bonding This maximum frame rate is only valid for 100k and 300k systems YECTRIS Next Generation X Ray Detectors Si sensor with pixelated pn diode structure CMO
21. the exposure time in seconds e Further information Details on how to control the detector from a specific environment e g at a synchrotron can be found in section 6 2 Details on how to trigger the detector with an external signal can be found in section 7 3 For information concerning the dead pixels and gaps please see section 9 For image manipulation with TVX please see section 12 15 YJECTRIS Next Generation X Ray Detectors 6 Control the Detector 6 1 From the Detector Server The Pilatus detector can be controlled from the delivered detector server Just follow the instructions in the Quick Start Guide Section 5 to start up the detector The runtvx command is a shell script which starts the actual programs Camserver and TVX It also handles the log files which can be found in the p2_det directory During the Camserver startup a connection to the detector is established and verified The TVX startup is carried out via the file called default gl This is a so called glossary file gl which is a convention used for files which are processed by TVX This default gl file stored in SHOME p2_det config makes several definitions short cuts which can be used further on in TVX For example the exposem command makes an endless loop and writes images in a temporary file see also section 12 This is a simple live view tool of TVX At the end of the startup glossary three more glossaries are called The first
22. to the detector This Without argument never may be used to force a reload of the trims set Threshold has not been This command builds a script in tmp setthreshold cam and set then loads it The data for building the script are read from p2_det config cam_data calibration def SetEnergy Energy eV none Simplified method to set gain and threshold 15 Setting the energy The requested energy is used to calculate appropriate gain and threshhold settings for the detector If energy is out of range a default is set and a warning issued If energy is omitted the current energy amp threshold settings are shown If energy is 0 the energy setting is reset The energy can be entered in 3 ways this command through the setthreshold command or through MXsettings wavelength val set If wavelength is set it is assumed to be definitive and SetEnergy and the energy option in setThreshold have no effect Only setenergy 0 will overcome this lock For finer control over detector settings use SetThreshold pathname of file Without argument once set Energy setting xxxx eV Settings xxx gain threshold xxxx eV vcmp x xxx V Trim file path to trim file abc bin Without argument never set Threshold has not been set 56 YECTRIS Next Generation X Ray Detectors K Stop data taking after current exposure ERR kill full path name of last image LdBadPixMap Filenam
23. 5 Rate correction is on tau xxxe 9 s cutoff xxxx A value of 0 0 turns off the in line rate correction counts The count rate correction value is threshold dependent and thus set by the SetThreshold commando to an appropriate value At very high counting rates gt 1e6 s Tau can vary with storage ring fill pattern Rate correction is invalid when the detector is synchronized to the bunch structure of a storage ring by an external enable signal In this case it is advised to set Tau to zero after setting the threshold SetAckint Number 0 Set the interval for acknowledgements over the socket 15 none or current setting This causes Camserver to acknowledge every n th image If N is omitted the current value is shown At the default n 0 only the last exposure of a series is acknowledged The initiating command is always acknowledged so for 1 or more images there is an acknowledgement before the start and at the end of a series There are some restrictions at high frame rate n cannot be too low Resettam Reset the camera 15 none DebTime Time s 0 Set the contact debounce time for external enable mode 15 Debounce time set to n n sec If t is not given the current setting is echoed This is useful when the external enable is not clean e g derived from a mechanical switch The external enable pulse must be shorter than 85 sec HeaderString String text none Give a string to be included in the ima
24. HWVersions 6 2 2 Testclients The detector can be controlled from any client which opens a_ socket connection to Camserver ZN Make sure TVX is disconnected type disconnect in TVX before you connect your own client The most simple client perhaps is telnet It is possible to test it on the detector server itself by executing telnet localhost 41234 Here localhost is the IP of the detector and 41234 the port where Camserver is listening to A basic test client written in C can be found under section15 Another test client called camclientt in p2_det programs tvx camera can also be used to issue commands to Camserver For more information please contact Dectris at support dectris com 18 YECTRIS Next Generation X Ray Detectors 7 How to use the Pilatus Detector through Camserver Camserver is a completely freestanding program that controls the detector and provides a simple user interface for atomic single function commands It is intended to provide a minimal but fully functional low level interface to camera hardware To get help on the Camserver commands use the help facility of TVX see section12 All commands in Camserver unlike TVX can be abbreviated to the minimum number of letters that make the command unambiguous below we use only the full names for clarity As in TVX commands are case insensitive but pathnames are case sensitive A full list of commands can be found in section 1
25. S chip technology gt Indium microbump bonding technology with 18 um bumps Figure 3 The detector module the basic element of all DECTRIS area detector systems The great advantage of this approach is that standard technologies are used for both the silicon sensor and the CMOS readout chips which guarantees highest quality Both processes are optimized separately as the best silicon substrates for X ray detection and for high speed high quality electronics are very different Moreover the small size of the pixel and the interconnection results in a very low capacitance which has the beneficial effect of reducing the noise and power consumption of the pixel readout electronics X ray data collection can be improved with detectors operating in single photon counting mode A hybrid pixel which features single photon counting comprises a charge sensitive preamplifier CSA which amplifies the signal generated in the sensor by the incoming X ray and a comparator Comp which produces a digital signal if the incoming charge exceeds a pre defined threshold The comparator feeds a 20 bit counter which then leads to completely digital storage and noiseless readout of the number of detected X rays in each pixel Figure 4 6 bit DAC cee 20 bit Counter Figure 4 Design of each pixel See text for details YJECTRIS Next Generation X Ray Detectors The fundamental unit of the DECTRIS detectors the module consists of a single ful
26. YECTRIS Next Generation X Ray Detectors USER MANUAL PILATUS Detector Systems s f pecas DECTRIS E l SM PILATUS 2 Version 1 4 YJECTRIS Next Generation X Ray Detectors Table of Contents 1 Document TTS OY pep ee ee ie ie he eee eee ee 3 IS EO FUN cece ce cee cp cep cele ede PE ewe cule eee ey ewe eve ASERNE eceueeepedeweccpeccucrees 3 2 How to use this Manual neuer 4 2 1 Address and support sees Eee ERE nnnm e ER 4 2 2 Explanation of Symbols sc ve ee ves veer vee ve ne eee rer cece vies sees sex sees veesveesvees seers 4 2 3 Convention for COMMMANS wiivenicensivniseniferise nines iiantienicaniienidenivexisantianlientih 5 2 AY DisclaiMe esere e aa ei a ae Aa E a aa eai ia 5 3 Warming ase ee ee ee Fre SEES ED E SENSE DER 6 4 System DES END 6 9 peer eter tenet ert Serre etre eee een bundede 7 A V OVE WW ay sasvous ecedee sven ree eee retret rear et arae yeas iet Kee Poet roet fret ORE TERESE REESE 7 4 2 Hardware ai nasties od itcadincnran sor ceacboraseantaiestaaiorbeesubniasbaniesasmadgouseasutoiasoucbeoenaels 7 43 SOWAT E eerie inae e AEAEE AAEE AEREE 11 4 3 1 Overview of TVX sccccecescnecccccesececccenectccresectcceeneceddeenectderenecddcnenebice 12 4 3 2 Overview of Camserver cicasscsisscronrnceenssemreniaciianatinetenmenadanabeents 12 4 3 3 Description of the File Structure and Configuration Files on the Pilatus Detector Server ccccccccccseeseeeeeeeeeeeeeeeeeeeeeeeeeseeeeeeensseeeeeee
