.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH CALIBRATION "1" "February 2018" "calibration from pyFAI version 0.15.0: 30/01/2018" "User Commands"
.SH NAME
calibration \- manual page for calibration from pyFAI version 0.15.0: 30/01/2018
.SH DESCRIPTION
usage: pyFAI\-recalib [options] \fB\-i\fR ponifile \fB\-w\fR 1 \fB\-c\fR calibrant.D imagefile.edf
.PP
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: Si_SRM640a,
CeO2, quartz, AgBh, CuO, Cr2O3, LaB6_SRM660c, Ni, CrOx, Si_SRM640d, LaB6, Si,
Si_SRM640, Si_SRM640c, alpha_Al2O3, Si_SRM640b, NaCl, LaB6_SRM660a, C14H30O,
Au, LaB6_SRM660b, mock, Si_SRM640e, TiO2, Al, PBBA, cristobaltite, ZnO 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=12.398419739640717keV.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 MAX_RINGS, \fB\-\-ring\fR MAX_RINGS
maximum number of rings to extract. Default: all
accessible
.TP
\fB\-k\fR, \fB\-\-keep\fR
Keep existing control point and append new
.PP
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 (\fB\-\-no\-gui\fR and \fB\-\-nointeractive\fR 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 \fB\-r\fR 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.
.SH "SEE ALSO"
The full documentation for
.B calibration
is maintained as a Texinfo manual.  If the
.B info
and
.B calibration
programs are properly installed at your site, the command
.IP
.B info calibration
.PP
should give you access to the complete manual.