calibration - DEPRECATED tool for refining the geometry of a
detector using a reference sample and a previously known calibration
file.
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: AgBh, Al, Au, C14H30O, CeO2, Cr2O3, CrOx, CuO, LaB6,
LaB6_SRM660a, LaB6_SRM660b, LaB6_SRM660c, NaCl, Ni, PBBA, Si, Si_SRM640,
Si_SRM640a, Si_SRM640b, Si_SRM640c, Si_SRM640d, Si_SRM640e, TiO2, ZnO,
alpha_Al2O3, cristobaltite, mock, quartz or search in the American
Mineralogist database: http://rruff.geo.arizona.edu/AMS/amcsd.php The
--calibrant option is mandatory !
- FILE
- List of files to calibrate
- -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=12.398419739640717keV.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
- -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.