Calibration tool: MX-calibrate¶
Purpose¶
Calibrate automatically a set of frames taken at various sample-detector distance.
This tool has been developed for ESRF MX-beamlines where an acceptable calibration is usually present is the header of the image. PyFAI reads it and does a “recalib” on each of them before exporting a linear regression of all parameters versus this distance.
Most standard calibrants are directly installed together with pyFAI. If you prefer using your own, you can provide a “d-spacing” file containing the spacing of Miller plans in Angstrom (in decreasing order). Most crystal powders used for calibration are available in the American Mineralogist database [AMD] or in the [COD].
Usage:¶
MX-Calibrate -w 1.54 -c CeO2 file1.cbf file2.cbf …
Options:¶
usage: MX-Calibrate -w 1.54 -c CeO2 file1.cbf file2.cbf …
Calibrate automatically a set of frames taken at various sample-detector distance. Return the linear regression of the fit in funtion of the sample- setector distance.
- positional arguments:
FILE List of files to calibrate
- optional arguments:
- -h, --help
show this help message and exit
- -V, --version
show program’s version number and exit
- -v, --verbose
switch to debug/verbose mode
- -c FILE, --calibrant FILE
file containing d-spacing of the calibrant reference sample (MANDATORY)
- -w WAVELENGTH, --wavelength WAVELENGTH
wavelength of the X-Ray beam in Angstrom
- -e ENERGY, --energy ENERGY
energy of the X-Ray beam in keV (hc=12.398419292keV.A)
- -P POLARIZATION_FACTOR, --polarization POLARIZATION_FACTOR
polarization factor, from -1 (vertical) to +1 (horizontal), default is 0, synchrotrons are around 0.95
- -b BACKGROUND, --background BACKGROUND
Automatic background subtraction if no value are provided
- -d DARK, --dark DARK
list of dark images to average and subtract
- -f FLAT, --flat FLAT
list of flat images to average and divide
- -s SPLINE, --spline SPLINE
spline file describing the detector distortion
- -p PIXEL, --pixel PIXEL
size of the pixel in micron
- -D DETECTOR_NAME, --detector DETECTOR_NAME
Detector name (instead of pixel size+spline)
- -m MASK, --mask MASK
file containing the mask (for image reconstruction)
- --filter FILTER
select the filter, either mean(default), max or median
- --saturation SATURATION
consider all pixel>max*(1-saturation) as saturated and reconstruct them
- -r MAX_RINGS, --ring MAX_RINGS
maximum number of rings to extract
- --weighted
weight fit by intensity
- -l DISTANCE, --distance DISTANCE
sample-detector distance in millimeter
- --tilt
Allow initially detector tilt to be refined (rot1, rot2, rot3). Default: Activated
- --no-tilt
Deactivated tilt refinement and set all rotation to 0
- --dist DIST
sample-detector distance in meter
- --poni1 PONI1
poni1 coordinate in meter
- --poni2 PONI2
poni2 coordinate in meter
- --rot1 ROT1
rot1 in radians
- --rot2 ROT2
rot2 in radians
- --rot3 ROT3
rot3 in radians
- --fix-dist
fix the distance parameter
- --free-dist
free the distance parameter
- --fix-poni1
fix the poni1 parameter
- --free-poni1
free the poni1 parameter
- --fix-poni2
fix the poni2 parameter
- --free-poni2
free the poni2 parameter
- --fix-rot1
fix the rot1 parameter
- --free-rot1
free the rot1 parameter
- --fix-rot2
fix the rot2 parameter
- --free-rot2
free the rot2 parameter
- --fix-rot3
fix the rot3 parameter
- --free-rot3
free the rot3 parameter
- --fix-wavelength
fix the wavelength parameter
- --free-wavelength
free the wavelength parameter
- --no-gui
force the program to run without a Graphical interface
- --gui
force the program to run with a Graphical interface
- --no-interactive
force the program to run and exit without prompting for refinements
- --interactive
force the program to prompt for refinements
- --peak-picker PEAKPICKER
Uses the ‘massif’, ‘blob’ or ‘watershed’ peak-picker algorithm (default: blob)
This tool has been developed for ESRF MX-beamlines where an acceptable calibration is usually present is the header of the image. PyFAI reads it and does a “recalib” on each of them before exporting a linear regression of all parameters versus this distance.