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].
MX-Calibrate -w 1.54 -c CeO2 file1.cbf file2.cbf ...
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.
-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.
$ MX-calibrate --help