NAME

       pyFAI-calib - calibration tool

DESCRIPTION

       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,  Si_SRM640b,
       Cr2O3,  AgBh, Si_SRM640, CuO, PBBA, alpha_Al2O3, 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)