--- name: "pyFAI-calib2" section: "1" platform: "linux" package: "pyfai" version: "0.20.0+dfsg1-3" release: "Debian 11 (Bullseye)" platforms: ["linux"] url: "https://new.carta.tech/pyFAI-calib2" --- # pyFAI-calib2(1) GUI tool for determining the geometry of a detector using a reference sample. ## NAME calibration - GUI tool for determining the geometry of a detector using a reference sample. ## DESCRIPTION usage: pyFAI-calib2 \[options\] input\_image.edf 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: AgBh, Al, Au, C14H30O, CeO2, Cr2O3, CrOx, CuO, LaB6, LaB6\_SRM660a, LaB6\_SRM660b, LaB6\_SRM660c, NaCl, Ni, PBBA, Pt, Si, Si\_SRM640, Si\_SRM640a, Si\_SRM640b, Si\_SRM640c, Si\_SRM640d, Si\_SRM640e, TiO2, ZnO, alpha\_Al2O3, cristobaltite, mock, quartz or search in the American Mineralogist database: http://rruff.geo.arizona.edu/AMS/amcsd.php ### 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 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)