27. a from stdin if FD_ISSET STDIN_FILENO amp rfd fgets buffer BUFSIZE stdin if stremp buffer exit n break Replace carriage return by null character if buffer strlen buffer 1 n buffer strlen buffer 1 0 Write to socket write s buffer strlen buffer 1 bzero buffer sizeof buffer II Data from socket else if FD_ISSET s amp rfd II Read from socket if read s buffer BUFSIZE 0 printf server not existing anymore exiting n break printf os n buffer bzero buffer sizeof buffer close s return 0 63
28. ally applied to each image that you take The bad pix mask is loaded every time the detector is trimmed via the SetThreshold command or any other command which calls this command To NOT apply this bad pixel mask automatically please insert a sign in front of the lines with a bpmap in the file nome det p2_det config cam_data calibrations def usually 9 times To remove this function temporally you can also use the command LdBadPixMap with a 0 as argument For further details please see Camserver command LdBadPixMap in section 1 9 1 1 Adding new Bad Pixels to the Mask It is possible that one or more noisy pixels can appear over time To add such a bad pixel to the mask you have to modify the actual bad pixel mask and put at the corresponding x y position a one This can be easily done with TVX To prevent loss of information make a backup of the old mask In a shell simply type as one line where DDMMYY is the actual date cp home det p2_det config calibration Mask badpix_mask tif home det p2_det contig calibration Mask baadpix_mask_untiIDDMMYY tif Then display the bad pixel mask with TVX In TVX disp nome det p2_det config calibration Mask badpix_mask tif Add the bad pixels e g at the coordinates x 17 y 126 by the following command In TVX pixifill 1 17 126 17 126 The coordinates are given twice because it is also possible to define a box which will be filled with the first value after the pix fill command
29. amserver window Thus direct typing is helpful for testing The reply from Camserver acknowledgement consists of a command index number followed by a space and either OK or ERR followed by another space and possibly a message The acknowledgement arrives after the requested action is completed typically in 1 2 ms some commands such as SetThreshold take longer especially for a big detector All acknowledgements end in 0x18 ASCII CAN without a newline there may be internal newlines in long messages Since there is no terminating linefeed MS Windows sockets must be opened in binary mode this is not a consideration for UNIX like systems Because of the socket connection protocol the camera hardware and server can reside on a different machine from the high level controller Camserver implements a token mechanism to prevent more than one outside process from having control over the hardware The Camserver window has full control at all times There is a debug facility to help with setting up the interface If you type dbgivi 5 the file camdbg out will contain many messages including the exact contents of socket messages Be sure to set dbgivi 1 the default before doing real work else camdbg out can grow without limit If there are difficult problems with the detector a run with dbg v 6 reproducing the error can be helpful for diagnosis Simply capture camdbg out and send it to DECTRIS The Camserver prog
30. be flagged with 1 in the final image To change the default behavior during startup please remove the line which contains Gapfill command from the startup file home det p2_det config startup g At TVX Camserver versions before TVX 7 2 70 110214 the SetThreshold command resets the Gapfill value to 0 From TVX 7 2 70 110214 on the previous state is remembered 33 YJECTRIS Next Generation X Ray Detectors 10 Adjust Crystallography Parameters The MxSettings command allows the user to store more information as comments or in the CBF template inside the image header of TIF and CBF images The principal usage of the MxSettings command is the following mxsettings parm_name value parm_name value It can be used to enter one or more of the following parameters with its value Available parameter names Wavelength Energy_range Detector_distance Detector_Voffset Beam_xy Beam_x Beam_y Flux Filter_transmission Start_angle Angle_increment Detector_2theta Polarization Alpha Kappa Phi Phi_ increment Chi Chi_increment Oscillation_axis N_ oscillations Start_position Position_increment Shutter_time and CBF_template_file It is possible to specify more than one parameter in each command and they can be in any order The parameters Beam_xy and Energy_range accept 2 values The parameter Oscillation_axis is text up to 18 chars e g X CW The command with no parameters will print the entire current lis
31. before the extension ExtTrigger file base name Arm the detector for an exposure or an exposure series started at the start 15 at start Starting externally file extension by one external trigger Before execution set timing parameters by the commands ExpTime and ExpPeriod To specify a delay between the trigger and the start of the exposure a Delay time can be set The time from arming the system until the arrival of the first trigger is unlimited Use K transmitted over the socket connection to interrupt this state at the end 7 triggered exposure s lt date amp time gt at the end full path name of last image 51 YECTRIS Next Generation X Ray Detectors ExtMtrigger file base name file extension Arm the detector for an exposure series where each exposure is started by an external trigger Set timing parameters by the commands ExpTime and ExpPeriod before execution Each exposure is trigged by the external trigger but uses the internal timer for the exposure time Individual exposures can be added up within one readout image by specifying NExpFrame prior to execution see Multiple Exposure Mode 7 3 5 The time from arming the system until the arrival of the first trigger is unlimited Use K transmitted over the socket connection to interrupt this state If the time between ExpPeriod and ExpTime is shorter than 13 ms and the ExpPeriod is shorter than 33 9 ms
32. d with standard arithmetic operators etc logical operators lt gt lt gt amp amp amp and special operators lt lt gt gt lt lt etc in arbitrarily complex expressions to perform sophisticated analyses and to construct custom scripts In case of doubt try it out you can t hurt anything Many commands in TVX require an input value or argument Without the declaration of a value the currently set value is shown li In this manual input values are shown in Italic Command or Macro Shows all commands It is divided in 5 parts Reserved Words do not use as variables External Procedures User Commands in current directory All TVX commands use man command to get a detailed description Defined variables amp strings This are macros which are created during startup e g in default gl use show macroname to see more details e User Variables assigned variables help command or _ Displays the help text for the command Help help is a man command good way to start Displays the definition of the macro ESC button Stop a running task and return to the TVX line interpreter CTRL C Full reset of TVX ZN Do not use this in Camserver YECTRIS Next Generation X Ray Detectors Command or Macro rbd imagepath path grafpath path expose exposure time in seconds exposem exposure time disp filename disp1 filename Read Back Detector Self
