Adxv User Manual - The Scripps Research Institute
Contents
1. Number of Colors Pixels which are greater than or equal to this value are displayed in a Yalow color This is used to show overloaded pixels When the Colormap is Heat these pixels are Blue and when the Colormap is Rainbow these pixels are Green m Adxv Propertibs Line Thickness ME A Interpolation O None Linear Over Sampling se T Plot Mode Plot Type Fa T 6 OF Image ig 18 Show Pixels gt 65000 Show Pixels lt 1 Resolution Rings jon Off JAnchorl Number of Colors 516 _ 32 _ 64 Max Tr Slab Combine Sum _ aAvg Close Selects how to combine slabs when multiple slabs from an hdf5 file are displayed Pixels which are smaller than this value are displayed in a Red color This is to show bad pixels i e with a value of 2 When the Colormap is Heat these pixels are Green and when the Colormap is Rainbow these pixels are Yellow Draw circles on the Image Window showing the resolution Default is 5 circles See the rings and rfont command line flags for more options Note that these resolution rings are not circular when 2 theta is non zero When Anchori1 is selected a circle is drawn about the beam center through the next point selected with the Left mouse button The diameter of this ring will change as the beam center is changed This is useful for fitting the beam center from ice rings or checking anisotropic scattering Number o2. The first line of the peaks file file is DPS PF A1 0 This is followed by pairs of Y X values For example DPS PF A1 0 614 36 796 76 542 30 798 36 579 09 791 72 672 28 573 30 If Adxv is started with the peaks adx command line option then a peaks adx file is also written This contains X Y I Sigma 796 76 614 36 362 67 798 36 542 30 231 83 791 72 579 09 202 38 573 30 672 28 172 72 In both cases the X Y values are in pixels Both the peaks file and peaks adx files are recognized by Adxv as spot files and may be used to display spot positions For example adxv test 1 001 img peaks file or adxv test 1 001 img peaks adx AdxvPredictions Automatic Peak Search Add Peaks Select this to manually add Max of Spots 30d AJ V spots Click on a spot in either the Image Min I Sigma 5 00 AY or Magnify Windows with the Left mouse Min Spot Spacing E A vi button to add a spot Ignore Ice Rings Spot Info Clicking on a spot displays the Fast Peak Search X and Y position of the spot in the text Avoid Zero Pixels boxes below the Left mouse button will remove it Find Peaks Remove Spots Clicking on a spot with Manual Peak Picking _ Add Peaks C Spot Info _ Remove Peaks Spot Info Hf ef Jeg When a denzo x file is loaded clicking on a spot with the Left mouse button will X mm EI display the HKL and X Y value of that spot y F e _
3. The following keys may be typed when using OpenGL graphics gl This will toggle turning lighting on and off The position and orientation of the data in the 3 D Magnify Window will be reset to its original state In line mode gl lines this will toggle between drawing the wire mesh with smooth lines slower or aliased lines faster When a surface is displayed this will toggle between drawing aliased and anti aliased polygons This will toggle between a wire mesh and surface display of the data Print help This will print a summary of the keys which may be pressed The Load Window This window is accessed by clicking File gt Load from the Control Window and is used to load files Image files Adxv spot adx denzo output x and CrystFEL geometry geom files may be loaded E Directory data lo arvai 052014 Ci Pattern Adxv Load img List File C3 1 00008 sp Stride LE Load a Directory where files are located nf HKL2000 OWE Rw RITTEN_FILES C3 1 UUUU aoe C3 1 00002 imq C3 1 00003 imq C3 1 00004 imq C3 1 00005 imq C3 1 0000B5 imq 3 SL 00007 ima ec C3 1 00008 imq C3 1 00012 imq C3 1 00013 imq C3 1 00014 imq C3 1 00015 imq C3 1 0001B5 imq C3 1 00017 imq C3 1 00018 imq C3 1 00018 imq C3 1 00022 imq C3 1 00023 imq C3 1 00024 img Se TS Pressing the List button will list all files which match the
4. ey 2 m t F e 2 i el 1 4 x 236 A ua J a Zo eset e J RES a ee f f rZ 40 M gt Saree d f E gt 4 I r o ge o e to p j DA UELLE DEN Det 1 J I ox e 1 B CU8 49A e l l f I f v ER S Le l et lo 2 Luis ae x bos E I gt I 4 e I T f L i e oW Y A I L 1 e 4 ee c pt r PPM stes SUE o M oe I 4 T ARE gt A 349 bs e zas J l l 1 2 s E en td 1 i 4 gs lt d I 1 t tuo P L e LI 4 p e Ma vo B 4 Image showing resolution rings Notice that the beam center is drawn as a red cross For this image 2 theta is non zero so the resolution rings are not circular Resolution rings may be turned on or off in the Properties Window which is discussed later The font used for the rings may be set with the rfont command line option If you want to draw only the rings without the resolutions printed you can use the rings only command line option Rings may also be drawn at specific resolutions with the rings command line option The following keys may be typed while the cursor is in the Image Window Arrow Keys lt SHIFT gt Middle mouse button lt SHIFT gt Right mouse button Raise the Load Window The File Load Window is displayed Adjust the histogram contrast in the Image
5. regular expression in the Pattern text field About 20000 files may be listed at once However if there are too many files you can list every 100 th file by making the pattern 01 img Regular expression s to filter which files are listed in the scrolling window to the right Some examples of patterns 0 img A C h5 lys3 cbf If Pattern is blank or all files are listed Directories are always listed Typing a carriage return will re scan the Directory for files matching the Pattern Directories are listed first followed by files Directory names have a trailing Single clicking a directory will change into that directory Clicking the directory will move one directory up Double clicking on a file will load and display that file E Directory data lo arvai 052014 Ci Pattern img List File C3 1 00008 img Load 44 gt Stride ho ES Adxv Load i HKL2000 C3 1 00001 imq C3 1 00002 irpa C3_1_O0 es Tma FU0004 img C3_1_90005 imq C3_1_00006 imq C31 00007 ime C3 1 00008 iImq C3 1 00012 imq C3 1 00013 imq C3 1 00014 imq C3 1 00015 imq C3 1 00015 imq C3 1 00017 imq C3 1 00018 imq C3 1 00018 imq C3 1 00022 imq C3 1 00023 Imq C3 1 00024 img es OVERWRITTEN_FILES Sort by Time Load and display the file in the text field to the left Sort Alphabetically You can type a file name into this text
6. ne ADXV User Manual pd er ds e O 4 Ew mns S x a uet Jase LL a gt A Version tl nop 2015 ET m se ES E A LU 5 E Fe P 4 Introduction History of Adxv Supported File Formats Notes for HDF5 files Starting Adxv Examples The Adxv Windows Control Image Magnify Load Save Output File Formats Line Histogram Info Image Header Predictions Statistics Settings Properties Background Socket Interface Beam Center File Frequently asked Questions Command line options Environment variables ON AANA HR W 11 11 17 20 25 31 32 33 39 42 45 46 49 52 54 55 56 58 64 Introduction Adxv is a program to graphically display and analyze 2 D area detector data It is optimized to display X Ray crystallography diffraction images Many common data formats are recognized including ADSC SMV IMG CBF and HDF5 The data may be displayed as a 1 D cross section 2 D image or 3 D surface Sequential images may be displayed as an animation The magnification contrast and color mapping are adjustable Displayed data may be saved in a variety of formats including ASCII SMV IMG TIFF JPEG and Postscript Adxv will run on most versions of Linux and OSX It is based on X11 Motif so an X server is required It will run on Windows if the Cygwin libraries have been installed and an X server is running Adxv is freely available to everyone There is no registration license or fee r
