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/kif/pyFAI/tree/master/calibration or search in the American Mineralogist database: [AMD] or in the [COD]. The –calibrant option is mandatory !
Calibrants available: Ni, CrOx, NaCl, Si_SRM640e, Si_SRM640d, Si_SRM640a, Si_SRM640b, Cr2O3, AgBh, Si_SRM640, CuO, PBBA, alpha_Al2O3, SI_SRM640c, quartz, C14H30O, cristobaltite, Si, LaB6, CeO2, LaB6_SRM660a, LaB6_SRM660b, LaB6_SRM660c, TiO2, ZnO, Al, Au
- it name or
- it’s pixel size or
- the spline file describing its distortion or
- the NeXus file describing the distortion
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)
pyFAI-calib [options] -w 1 -D detector -c calibrant imagefile.edf
-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=12.398419292keV.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
PONI-files are ASCII files and each new refinement adds an entry in the file. So if you are unhappy with the last step, just edit this file and remove the last entry (time-stamps will help you).
$ pyFAI-calib --help
usage: pyFAI-calib [options] -w 1 -D detector -c calibrant.D imagefile.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: Ni, CrOx, NaCl, Si_SRM640e,
Si_SRM640d, Si_SRM640a, Si_SRM640c, alpha_Al2O3, Cr2O3, AgBh, Si_SRM640, CuO,
PBBA, Si_SRM640b, mock, quartz, C14H30O, cristobaltite, Si, LaB6, CeO2,
LaB6_SRM660a, LaB6_SRM660b, LaB6_SRM660c, TiO2, ZnO, Al, Au or search in the
American Mineralogist database: http://rruff.geo.arizona.edu/AMS/amcsd.php The
--calibrant option is mandatory !
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
-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=12.398419292keV.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
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)
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.
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 test-suite of pyFAI. To download them from internet, run
python setup.py build test
Downloaded test images are located in tests/testimages