33. difficult to restore uncorrected data from a corrected image Alternatively crystallographic processing programs such as XDS can correct for variations in detector sensitivity which has a similar effect as a flat field correction 49 YJECTRIS Next Generation X Ray Detectors 6 Bad Pixels The software permits reading a bad pixel mask and flagging defective pixels as 2 in the data The gaps between the modules can optionally be flagged with 1 zero is the default Both of these flags are used by XDS 50 YECTRIS Next Generation X Ray Detectors 14 Camserver Commands The following list presents the Camserver commands with a short description For detailed usage of the detector system please see sections 7 through 11 Command Arguments Description Socket Socket connection unit connection return text default values return code Exposure fie base name Make an exposure at the start 15 at start starting xxx file extension second background ExpTime ExpPeriod ImgPath and Nlmages have to be set lt date amp time gt beforehand to the desired values The image is written to the specified file base name relative to ImgPath or to an absolute at the end 7 at the end full path name path if given The format of the image is derived from the of last image filename extension if given tif cbf or edf otherwise a raw image is written If an exposure series is set up NImages gt 1 an image number is inserted
34. e text none Load a mask image giving bad pixels to be flagged Filename must be a full pathname If filename is not given the current setting is shown If filename is 0 or off the pixel flagging function is turned off The maximum number of bad pixels is 5000 the flag value is 2 15 none or pathname LdFlatField Filename text none Load the flat field correction file Filename must be a full pathname File must be a 32 bit floating point TIFF image If filename is not given the current setting is shown If filename is 0 or off the flat field function is turned off The image is pixel wise multiplied by the correction file 15 none or pathname GapFill Number 0 1 0 Set the value to be used in pixels between modules This only applies to multi module detectors Number can only be 0 or 1 If n is omitted the current value is printed For TVX 7 2 70 110214 and earlier The SetThreshold command resets the Gapfill value to 0 15 Detector gap fill is nn THread Channel n all Read one of the temperature and humidity sensors Channels are numbered 1 6 on the first detector control board 7 12 on the second If channel is not specified 0 is addressed If no sensor is connected 99 is printed 215 temperature and humidity 57 YECTRIS Next Generation X Ray Detectors Tau Time s 0 Control in line count rate correction 1
35. e directory given by imagepath move fn1 fn2 Integrate histogram lo hi int The basic image manipulation command In the simple form shown this copies an image to a new name or directory However fn2 can be any arithmetic expression of images and constants integrate the pixels selected by the current selection tool box butterfly includes straight line case or spot annulus tool and show the resulting graph Usage integrate IM graph name For the butterfly the graph name can be given as the second parameter in this case the image name must be specified In other cases the default image is used if no image is specified Histogram of the pixels selected by the box tool on the image Alternatively specify the image and region of interest on the command line Usage histogram IM lo hi int x1 y1 x2 y2 graph_name where lo is the first value to use hi is the last value and int is the interval If IM is not specified the default IM is used x1 y1 x2 y2 are the coordinates of the box to be histogrammed If no graph_name is specified the histogram is placed in file hist n dat in the default graph directory where n rotates through the values 0 5 This file can be then be moved to a permanent file by a command such as move myhist hist1 The histogram parameters are remembered so subsequent operations with the same parameters can be obtained by just typing histogram If the coordinates are
36. ed image file format extension is present tif edf cbf the file will be created in that format Otherwise a raw image is produced For multiple exposure series NImages gt 1 the typed name is used as a basename again the extension if given is used to set the image format The following examples show the interpretation of the basename basename files produced test6 tif test6_00000 tif test6_00001 tif test6_ tif test6_00000 tif test6_00001 tif test6_000 tif test6_000 tif test6_001 tif test6_014 tif test6_014 tif test6_015 tif test6_0008 tif test6_0008 tif test6_0009 tif test6 2 0035 tif test6 2 0035 tif test6 2 0036 tif test6 014B tif test6 014B 00000 tif test6 014B 00001 tif l e the numbers following the last are taken as a format template and as a start value The minimum number of digits in the format is 3 there is no maximum the default is 5 The format is also constrained by the requested number of images 2 Maximum time out during fast exposures gt 30 Hz Due to the Gigastar communication between the detector and the computer it is necessary that the first pulses arrives on the detector within the DMA Direct Memory Access timeout Since this DMA timeout can vary from detector to detector it is displayed during Camserver start e g Maximum DMA timeout 8 1 s See also section 7 3 1 for details 3 Tolerant pulse repetition lt 30 Hz TVX versions TVX 7 2 70 110214 and
37. en exposures ExpPeriod minus ExpTime must be gt 13 ms This mode of operation is especially well suited for long exposure times but with adequate time between exposures If the exposure time or the read out time exposure period minus exposure time are short the system must predict the end of the exposure and the beginning of the next exposure with some accuracy the requirement for accuracy becomes more stringent as the exposure time becomes longer while the time between exposures is held short In most circumstances there is at least a 30 tolerance on the timing parameters input to Camserver as compared to the time actually generated by the external pulse generator However bigger differences can cause an error This is especially the case if the delays add up to more than the timeout of the communication protocol DMA timeout displayed during startup of Camserver either 8 or 16 seconds Frame Rate lt 30 Hz only in TVX 7 2 70 110214 or later If the exposure period is more than 33 9 ms less than 30 Hz AND the read out time is more than 13 ms it is possible to have large variations in the times which are set in Camserver and the applied pulses on the trigger input of the camera Moreover there is no timeout after executing a trigger command in Camserver the detector will wait until a signal arrives This state can only be 22 YJECTRIS Next Generation X Ray Detectors interrupted by transmitting a K to Camserver
38. enenssesvnenvees 32 9 1 Using the Bad Pixel Mask iicscccccicccdenccentdencdeetienctenstenslenttanstentteesteestentinds 32 9 1 1 Adding new Bad Pixels to the Mask seseeeeeeeeeeeeeeeeeeeeeeee 32 9 1 2 Make anew Bad Pixel Mask from an Uniform Illumination 33 9 2 Flag the Module Gaps Only for Multi Module Detectors 33 10 Adjust Crystallography Parameters ccccccccccseneseeeseeeseereeeeeeeeeeeeeeees 34 VI is 9 made eee eet eer mee a eee eee S 35 11 1 Using the Flat Field Correction Image in Camserver 0000eeeeee0000 35 11 2 Creating a new Flat Field Image esserne 36 11 3 Using the Flat Field Correction Image in TVX eeeeeeeeeeeeeee eee eeee 36 YJECTRIS Next Generation X Ray Detectors 12 How to Use the Pilatus Detector through TVX ccccccccceeeeeeeeeeeeeeeeeeeeees 37 12 1 Description of the Image Display cccceeeeeeeeeeeeeeteeeeeeeeeeeeeee 40 12 2 Analysis commands aos eneee eeen 44 123 Maske eee ere ee ener eee ree ee nee reer 45 12 4 User defined commands cccncic nore ana nnennamndaen 47 12 5 Glossary fil S ren mR ene 48 126 Example srania eao a a aea aiaa 48 13 Factory Calibration and Correction ccccccceceeeeeceneeeeeeeeeeeeeeeeenneeeeeeees 49 14 Camserver Commands as ee ee eee ele ie ee 51 15 Camserver Test Client 0 ccccccceccecceeccecceecceccececeeceeceeeceeceeeateceeeateneesess 62 YECTRIS Next G
