Calibration tool: pyFAI-recalibΒΆ

pyFAI-recalib is now obsolete. All feature provided by it are now available as part of pyFAI-calib.

$ pyFAI-recalib --help
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: Ni, CrOx, NaCl,
Si_SRM640e, Si_SRM640d, Si_SRM640a, Si_SRM640c, alpha_Al2O3, Cr2O3, TiO2,
Si_SRM640, CuO, PBBA, Si_SRM640b, mock, quartz, C14H30O, cristobaltite, Si,
LaB6, CeO2, LaB6_SRM660a, LaB6_SRM660b, LaB6_SRM660c, AgBh, 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 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 Debye-
Sherrer 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 --no-
interactive 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.

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