pyFAI-calib21

Gui tool for determining the geometry of a detector using a reference sample.

Overview

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)

Releases

2 releases since Debian 10 (Buster); the text changed 1 time.

--gl since Debian 11 (Bullseye); --opengl since Debian 11 (Bullseye).