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].

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.