Calibration tool: pyFAI-calib

Purpose

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).

If you are using a standard calibrant, look at https://github.com/silx-kit/pyFAI/tree/master/calibration or search in the American Mineralogist database: [AMD] or in the [COD]. The –calibrant option is mandatory !

Calibrants available: Ni, CrOx, NaCl, Si_SRM640e, Si_SRM640d, Si_SRM640a, Si_SRM640b, Cr2O3, AgBh, Si_SRM640, CuO, PBBA, alpha_Al2O3, SI_SRM640c, quartz, C14H30O, cristobaltite, Si, LaB6, CeO2, LaB6_SRM660a, LaB6_SRM660b, LaB6_SRM660c, TiO2, ZnO, Al, Au

You will need in addition:

  • The radiation energy (in keV) or its wavelength (in A)

  • The description of the detector:

  • it name or

  • it’s pixel size or

  • the spline file describing its distortion or

  • the NeXus file describing the distortion

Many option are available among those:

  • dark-current / flat field corrections

  • Masking of bad regions

  • reconstruction of missing region (module based detectors), see option -r

  • Polarization correction

  • Automatic desaturation (time consuming!)

  • Intensity weighted least-squares refinements

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)

Usage:

pyFAI-calib [options] -w 1 -D detector -c calibrant imagefile.edf

Options:

-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

-c FILE, --calibrant FILE

Calibrant name or file containing d-spacing of the reference sample (MANDATORY, case sensitive !)

-w WAVELENGTH, --wavelength WAVELENGTH

wavelength of the X-Ray beam in Angstrom. Mandatory

-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 None (no correction), synchrotrons are around 0.95

-i FILE, --poni FILE

file containing the diffraction parameter (poni-file). MANDATORY for pyFAI-recalib!

-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

-D DETECTOR_NAME, --detector DETECTOR_NAME

Detector name (instead of pixel size+spline)

-m MASK, --mask MASK

file containing the mask (for image reconstruction)

-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-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

--fix-wavelength

fix the wavelength parameter. Default: Activated

--free-wavelength

free the wavelength parameter. Default: Deactivated

--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.

--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

--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

-p PIXEL, --pixel PIXEL

size of the pixel in micron

Tips & Tricks

PONI-files are ASCII files and each new refinement adds an entry in the file. So if you are unhappy with the last step, just edit this file and remove the last entry (time-stamps will help you).

Example of usage:

Pilatus 1M image of Silver Behenate taken at ESRF-BM26:

pyFAI-calib -D Pilatus1M -c AgBh -r -w 1.0 test/testimages/Pilatus1M.edf

We use the parameter -r to reconstruct the missing part between the modules of the Pilatus detector.

Half a FReLoN CCD image of Lantanide hexaboride taken at ESRF-ID11:

pyFAI-calib -s test/testimages/halfccd.spline -c LaB6 -w 0.3 test/testimages/halfccd.edf -g 250

This image is rather spotty. We need to blur a lot to get the continuity of the rings. This is achieved by the -g parameter. While the sample is well diffracting and well known, the wavelength has been guessed. One should refine the wavelength when the peaks extracted are correct

All those images are part of the test-suite of pyFAI. To download them from internet, run

python setup.py build test

Downloaded test images are located in tests/testimages