7. This was written with the X11 Motif libraries Over the years Adxv has slowly evolved by adding more features supporting more data formats and supporting the latest computers and operating systems Adxv There is no substitute Supported File Formats Format File Extension ADSC SMV IMG 16 and 32 bit integer img Bruker sfrm CBF Standard and mini CBF cof EDF edf Fuji Image Plate Fuji HDF5 h5 hdf5 MarCCD mccd Mar Image Plate image marxxxx NUMPY hpy R AXIS OSC TIFF 8 16 32 Bits Pixel with 1 Sample Pixel Af ttf Raw binary 8 16 32 bit integer and 32 bit float any Adxv spot file adx Cheetah pixelmap file AS CrystFEL geometry file geom Denzo x file x Adxv recognizes many file formats based on the file header so the file extension can be anything Files which have been compressed with gzip compress or bzip may be read without uncompressing them The internal data representation of Adxv is 32 bit signed integer If an input data format is floating point and the data values are very small or very large you may want to run Adxv with the iscale command line option to multiply the data by a scale factor before conversion to integer Notes for HDF5 files HDF5 files are containers for two kinds of objects Datasets and Groups Datasets contain multidimensional arrays of data and Groups are container structures which may contain Datasets or other Groups Groups are analogous to directories and Data
8. Window The contrast of the visible portion of the data in the Image Window is automatically adjusted Note that if the entire image is not visible only the pixels visible in the Image Window are used to adjust the contrast Toggle lighting on and off in the Magnify Window When using OpenGL graphics this will toggle turning lighting on and off Adjust the histogram contrast in the Magnify Window The contrast of the Magnify Window is automatically adjusted Toggle turning predictions on and off When predictions are displayed this will toggle displaying them or not displaying them Reset the display in the 3 d magnify window The position and orientation of the data inthe 3 d magnify window is reset to its original state Toggle smoothing in the Magnify Window When using OpenGL graphics in line mode gl lines this will toggle between drawing the wire mesh with smooth lines slower or aliased lines faster When a surface is displayed this will toggle between drawing aliased and anti aliased polygons Toggle between wire mesh and surface display in the Magnify Window When using OpenGL graphics this will toggle between a wire mesh and surface display of the data Adjust the cursor position Pressing the arrow keys up down left right will move the cursor by one pixel If the Plot Type is Circle set under Edit gt Properties the arrow keys will translate the center of the circle by one pixel Print help This will print
9. and keep the values as they are check the box under Fix and next to the relevant parameter AqwSettings Distance 179 956 mm _ Pixel Size 0 10259 mm esl Wavelength 1 03316 A Here the Wavelength is fixed so a value read in from a new image will not change this 2 Theta _ Horiz 0 00 deg aco pri 2 theta may be Horizontal or Vertical When Horizontal the detector rotates about a a lus vertical axis and when Vertical x 1525 q 2 the detector rotates about a lt q b 3 a horizontal axis v IE v pixels Small Spots Fix Contrast Close Adwsettings Distance 179 956 mm Pixel Size 0 10259 mm Wavelength 1 0331 E A 2 Theta dea _ Hori 0 00 eg O Vert Beam Cener isos lt gt pixels Small Spots qm Fix Contrast Fix si Ei E The position of the beam center may be moved by 1 pixel by clicking the appropriate arrow button The coordinates of the beam center may be entered and displayed in the text boxes to the left in either millimeters or pixels by selecting mm or pixels respectively When Small Spots is checked there is more smoothing of the image displayed in the Image Window If spots are small and every n th pixel is simply displayed without smoothing then some spots may not be visible This only affects the display in the Image Window not the Magnify Window See examples on the next page When
10. falls between pixels it s value may be either the closest pixel or interpolated from close pixels Number of points drawn per pixel of length The line may be displayed as individual points a line connecting points or a stair step centered on each pixel The plot will be a straight line where the first point is selected with the Left mouse button The mouse is then dragged and the end point is where the mouse button is released 3 Adkv Properties J The Left mouse button will select the center of a circle As the mouse is dragged the radius of the circle Thickness AY increases When the mouse button peres is released a circular arc of data will be drawn from O to 360 degrees Over Sampling 1 22 J408 around the circle The plot is Plot Mode ros ne amp Pixel counter clockwise starting from the Plot Type x 6 9 right side Image W Show Pixels gt Jesoog Show Pixels lt T Resolution Rings zon Off Ancho 7 Same as above except the edge of the circle is selected and the mouse 64 O Max is then dragged to select the center Slab Combine Sum _ aAvg Close As above the center of a circle is selected with the Left mouse button and the mouse is dragged to select the radius The horizontal axis of the plot is radius i e distance from the center of the circle The value at each radius is the circularly averaged pixel intensity at that radius May be useful for SAXS Line
11. field or select one with the mouse from the list on the right To load a file you can either click the Load button type a carriage return in the text field or double click on the file in the list on the right Pressing the Right mouse button in the file list section brings up a menu where you can choose to sort files alphabetically or by modification time The default is alphabetical When files are listed they are not sorted absolutely alphabetically Sorting also takes into account run numbers and these are sorted from small to large For example files are sorted like this data 1 001 img data 2 001 img data 10 001 img data 11 001 img not like this data 10 001 img data 11 001 img data 1 001 img data 2 001 img When Sort by Time is selected more recent files are listed first regardless of file name Directories are still listed first To re scan files in a directory press the List button or type a carriage return in the Pattern text field Load and display the next file In this case the next file to load will be C3 1 00013 img This is because the current file is number 8 and the stride is 5 If instead the left previous arrow button is pressed then file number 3 would be loaded When a new file is loaded if the Line or Magnify Windows are displayed their contents will be updated to reflect the data in the new file This also applies to movie mode Adxv Load EH Directory data lo ar
