ADXV(LOCAL) ADXV(LOCAL) NAME adxv - display area detector images under the X Window System SYNOPSIS adxv [options] [filename [predictions] ] DESCRIPTION The adxv program graphically displays and enhances selected regions of a two dimensional data file. The following file formats are supported: Format Extension ADSC / SMV .img Mar image plate .image Mar345 image plate .marxxxx Mar ccd .mccd Raxis2 / Raxis4 .raxis Fuji image plate .fuji CBF .cbf Adxv prediction .adx Denzo prediction .x File formats are typically identified by the file name extension or informa- tion in the file header. In the case of Fuji image plate images the -fuji or -fuji10bit command line option is required. If Mar ccd image files do not have the extension .mccd then the -marccd command line option is required. Files stored as raw binary unsigned char, unsigned short, signed short or signed integer values may also be read (see options -nx, -ny, -uchar, -ushort, -short and -int). Files which have been compressed with bzip2(1), compress(1) or gzip(1) may be read without uncompressing them. Displayed data may be saved in a variety of formats including ascii, binary SMV, TIFF and Postscript. The current version of adxv is 1.9.5. OPTIONS -autoload Automatically load images listed in the file $XFORMSTATUSFILE. This file should contain one line with two values, an integer number and a 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 I/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. -border Draw a 1 pixel border around the image. Default is -noborder. -colormap Create a new colormap instead of using the default one. -colors Gray|Heat|Rainbow Defines the initial colormap colors. Default is Gray. -debug Print debugging information. -distance x Specify the crystal to detector distance in mm. Default is read from the image header. -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. -fix_contrast Do not automatically re-adjust the contrast as each new image is read in. This may also be set in the Settings Window. -flip H | V Flip the image about a Horizontal or Vertical axis. -fuji Input is a Fuji image plate image. -fuji10bit Input is a Fuji 10bit image plate image. -gl -use_gl If available, use OpenGL to render 3-d graphics in the Magnify Window. -gl_lines 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 rep- resentation. -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. -ifont fontname Text font to use in the Image Window. -int -raw Input is raw binary signed integers (4 bytes/pixel). -invert_colors Invert the colormap colors. -itext Draw the text in the Image Window within a white rectangle. Default is to individually outline each character. -level1 Output level1 postscript files. Default is level2. -marccd Input is a Mar ccd image. -mosflm Mimic the Mosflm coordinate system. Shortcut for: -rotate 90 -flip V -scan_origin_px LR -scan_origin_mm LR -ncolors N Use N colors for the colormap. Default is 64. If N=0, use the maximum possible. -newpixmap Create a new pixmap when a new image is read. The default is to only create a new pixmap if the new image is a different size. -noborder Do not draw a 1 pixel border around the image (default). -nofp Do not attempt to pre-pend $MARHOME/fonts to the X font path. -no_adxv_beam_center If there is a file called .adxv_beam_center in the image directory, this file will be read to determine the beam center. If this file does not exist, it will be created by adxv. This option causes adxv to nei- ther read nor create the .adxv_beam_center file. -nopixmap Use a Window instead of a Pixmap in the Image Window. -norotate Do not rotate mar .image files 90 degrees before displaying. -nosmooth When the image scale factor is less than one, do not smooth the dis- played 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. -nozi Use memory buffering only if the scale factor is 0.5 or less and there is a readonly visual. With -nozi less memory is used, but redraws are slower. -nx N Number of pixels in the horizontal direction (required for raw binary data). -ny N Number of pixels in the vertical direction (required for raw binary data). -oldcontrast Use older automatic contrast adjustment. -overload N Pixel overload value. Default is 65000. Pixels larger than this are drawn as yellow. This may also be set in the Properties Window. -pixelsize p The pixel size in mm. Default is read from the image header. -ps Display the Prediction Window at startup. -rfont fontname Font to use for resolution rings. -rotate 90 | 180 | 270 Rotate the image before displaying it. -sa Standalone mode. This reads an image file, automatically writes a tiff file and then exits. It requires an input image file and output tiff file as the last two arguments, respectively. The tiff file must end in .tif or .tiff. -scan_origin_mm UL | UR | LL | LR The scan origin for mm coordinates displayed in the Image Window. Default is LL (Lower Left). See also -fast_scan_mm. -scan_origin_px UL | UR | LL | LR The scan origin for pixel coordinates displayed in the Image Window. Default is UL (Upper Left). See also -fast_scan_px. -short -sshort Input is raw binary signed shorts (2 bytes/pixel). -skip N Skip N bytes before reading raw binary data. May be used to skip a file header. -small_cursor Use a smaller crosshair cursor. -socket Adxv will listen for a socket connection on port number 8100. The port number may be set with the ADXV_DISPLAY_PORT environment variable. -swab -swap -swapbytes Swap the two 8-bit halves of a 16-bit word -swap_beam_center Swap x and y position of the beam center -swaw Swap the two 16-bit halves of a 32-bit word -twotheta theta 2-Theta angle in degrees. Default is read from the image header. -uchar Input is raw binary unsigned chars (1 byte/pixel). -ushort Input is raw binary unsigned shorts (2 bytes/pixel). -verbose Verbose output. -visual visualclass | visualid Visual Class or ID to use. See xdpyinfo(1) or glxinfo(1). -wavelength w X-Ray wavelength in angstroms. Default is read from the image header. USAGE The program may be started with an optional file name, which will be read and displayed: 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 mm and pixels. The resolution (in A) and I/Sigma of the region under the cursor is also displayed. 