Calibrate automatically a set of frames taken at various sample-detector distance.
This tool has been developed for ESRF MX-beamlines where an acceptable calibration is usually present is the header of the image. PyFAI reads it and does a “recalib” on each of them before exporting a linear regression of all parameters versus this distance.
Most standard calibrants are directly installed together with pyFAI. If you prefer using your own, you can provide a “d-spacing” file containing the spacing of Miller plans in Angstrom (in decreasing order). Most crystal powders used for calibration are available in the American Mineralogist database [AMD] or in the [COD].
MX-Calibrate -w 1.54 -c CeO2 file1.cbf file2.cbf ...
usage: MX-Calibrate -w 1.54 -c CeO2 file1.cbf file2.cbf ...
Calibrate automatically a set of frames taken at various sample-detector distance. Return the linear regression of the fit in funtion of the sample- setector distance.
| -h, --help | show this help message and exit |
| -V, --version | show program’s version number and exit |
| -v, --verbose | switch to debug/verbose mode |
| -c FILE, --calibrant FILE | |
| file containing d-spacing of the calibrant reference sample (MANDATORY) | |
| -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=12.398419292keV.A) | |
| -P POLARIZATION_FACTOR, --polarization POLARIZATION_FACTOR | |
| polarization factor, from -1 (vertical) to +1 (horizontal), default is 0, synchrotrons are around 0.95 | |
| -b BACKGROUND, --background BACKGROUND | |
| Automatic background subtraction if no value are provided | |
| -d DARK, --dark DARK | |
| list of dark images to average and subtract | |
| -f FLAT, --flat FLAT | |
| list of flat images to average and divide | |
| -s SPLINE, --spline SPLINE | |
| spline file describing the detector distortion | |
| -p PIXEL, --pixel PIXEL | |
| size of the pixel in micron | |
| -D DETECTOR_NAME, --detector DETECTOR_NAME | |
| Detector name (instead of pixel size+spline) | |
| -m MASK, --mask MASK | |
| file containing the mask (for image reconstruction) | |
| --filter FILTER | |
| select the filter, either mean(default), max or median | |
| --saturation SATURATION | |
| consider all pixel>max*(1-saturation) as saturated and reconstruct them | |
| -r MAX_RINGS, --ring MAX_RINGS | |
| maximum number of rings to extract | |
| --weighted | weight fit by intensity |
| -l DISTANCE, --distance DISTANCE | |
| sample-detector distance in millimeter | |
| --tilt | Allow initially detector tilt to be refined (rot1, rot2, rot3). Default: Activated |
| --no-tilt | Deactivated tilt refinement and set all rotation to 0 |
| --dist DIST | sample-detector distance in meter |
| --poni1 PONI1 | poni1 coordinate in meter |
| --poni2 PONI2 | poni2 coordinate in meter |
| --rot1 ROT1 | rot1 in radians |
| --rot2 ROT2 | rot2 in radians |
| --rot3 ROT3 | rot3 in radians |
| --fix-dist | fix the distance parameter |
| --free-dist | free the distance parameter |
| --fix-poni1 | fix the poni1 parameter |
| --free-poni1 | free the poni1 parameter |
| --fix-poni2 | fix the poni2 parameter |
| --free-poni2 | free the poni2 parameter |
| --fix-rot1 | fix the rot1 parameter |
| --free-rot1 | free the rot1 parameter |
| --fix-rot2 | fix the rot2 parameter |
| --free-rot2 | free the rot2 parameter |
| --fix-rot3 | fix the rot3 parameter |
| --free-rot3 | free the rot3 parameter |
| --fix-wavelength | |
| fix the wavelength parameter | |
| --free-wavelength | |
| free the wavelength parameter | |
| --no-gui | force the program to run without a Graphical interface |
| --gui | force the program to run with a Graphical interface |
| --no-interactive | |
| force the program to run and exit without prompting for refinements | |
| --interactive | force the program to prompt for refinements |
| --peak-picker PEAKPICKER | |
| Uses the ‘massif’, ‘blob’ or ‘watershed’ peak-picker algorithm (default: blob) | |
This tool has been developed for ESRF MX-beamlines where an acceptable calibration is usually present is the header of the image. PyFAI reads it and does a “recalib” on each of them before exporting a linear regression of all parameters versus this distance.
$ MX-calibrate --help
usage: MX-Calibrate -w 1.54 -c CeO2 file1.cbf file2.cbf ...
Calibrate automatically a set of frames taken at various sample-detector
distance. Return the linear regression of the fit in funtion of the sample-
setector distance.
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
-v, --verbose switch to debug/verbose mode
-c FILE, --calibrant FILE
file containing d-spacing of the calibrant reference
sample (MANDATORY)
-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=12.398419292keV.A)
-P POLARIZATION_FACTOR, --polarization POLARIZATION_FACTOR
polarization factor, from -1 (vertical) to +1
(horizontal), default is 0, synchrotrons are around
0.95
-b BACKGROUND, --background BACKGROUND
Automatic background subtraction if no value are
provided
-d DARK, --dark DARK list of dark images to average and subtract
-f FLAT, --flat FLAT list of flat images to average and divide
-s SPLINE, --spline SPLINE
spline file describing the detector distortion
-p PIXEL, --pixel PIXEL
size of the pixel in micron
-D DETECTOR_NAME, --detector DETECTOR_NAME
Detector name (instead of pixel size+spline)
-m MASK, --mask MASK file containing the mask (for image reconstruction)
--filter FILTER select the filter, either mean(default), max or median
--saturation SATURATION
consider all pixel>max*(1-saturation) as saturated and
reconstruct them
-r MAX_RINGS, --ring MAX_RINGS
maximum number of rings to extract
--weighted weight fit by intensity
-l DISTANCE, --distance DISTANCE
sample-detector distance in millimeter
--tilt Allow initially detector tilt to be refined (rot1,
rot2, rot3). Default: Activated
--no-tilt Deactivated tilt refinement and set all rotation to 0
--dist DIST sample-detector distance in meter
--poni1 PONI1 poni1 coordinate in meter
--poni2 PONI2 poni2 coordinate in meter
--rot1 ROT1 rot1 in radians
--rot2 ROT2 rot2 in radians
--rot3 ROT3 rot3 in radians
--fix-dist fix the distance parameter
--free-dist free the distance parameter
--fix-poni1 fix the poni1 parameter
--free-poni1 free the poni1 parameter
--fix-poni2 fix the poni2 parameter
--free-poni2 free the poni2 parameter
--fix-rot1 fix the rot1 parameter
--free-rot1 free the rot1 parameter
--fix-rot2 fix the rot2 parameter
--free-rot2 free the rot2 parameter
--fix-rot3 fix the rot3 parameter
--free-rot3 free the rot3 parameter
--fix-wavelength fix the wavelength parameter
--free-wavelength free the wavelength parameter
--no-gui force the program to run without a Graphical interface
--gui force the program to run with a Graphical interface
--no-interactive force the program to run and exit without prompting
for refinements
--interactive force the program to prompt for refinements
--peak-picker PEAKPICKER
Uses the 'massif', 'blob' or 'watershed' peak-picker
algorithm (default: blob)
This tool has been developed for ESRF MX-beamlines where an acceptable
calibration is usually present is the header of the image. PyFAI reads it and
does a "recalib" on each of them before exporting a linear regression of all
parameters versus this distance.