Calibration tool: MX-calibrate
Purpose
MX-Calibrate - calibrate the distance of a detector from a set of powder diffraction patterns 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].
Nota: this tool is deprecated in favor of the jupyter notebook found in the documentation (with the same name).
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- detector distance.
Options:
- -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=12.398419843320026keV.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.