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.