12. image is 19 the size of the entire image so about every 5 pixel is displayed Loading C3 1 00001 imqg If Adxv is started with the verbose flag more 3072 x 3072 pixels Distance 180 mm Lambda 1 033 information is printed Mink O at 0 0 Maxl 65535 at 16512 1005 of 1 pixels O The x y position of the smallest and largest pixels of 2 pixels 0 The number of 1 and 2 pixels The standard deviation sigma of all the pixels 4 gl 186 Sigma 345 5 95 Overflows 19 Spots Scale factor 0 19 The Image Window The The Image Window graphically displays the image using a grayscale colormap Larger pixel values are darker and smaller pixel values are lighter As the mouse is moved around the Image Window the position of the cursor is displayed in both mm and pixels The resolution in A and the Sigma of the region under the cursor is also displayed The beam center is drawn as a red cross in both the Image and Magnify windows The left mouse button may be pressed dragged along the window and then released to produce a 1 d plot in a separate Line Window The middle mouse button may be pressed and dragged to pan the image if the image does not fit in the window Pressing the right mouse button will magnify and display the area under the cursor ina separate Magnify Window If the lt SHIFT gt key and Right mouse button are pressed simultaneously the Control Window will be raised If the mouse has
13. pixels The displayed X Y value may be selected to be mm or pixels but the output peaks file Show Predictions Close is always pixels Un checking this box will turn off the display of spots Same lM as typing p in the Image or Magnify Windows The Statistics Window This window is accessed by clicking View gt Statistics in the Control Window When the Right mouse button is clicked in either the Image or Magnify Windows Statistics of data in a box centered on the mouse position are calculated and displayed Adw Statistics Box Size 11 X Pixels Center of Mass 755 59 1752 47 Pixels 7 57 133 58 mm Average 53 22 Std Deviation 1320 13 Close Box Size specifies the area of the region over which to calculate statistics If the area of the Box is O then all the pixels in the Magnify Window are used The Center of Mass is displayed in both Pixels and mm The Average pixel value as well as the Standard Deviation are calculated and displayed The Settings Window This window is accessed by clicking Edit gt Settings in the Control Window Distance and Pixel Size are in millimeters Wavelength is in Angstroms and 2 Theta is in degrees The beam center may be entered and displayed in pixels or millimeters depending on the setting of the adjacent radio box When a new image is displayed these values may be overwritten by values in the image header To avoid this
14. reads an image file automatically writes a jpeg tiff or img file and then exits It requires an input image file and output file name as the last two arguments respectively The output filename extension tiff jpeg or img specifies the output format sa crop WxH X Y In standalone mode sa this will crop the output image The upper left corner is XY and the output dimensions are W x H pixels Use stat instead of d type field to determine the file type scan_origin mm UL UR The scan origin for mm coordinates displayed in the LL LR Image Window Default is LL Lower Left See also fast scan mm scan origin px UL UR LL The scan origin for pixel coordinates displayed in the LR Image Window Default is UL Upper Left See also fast scan px Input file is raw binary signed shorts 2 bytes pixel show underload Show pixels below a threshold See Properties Window Skip N bytes before reading raw binary data May be used to skip a file header slab combine Sum Avg Sum or Average data when combining multiple slabs Default is Sum Applies to multi dimensional hdf5 data First slab of multi dimensional hdf5 data to display Number of slabs of multi dimensional hdf5 data to merge and display Slower routine to open CBF files Use a smaller crosshair cursor in the Image Window Better image display for images with small spots Output img files will be 32 bit signed integer instead of 16 b
15. set the Max and Min contrast values in the textboxes to the right will be drawn in a Bold font Adxv Control File View Edit Help Scale 550 _ 100 Auto Magnify _ 3 D Pixels _ Values Magnification 1 JM JM Q8 16 _ 32 64 2 Loading C3_1_00001 img 3072 x 3072 pixels Distance 180 mm Lambda 1 033 4 Maxi 65535 Avgl 186 95 Overflows 19 Spots Scale factor 0 19 This selects how data is displayed in the Magnify Window If 3 D is selected the data is displayed as a wire mesh Pixels displays magnified pixels and Values prints only numbers See examples on Page 22 Magnification factor of pixels drawn in the Magnify Window 8 means that each pixel in the raw data is magnified 8 times and is drawn as an 8x8 pixel box in the Magnify Window The range of magnifications is from 1 to 128 See examples on Page 21 There is more information about magnification types and factors in the Magnify Window section page 20 Information about the image which was loaded Max is the largest pixel value in the image Avgl is the average pixel value Overflows is the number of pixels which have overflowed the linear range of the detector Spots is the number of groups of contiguous pixels which are overflowed i e each spot may contain multiple overflowed pixels Scale factor is how much the image was scaled to fit in the Image Window when the Scale mode is Auto In this case the
16. window may display either a histogram or a 1 d cross section of the data Whichever is displayed in the Line window will be saved b AdwSwe i EE nomc arval tesf HB Directory and File where the q saved data will be written File fc3_1_00001 ps Window Format Image o Ascii J Magnify J Binary _ Line Postscript _ Tiff J Jpeg Selects which format the data will be saved as See Output File Formats below for more information about these choices Selects which window data will be saved from 31 Output File Formats Ascii For the Image and Magnify Windows the output is NX columns and NY rows where NX is the width in pixels and NY is the height For example here is the output of a 5x5 pixel region displayed in the Magnify Window 443 462 387 439 413 439 2156 1566 472 425 488 25600 19114 757 420 451 563 609 483 431 396 415 410 440 424 For the Line window there is a short header followed by pairs of X Y values where X is the distance in pixels and Y is the value For example Line from image home arvai test images pilatus cbf Start 1280 1119 End 1290 1119 Linewidth 1 Interpolation 1 H O 406 000000 1 469 000000 2 449 000000 3 488 000000 4 25600 000000 5 19114 000000 6 420 000000 7 410 000000 8 393 000000 9 434 000000 Note that the x coordinate distance is relative to the Start position in the header Binary This is only an option for the Im
17. 1 595 518 467 430 412 416 1064 772 575 495 452 431 421 407 398 411 380 392 377 331 408 700 575 489 Values Notice that when the magnification is 32 or larger the pixel values are printed in each pixel Depending on the number of digits needed for each value a larger or smaller font may be used so that the value will fit within a pixel For Values the magnification setting is disabled The magnification depends on how many pixels can be fit in the Magnify Window and is usually about 32 N N The Magnify Window when using GL gl command line option BEN Adxv Magnify lt rad10 gt Pixels The colormap is Heat Adxv Magnify lt rad10 gt 3 D Wire Mesh Type w to toggle between wire mesh and surface display BE Adxv Magnify lt rad10 gt 3 D Surface Type I to toggle lighting on and off The following keys may be typed in the Magnify Window Arrow Keys lt SHIFT gt Middle mouse button lt SHIFT gt Right mouse button Raise the Load Window Adjust the contrast to optimize display of the contents of the Magnify Window Toggle display of spots on off Reset orientation of 3 D display Adjust the cursor position Pressing the arrow will move the cursor by one pixel Print help This will print a summary of the keys which may be pressed Set the beam center to the current mouse position Prints the distance between successive Right mouse button clicks to the terminal
