img2r commands

You may also visit the explanation of internal commands: aliases, flowcontrol etc.

List of commands

abort

Syntax: abort state
Default: abort off
If state=off, warnings are not fatal. If state=on a warning will abort the program.

badrespons

Syntax: badrespons n
Default: not used
Sets the bad respons threshold to n. Pixels from theb images with a value less than n will be ignored.

contour

Syntax: contour name
Creates:

debug

Syntax: debug state
Default: debug off
If state=on a lot more output will be given.

display

Syntax: display
If images have been read, prints the map on screen.

correct

Syntax: correct none/normal/full/debug
Default: correct normal
Allows command and option corrections. Commands and options are only corrected if input originates from the keyboard, and output is sent to the screen.

exit

Exit program.

ideal

Syntax: ideal state
Default: ideal off
If state=on and if the detector distance is known, the conversion of image pixels to millimeters will correct for detector oriention offsets. output will be given. The detector distance will be set by reading an image.

low

Syntax: low n
Default: low 0
Controls the use of low images. The contents of the low images will be subtracted from every image.

maxdim

Syntax: maxdim n
Default: maxdim 100
Sets the dimension of the reciprocal lattice to -n:n for all three directions. A scalefactor will be calculated to map reciprocal vectors c to the limits of the reciprocal map set by maxdim.
The number of pixels in the reciprocal lattice will become (2n+1)³. Note, the default value of 100 correspons to 8 million pixels. With every pixel 4 bytes this will lead to two 32 MB arrays and a cnt file of 32 MB. Setting maxdim to 400 leads to 2 GB arrays.

normalize

Syntax: normalize
While reading the images, the intensities are summed into virtual pixels in the reciprocal lattice. In the end, the accumulated intensities will be normalized, by dividing them by the number of contributing pixels. The command normalize will perform this normalization. Normally, this is not needed, as the normalization will be performed by the contour command, if neccessary. But you may want to do a manual normalize before inspecting intermediate results (with f.e. display)

outputlevel

Syntax: outputlevel none/normal/full/debug
Default: outputlevel normal
Controls the amount of output.

read

Syntax: read images
Reads and processes images. Wildcharacters as * and ? are allowed, as are constructions using [], like s0[135]f* or s0[1-5]f*.

status

Syntax: status images
Prints the values of various parameters

thmax

Syntax: thmax f
Default: thmax 27.5
Sets the maximum resolution (in theta) of the reciprocal map to f, in degrees. A scalefactor will be calculated to map reciprocal vectors c to the limits of the reciprocal map set by maxdim.

trace

Syntax: trace state
Default: trace off
If state=on img2r will print a trace of all the routines while processing images.
img2r overview
from images to density map
EVPY Suite Overview