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" 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 properties of the displayed image. In the upper left of this window is a graphical display of the current color map and just to the right of this is a vertical slider. Dragging the slider will adjust the contrast of the image. Pixel values larger than the numerical value above the slider are drawn as black (or the top 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, colormap, and Magnify Window display. The magnification factor used to display data in the Magnify Window may be adjusted as can the format of the displayed data. If Values is selected, then simply raw numbers will be displayed. If Pixels is selected, then a magnified view of the pixels in the Image Window is displayed. If 3-d is selected, the data is displayed as a three-dimensional wire mesh. If the -gl command line option was used, a wire mesh or polygonal surface will be drawn using OpenGL. If the Control Window is not visible, simultaneously pressing the key and the right mouse button in either the Image or Magnify Window will raise the Control Window to the top. In the Image Window, if the key is pressed while also pressing the left mouse button, 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 of a lattice or estimate how far to rotate a crys- tal to align a zone. The following keys may be typed while the cursor is in the Image Window: f Raise Load Window. The File Load Window is displayed. h Adjust histogram contrast in the Image Window. The contrast of the visible portion of the Image Window is auto- matically adjusted. l Toggle lighting on and off in the Magnify Window. When using OpenGL graphics, this will toggle turning lighting on and off. m Adjust histogram contrast in the Magnify Window. The contrast of the Magnify Window is automatically adjusted. P | p Toggle turning predictions on and off. When predictions are displayed, this will toggle displaying them or not displaying them. r Reset the display in the 3-d magnify window The position and orientation of the data in the 3-d magnify window is reset to its original state. s 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 tog- gle between drawing aliased and anti-aliased polygons. w Toggle between wire mesh and surface display in the Magnify Win- dow. When using OpenGL graphics, this will toggle between a wire mesh and surface display of the data. Arrow Keys Adjust the cursor position. Pressing the arrow keys (up, down, left, right) will move the cur- sor by one pixel. If the Plot Type is Circle (set under Edit->Properties), the arrow keys will translate the center of the circle by one pixel. ? Print help. This will print a summary of the keys which may be pressed. Spots may be overlaid on an image by reading a .adx format prediction file. The format of this file is very simple. The file name extension must be .adx and it simply contains pairs of values which specify the x and y position (in pixels) of a spot. EXAMPLES Display an ADSC .img file: adxv nnos6_1_001.img Display 1152x1152 binary unsigned short data, skip 2048 byte header and swap bytes: adxv -nx 1152 -ny 1152 -ushort -skip 2048 -swap Specify a PseudoColor visual: adxv -visual PseudoColor Specify an exact visual and use OpenGL for the 3-d display: adxv -visual 0x26 -gl To make nice figures, scale the image to 100%, show the resolution rings and save as tiff or postscript: adxv -ncolors 0 -rfont "-*-lucidatypewriter-bold-r-normal- sans-180-*-*-*-*-*-*-*" The -rfont option is needed when the image is scaled to 100% and saved as a tiff or postscript file since otherwise the text for the resolution rings will be small compared to the image size. Display an image file and overlay predictions from denzo: adxv ../nnos6_1_001.img x/nnos6_1_001.x Automatically save an image as a color tiff file and then exit: adxv -sa -colors Heat myo_4_001.img myo_4_001.tif ENVIRONMENT VARIABLES ADXV_DISPLAY_PORT Port to listen for a socket connection. Default is 8100. ADXV_PATTERN Pattern to list new images. Default is *.img. ADXV_SHOW_PIXELS Pixel overload value. Pixels larger than this are drawn in yellow. Default is 65000, but may be changed in the Property Window. DISPLAY Set the default host and display number. MARHOME If $MARHOME/fonts exists then this will be pre-pended to the X Font Path. See -nofp. XFORMSTATUSFILE File which specifies images to automatically load (see -autoload). DIAGNOSTICS Error messages are meant to be self-explanatory. AUTHOR Written by Andrew Arvai SEE ALSO mosflm(1L), xdpyinfo(1), glxinfo(1) 4th Berkeley Distribution 04/12/05 ADXV(LOCAL)