18. 1_00001 img 3072 x 3072 pixels Distance 180 mm Lambda 1 033 Maxi 65535 Avgi 186 95 Overflows 19 Spots Scale factor 0 19 See examples below 11 Adxv 64phr native 1 001 20 100 The Image Window showing the same image displayed at different scales When the scale is 25 or larger the image does not fit completely inside the Image Window In this case you can press and hold the Middle mouse button to move the image around The beam center is drawn as a red cross in each image E E AdwContod Adjusts the colormap of the image File View Edit Help displayed in the Image and Magnify Scale Windows For example with Heat larger 225 50 100 Auto gos pixel values are light Yellow intermediate a values are Orange and smaller values are seg dark Red Colormar Gray _ Heat _ Rainbow 300 agnify 240 IRD 180 Pikels 120 bE Values Magnification 4 O8 516 332 364 2 Loading C3M 1 00001 img 3072 x 307 pixels Heat Rainbow Distance 18 mm Lambda 1 033 Maxl 55535 vgl 185 95 Overflows M9 Spots Scale factor 0 49 This inverts the colormap For example with Gray larger pixel values are Black When Invert is selected larger pixel values are White See examples of different colormaps below Gray Gray Invert 13 The Image Window showing different colorm
19. Fix Contrast is checked the image contrast is not automatically adjusted for each image as it is loaded The may also be set from a pulldown menu selected by clicking the Right mouse button in the colormap drawing area of the Control Window Effect of smoothing on an image which is scaled to 50 No smoothing every other pixel is displayed This can be selected with the nosmooth command line option This is the default setting There is no smoothing when the image is scaled to 100 and there is progressively more smoothing as the image scale is decreased More smoothing about twice the default This can be selected with the small spots command line option or by checking the Small Spots checkbox in the Settings Window The Properties Window This window is accessed by clicking Edit gt Properties in the Control Window The upper set of properties affect the display of the Line Window and the lower set affect the display of the Image Window Adxy Properties 0 Line Thickness ME A Interpolation Over Sampling Plot Mode _ Dots _ Line Pixe we L7 OLEO Image W Show Pixels gt Jesoog v 1 Show Pixels lt Resolution Rings 50n Off _ Anchort Number of Colors 316 _ 32 _ 64 Max wr Slab Combine Sum _ aAvg Close Number of pixels orthogonal to the line direction which are averaged to form each point displayed in the Line Window When a point
20. IN none VERSION 15 ADC slow HDRBLKS 15 DATE Sun Jun 8 13 46 13 1997 TIME 150 00 DISTANCE 50 000 OSC RANGE 1 000 PHI 0 000 OSC START 0 000 TYPE Omega Scan Image SITE BRUKER21 MODEL D85 with FIXED CHI USER BrukerAdministrator SAMPLE SETNAME RUN 1 SAMPNUM O TITLE TITLE TITLE TITLE TITLE TITLE TITLE Adxv Info lt radi0 gt HHHCBF VERSION 1 5 CBFlib v0 7 8 data 1327225845 00000 array data header convention PILATUS 1 2 _array_ data header contents Bruker Detector PILATUS 6M S N 60 0113 2012 01 22 102 07 29 073 Pixel size 172e 6 m x 172e 6 m Silicon sensor thickness 0 000320 m Exposure time 1 9977000 s Exposure period 2 0000000 s Tau 199 1e 09 5 8 Count cutoff 1179359 counts 8 Threshold setting 5300 ev Gain setting mid gain vrf 0 200 Close Close mini CBF i y Adxv Info lt radi0o gt NUMPY NUM PY 1 0 i CT 1 Mar CCD deser lt f8 fortran order False GAhigh 1 033 mccd ISDE DD iuan total_pixels_x 4096 total_pixels_y 4096 bytes_per_pixel 2 bytes per record 8192 bits per pixel 15 data type 0 saturation 65535 overflow_location 0 over 8 bits 0 no_overflows 0 distance 300 beam x 2048 beam v 2048 E adumo d biosaxsMetadata edf EDF_DataBlockID O Image Psd EDF_BinarySize 4092732 EDF_HeaderSize 1536 ByteOrder LowByteFirst Dat
21. a scroll wheel then in Pixels and 3 D mode the scroll wheel can be used to adjust the magnification factor in the Magnify Window from 1 to 128 If the lt SHIFT gt key and Left mouse button are pressed simultaneously a position on the image is selected Once three positions have been selected the angle between two consecutive lines described by those three positions will be printed to the standard output If two of the three positions are identical the horizontal and vertical angle relative to the crystal origin between the two points is printed If all three points are identical the horizontal and vertical angle required to rotate that point to the beam center is printed These options were useful in the old days to measure the angles ofa lattice or estimate how far to rotate a crystal to align a zone If the SHIFT key and Middle mouse button are pressed simultaneously the beam center will be set to the cursor position This may also be done in the Magnify Window With the cursor is in the Image Window two numbers followed by a carriage return may be typed and the Magnify Window will be raised and centered on that x y pixel position If the Right mouse button is pressed while the SHIFT key is also pressed then the distance between successive clicks in pixels and mm will be printed to the terminal Adxv LY_140429a_1_0001 img gz EE P ac f m M 1 82A 38 B BUE W d a E aA a Ls 1 91 E E
22. a summary of the keys which may be pressed Set the beam center to the current cursor position Raises the Control Window Also prints the distance between successive Right mouse button clicks to the terminal The Magnify Window The Magnify Window displays a magnified portion of the data from the Image Window Pressing the right mouse button in the Image Window draws a box and displays a magnified view of the data within that box in a separate Magnify Window The format of the displayed data may be selected by toggle buttons in the Control Window see examples below The default is Pixels where each pixel in the image is scaled by a magnification factor and displayed If the magnification factor is 32 or larger the value of each pixel will also be printed within each pixel If Values is selected then only pixel values will be printed not a magnified image If 3 D is selected then a three dimensional wire mesh representation of the data will be displayed The function of the mouse buttons is different with the different display modes In Values mode the Left and Right mouse buttons have no effect The Middle mouse button will pan the displayed data around the image In Pixels mode the Left mouse button will draw a line or circle depending on the Plot Type setting in the Properties Window The Middle mouse button again pans around the image and the Right button has no effect In 3 D mode the Left mouse button rotates the wire mesh Th
23. aType SignedInteger 81 Dim 1 Dim 2 1043 Image D HeaderID EH 000000 000000 000000 Size 4092732 VersionNumber 0 10 Date Wed May 12 16 13 16 2010 count time 20 000000000 Diuvol cize 1728 E m x 172e 6 m ET LCLS f_11_ENRC 1 01856e 312 LCLS f_12_ENRC 6 95329e 310 Close LCLS f_21_ENRC 6 95329e 310 LCLS f 22 ENRC 6 93648e 310 ALCLS fiducial 62214 LCLS machineTime 1298270150 LCLS phaseCavitvCharge1 6 93645e 310 LCLS phaseCavityCharge2 O LCLS phaseCavityTime1 2 32705e 319 LCLS phaseCavityTime2 5 083e 317 LCLS photon_energy_eV 3385 21 LCLS photon_wavelength_4 1 32106 data data data data raw data data rawdata 1480 x 1552 HST_STD_II6LE processing processing hitfinder processing hitfinder peakinfo 121 x 3 H5T Close land HDF5 2 EDF With an hdf5 file header entries with 2 or more dimensions are displayed in a bold font If you double click one of these with the Left mouse button then Adxv will load that dataset Adxv will also remember the dataset name and will try to load it from future hdf5 files Dataset name If starting Adxv Data type In this case F32LE with the hdf5dataset command is floating point 32 bit little line argument this is the name endian you would use A 7 Double click to LCLS load this dataset LCLS fhoton energy ev 3000 ALCLS Bhoton_wavelength_4 24 1328 data
