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

Usage:

pyFAI-calib2 [options] [input_image.edf]

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=12.398419843320026keV.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 are also produced. (.dat and .azim files)