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calibration - manual page for calibration from pyFAI version 0.15.0: 30/01/2018


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: PBBA, Si_SRM640a, LaB6_SRM660a, Si_SRM640c, TiO2, CuO, AgBh, mock, Au, Si_SRM640b, Si_SRM640d, NaCl, Si_SRM640, CeO2, LaB6_SRM660b, Si_SRM640e, LaB6, Al, Ni, LaB6_SRM660c, CrOx, alpha_Al2O3, ZnO, Cr2O3, Si, quartz, C14H30O, cristobaltite or search in the American Mineralogist database: The --calibrant option is mandatory !

positional arguments:

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 !)
wavelength of the X-Ray beam in Angstrom. Mandatory
-e ENERGY, --energy ENERGY
energy of the X-Ray beam in keV (hc=12.398419739640717keV.A).
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!
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
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 the distance parameter
free the distance parameter. Default: Activated
fix the poni1 parameter
free the poni1 parameter. Default: Activated
fix the poni2 parameter
free the poni2 parameter. Default: Activated
fix the rot1 parameter
free the rot1 parameter. Default: Activated
fix the rot2 parameter
free the rot2 parameter. Default: Activated
fix the rot3 parameter
free the rot3 parameter. Default: Activated
fix the wavelength parameter. Default: Activated
free the wavelength parameter. Default: Deactivated
Allow initially detector tilt to be refined (rot1, rot2, rot3). Default: Activated
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)
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
force the program to run without a Graphical interface
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.
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)


The full documentation for calibration is maintained as a Texinfo manual. If the info and calibration programs are properly installed at your site, the command
info calibration

should give you access to the complete manual.

February 2018 calibration from pyFAI version 0.15.0: 30/01/2018