24. age Window The entire image is written regardless of how much is visible The output format is ADSC img format There is an ASCII header which looks like this HEADER_BYTES 512 DIM 2 SIZE1 2463 SIZE2 2527 TYPE unsigned_short BYTE ORDER little endian DISTANCE 80 001 PIXEL SIZE 0 172000 WAVELENGTH 0 980800 PL The header is padded to HEADER BYTES bytes and is then followed by the raw data which is 16 bit unsigned shprt The output data will be signed 32 bit integer if Adxv is started with the smv32bits command line option In this case the header is slightly different with TYPE long integer Images may also be converted to and saved as img files with the sa command line option See examples on pages 9 and 10 Here is a library and documentation to read write ADSC SMV IMG files http www scripps edu arvai adxv data smv tar gz Postscript Writes level2 color postscript If Adxv is started with the levell command line option then level1 postscript will be written Tiff Tagged image file format Jpeg Standard JPEG format The Line Histogram Window The Line Window displays a 1 D cross section plot of data from the Image or Magnify Windows Pressing and dragging the left mouse button in the Image or Magnify Window will draw a rubberband line When the mouse button is released the data selected by that line will be displayed as a 1 D plot in the Line Window The horizontal scale
25. al Moving Average w Radial Symmetry about Beam Center Apply to Select whether the Original background is applied to the Original image or the close Displayed currently Displayed image Image The difference is that the currently displayed image may already have had some background subtracted The background may be calculated using a Local moving average or based on Radial symmetry about the beam center For the later make sure the beam center is correct The Socket interface When Adxv is started with the socket command line option it will listen for a connection on port 8100 Commands may be sent to Adxv over this connection Commands can be sent to load images display spots or raise windows Below is a list of commands which can be sent box xy Size of box drawn around spots define_type n color lt color gt radius Define a spot type Color is one of red green lt radius gt or Blue Radius is in pixels load_image lt image file gt Load an image file load spots N Read N spots x y type Spot at pixel position x y end_of_pack End of spot data raise_ window lt window gt Raises a Window lt window gt must be one of Control Image Magnify Line or Load exit Exit Adxv Here is an example http www scripps edu arvai adxv data adxv socket example c To run cc o adxv socket example adxv socket example c adxv socket amp adxv socket example This will load an image file displ
26. aps 14 Rainbow Pixel values larger than this value are drawn as Black This may also be set and displayed in the Histogram Window Graphical display of pixel value vs color mapping For example a pixel File View Edit Help value of 360 will be drawn in Scale medium gray and a pixel value of 120 Tak Gentle carn Auto will be drawn in light gray The l Middle mouse button may be pressed shih and dragged in this window to stretch and adjust the colormap The behavior is analogous to stretching a rubber sheet Selecting a different colormap or moving the contrast Slider will reset the colormap Fix Contrast Magnify Auto 23 D Pixels _ Values TA Slider to adjust the contrast MN 2 NM Dragging this up increases the contrast and dragging it down Loading C3_1_0 001 img 3072 x 3072 pixels decreases the contrast Distance 180 mgm Lambda 1 033 4 Maxl 55535 Awglh 185 35 Overflows P9 Spots Scale factor 0 75 Pixel values smaller than this are drawn as White May also be set and displayed in the Histogram Window If the Right mouse button is pressed in the colormap drawing area this popup menu appears Selecting Fix Contrast will not automatically update the contrast setting for each image as it is loaded The Max and Min contrast settings will remain as from the last image loaded or as set by the user This may also be set in the Settings window When Fix Contrast is
27. ay 4 spots of various sizes and colors and raise the Load Window You will need to change the name of the image file in the code An example image is available here http www scripps edu arvai adxv data da1 img gz The Beam Center File Whenever Adxv reads an image file it checks to see if there is a adxv_beam_center file in the directory where the image is being loaded from If this file exists then it will be used to set the beam center The reason for this is that sometimes the beam center written in the image header is not correct If it is adjusted one time then all images in that directory will be displayed with the correct beam center If the adxv beam center file does not exist or if the user adjusts the beam center in Adxv then this file will be written The file contains 4 ascii numbers beam x beam y nx ny beam x and beam y are the coordinates of the beam center and nx and ny are the image dimensions For the beam center to be used the image dimensions of the displayed image must match nx and ny To not read or write the adxv beam center file Adxv can either be started with the no adxv beam center command line option or the NO ADXV BEAM CENTER environment variable may be set Frequently asked Questions Is there any license or fee for using Adxv No it is free for anyone to use Where can download adxv from www scripps edu arvai adxv html What if Adxv complains about missing fonts You can install the
28. data data 1456 x 1456 HST_IEEE_F32LE H5Z FILTER DEFLATE Dimensions of the data array in pixels Filter if any needed to decompress the data In additions to the standard HDF5 filters Adxv will also recognize the LZ4 filter The Predictions Window This window is accessed by clicking View gt Predictions in the Control Window Spots can be automatically or manually picked and displayed Adw Predictions Max of Spots specifies the maximum Autamatir Paak Search number of spots to find All the found f spots are sorted based on l Sigma and the Max of Spots 300 ROUND ee Av largest are saved If Max is set to O then all Min l sigma 500 Al V spots are kept Min Spot Spacing E AY Ignore Ice Rings Min 1 Sigma saves only spots larger than the specified l Sigma Fast Peak Search q ql Avoid Zero Pixels Min Spot Spacing saves only the larger of two spots if they are too close Distance is Find Peaks in pixels Ignore Ice Rings will not use spots near ice rings Manual Peak Picking _ Add Peaks Spot Info Fast Peak Search uses a different peak gt Remove Peaks search algorithm Avoid Zero Pixels ignores spots near pixels Spot Info which have a value of O H K When Find Peaks is clicked spots will be A mm searched saved in a files called peaks file Y pixels and then displayed on the image with a box around each spot _ Show Predictions Close
