.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.48.5.
.TH CALIBRATION "1" "November 2021" "calibration from pyFAI version 0.20.0: 21/01/2021" "User Commands"
.SH NAME
calibration \- CLI tool for determining the geometry of a detector using a reference sample.
.SH DESCRIPTION
usage: pyFAI\-calib [options] \fB\-w\fR 1 \fB\-D\fR detector \fB\-c\fR calibrant.D imagefile.edf
.PP
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: AgBh, Al, Au, C14H30O, CeO2, Cr2O3,
CrOx, CuO, LaB6, LaB6_SRM660a, LaB6_SRM660b, LaB6_SRM660c, NaCl, Ni, PBBA, Pt,
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
\fB\-\-calibrant\fR option is mandatory !
.SS "positional arguments:"
.TP
FILE
List of files to calibrate
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-V\fR, \fB\-\-version\fR
show program's version number and exit
.TP
\fB\-o\fR FILE, \fB\-\-out\fR FILE
Filename where processed image is saved
.TP
\fB\-v\fR, \fB\-\-verbose\fR
switch to debug/verbose mode
.TP
\fB\-c\fR FILE, \fB\-\-calibrant\fR FILE
Calibrant name or file containing d\-spacing of the
reference sample (MANDATORY, case sensitive !)
.TP
\fB\-w\fR WAVELENGTH, \fB\-\-wavelength\fR WAVELENGTH
wavelength of the X\-Ray beam in Angstrom. Mandatory
.TP
\fB\-e\fR ENERGY, \fB\-\-energy\fR ENERGY
energy of the X\-Ray beam in keV
(hc=12.398419843320026keV.A).
.TP
\fB\-P\fR POLARIZATION_FACTOR, \fB\-\-polarization\fR POLARIZATION_FACTOR
polarization factor, from \fB\-1\fR (vertical) to +1
(horizontal), default is None (no correction),
synchrotrons are around 0.95
.TP
\fB\-i\fR FILE, \fB\-\-poni\fR FILE
file containing the diffraction parameter (poni\-file).
MANDATORY for pyFAI\-recalib!
.TP
\fB\-b\fR BACKGROUND, \fB\-\-background\fR BACKGROUND
Automatic background subtraction if no value are
provided
.TP
\fB\-d\fR DARK, \fB\-\-dark\fR DARK
list of comma separated dark images to average and
subtract
.TP
\fB\-f\fR FLAT, \fB\-\-flat\fR FLAT
list of comma separated flat images to average and
divide
.TP
\fB\-s\fR SPLINE, \fB\-\-spline\fR SPLINE
spline file describing the detector distortion
.TP
\fB\-D\fR DETECTOR_NAME, \fB\-\-detector\fR DETECTOR_NAME
Detector name (instead of pixel size+spline)
.TP
\fB\-m\fR MASK, \fB\-\-mask\fR MASK
file containing the mask (for image reconstruction)
.TP
\fB\-n\fR NPT, \fB\-\-pt\fR NPT
file with datapoints saved. Default: basename.npt
.TP
\fB\-\-filter\fR FILTER
select the filter, either mean(default), max or median
.TP
\fB\-l\fR DISTANCE, \fB\-\-distance\fR DISTANCE
sample\-detector distance in millimeter. Default: 100mm
.TP
\fB\-\-dist\fR DIST
sample\-detector distance in meter. Default: 0.1m
.TP
\fB\-\-poni1\fR PONI1
poni1 coordinate in meter. Default: center of detector
.TP
\fB\-\-poni2\fR PONI2
poni2 coordinate in meter. Default: center of detector
.TP
\fB\-\-rot1\fR ROT1
rot1 in radians. default: 0
.TP
\fB\-\-rot2\fR ROT2
rot2 in radians. default: 0
.TP
\fB\-\-rot3\fR ROT3
rot3 in radians. default: 0
.TP
\fB\-\-fix\-dist\fR
fix the distance parameter
.TP
\fB\-\-free\-dist\fR
free the distance parameter. Default: Activated
.TP
\fB\-\-fix\-poni1\fR
fix the poni1 parameter
.TP
\fB\-\-free\-poni1\fR
free the poni1 parameter. Default: Activated
.TP
\fB\-\-fix\-poni2\fR
fix the poni2 parameter
.TP
\fB\-\-free\-poni2\fR
free the poni2 parameter. Default: Activated
.TP
\fB\-\-fix\-rot1\fR
fix the rot1 parameter
.TP
\fB\-\-free\-rot1\fR
free the rot1 parameter. Default: Activated
.TP
\fB\-\-fix\-rot2\fR
fix the rot2 parameter
.TP
\fB\-\-free\-rot2\fR
free the rot2 parameter. Default: Activated
.TP
\fB\-\-fix\-rot3\fR
fix the rot3 parameter
.TP
\fB\-\-free\-rot3\fR
free the rot3 parameter. Default: Activated
.TP
\fB\-\-fix\-wavelength\fR
fix the wavelength parameter. Default: Activated
.TP
\fB\-\-free\-wavelength\fR
free the wavelength parameter. Default: Deactivated
.TP
\fB\-\-tilt\fR
Allow initially detector tilt to be refined (rot1,
rot2, rot3). Default: Activated
.TP
\fB\-\-no\-tilt\fR
Deactivated tilt refinement and set all rotation to 0
.TP
\fB\-\-saturation\fR SATURATION
consider all pixel>max*(1\-saturation) as saturated and
reconstruct them, default: 0 (deactivated)
.TP
\fB\-\-weighted\fR
weight fit by intensity, by default not.
.TP
\fB\-\-npt\fR NPT_1D
Number of point in 1D integrated pattern, Default:
1024
.TP
\fB\-\-npt\-azim\fR NPT_2D_AZIM
Number of azimuthal sectors in 2D integrated images.
Default: 360
.TP
\fB\-\-npt\-rad\fR NPT_2D_RAD
Number of radial bins in 2D integrated images.
Default: 400
.TP
\fB\-\-unit\fR UNIT
Valid units for radial range: 2th_deg, 2th_rad,
q_nm^\-1, q_A^\-1, r_mm. Default: 2th_deg
.TP
\fB\-\-no\-gui\fR
force the program to run without a Graphical interface
.TP
\fB\-\-no\-interactive\fR
force the program to run and exit without prompting
for refinements
.TP
\fB\-r\fR, \fB\-\-reconstruct\fR
Reconstruct image where data are masked or <0 (for
Pilatus detectors or detectors with modules)
.TP
\fB\-g\fR GAUSSIAN, \fB\-\-gaussian\fR 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.
.TP
\fB\-\-square\fR
Use square kernel shape for neighbor search instead of
diamond shape
.TP
\fB\-p\fR PIXEL, \fB\-\-pixel\fR PIXEL
size of the pixel in micron
.PP
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)