crysm
Collection of scripts for CRED. PETS specific commands are prefixed by pets-, XDS specific commands by xds-
Usage:
console
$ crysm [OPTIONS] COMMAND [ARGS]...
Options:
--install-completion: Install completion for the current shell.--show-completion: Show completion for the current shell, to copy it or customize the installation.--help: Show this message and exit.
Commands:
pets-calibrate-angles: Calibrate the angle of each image based on...find-center-cross-correction: Find central cross intensity correction...pets-correct-center-cross: Correct central cross of a dataset given...pets-correct-center-cross-calibration: Correct the center cross of a single...pets-mark-dead-pixels: Open an interactive matplotlib window to...pets-create-beamstop: Create a beamstoppets-solve: Runs SHELXT on the given project using the...xds-calibrate: Print lines to add to XDS.INP to correct...compare-hkl: Compare the indexed reflections in...plot-hkl: Plot the distribution of indexed peaks in...plot-camel: Plot the rocking curve from a .cml-file
crysm pets-calibrate-angles
Calibrate the angle of each image based on the timestamps in their metadata. Generates
Example usage: crysm pets-calibrate-angles
Usage:
console
$ crysm pets-calibrate-angles [OPTIONS]
Options:
--range FLOAT: Estimaged percentage of total angle range really spanned [default: 100]--skip / --no-skip: Skip first frame after defocus [default: no-skip]--plot / --no-plot: Plot timestep histogram [default: no-plot]--help: Show this message and exit.
crysm find-center-cross-correction
Find central cross intensity correction factor from a flatfield image. Supported formats are .tiff or .mib
Example usage: crysm finc-center-cross-correction flatfield.mib
Usage:
console
$ crysm find-center-cross-correction [OPTIONS] FLATFIELD_IMAGES...
Arguments:
FLATFIELD_IMAGES...: Flatfield images to use for calibration [required]
Options:
--help: Show this message and exit.
crysm pets-correct-center-cross
Correct central cross of a dataset given the intensity correction factor and the number of pixels in the gap.
Example usage: crysm pets-correct-center-cross --additional-pixels 2
--correction-factor 2.196 --central-four-factor 4.051
Usage:
console
$ crysm pets-correct-center-cross [OPTIONS]
Options:
-a, --additional-pixels INTEGER: How many pixels should be added to thecenter to correct the geometry of the images. [required]-c, --correction-factor FLOAT: How much more intense a center cross pixel is than a regular pixel [required]-C, --central-four-factor FLOAT: How much more intense the four central pixels are than a regular pixel [required]--help: Show this message and exit.
crysm pets-correct-center-cross-calibration
Correct the center cross of a single image, used for correcting calibration images.
Example usage: crysm pets-correct-center-cross-calibration --additional-pixels 2
flatfield.mib flatfield_2px_corrected.tiff
Usage:
console
$ crysm pets-correct-center-cross-calibration [OPTIONS] INPUT OUTPUT
Arguments:
INPUT: Input image [required]OUTPUT: Output image [required]
Options:
--additional-pixels INTEGER: How many pixels should be added to thecenter to correct the geometry of the images. [required]--correction-factor FLOAT: How much more intense a center cross pixel is than a regular pixel--central-four-factor FLOAT: How much more intense the four central pixels are than a regular pixel--help: Show this message and exit.
crysm pets-mark-dead-pixels
Open an interactive matplotlib window to mark pixels as dead. Double click to mark a pixel as dead. Use "a" and "d" as arrow keys to rotate through the dataset.
Example usage: crysm pets-mark-dead-pixels
--correction-factor 2.196 --central-four-factor 4.051
Usage:
console
$ crysm pets-mark-dead-pixels [OPTIONS] IMAGE
Arguments:
IMAGE: Image to look at to find the dead pixels [required]
Options:
-d, --dead-pixels PATH: PETS generated file of initial dead pixels--help: Show this message and exit.
crysm pets-create-beamstop
Create a beamstop
Usage:
console
$ crysm pets-create-beamstop [OPTIONS] OUTPUT
Arguments:
OUTPUT: File to store beamstop in [required]
Options:
-w, --image-width INTEGER: Width of image in pixels, after eventual widening of the cross [required]-b, --beamstop-width INTEGER: Width of beamstop in pixels [required]-k, --beamstop-kind [cross|square]: Type of beamstop, either "cross" or "square" [default: cross]--help: Show this message and exit.
crysm pets-solve
Runs SHELXT on the given project using the generated .hkl and .ins files from newest integration. Adds elements to .ins file and runs with the Laue group found in .pts2 file Any arguments can be added after the .pts2 file and will be passed on to SHELXT, overriding the defaults set by crysm:
crysm pets-solve pets.pts2 -l4 -a"0.5"
Usage:
console
$ crysm pets-solve [OPTIONS] PETS_FILE
Arguments:
PETS_FILE: Pets .pts2 file to read the Laue class from [required]
Options:
-m, --composition TEXT: Composition of substance, e.g. SiO or Si2O4. Case sensitive. [required]--help: Show this message and exit.
crysm xds-calibrate
Print lines to add to XDS.INP to correct the rotation axis and detector distance
Usage:
console
$ crysm xds-calibrate [OPTIONS]
Options:
--pixel-size FLOAT: Calibrated pixel size, depends on camera length.Suggested values: 120cm -> 0.00947, 150cm -> 0.007929, 200cm -> 0.006167 [default: 0.007929]--rotation-axis FLOAT: Rotation axis in degrees. Default 231 degrees. [default: 231]--help: Show this message and exit.
crysm compare-hkl
Compare the indexed reflections in SMV/INTEGRATE.HKL and pets.hkl
Usage:
console
$ crysm compare-hkl [OPTIONS]
Options:
--help: Show this message and exit.
crysm plot-hkl
Plot the distribution of indexed peaks in a pets .hkl-file
Usage:
console
$ crysm plot-hkl [OPTIONS]
Options:
--filename PATH--help: Show this message and exit.
crysm plot-camel
Plot the rocking curve from a .cml-file
Usage:
console
$ crysm plot-camel [OPTIONS] FILENAME
Arguments:
FILENAME: The .cml file to plot [required]
Options:
--help: Show this message and exit.