29. e Middle mouse button translates the mesh in X Y within the Magnify Window The Right mouse button is used to scale the wire mesh in the Z direction If Control Right mouse button is pressed this will scale the wire mesh in all dimensions If the mouse has a scroll wheel then in Pixels and 3 D mode the scroll wheel can be used to adjust the magnification factor from 1 to 128 If Adxv is started with the gl command line then OpenGL graphics is used for 3 D mode r E 9 407 374 352 348 328 320 303 300 304 2 369 344 338 330 328 319 aos 408 365 345 334 322 EE 413 359 331 3 462 391 OS 435 408 412 416 398 411 408 331 ANA bom r dm ae Magnify Window as the magnification increases from 1 to 128 The magnification mode is Pixels x 64 x 128 21 Comparison between Pixels 3 D and Values Adxw Magnify Pixels isa dl lini p ud m 3 D The same data is shown with Magnification set to Pixels left and 3 D right The magnification is 4 in both cases Pixels Adxw Magnify 370 346 343 342 338 310 5 294 305 311 29 423 407 374 352 348 328 320 303 300 304 537 513 448 406 369 344 338 330 328 319 929 718 538 495 468 408 365 345 334 322 1789 1223 918 723 668 600 500 413 353 331 4542 1874 1300 1197 1128 994 786 594 462 331 3608 1517 1046 929 890 791 649 503 435 408 1966 1100 766 63
30. ead The default is to only create a new pixmap if the new image is a different size norotate Do not rotate mar image files 90 degrees before displaying When the image scale factor is less than 0 25 do not smooth the displayed image When a large image is scaled down small spots may not be visible if simply every n th pixel is displayed Smoothing is on by default nolabelPixmap Labels are not drawn from Pixmaps numpy Input file is NUMPY format Number of pixels in horizontal fast direction ny N Number of pixels in vertical slow direction Open files with O DIRECT for faster I O Constant to add to all pixel values oldcontrast Use older automatic contrast adjustment overload N Pixel overload value Pixels larger than this are drawn as yellow This may also be set in the Properties Window parallel Use multiple processors up to 16 peaks adx Write peaks adx X Y I Sigma for peak search pixelmap lt geometryfile gt CrystFEL geometry file or Cheetah pixelmap file pixelsize X Pixelsize mm printheader Print image header to the standard output Display the Prediction Window at startup Line Window horizontal scale is in q space units rfont lt fontname gt Font to use for resolution rings rings res1 res2 Display resolution rings rings only Draw only the rings not the resolutions rotate 90 180 270 Rotate the image 90 180 or 270 degrees before displaying it Standalone mode This
31. eedback Adxv crashes in with Library not loaded usr X11 lib libXt 6 dylib In OSX 10 10 Yosemite the X11 libraries were moved from usr X11 to opt X11 You can make a symbolic link from opt X11 to usr X11 In s opt X11 usr X11 What if none of the binaries run on my machine or I find a bug Contact me at arvai scripps edu What if want to donate money to fund Adxv support and development Definitely contact me Command line options autoload Automatically load images listed in the file SXFORMSTATUSFILE This file should contain one line with two values an integer number and file name This file is checked every two seconds and when the integer number changes the specified file name is loaded and displayed auto_sigma As the cursor moves across the Image Window the Sigma of the region under the cursor is calculated more accurately but more slowly This is done by default in the Magnify Window beam_center x y Specify the beam center in mm Default is read from the image header beam_center_pixels x y Specify the beam center in pixels Default is read from the image header oier CE oma O O ar rotenone contrast Min Max Set the initial values for the contrast setting Default is automatic Print debugging information Delay in milliseconds for displaying images in movie mode display DISPLAY X11 display to use Specify the crystal to detector distance in mm Default is read from the ima
32. equired to use it You can download it from www scripps edu arvai adxv html This manual is available here www scripps edu arvai adxv AdxvUserManual pdf The current version of Adxv is 1 9 10 A Brief History of Adxv In 1992 The Scripps Research Institute TSRI got a new Mar Image Plate Scanner It was a great detector although it used the VMS operating system and the display software XIPS was not so great So wrote a program called Xvip to display images on our Unix Sun workstations Xvip was written in C and used the X11 Xview graphics libraries File Save Show Quit Scale Contrast 100 Min Mas d 75 amp 29 50 25 Auto Color On Off Magnify 4 8 16 32 Predict On Off Pixel Value zd Loading home arvai andy 2 1 001 1mage z Distance 230 mm Lambda 1 540 4 d 2000 x 2000 pixels O overflows Joo MaxI 64391 AvgI 6 vi Scale factor 0 31 Xvip circa 1993 Our Sun workstations were monochrome so grayscale images were displayed using dithering When we got color workstations modified Xvip to work with grayscale and color A later version of Xvip was given to Mar Research which evolved into what is now their MarView display program In 1993 in collaboration with ADSC created a version of Xvip which was better suited for SAXS data This program was called Marvip In 1994 combined the best features of Xvip and Marvip into the first version of Adxv
33. f colors to use for the colormap when displaying the image The Background Window This window is accessed by clicking Edit gt Background in the Control Window You can display the background of an image as well as subtract or divide the background from an image This may also be used to add or subtract images Display will calculate and display the background of the current image Divide will divide the current image by either a file or a calculated background Subtract will subtract the background either calculated or read from a file from the current image The percentage of the background to subtract may be specified 50 specifies half the background will be subtracted If the percentage is negative the background is added For example 100 can be used to sum two images Select whether the background is read from a file or calculated from the current image Background Source _ Display _ File _ Divide Calculate Subtract 100 0 Bacharpuni File Directory tiis Background Calculation Local Moving Average _ Radial Symmetry about Beam Center Apply to Original Close Displayed Image Background Source v Display File w Divide w Calculate Subtract 100d If File is selected as the Source then the Directory Background File and File are specified here Directory home arvai test File C3 1 00001 imd Background Calculation Loc
34. ge header Input file is Binary doubles fast scan mm H V Specify the fast scanning direction for mm coordinates displayed in the Image Window Default is H Horizontal See also scan origin mm fast scan px H V Specify the fast scanning direction for pixel coordinates displayed in the Image Window Default is H Horizontal See also scan origin px find peaks Run peak search and exit Do not automatically re adjust the contrast as each new image is read in This may also be set in the Settings Window mon mesas 000 tah mweafunmeeptemae mum npr fein Fa 100 mage piae rrago gl If available use OpenGL to render 3 d graphics in the use gl Magnify Window Draw OpenGL 3 d graphics as a wire mesh Typing w in the Magnify Window will also toggle between a wire mesh or polygonal surface representation gl_quad_strip_bug Draw the 3 d polygonal surface using GL QUADS instead of GL QUAD STRIP This works around a bug in some X Servers hdf5dataset lt dataset gt Name of HDF5 data set i e data hist32bits Larger dynamic range for histogram slower ifont lt fontname gt Text font to use in the Image Window Input file is raw binary signed integers 4 bytes pixel Mimic Mosflm s coordinate system Shortcut for rotate 90 flip V scan origin px UL scan origin mm UL Use N colors for the colormap Default is 1024 If N20 use the maximum possible newpixmap Create a new pixmap when a new image is r
