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.