MX-calibrate - Online in the Cloud

PROGRAM:

NAME

MX-calibrate - Validate detector position for MX beamlines

DESCRIPTION

Calibrate automatically a set of frames taken at various sample-detector distance. Return
the linear regression of the fit in funtion of the samplesetector 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.

Use MX-calibrate online using onworks.net services