39. eneration X Ray Detectors 1 Document History Actual document version Date statue prepared ohecked released 1 1 Changes Version Date Changes 1 1 31 08 2007 Various improvements 1 2 06 02 2009 Various improvements 1 2 1 28 09 2010 Various improvements 1 3 23 08 2011 Major revision 1 4 01 05 2013 Various improvements YECTRIS Next Generation X Ray Detectors 2 How to use this Manual Before you start to operate the PILATUS detector system please read this manual thoroughly The user manual and the technical specification together form the user documentation 2 1 Address and support DECTRIS Ltd Neuenhoferstrasse 107 5400 Baden Switzerland Phone 41 56 500 21 02 Fax 41 56 500 21 01 Email support dectris com Should you have questions concerning the system or its use please contact us via phone mail or fax A Do not ship the system Back before you receive the necessary transport and shipping information 2 2 Explanation of Symbols Symbol Caution Please follow the instructions carefully to prevent AN equipment damage or personal injury Important or helpful notice S AC current ANAI YECTRIS Next Generation X Ray Detectors 2 3 Convention for Commands Example Description O Z O O O OOS O Shell commands are written in blue and italic Camserver commands are written italic dip TVX commands are written in bold italic posem TVX macros a
40. er and password see additional sheet in your user documentation e Open a shell e Change to the p2_det directory All following paths are given relative to this cd p2_det e Run TVX by typing Jruntvx After the initialization up to 30s you should get the following screen IX image _00001 1if elie x X wx aie fx la Please edit trim gls trimcalc sh for the number of banks Filemenu editmenu imagemenu U o 1048575 2 a ma mm 7 npy 195 ee Fe ota RS italien nner aia setvcmpme scan j mimjveca Lvl forich 0z scht do pointer gt image gt set bibana venp ch Lv define 1 setvenpchip scan v b n ctset b b _m m _veca v set b b _n n vemp c v define 1 setvtrmmod scan v b mzset b b _m m _vtrm v b Need to individually set dacs for each module for offset to be implemented patios ie scan vifor b 1 b lt nb 1 b for m 1 m lt nmzm set b b _m m vrf v I define 1 setveal scan y3for b 1sb lt nb 1sb for nJ_veal v define 1 setvadj scan v3for b 1sb lt nb 1sb for m 1 mJ_vadj v define 1 setdac set B15 M7 vtrm 1 8 set B15 M7 vrfs 0 7zset B15 M7 vdel 0 83seturf 0 2 setvcal 0 3 setvemp 0 7 setvadj 1 15 nmzm set b b _m nmzm set b b _m i define 1 vcalscan setvenp 0 3 for v 07v lt 0 3 v 0 02 v ssetveal v calibdet mask file define 1 ldm maskimg basepath correct goodpix_mask tif
41. es 13 5 Quick Start Guide cite ce hee ee eee 14 6 Control the Detector sc panier ee eons 16 6 1 From the Detector Server cccccccceecceeeeseeeeeeeeeeeeeeaeeseeeeeeeeeeeeees 16 6 2 From a Specific Environment 0 1s2cccisccacsssccssssscacscecetessssssdeneencdiorsas 16 6 2 1 Steps to Bring Up a PILATUS Detector in a New Environment 17 6 22 TESS ES coset 18 7 How to use the Pilatus Detector through Camservet seerne 19 7 1 Main CommandS sss ciscecstursscscaciccantrabasetacan sniateneSonnswseiun xeueascdascwsaderetoneds 19 feki VARWADICS ee ee ecanen Ueeraleatenins 20 T 2 Image TONES cee ees eee E E EEEE 20 7 3 External Triggering u u ssseeeererereerreeeeenee renerne rer on ostseniaosion 22 7 3 1 Necessary Camserver Time Settings sssssseeeeennnnnnnnnnnnnnnn 22 7 3 2 External Trigger Mode W W M u ssssss sneen 23 7 3 3 External Multi Trigger Mode u sssssss sneen nnnnnnn 25 7 3 4 External Enable Mode ccccccsceseeeseeeeeeeeeeeeeeeeseeeeeeeeeeeeees 26 7 3 5 Multiple Exposure Mode ccccccccseesseeeeeeeeeeeeeeeesseeeeeeeeeeeeees 28 9 Iimming the Detector en cae ee ae 29 8 1 Princip IE 5 emer e eee VC TERT eek eter TnI 29 8 2 Simple Trimming Method each cease cena centeeeaents 29 8 3 Set the Threshold with more Control cceeeeeeeeeeeeeeeeeeeeeeeeeeeees 30 9 Bad Pixel Mask and Module Gaps asics vecessunseasveissices ver bieuivsksvenseeed
42. ge header 15 none The maximum length is 68 characters no formatting permitted Enclose the text in quotes to transmit non alpha characters YECTRIS Next Generation X Ray Detectors DiscardMultilm yes no no Discard multiple images 15 status During too fast images collections it can happen that the system loses images It is possible to sum the counted photons in the following image or zero this no n O Multiple images will be preserved yes y 1 Multiple images will be zeroed Exit Quit Close the socket connection none Df Show the number of 1 KB blocks available on ImgPath 5 1K blocks available Deb_init Attempt full re initialize of the dcb detector control board 15 dbglvl 1 ExpEnd Return the filename with which the exposure ended 6 full path name of last image CamSetup Report camera setup 2 Camera definition Camera name Camera state Target file Time left Last image Master PID is Controlling PID is Exposure time Last completed image Shutter is Telemetry Report camera telemetry 18 Image format and additional camera messages Version Print the TVX Camserver version 24 version ShowPID Show the PID of the process receiving the command 16 the pid 59 YECTRIS Next Generation X Ray Detectors 1 file_base_name Exposure commands take a filename or file basename as their argument For single images the filename is used as typed if a recogniz
43. igher than the threshold energy will be counted by the detector whereas photons with an energy below this threshold will be cut off and therefore not counted This transition is not perfectly sharp and follows an s shaped curve with a derivative of about 1keV FWHM This means that if you set the threshold energy at exactly the incoming monochromatic energy you will count 50 of the X rays At higher energies the asymptote of this s shape is not a constant but still slightly increasing due to various reasons As mentioned before the optimum of the threshold value is at 50 of the incoming energy This arises from the fact that it is possible that an X ray will be absorbed at the boundary between two pixels and the charge is divided to both of them If the threshold energy is set below 50 of the incoming X ray energy it is possible that one photon is counted twice in two neighboring pixels Best usage For the mentioned reasons it is best to set the threshold energy for the Pilatus detector between 50 and 80 of the incoming X ray energy The upper limit of 80 is not a hard criterion but above that the energy resolution gets worse Moreover one should not set the threshold much closer than 1keV to the incoming X ray energy due to the suppression of the primary incoming energy However it is not a problem to set the threshold e g to 60 of the incoming energy At this threshold there are only about 3 10 depending on the energy fewer counts
44. ignificant approaching 10 s above 2 10 s the conversion is cut off at a saturation value This value is printed in the header and can be used as a flag in analysis software Rate correction is optionally turned off in the control software e g triggering on short single X ray bursts 3 Distortion only for Multi Module Systems A text file with a map of the offset in position and angle of each module with respect to some common origin will be provided The processing program must incorporate this information using it as a lookup table to map sought reciprocal space positions onto detector positions However due to the high manufacturing quality of the detector and the direct detection geometrical distortions are minimal and excellent results are obtained without correction 4 Parallax The silicon sensor is 0 320 mm thick The parallax correction as a function of energy and angle of incidence has been well modeled and is about 1 pixel displacement at an angle of incidence of 45 deg Parallax actually improves spatial resolution because a spot that is spread over a few of pixels can be localized better than a spot in just 1 pixel 5 Flat Field Different modules in a multi module detector differ in sensitivity This calibration needs to be done as a function of beam energy and energy to threshold ratio The flat field map can be loaded into the detector controller which performs the correction as the data is read however it is
