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)