35. he autoload command line option Maximum number of threads to use when the parallel command line option is used Max is 16
36. ictions The options which may be specified on the command line are listed starting on page 58 Following any command line options is the name of an image file to load After the image file a file with spot positions may also be specified For example to display an image you can do adxv test 1 001 img Two windows will appear the Control Window and the Image Window The Image Window graphically displays the image using a grayscale colormap Larger pixel values are darker and smaller pixel values are lighter As the mouse is moved around the Image Window the position of the cursor is displayed in both millimeters and pixels The resolution in Angstroms and l Sigma of the region under the cursor are also displayed In the Image Window the Left mouse button may be pressed dragged and then released to produce a 1 d cross section plot This plot will be displayed in a new Line Window The middle mouse button may be pressed and dragged to pan around the image Pressing the right mouse button will magnify and display the area under the cursor in a separate Magnify Window The Control Window may be used to modify the appearance of the displayed image In the center of this window is a graphical display of the pixel to color mapping and immediately to the right of this is a vertical slider Dragging the slider will adjust the contrast of the image Pixel values larger than the value in the text box above the slider are drawn as black or the t
37. image View gt Histogram gt Image may be selected The horizontal scale is pixel value and the vertical scale is number of pixels Two vertical dashed lines are drawn at the pixel values displayed above and below the contrast slider in the Control Window and represent the min and max pixels values in the colormap Values below the min pixel value are drawn as white and values above the max value are drawn as black Pixel values intermediate to these values are drawn as a grayscale 3 De 04 M The Left Mouse button can be Ea mA used to adjust the min pixel value slider and the Right P Dern Mouse button will adjust the 3 De 04 N max value The Middle mouse button will adjust the vertical 0 0e 04 200 400 600 300 scale of the plot A small red cross is drawn at the horizontal position of the cursor The X and Y values of this coordinate are displayed in the upper right The left and right arrow keys may be pressed to move the cursor 1 pixel in each direction The Info Window This window is accessed by clicking View Image Header in the Control Window This will show the image header for the displayed image Below are some example image headers for various image formats Adxv Info lt rad10 gt ADSC img qi img HEADER BYTES 512 DIM 2 ARE eee SETTE e TyPE unsigned short SIZE1 1152 Ada info Info Ams SIZE2 1 152 PIXEL SIZE20 0870 FORMAT 100 B
38. is millimeters and the vertical scale is pixel value The total length of the displayed data in millimeters is shown in the upper right An estimate of the crystal lattice length based on distance between adjacent peaks is also shown Pressing the Left mouse button will display the X and Y coordinates Pressing and dragging the Middle mouse button will adjust the vertical scale of the plot Total length of data millimeters HE 16000 Length 14 6 mm 12000 Lattice 117 9 A 8000 4000 0 jg 000 6000 3000 12000 This spot spacing corresponds to this reciprocal lattice spacing Magnifying a region of an image and then plotting a cross section through it Oe 1 995 5 Adxv C3_1_00001 img Bll Adxv Magni p a al E Adxv Line Bll UM Lattice 128 2 A 12000 16000 8000 4000 36 0 0 3000 6000 3000 12000 Overloaded pixels are drawn in Yellow Notice the cross section has a flat top S r Adxv home arvai test images C3 100001 img la 4 D sumal AM a Length 4 2 mm Adxv Line inim 40000 20000 2200 The Line Window may also display a histogram of the data in the Image or Magnify Windows This is selected from the View gt Histogram pulldown menu in the Control Window The histogram of either the Magnify Window View gt Histogram gt Magnify or the entire
39. it unsigned short socket port_number Adxv will listen for a socket connection on port number 8100 The port number may be set with the ADXV DISPLAY PORT environment variable spindle orient H V Spindle Orientation for DPS spindle rot clock anti Spindle Rotation for DPS Number of Slabs Files to step when loading the next image swab Swap the two 8 bit halves of each 16 bit word swap swapbytes EO ET veiw soneto mo behaves ofeach word cw meten 000 aa oweTrtfefemersibesrhumenr ERN 2 Theta angle in degrees Default is read from the image header m a be set in Properties Window Visual Class or ID to use See xdpyinfo 1 or glxinfo 1 wavelength X X Ray wavelength in angstroms Default is read from the image header Environment Variables ADXV_DISPLAY_PORT ADXV_PATTERN ADXV SHOW PIXELS DISPLAY MARHOME NO ADXV BEAM CENTER XFORMSTATUSFILE OMP_NUM_THREADS Port to listen for a socket connection Default is 8100 Also set with socket command line argument Pattern to list new images in the Load Window Default is img Pixel overload value Pixels larger than this are drawn in yellow Default is 65000 but may be changed in the Property Window Set the default host and display number If SMARHOME fonts exists then this will be prepended to the X Font Path See nofp Do not read or write the adxv beam center file File which specifies images to automatically load see t
40. l Window is not visible simultaneously pressing the lt SHIFT gt key and the right mouse button in either the Image or Magnify Window will raise the Control Window to the top Examples Display an image and overlay spots from a adx file adxv Thau2 1 031 img Spots adx Draw resolution rings at 4 specific resolutions adxv rings 8 3 5 2 1 5 trypsin 2 001 img Display 1152x1152 binary unsigned short data skip 2048 byte header and swap bytes adxv ushort nx 1152 ny 1152 skip 2048 swap test 001 raw Display an image and denzo predictions adxv nnos6 1 001 img nnos6 1 001 x Specify an exact visual id and use OpenGL for the 3 D display adxv visual 0x26 gl Read an HDF5 file and specify which dataset to display adxv hdf5dataset entry 1 image 1 data cxidb 3 cxi Convert an image from CBF to IMG adxv smv32bits sa G8 1 00001 cbf G8 1 00001 img Automatically save an image as a 1 10 scale jpeg file adxv sa jpeg scale 0 1 nnos6 001 img nnos6 001 jpeg Crop a 100x100 pixel region where the upper left corner is at x 200 y 300 from an hdf5 file and save it as a 32 bit img file adxv smv32bits sa sa crop 100x100 200 300 dark h5 dark img Display CSPAD data and use a CrystFEL detector geometry file to correct the image adxv pixelmap cspad geom CxiDs1 image h5 Display CSPAD data and use a Cheetah pixelmap file to correct the image adxv pixelsize 0 110 pixelmap pixelmap h5 CxiDs1 image h5 Use a larger font for the reso