45. ition of the cursor x 774 y 1006 Intensity 1030918 and intensity of the pixel Figure 13 Image display from TVX 40 YECTRIS Next Generation X Ray Detectors sliders Define the color and the contrast of the image For every value of a pixel a color from a lookup table will be displayed With the two left sliders the cut off for the low and high values can be set Values outside this range are displayed with the same color The third slider defines the contrast factor The sliders can be moved with the mouse or by putting the mouse on the slider and adjusting the value with the left and right cursor buttons They can also be set from the command line using the disp command use man disp zoom A magnification can be chosen and the enlarged area is shown in a new window The zoom outline in the main window can be positioned by clicking or dragging with the mouse with the right button depressed pointer normal pointer annulus Allows analysis of circular areas The sizes of the circles can be adjusted with the mouse or directly by the setting the values in the image window box Allows analysis of rectangular areas Move the box with the right mouse or place the center of the box with the left mouse button The size of the box can be adjusted with the mouse or directly by setting the values in the image window butterfly Allows analysis of special shaped areas The shape of the area can be adjusted with the mouse or directly b
46. later are much more tolerant against variations in the trigger sequence for slow frame rates lt 30 Hz The provided signal to the external trigger input on the detector can deviate from the adjusted ExpTime and ExpPeriod more than the usual 30 However the trigger signal must be still logical e g a too early trigger signal during the ExpTime in the ExtMTrigger mode will be ignored This may cause that at the end of the series the detector is still is waiting for one trigger pulse 4 Only available in TVX versions TVX 7 2 70 101111 and newer 5 Automatically set by the SetThreshold command 6 The command NFramelmg is only available at TVX versions TVX 7 2 70 110331 and older It controls or queries the number of frames to be summed to an image n frames readouts are summed in software into a single image The frames are individually rate corrected The resulting dynamic range is up to 31 bits The maximum pixel value is 2432 It can be used with an integer number and will write back a return code of 15 and the following message Frames per image set to nn 7 Only available in TVX versions TVX 7 3 13 121212 and newer 60 YECTRIS Next Generation X Ray Detectors 61 YJECTRIS Next Generation X Ray Detectors 15 Camserver Test Client FEER SES EEN SES ERE a a SES SES SER REAR wee aman en EEN Name cam_client c Created by Sebastian Commichau May 2009 Modified by Stefan Brandstetter Feb 2011 Purpose
47. loat input object returns a 32 bit integer mask Because the generated file is a normal image you can use any of the image manipulation tools supplied in TVX to alter your mask image if you wish Declare inquire about or turn off the current mask image Usage maskimg im or maskimg 0 If present the mask is used to blank out bad pixels in statistical routines such as box integrate spot amp histogram Zeros in the mask are excluded from the analysis non zeroes are included With no argument displays the current mask image name if any With numeric argument e g 0 turn off the mask image Ldm is short for load mask a macro and uses the maskimg command and the factory produced mask stored in HOME p2_det correct goodpix_mask tif Set pixels in M to value using the current box coordinates as a template This permits you to manually alter a mask image based on observations on a different image Alternatively the box coordinates can be specified as described in section 9 1 1 li If the command deleteallobjs is used after you have loaded a mask image your maskimg will be reset of course the stored image is untouched 46 YECTRIS Next Generation X Ray Detectors 12 4 User defined commands TVX supports complex C like commands in the command line Example To display a series of images as a movie format 2 for i 0 i lt 100 i disp1 image_OOO i wait 0 5 Displays image_00000 to i
48. ly depleted monolithic silicon sensor with an 8 x 2 array of CMOS readout chips bump bonded to it Each sensor is a continuous array of 487 x 197 94965 pixels without dead areas and covers an active area of 83 8 x 33 5 mm The readout chips are wire bonded to the underlying print which is glued to the mounting bracket Together with its readout control electronics the sensor with readout chips forms the complete module Figure 3 10 YJECTRIS Next Generation X Ray Detectors 4 3 Software The operating software for the PILATUS detector system consists of two components e TVX Data analysis software and control program e Camserver Operating software for the detector hardware These two software packages are normally installed on one detector server and communicate with each other through an internal socket connection PILATUS TVX TCP IP Camserver XX Figure 5 Normal operation with TVX and Camserver on one computer It is also possible to operate the detector without TVX and access Camserver directly via a socket connection from another PC Socket interface TCP IP PILATUS _ E Figure 6 Operation with TVX and Camserver on separate computers 11 YJECTRIS Next Generation X Ray Detectors 4 3 1 Overview of TVX TVX is a free open source data acquisition and control software suite tailored to X ray science TVX is an attempt to pr
49. mage_00099 and waits 0 5 seconds between each picture The brackets mean to substitute the enclosed argument as text with the number of digits specified by the format With define one can create custom commands for the current session and eventually save them for reuse Example define test1 format 2 for i 0 i lt 100 i disp1 image 000 i wait 0 5 define Define a name value or command which can be used in name string the current session They are not saved when TVX define name value closes save myfile gl Saves the currently defined commands in myfile gl as text Such files are called glossaries Glossaries may also have executable commands edited in following all the definitions these are preserved when the file is overwritten get myfile gl Load the definitions from myfile gl and execute any commands appended after the definitions 47 YJECTRIS Next Generation X Ray Detectors 12 5 Glossary files When TVX is started a glossary is automatically started up called home det p2_det contig default gl In this glossary the main commands for using the detector are defined Three other glossaries are called from default g all in config det_spec gl Detector specific definitions In case of multi module detectors number of banks modules tools for addressing modules and analyzing module specific data user gl User specific commands startup gl Commands which are automatically loaded at
50. oscope image of an external enable Orange enable signal of the detector Green external gate In this example using external enable N mages was set to 3 Because external enable gates the counter directly it does not rely upon the detector s internal clock This means that the Delay between the enable and start of exposure is negligible and mostly given by the rise time of the enable provided to the detector This can be seen in the oscilloscope image below 26 YECTRIS Next Generation X Ray Detectors low high 8 5m OC x DC 0 94 v 5 V fon O NORMAL Figure 11 Oscilloscope trace of the typical delay between enable signal and exposure Orange enable signal of the detector Green trigger 27 YECTRIS Next Generation X Ray Detectors 7 3 5 Multiple Exposure Mode i This mode is useful to capture data from a rapidly repeating event which generates only a few X rays per pixel for each event such as pump probe experiments For example it is possible to synchronize to the bunch structure of a storage ring providing that an appropriate gate is available from the ring control system The data are accumulated in the pixel and read out after a certain number e g 2507000 of events is collected To use this mode set the variable nexpframe to the desired value The default value is 1 all exposure modes use this variable If the detector is used in this mode and it is synchronized to the bunch structure of a sto
