img2r commands
You may also visit the explanation of
internal commands: aliases, flowcontrol etc.
Syntax: abort state
Default: abort off
If state=off,
warnings are not fatal.
If state=on a warning
will abort the program.
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.
Syntax: contour name
Creates:
Syntax: debug state
Default: debug off
If state=on a lot more
output will be given.
Syntax: display
If images have been read, prints the map on screen.
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.
- none
No correction will be applied
- normal
Commands and options will be corrected.
- full
As before plus possible corrections are printed
- debug
As before plus all available commands/options are printed
Exit program.
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.
Syntax: low n
Default: low 0
Controls the use of low images. The contents of the low images
will be subtracted from every image.
- low 0
No low image
- low 1
Low images will be read while images are being processed.
Each scan a separate low image. These images can be created by
low3.
The low data will be subtracted from every image.
- low 2 cntfile
Read cntfile containing low data. Such an image
can be created by imagesum.
The low data will be subtracted from every image.
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.
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)
Syntax: outputlevel none/normal/full/debug
Default: outputlevel normal
Controls the amount of output.
- none
- normal
- full
- print image header
- print goniometer and detector information for first images of a scan
icr plots
- debug
- Print cvectors
- Print conversion from mm to cvectors
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*.
Syntax: status images
Prints the values of various parameters
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.
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