Calibration tool: pyFAI-calib2

Calibration - GUI tool for determining the geometry of a detector using a reference sample.

Please have a look at the Calibration of a diffraction setup using the Graphical User Interface (GUI) for a 5 minutes introduction.

Purpose

Calibrate the diffraction setup geometry based on Debye-Sherrer rings images without a priori knowledge of your setup. You will need to provide a calibrant or a “d-spacing” file containing the spacing of Miller plans in Angstrom (in decreasing order).

Calibrants available: Ni, CrOx, NaCl, Si_SRM640e, Si_SRM640d, Si_SRM640a, Si_SRM640c, alpha_Al2O3, Cr2O3, AgBh, Si_SRM640, CuO, PBBA, Si_SRM640b, quartz, C14H30O, cristobaltite, Si, LaB6, CeO2, LaB6_SRM660a, LaB6_SRM660b, LaB6_SRM660c, TiO2, ZnO, Al, Au or search in the American Mineralogist database.

Usage:

pyFAI-calib2 [options] [input_image.edf]

Everything can be set by the GUI, but here are the command-line arguments.

Options:

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
-o FILE, --out FILE
	Filename where processed image is saved
-v, --verbose	switch to debug/verbose mode
--debug	Set logging system in debug mode
--opengl, --gl	Enable OpenGL rendering (else matplotlib is used)
-c FILE, --calibrant FILE
	Calibrant name or file containing d-spacing of the reference sample (case sensitive)
-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=12.398419739640717keV.A).
-P POLARIZATION_FACTOR, --polarization POLARIZATION_FACTOR
	polarization factor, from -1 (vertical) to +1 (horizontal), default is None (no correction), synchrotrons are around 0.95
-D DETECTOR_NAME, --detector DETECTOR_NAME
	Detector name (instead of pixel size+spline)
-m MASK, --mask MASK
	file containing the mask (for image reconstruction)
-p PIXEL, --pixel PIXEL
	size of the pixel in micron
-s SPLINE, --spline SPLINE
	spline file describing the detector distortion
-n NPT, --pt NPT
	file with datapoints saved. Example: basename.npt
-i FILE, --poni FILE
	file containing the diffraction parameter (poni-file) [not used].
-b BACKGROUND, --background BACKGROUND
	Automatic background subtraction if no value are provided [not used]
-d DARK, --dark DARK
	list of comma separated dark images to average and subtract [not used]
-f FLAT, --flat FLAT
	list of comma separated flat images to average and divide [not used]
--filter FILTER
	select the filter, either mean(default), max or median [not used]
-l DIST_MM, --distance DIST_MM
	sample-detector distance in millimeter. Default: 100mm
--dist DIST	sample-detector distance in meter. Default: 0.1m
--poni1 PONI1	poni1 coordinate in meter. Default: center of detector
--poni2 PONI2	poni2 coordinate in meter. Default: center of detector
--rot1 ROT1	rot1 in radians. default: 0
--rot2 ROT2	rot2 in radians. default: 0
--rot3 ROT3	rot3 in radians. default: 0
--fix-wavelength
	fix the wavelength parameter. Default: Activated
--free-wavelength
	free the wavelength parameter. Default: Deactivated
--fix-dist	fix the distance parameter
--free-dist	free the distance parameter. Default: Activated
--fix-poni1	fix the poni1 parameter
--free-poni1	free the poni1 parameter. Default: Activated
--fix-poni2	fix the poni2 parameter
--free-poni2	free the poni2 parameter. Default: Activated
--fix-rot1	fix the rot1 parameter
--free-rot1	free the rot1 parameter. Default: Activated
--fix-rot2	fix the rot2 parameter
--free-rot2	free the rot2 parameter. Default: Activated
--fix-rot3	fix the rot3 parameter
--free-rot3	free the rot3 parameter. Default: Activated
--npt NPT_1D	Number of point in 1D integrated pattern, Default: 1024
--npt-azim NPT_2D_AZIM
	Number of azimuthal sectors in 2D integrated images. Default: 360
--npt-rad NPT_2D_RAD
	Number of radial bins in 2D integrated images. Default: 400
--qtargs QTARGS
	Arguments propagated to Qt
--tilt	Allow initially detector tilt to be refined (rot1, rot2, rot3). Default: Activated
--no-tilt	Deactivated tilt refinement and set all rotation to 0
--saturation SATURATION
	consider all pixel>max*(1-saturation) as saturated and reconstruct them, default: 0 (deactivated)
--weighted	weight fit by intensity, by default not.
--unit UNIT	Valid units for radial range: 2th_deg, 2th_rad, q_nm^-1, q_A^-1, r_mm. Default: 2th_deg
--no-gui	force the program to run without a Graphical interface
--no-interactive
	force the program to run and exit without prompting for refinements
-r, --reconstruct
	Reconstruct image where data are masked or <0 (for Pilatus detectors or detectors with modules)
-g GAUSSIAN, --gaussian GAUSSIAN
	Size of the gaussian kernel. Size of the gap (in pixels) between two consecutive rings, by default 100 Increase the value if the arc is not complete; decrease the value if arcs are mixed together.
--square	Use square kernel shape for neighbor search instead of diamond shape

Tips & Tricks

The output of this program is a “PONI” file containing the detector description and the 6 refined parameters (distance, center, rotation) and wavelength. An 1D and 2D diffraction patterns can also produced. (.dat and .azim files)