Calibration tool: pyFAI-calib
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).
If you are using a standard calibrant, look at https://github.com/silx-kit/pyFAI/tree/master/calibration or search in the American Mineralogist database: [AMD] or in the [COD]. The –calibrant option is mandatory !
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: http://rruff.geo.arizona.edu/AMS/amcsd.php
- You will need in addition:
The radiation energy (in keV) or its wavelength (in A)
The description of the detector:
it name or
it’s pixel size or
the spline file describing its distortion or
the NeXus file describing the distortion
- Many option are available among those:
dark-current / flat field corrections
Masking of bad regions
reconstruction of missing region (module based detectors), see option -r
Polarization correction
Automatic desaturation (time consuming!)
Intensity weighted least-squares refinements
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)
Usage:
pyFAI-calib [options] -w 1 -D detector -c calibrant.D imagefile.edf
options:
- -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
- -c FILE, –calibrant FILE
Calibrant name or file containing d-spacing of the reference sample (MANDATORY, case sensitive !)
- -w WAVELENGTH, –wavelength WAVELENGTH
wavelength of the X-Ray beam in Angstrom. Mandatory
- -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
- -i FILE, –poni FILE
file containing the diffraction parameter (poni-file). MANDATORY for pyFAI-recalib!
- -b BACKGROUND, –background BACKGROUND
Automatic background subtraction if no value are provided
- -d DARK, –dark DARK
list of comma separated dark images to average and subtract
- -f FLAT, –flat FLAT
list of comma separated flat images to average and divide
- -s SPLINE, –spline SPLINE
spline file describing the detector distortion
- -D DETECTOR_NAME, –detector DETECTOR_NAME
Detector name (instead of pixel size+spline)
- -m MASK, –mask MASK
file containing the mask (for image reconstruction)
- -n NPT, –pt NPT
file with datapoints saved. Default: basename.npt
- –filter FILTER
select the filter, either mean(default), max or median
- -l DISTANCE, –distance DISTANCE
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-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
- –fix-wavelength
fix the wavelength parameter. Default: Activated
- –free-wavelength
free the wavelength parameter. Default: Deactivated
- –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.
- –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
- –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
- -p PIXEL, –pixel PIXEL
size of the pixel in micron
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)
Example of usage:
Pilatus 1M image of Silver Behenate taken at ESRF-BM26:
pyFAI-calib -D Pilatus1M -c AgBh -r -w 1.0 test/testimages/Pilatus1M.edf
We use the parameter -r to reconstruct the missing part between the modules of the Pilatus detector.
Half a FReLoN CCD image of Lantanide hexaboride taken at ESRF-ID11:
pyFAI-calib -s test/testimages/halfccd.spline -c LaB6 -w 0.3 test/testimages/halfccd.edf -g 250
This image is rather spotty. We need to blur a lot to get the continuity of the rings. This is achieved by the -g parameter. While the sample is well diffracting and well known, the wavelength has been guessed. One should refine the wavelength when the peaks extracted are correct
All those images are part of the benchmark suite of pyFAI. To download them from internet, run the benchmark:
pyFAI-benchmark
Downloaded test images are located in /tmp/pyFAI_testdata_${USER}