Calibration tool: pyFAI-recalib¶
pyFAI-recalib is now obsolete. All feature provided by it are now available as part of pyFAI-calib.
calibration - DEPRECATED tool for refining the geometry of a detector using a reference sample and a previously known calibration file.
DESCRIPTION¶
usage: pyFAI-recalib [options] -i ponifile -w 1 -c calibrant.D imagefile.edf
Calibrate the diffraction setup geometry based on Debye-Sherrer rings images with a priori knowledge of your setup (an input PONI-file). 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: 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=12.398419843320026keV.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 MAX_RINGS, –ring MAX_RINGS
- maximum number of rings to extract. Default: all accessible
- -k, –keep
- Keep existing control point and append new
The main difference with pyFAI-calib is the way control-point hence DebyeSherrer rings are extracted. While pyFAI-calib relies on the contiguity of a region of peaks called massif; pyFAI-recalib knows approximatly the geometry and is able to select the region where the ring should be. From this region it selects automatically the various peaks; making pyFAI-recalib able to run without graphical interface and without human intervention (–no-gui and –nointeractive options). Note that `pyFAI-recalib` program is obsolete as the same functionality is available from within pyFAI-calib, using the `recalib` command in the refinement process. Two option are available for recalib: the numbe of rings to extract (similar to the -r option of this program) and a new option which lets you choose between the original `massif` algorithm and newer ones like `blob` and `watershed` detection.