pyFAI-recalib - Online in the Cloud

PROGRAM:

NAME

pyFAI-recalib - Deprecated

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: 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 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 functionnality 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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