51. ovide a flexible user interface that is easily adapted to control a broad range of 2 D X ray detectors as well as a powerful collection of analysis tools The suite operates by distributing the tasks of data analysis and hardware control between two separate programs The first program which is referred to as TVX contains the user interface and analysis tool suite The other which is referred to as the Camserver is responsible for controlling the hardware of the specific data acquisition system These two programs communicate over a TCP IP connection as shown in Figure 5 and thus do not need to run on the same machine see Figure 6 An added benefit of this model is that it allows the experimenters to do their analysis wherever and whenever it is most convenient for them be it at the beam line while the data are being taken or back at their home institution or corporation TVX compiles and operates on Linux Camserver requires specific camera hardware for operation 4 3 2 Overview of Camserver Camserver is a freestanding program that controls the Pilatus detector and provides a simple user interface for atomic single function commands It is intended to provide a minimal but fully functional low level interface to camera hardware On invocation Camserver takes a single command line argument the path to its resource file by default called camrc Camserver will also use the same path to open its debugging file camdbg out
52. priately the determined trim parameters have to be applied with one of the methods described below Every detector is calibrated at the factory 8 2 Simple Trimming Method The easiest method to trim the detector is to use the SetEnergy command Use the command SetEnergy and supply the information of the incoming X ray energy in electron volts as an argument This will condition trim the detector in most appropriate way for your measurement SetEnergy energy SetEnergy set or query the simplified gain and threshold setting Usage SetEnergy energy in eV If energy is out of range a default is set and a warning issued The requested energy is used to calculate appropriate gain and threshold settings for the detector This command internally uses the SetThreshold command to set the threshold For finer control over detector settings use SetThreshold This command allows you to operate the detector in the best manner after issuing only one command 29 YJECTRIS Next Generation X Ray Detectors 8 3 Set the Threshold with more Control In order to have more control over the threshold the SetThreshold command can be used Background The detector systems require that an energy threshold is set This threshold is usually set to 50 of the incoming X ray energy for reasons which are explained below However it is also possible to set the threshold at an arbitrary energy What happens All X ray photons with an energy h
53. rage ring high count rate the rate correction is probably invalid and it is advisable to turn it off see Tau in section Camserver Commands In the following example nexpframe 2 is set The detector will take exposures in the same way as described for external enable also possible with external trigger and external multi trigger but will additively bundle 2 exposures in each readout If N mages is defined to be 3 and nexpframe is defined to be 2 then the detector will take 6 exposures and generate 3 images It is necessary to provide 6 pulses or positive edges to achieve a successful readout only a single pulse is required for the ExtTrigger mode O NORMAL Figure 12 Oscilloscope image of the multiple exposure mode Orange enable signal of the detector Green external gate 28 YJECTRIS Next Generation X Ray Detectors 8 Trimming the Detector 8 1 Principle PILATUS detectors possess an adjustable energy threshold which has to be set due to the working principle of the detector This threshold is controlled by the comparator voltage of the detector chip Furthermore the threshold of every pixel can be individually trimmed with six trim bits 6 bit DACs which allow 2 64 different values The magnitude of the influence of these trim bits is determined by the trim voltage of each chip Since the process of threshold trimming is rather complex it is done during factory calibration To be able to operate the detector appro
54. ram of the PILATUS detector provides a simple to use interface for either EPICS or SPEC Several clients for these protocols have been written at the Swiss Light Source SLS at the Paul Scherrer Institut PSI and by Mark Rivers of the University of Chicago http cars9 uchicago edu software epics pilatusRO IDoc html 6 2 1 Steps to Bring Up a PILATUS Detector in a New Environment 1 If needed change the hostname to be compatible with the local network This can be done conveniently in SuSE linux with YAST2 or directly with vi 2 Set up the detector on the network if needed Note that the detector does not require an external network 3 Configure Camserver and the client TVX as needed Probably the defaults will be adequate but many parameters can be adjusted in camrc and tvxrc both of which reside in the HOME p2_det directory 4 Start the detector by runivx in the HOME p2_det directory 17 YJECTRIS Next Generation X Ray Detectors 5 If you are using your own client see section 6 2 2 for Camserver e g SPEC or EPICS disconnect TVX type disconnect in TVX This can be done automatically in the startup script after the test images are shown Connect your client and begin issuing commands see section 1 Further sources of information can be found in HOME p2_det programs tvx docs To see the details of the current configuration of Camserver check the hardware version file in HOME p2_det config camstat
55. re written in underlined bold italic 2 4 Disclaimer DECTRIS has carefully compiled the contents on this manual according to the current state of knowledge Damage and warranty claims arising from missing or incorrect data are excluded DECTRIS bears no responsibility or liability for damage of any kind also for indirect or consequential damage resulting from the use of this system DECTRIS is the sole owner of all user rights related to the contents of the manual in particular information images or materials unless otherwise indicated Without the written permission of Dectris it is prohibited to integrate the protected contents published in these applications into other programs or other Web sites or to use them by any other means DECTRIS reserves the right at its own discretion and without liability or prior notice to modify and or discontinue this application in whole or in part at any time and is not obliged to update the contents of the manual YJECTRIS Next Generation X Ray Detectors 3 Warnings PAN Please read these warnings before operating the detector Before turning the power supply on check the supply voltage against the label on the power supply Using an improper main voltage will destroy the power supply and damage the detector Power down the detector system before connecting or disconnecting any cable Make sure the cables are connected and properly secured Avoid pressure or tension on the cables