41. le ao ve combine slabs sum G4 2 offoos hs Load 548 00006 h5 ue average Rad be 4 2 00007 h5 specified in the Slab Slabs Properties Window G4 2 00012 h5 G4 2 00013 h5 i i TAV G4_2_00014 h5 44 lt q M G4 2 O0015 h5 G4 2 00016 h3 G4 2 O0017 h5 Slabs Stride Ei G4_2_00018 h5 G4 2 00019 h5 G4 2 O0020 h5 G4 2 O0021 h5 Cl se E M TM If this checkbox is checked then the forward and backward arrows will display the next slab of data not the next file For example if you are displaying slab 1 the stride is 3 and you click the forward arrow button then slab 4 will be displayed If there are no more slabs then the next file will be displayed Here a file G4_2_00001 h5 is loaded which contains a total of 5 slabs The first slab to display is 2 and the number of slabs to combine is 3 E Directory data jatlab arvai Oo2014 G4 01 h5E List gt 0000 h5 _2_09f701 h5 AS File h5 G4_2_00901 hS Load Slab Slabs zd G4_2_00901 h5 Z 3 AI V 5270100155 Gd 2 01101 h5 G4 2 01201 h5 Gd 2 01301 h5 d 5 G4 2 01401 h5 G4 2 01501 h5 G4 2 01601 h5 Slabs Stride fr G4 2 01701 h5 G4 2 01801 h5 G4 2 01901 h5 G4 2 02001 h5 Close Il A The Save Window This window is accessed by clicking File gt Save in the Control Window Data from the Image Magnify and Line windows may be saved to a file in various formats The Line
42. lution rings This will help if you have a large image scale to 10096 and then save as jpg or tiff Here s a short script to make a movie from a series of images bin csh foreachi lyso img adxv sa Si tmp Si r jpg end ffmpeg r 25 i tmp lyso 9603d jpg vb 20M lyso mpg The Control Window 4 Histogram F Image Image Header TFETI gnify The top row contains a menu bar Load Selecting one of these menu buttons will display a pull down menu The items in these pull down menus will be discussed later Statistics Settings Properties Background Exit File View Edit Help Scale 325 _ 50 _ 100 Auto Adjusts the scale of the image in the Image Display Window When the scale is 100 every pixel is displayed so that 1 pixel in the image is 1 pixel on the screen When the scale is 25 every 4th pixel in the image is displayed on the screen For example if the image is 3072x3072 pixels and the scale is 2596 then the image displayed on the screen will be 768x768 pixels When Auto is selected the image is scaled so it fits inside the Image Window The scale is calculated as the width of the image divided by the width of the Image Window For example if the Image Window is 600 pixels wide and the image is 3072 pixels wide the scale will be 600 3072 0 195 _ Values 4 8 NE 232 984 2 Loading C3_
43. missing fonts from these packages xorg x11 fonts 75dpi noarch xorg x11 fonts IS08859 1 75dpi noarch You can also download all the fonts Adxv needs from http www scripps edu arvai adxv fonts tar gz Put this file in a directory i e usr share adxvfonts and type gunzip stdout fonts tar gz tar xvf Then run Adxv with the font path option adxv fp usr share adxvfonts What if download Adxv and get adxv Permission denied chmod x adxv What if the Image Window doesn t refresh correctly under NX This is a bug in NX and should be fixed in newer versions of the NX server Try typing Ctrl Alt E to toggle lazy encoding Depending on the version of NX try adding one of the following options on the machine which is running the nxserver usr NX etc node cfg AgentExtraOptions defer 0 etc nxserver node conf AGENT EXTRA OPTIONS X defer 0 Other things to try adxv nopixmap adxv nopixmap nobs Complain to nomachine https www nomachine com report issues As a last resort contact me arvai scripps edu Is there a version of Adxv which runs under Windows If you install cygwin http Ly ygwin http CVg and the x server packages D X cygwin ETT TETTE Cygwin x Iren utut L then the cygwin version of Adxv s d WO dxv was compiled under Windows is will also run under Windows 7 buto nly if you install the 32 bit version of cygwin Thanks to Dr Ilya Prantsuzov for this f
44. op color in the colormap and pixel values smaller than the value below the slider are drawn as white or the bottom color in the colormap There are radio buttons to adjust the image scale and colormap The default Scale is Auto and this will scale the image so it fits inside the Image Window If 100 is selected then each pixel in the image will be drawn as 1 pixel on the screen If 50 is selected then every other pixel in the image will be drawn There are 3 choices for colormap Gray Heat and Rainbow Each of these may be inverted For example if the Gray color map is inverted then large pixels are White and small pixels are Black The magnification factor used to display data in the Magnify Window may be adjusted from 1 to 128 If this is set to 8 then each pixel in the image will be drawn as an 8x8 pixel in the Magnify Window The data in the Magnify Window may be displayed as Values Pixels or 3 D If Values is selected then only numbers will be displayed If Pixels is selected then a magnified view of the pixels is displayed If 3 D is selected the data is displayed as a three dimensional wire mesh Other Adxv windows can be accessed from the Control Window Clicking with the Left mouse button on the menu bar at the top of the Control Window will display a menu with choices of Windows to display Each of these windows as well as the Control Window and Image Window will be shown and explained in more detail later If the Contro
45. sets are like files By default Adxv will try to open the following Datasets in an hdf5 file data data data intensities real entry data entry data data entry 1 data 1 data entry 1 image 1 data entry 1 instrument 1 detector 1 data entry instrument detector data If none of these are found the Info Window is raised and you can examine the file header to find the dataset name You can either double click on the dataset or next time you can start Adxv with Adxv Info lt rad10 gt adxv hdf5dataset datasetname In the Info Window to the right the fentry data x 2463 values fentry data y 2527 values dataset name is entry data data Pentre io nb ERR UR entry end time 2013 02 08T12 03 13 589 entry instrument An hdf5 file may contain multiple fentry instrument attenuator fentry instrument attenuator attenuator_ transmissi datasets each of which will be fall hd EL LULA ods entry instrument detector beam center x 0 2124 highlighted in a bold font in the Info entry instrument detector beam center y 0 2200 Window fentry instrument detector count time 0 1975 0 1 fentry instrument detector dead time 1 991e 07 fentry instrument detector depends on entry ins pan pen PILATUS BN For more information about hdf5 files see page 29 Load Window and page 41 Info Window Starting Adxv The usage to start Adxv from the command line is adxv options file pred
46. vai 052014 CZ Pattern uf HKL2000 imd List OVERWRITTEN FILES C3 1 00001 imq C3 1 00002 imq File C3 1 00003 imq S if th C3 1 00004 imq pecily every nt C3_1_00008 imd Load C3 1 00005 imq i C3_1_00006 imq file to load For gotten example if the Stride is 10 then C3 1 00010 ima ux e AMG every 10 th file will C3_1_00012 imq be loaded If the E371 700014 Ime 44 4 bb c3 1 00014 ima Stride is 1 then LJ 1 090 12 1mq C3 1 00016 imq every file will be stride 5 amp 3 1 00017 ima CM 00018 ima loaded C3 N90019 ima C3 1 Q022 im Close 3 i Movie mode Continually load and display the next file Press again to stop In this case the Stride is 5 so every 5 th file 8 13 18 etc will be continually loaded and displayed If files are displayed too quickly a pause can be added between them with the delay command line option With three dimensional hdf5 data the Load Window will automatically show two additional text fields and a checkbox These are used to select which slab s to display Specify the first slab to display Each slab is a 2 d array of data If the data is 100x2527x2463 pixels then there are 100 slabs of data where each slab is 2527x2463 pixels Adxv Load Directory Number of slabs to data jatlab aryai 023014 G4 combine and display If Slabs is 5 then 5 Pattern XDS slabs are summed and List Se mt displayed How to Fi
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