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doc/source/man/pyFAI-calib2.rst
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@ -13,16 +13,16 @@ 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, alpha_Al2O3, Cr2O3, AgBh, Si_SRM640, CuO, PBBA,
Si_SRM640b, mock, 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
Calibrants available: ``Ni``, ``CrOx``, ``NaCl``, ``Si_SRM640e``, ``Si_SRM640d``, ``Si_SRM640a``,
``Si_SRM640c``, ``alpha_Al2O3``, ``Cr2O3``, ``AgBh``, ``Si_SRM640``, ``CuO``, ``PBBA``,
``Si_SRM640b``, ``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>`_.
Usage:
------
pyFAI-calib2 [options] [input_image.edf]
``pyFAI-calib2 [options] [input_image.edf]``
Everything can be set by the GUI, but here are the command-line arguments.
@ -30,171 +30,97 @@ Options:
--------
positional arguments:
FILE List of files to calibrate
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
--debug
Set logging system in debug mode
-c FILE, --calibrant FILE
Calibrant name or file containing d-spacing of the reference sample (case sensitive)
-w WAVELENGTH, --wavelength WAVELENGTH
wavelength of the X-Ray beam in Angstrom.
-e ENERGY, --energy ENERGY
energy of the X-Ray beam in keV (hc=12.3984197396keV.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
-D DETECTOR_NAME, --detector DETECTOR_NAME
Detector name (instead of pixel size+spline)
-m MASK, --mask MASK
file containing the mask (for image reconstruction)
-p PIXEL, --pixel PIXEL
size of the pixel in micron
-i FILE, --poni FILE
file containing the diffraction parameter (poni-file).
-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
-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-wavelength
fix the wavelength parameter. Default: Activated
--free-wavelength
free the wavelength parameter. Default: Deactivated
--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
--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
--qtargs QTARGS
Arguments propagated to Qt
--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.
--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
-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
--debug Set logging system in debug mode
--opengl, --gl Enable OpenGL rendering (else matplotlib is used)
-c FILE, --calibrant FILE
Calibrant name or file containing d-spacing of the
reference sample (case sensitive)
-w WAVELENGTH, --wavelength WAVELENGTH
wavelength of the X-Ray beam in Angstrom.
-e ENERGY, --energy ENERGY
energy of the X-Ray beam in keV
(hc=12.398419739640717keV.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
-D DETECTOR_NAME, --detector DETECTOR_NAME
Detector name (instead of pixel size+spline)
-m MASK, --mask MASK file containing the mask (for image reconstruction)
-p PIXEL, --pixel PIXEL
size of the pixel in micron
-s SPLINE, --spline SPLINE
spline file describing the detector distortion
-n NPT, --pt NPT file with datapoints saved. Example: basename.npt
-i FILE, --poni FILE file containing the diffraction parameter (poni-file)
[not used].
-b BACKGROUND, --background BACKGROUND
Automatic background subtraction if no value are
provided [not used]
-d DARK, --dark DARK list of comma separated dark images to average and
subtract [not used]
-f FLAT, --flat FLAT list of comma separated flat images to average and
divide [not used]
--filter FILTER select the filter, either mean(default), max or median
[not used]
-l DIST_MM, --distance DIST_MM
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-wavelength fix the wavelength parameter. Default: Activated
--free-wavelength free the wavelength parameter. Default: Deactivated
--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
--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
--qtargs QTARGS Arguments propagated to Qt
--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.
--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
Tips & Tricks
-------------

2
doc/source/man/pyFAI-drawmask.rst
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@ -1,6 +1,8 @@
Mask generation tool: pyFAI-drawmask
====================================
.. _pyFAI-drawmask:
Purpose
-------

64
doc/source/man/pyFAI-integrate.rst
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@ -4,7 +4,7 @@ Integration tool: pyFAI-integrate
Purpose
-------
PyFAI-integrate is a graphical interface (based on Python/Qt4) to perform azimuthal integration
PyFAI-integrate is a graphical interface (based on Python/Qt5) to perform azimuthal integration
on a set of files. It exposes most of the important options available within pyFAI and allows you
to select a GPU (or an openCL platform) to perform the calculation on.
@ -16,36 +16,46 @@ to select a GPU (or an openCL platform) to perform the calculation on.
Usage
-----
pyFAI-integrate [options] file1.edf file2.edf ...
``pyFAI-integrate [options] file1.edf file2.edf ...``
Options:
--------
-h, --help show this help message and exit
-V, --version show program's version number and exit
-v, --verbose switch to verbose/debug mode
-o OUTPUT, --output OUTPUT
Directory or file where to store the output data
-f FORMAT, --format FORMAT
output data format (can be HDF5)
-s SLOW, --slow-motor SLOW
Dimension of the scan on the slow direction (makes
sense only with HDF5)
-r RAPID, --fast-motor RAPID
Dimension of the scan on the fast direction (makes
sense only with HDF5)
--no-gui Process the dataset without showing the user
interface.
-j JSON, --json JSON Configuration file containing the processing to be
done
--monitor-name MONITOR_KEY
Name of the monitor in the header of each input files.
If defined the contribution of each input file is
divided by the monitor. If the header does not contain
or contains a wrong value, the contribution of the
input file is ignored. On EDF files, values from
'counter_pos' can accessed by using the expected
mnemonic. For example 'counter/bmon'.
positional arguments:
FILE Files to be integrated
optional arguments:
-h, --help show this help message and exit
-V, --version show program's version number and exit
-v, --verbose switch to verbose/debug mode
--debug Set logging system in debug mode
-o OUTPUT, --output OUTPUT
Directory or file where to store the output data
-f FORMAT, --format FORMAT
output data format (can be HDF5)
-s SLOW, --slow-motor SLOW
Dimension of the scan on the slow direction (makes
sense only with HDF5)
-r RAPID, --fast-motor RAPID
Dimension of the scan on the fast direction (makes
sense only with HDF5)
--no-gui Process the dataset without showing the user
interface.
-j JSON, --json JSON Configuration file containing the processing to be
done
--monitor-name MONITOR_KEY
Name of the monitor in the header of each input files.
If defined the contribution of each input file is
divided by the monitor. If the header does not contain
or contains a wrong value, the contribution of the
input file is ignored. On EDF files, values from
'counter_pos' can be accessed by using the expected
mnemonic. For example 'counter/bmon'.
--delete Delete the destination file if already exists
--append Append the processing to the destination file using an
available group (HDF5 output)
--overwrite Overwrite the entry of the destination file if it
already exists (HDF5 output)
Tips & Tricks:
--------------