56. s a script in tmp setthreshold cmd and then loads it The following table shows more details on the three different gains The optimum energy range for their application the corresponding amplifier voltage Vrf and the time structure used for rate correction Tau Details on the latter can be found in section 1 aan vv highg 0 15 Slow setting with high gain for best resolution at low energies 4 5 keV midg 0 2 Standard setting for energies between 5 7 keV lowg 0 3 Fast setting with low gain for best performance at high energies and high rates 7 18 keV The directories with the trim files are stored in home det p2_det contig calibration The information about the relevant trimfiles is stored in home det p2_det contig cam_data calibrations def In this file the names of the trimfiles and the corresponding parameters are stored 31 YJECTRIS Next Generation X Ray Detectors 9 Bad Pixel Mask and Module Gaps During factory calibration the bad pixels non responding or noisy are determined and stored in a tif image This image contains 0 for good pixels and 1 for bad pixels Once the bad pixel mask is loaded bad pixels are flagged with 2 in the final image This can be desired or not since once the pixels are flagged their data are lost It is also easy to incorporate these data as a post acquisition step 9 1 Using the Bad Pixel Mask The bad pixel mask created during factory tests is automatic
57. specified on the command line the parameters must also be specified If the file name is specified either the image name must also be given or 3 or 7 numeric parameters must be specified In the integral mode the integral is written to hist n 1 dat if the name is specified it is appended with _i for the integral See also histset 44 YECTRIS Next Generation X Ray Detectors Print statistics from the current box selection tool on the image Alternatively specifiy image name and box coordinates on the command line Usage box IM x1 y1 x2 y2 If IM is not given the default IM is used x1 y1 x2 y2 are the coordinates of box to be examined If not given use the box selection tool on image If given the box selection tool is created or updated on the image if it is displayed If the box is set with the mouse pox and integrate give the same result Several system variables are set counts total counts in box area mean minimum maximum stdev rms var variance xcen amp ycen centroid box_x1 box_x2 box_y1 amp box_y2 corners of box boxall Print statistics from the whole current image format n1 n2 Control the number of digits to be printed n1 or the number of decimal places n2 deleteallobjs Delete the TVX record of all objects the objects themselves are untouched Images are stored in the TVX memory up to the limit specified in tvxrc which can consume significan
58. st1 test2 a new directory is NOT created 10 the path Nimages Number 1 Set the number of images for an automatic sequence Maximum number of images is 65535 15 N images set to nn Delay Time s 0 dcb Number Set the delay from the external trigger until start of the first exposure The time must be shorter than 64 s The delay is reset to 0 for ordinary exposures and external enable In a multi dcb detector control board detector the dcb s can be individually delayed If dcb number is not given t is applied to all dcb s Delays of successive dcb s are cumulative e g the sequence Delay 0 0 0 Delay 0 1 1 Delay 0 1 2 results in dcb 2 starting 0 2 s after the trigger not 0 1 s ExpPeriod gt ExpTime max_delay readout_time where max delay 0 2 s in the above example and readout_time 0 00228 s 15 Delay time set to n n sec Or dcb 0 delay time set to 0 000000 sec for all dcb s 54 YECTRIS Next Generation X Ray Detectors NExpFrame Number 1 Set the number of exposures to accumulate per frame read out This is a method summing up images within the detector chip A value gt 1 is a waste of X rays except when using external enable or external multi trigger to synchronously capture an event If nexpframe gt 1 the reported measured exposure time applies to the last exposure only The maximum possible number is 2 32 1 15
59. startup e g setdac rbd calibdet For usage at the beamline usually the last command is Disconnect which allows remote control of Camserver 12 6 Example The following line is a simple example of using TVX to create a flat field correction file corr tif out of a high intensity count image image_00001 tif After you recorded the image with adequate statistics and stored it in Home p2_det images you can use the following commands disp image_00001 tif Idm boxall convert image 00001 tif corr image float tif float move corr tif mean corr image float tif If the image 00001 tif was an appropriate flat image see section 11 for details the 5 lines create a proper correction image corr tif which can be used for flat field correction 48 YJECTRIS Next Generation X Ray Detectors 13 Factory Calibration and Correction The following calibrations are done at the DECTRIS premises 1 Threshold Calibration The PILATUS detector systems come fully calibrated See the system information sheet in your user handbook for more information about the calibrated energies and settings The discriminator thresholds in the individual pixels are set by an automated procedure described above 2 Rate Correction The counter in the pixels is a classical paralyzable counter with a dead time that depends on the gain amplifier settings The correction required is negligible up to 10 counts s pixel but becomes quite s
60. t If only one parameter without value is given the corresponding value is printed In an automatic sequence starting values are automatically incremented by their corresponding increments Start_angle is incremented by Angle_increment Phi by Phi_increment Chi by Chi_increment and Position by Position_increment The values of these parameters may alternatively be specified in the CBF header template The parameter CBF template file gives the full path to the template Note that the CBF template may be used to set variables even when TIFF images are to be written MXsettings CBF template file 0 can be used to turn off this setting See also the cbf template HOWTO txt in the HOME p2_det tvx docs directory for more information 34 YJECTRIS Next Generation X Ray Detectors 11 Flat Field Image 11 1 Using the Flat Field Correction Image in Camserver The flat field images recorded during factory calibration are NOT automatically applied to the images that you take Cli The factory recorded flat field is only appropriate to use at the energy and threshold settings at which it is recorded no special correction recommended usage only at 100K and 300K detectors The energy and threshold values are encoded in the directory name where the correction file FFcorr tif is stored and these directories are located in home det p2_det conftig In the following example FF_pxxxkyyyy_E8p0_T5p0_ vrf_m0p2 E8p0 stands for an incoming X ray
61. t resources use this command to free up memory In addition one can create files with identical names in various directories To avoid the necessity of always specifying full path names use this command to clear the TVX memory deleteobj filename Deletes the specified object from the TVX memory The file on disk is untouched Specify a mask image to be used by many TVX commands such as box and histogram See below 12 3 Mask files Setting a mask image is useful when you are looking at the statistics of images from the detector Pixels in the detector that are either dead too noisy or behave in a non desirable manner can be masked out After a pixel has been masked it will no longer be considered when using statistical routines in TVX to analyze your image so that your results will not be distorted by pixels with too high or too low values A mask file is an image file that uses only two distinct values for each pixel Every pixel that is to be masked out is given a value of 0 every other pixel is given a value of 1 You can create a mask file from another image by using the command mkmask 45 YECTRIS Next Generation X Ray Detectors mkmask pixlfill IM value Make a mask from an image between two limits inclusively Usage mkmask IM IMout low high The result is a mask of 1 s and 0 s which can be used to select pixels of an image by multiplication If no image is supplied the default is used Note that a f
