# 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/kif/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:

    $ pyFAI-calib --help

### 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