xds Command-line Options

xds [-z <zoomfactor>] [-r <aspectratio>] [-hqMPRI] 
        [-A <activationfile> ] 
        [-E <activationfile> ] 
        [-v <overlayfile>] [-m <colormapfile>] [-l <logfile>]
        [-L <black_dataval>] [-H <white_dataval>] [-C <cycle_length>]
        [-s <startimagenum>] [-# <numimages>] [-e <endimagenum>]
        <imagefile.ext> [[-s <n>] [-e <n>] [-# <n>] <file2.ext2>] ...

  [-b] bilinear interpolation mode.
  [-u] Turn on background loading. Load/Unload X Server memory.
  [-z <n>] Increase image size by a factor of <n> in linear dimensions.
  [-r <float>] Make the pixels <float> times larger in the vertical direction.
  [-h] Print help information. (Same as 'h' key).
  [-q] Toggle quiet mode (don't print statistics). (Same as 'Q' key).
  -[M]|[P]|[R]|[I] Define data as complex and select mag, phase, real, 
       or imaginary. (Same as '1 D', '2 D', '3 D', and '4 D' respectively.)
  [-E <file>] Filename for overlay color image, 0-100 linear scale.
  [-A <file>] Filename for statistical image (KS_grinder or T_grinder output)
  [-v <file>] Filename for overlay data (ascii x,y pairs) or seg .otl file.
  [-m <file>] Filename to load 256 ascii triples as 0-65535 rgb color map.
  [-c <file>] Load colors as for -m <file>, but with windowable grays.
              Data file then must vary only [0..255], interpreted as colors.
  [-l <file>] Filename to save log data into (output of 's' command).
  [-f <file>] Filename for Plot Commands in Image window (see sample plotter file).
  [-g <file>] Filename for Plot Commands in Graph window (see sample plotter file).
  [-B <thickness>] Big graph lines and cursor for visual impact.
  [-W] Auto window and level each window individually (for disparate images).
  [-L <float>],[-H <float>] User-defined data limits to force image contrast.
              Data outside this range will be displayed as black or white.
  [-C <n>] Treat loaded data as cycles of length <n> plotted in graph window.
  [-s <n>] Start loading at image <n>, where n starts at 0.
  [-# <n>]|[-e <n>] Load the following file for <n> images or at image <n>.
  <imagefile.ext> Image stack filenames, named with appropriate extension;
  Input files must be acceptable to read_image(), or ANMR .im files.
  N.B.  The -s, -e, -# parameters apply only to SUBSEQUENT files, and until
        replaced. e.g. xds -s 0 -# 10 f1.bshort -s1 -#10 f2.bshort
        reads 20 images, but the second -#10 is redundant.

xds Interactive Commands

MOUSE ACTIONS

Button 1: Draw rectangle in selected Overlay (for ROI choice).
Button 2: Grayscale window (move horizontal), Center level (move vertical).
Button 3: Animate sequence. Move horizontal to change speed.
Button 1 in Graph Window: Move to image corresponding to this time point.
Button 1 double click in Graph Window: Increment the cycle focus (use with -c)

KEYBOARD ACTIONS:

[<n> signifies a typed integer; default is 0]
N: Toggle `No Deviations, Local Scale' mode: graph always utilizes full range.
M: toggle dynamic color lookup table mode.
spacebar: Toggle showing of overlay vs. masking out area outside ROI.
<n> RETURN: go to image number <n>.
<n> D: Choose display type <n>, where 0=scalars, 1=mag, 2=phase, 3=re, 4=im.
<n> R: Choose reference type <n> with current image as reference point, where <n> = 0 for NONE, 1:SUBTRACTION, 2:RATIO, 3: -LOG(RATIO).
f: Write out current image as a .flt file, with filename <imagefile>_<n>.flt
a: toggle animation as if holding down mouse button 3.
u: Toggle background loading/unloading of server data, to conserve memory.
+ or =: Increment image number and display; also <n> + to inc by <n>.
-: Decrement image number and display; also <n> - to inc by <n>.
r: Reload and bin the image stack with current window & level, choosing optimal pixel bins for viewing data within the current window & level.
P: Reload image stack, resetting to the pristine window/level state.
w: Auto window and level stack to the currently-active overlay region.
W: Auto window and level the current image separately, not the stack.
n: Toggle image number display.
g: Create or toggle activity of time-course graph display.
h: Print help summary (this page).
Q: Toggle quiet mode.
B: Cycle through Big Lines modes for increased visibility of graphs.
q: Quit (after typing 'y' to verify).

STATISTICS OPERATIONS: (after reading in a -A stats overlay)

A: Toggle showing activation overlay
<n> ^L: (control-L) Set low activation threshold (default 4.6, or p=0.01)
<n> ^H: (control-H) Set high activation threshold (default 20)
<n> ^A: (control-A) Change p-value for show-through w/o changing colormap.
^T: (control-T) Cycle through viewing (both, + only, - only, abs(A)) activations.

OVERLAY OPERATIONS: (Button 1 to draw rectangles)

o: Load command-line -o file data into the working overlay set.
O: Rewrite (save) current overlay set data as the -o file in ascii int pairs.
<n> z: Set working overlay to overlay <n> (a single overlay, <n> is 0-3).
<n> Z: Toggle overlay <n> in/out of working set (multiple active overlays).
x: Set pixel at pointer into the overlay.
X: Toggle pixel at pointer into or out of the overlay.
c: Clear pixel at pointer out of the overlay.
C: Clear the current overlay completely. (w and W above also work on ROI if selected.)
d<n>: Mark a square region n by n pixels in size.
HJKL: Move the overlays left,right,up,down.
s: Report statistics (mean and stdev) for overlayed area for image stack; show mean and stdev on graph as well.
S: Prints overlay stats for current image to stdout if not in Quiet mode.