62. te existing data 23 o NORMAL Figure 8 Oscilloscope trace of an external trigger Orange enable signal of the detector Green trigger In Figure 8 the upper trace is the exposure enable signal the lower trace is from the pulse generator being used as a trigger For this external trigger Nimages is 3 the Delay is 0 005 s ExpTime is 0 016 s and ExpPeriod is 0 06 s Note that only the first positive edge of the trigger is used in this example Because the external trigger relies upon the module s internal clock signal to start the timing of the exposure there is a delay and jitter between the trigger signal and the start of the first exposure The maximum jitter is 15 ns with an average delay of 177 ns see Figure 9 Fall 2 delay oc 0 94 V ae O NORMAL Figure 9 Delay and jitter Orange enable signal of the detector Green trigger 24 YJECTRIS Next Generation X Ray Detectors 7 3 3 External Multi Trigger Mode External multi trigger mode is started with the command ExtMTrigger imagename tif where imagename tif is the name of the images you wish to be taken The image name will be imagename_00000 tif unless otherwise specified If Nimages gt 1 the image number will be incremented for each image in the series After issuing the ExtMTrigger imagename tif command the detector will monitor and take a number of images defined below on the level of the trigger pulse The se
63. test of the digital part of the detector Sends a digital pattern to each pixel reads it out and displays the image Use this command always after a startup Every pixel shows 1000 counts Self test of the detector Sends 100 calibrate pulses to the analog part of each pixel reads back the recorded values as an image and displays the result li Every pixel shows 100 counts Sets all Digital Analog Converters DAC to the predefined values Use this command always after a startup Image Path Without the input of a path it displays the current default path With a declaration it changes the default path for images The imagepath command also sets the autoname to the new path The keyword image path can be used in expressions as image path Display or change the default path for graphs The keyword grafpath can be used in expressions as grafpath expose 1 makes an image with an exposure time of 1 sec Shortest exposure time gt 0 000 001s Shows the exposed image and its name immediately after completion continuous camera mode without saving images Takes images until any key is pressed The last image is stored in temp tif Display an image see Section12 1 Opens up to 3 windows with successive invocations Displays an image reusing the last window Useful in loops 38 YECTRIS Next Generation X Ray Detectors Command or Macro graf fn1 fn2 fn3 Graph up to 3 graphs in a window
64. ttings that are necessary for external multi triggering are Nimages ExpTime ExpPeriod Delay optional After receiving a trigger on the positive edge the detector will wait a period of time defined by Delay take an exposure as defined by ExpTime readout the image and will rearm to take another images This will be repeated Nimages times The image number is only incremented during an exposure series if you reissue the command ExtTrigger imagename tif it will start writing images from imagename_00000 tif and overwrite existing data 25 YECTRIS Next Generation X Ray Detectors 7 3 4 External Enable Mode External enable mode is started with the command ExtEnable imagename tif where imagename tif is the name of the images you wish to be taken The first image name will be imagename_00000 tif unless otherwise specified lf Nimages gt 1 the image number will be incremented for each image in the series After issuing the ExtEnable imagename tif command the detector will monitor and take a number of images defined by Nimages gated on the level of the trigger pulse i The settings that are necessary for external enable mode are e Nimages e ExpTime e ExpPeriod N The image number is only incremented during an exposure series if you reissue the command ExtEnable imagename tif it will start writing images from imagename_00000 tif and overwrite existing data Oo NORMAL Figure 10 Oscill
65. ul only in special cases reverse The values are reversed X rays in the image become black rather than white Useful for crystallographic images Several test images and graphs are included in the system i imagepath examples disp gray20bit tif Try the following grafpath examples grafdemo More examples are in home det p2_det programs tvx test images and nhome det p2_det programs tvx test graphs 42 YECTRIS Next Generation X Ray Detectors Example Butterfly selection tool This selection tool is useful for straight line integrations densitometer traces and for integrating small angle scattering patterns from either a line or a point X ray source filemenu editmenu imagemenu helpmenu 0 1048575 20 xi a butterfly image is hesss play 21 7 dir 35 8 sep 30 x 342 y 936 Intensity 958806 Figure 14 Example of a the butterfly selection tool The size and position can be adjusted directly with the mouse or by typing the values directly into the boxes The circle is used only as a positioning aid Use the keyword integrate in the TVX window to display the result 43 YECTRIS Next Generation X Ray Detectors 12 2 Analysis commands TVX offers a large variety of image analyzing and processing commands The most important commands are described in this document All created numeric data are stored in the directory given by grafpath image data are stored in th
66. xel is recommended The longer the exposure time the better the statistics e Divide the mean value of the recorded flat field image by the image itself To perform this operation with TVX see section 12 6 e The resulting image should contain values of around 1 To use the flat field file please see the previous section 11 1 11 3 Using the Flat Field Correction Image in TVX To apply the correction to an existing image issue the command move new_image image limi Where new image is the new image that will be created and image is the image that is to be corrected When you first ask for an intensity correction TVX asks for a file which becomes permanent until exiting the program The command setint correction image can be used to change it By default the file is assumed to be in p2_det correct By explicitly stating the path and image you can specify an image in a different directory Issuing the command setint without any argument will list the currently used correction image if any 36 YECTRIS Next Generation X Ray Detectors 12 How to Use the Pilatus Detector through TVX TVX is a powerful tool for data acquisition and analysis This section describes only the most commonly used commands in TVX All commands are case insensitive however filenames are case sensitive An object in TVX may be an image or a graph Many commands such as move will work on objects of either kind Objects can be combine
67. y the setting the values in the image window The circle is only for alignment purposes Line Distance measuring tool Requires that the correct pixel size be set in detector setup file p2_det tvxrc resolution Resolution circles for crystallographic patterns Calculates the resolution of the image The correct parameters for the detector should be set in the detector setup file or from the command line det_dist lamdba and pixel size Display mode grays color lookup table with gray scale color lookup table with a spectral distribution blue and 41 D Next Generation X Ray Detectors black near zero red fading to pink and white at the high end thermal color lookup table going from blue through yellow and red but no greens decades The values between Min and Max are displayed linearly but with the scale wrapping around Scal number of times Thus Scal 1 is linear Scal 5 covers the range Min to Max with 5 linear segments going from 0 to 255 0 to 255 etc This gives lots of artificial contrast that is good for smoothly varying SAXS data but is otherwise rather non intuitive power The image is displayed between Min and Max using the transfer function grays value min max min Scal 15 grays is usually 256 Thus a small value of Scal 3 gives a very steep transfer function at low values and very little contrast at high values Scal 15 is a linear transfer function Scal gt 15 is usef

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