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)