Eiger2CBF

Purpose

Convert a multiframe HDF5 Eiger data file into several CBF files.

Portable image converter based on FabIO library to export Eiger frames (lima or eiger) to CBF which mimic the header of a Dectris Pilatus detector.

Usage:

eiger2cbf [-h] [-V] [-v] [–debug] [-o OUTPUT] [-m MASK] [-O OFFSET] [-D DUMMY] [–pilatus] [–dry-run] [-e ENERGY] [-w WAVELENGTH] [-d DISTANCE] [-b BEAM BEAM] [–alpha ALPHA] [–kappa KAPPA] [–chi CHI] [–phi PHI] [–omega OMEGA] [–rotation ROTATION] [–transpose] [–flip-ud] [–flip-lr] [IMAGE …]

Positional arguments:

IMAGE: File with input images

Options:

-h, –help: show this help message and exit
-V, –version: output version and exit
-v, –verbose: show information for each conversions
–debug: show debug information

Main arguments:

-o OUTPUT, –output OUTPUT: output directory and filename template: eiger2cbf/frame_{index:04d}.cbf
-m MASK, –mask MASK: Read masked pixel from this file
-O OFFSET, –offset OFFSET: index offset, CrysalisPro likes indexes to start at 1, Python starts at 0 (default)
-D DUMMY, –dummy DUMMY: Set masked values to this dummy value
–pilatus: Select an image shape similar to Pilatus detectors for compatibiliy with Crysalis

Optional behaviour arguments:

–dry-run: do everything except modifying the file system

Experimental setup options:

-e ENERGY, –energy ENERGY: Energy of the incident beam in keV
-w WAVELENGTH, –wavelength WAVELENGTH: Wavelength of the incident beam in Angstrom
-d DISTANCE, –distance DISTANCE: Detector distance in meters
-b BEAM BEAM, –beam BEAM BEAM: Direct beam in pixels x, y

Goniometer setup:

–alpha ALPHA: Goniometer angle alpha value in deg. Constant, angle between kappa and omega.
–kappa KAPPA: Goniometer angle kappa value in degrees or formula f(index) -80 + 2*index
–chi CHI: Goniometer angle chi value in degres or formula f(index)
–phi PHI: Goniometer angle phi value (inner-most rotation) in degrees or formula f(index) -180+0.7*index
–omega OMEGA: Goniometer angle omega value (outer-most rotation) in degrees or formula f(index) -180+0.5*index

Image preprocessing:

Images are patched onto the center of a square frame, and transformation are applied in this order:

–rotation ROTATION: Rotate the initial image by this value in degrees. Must be a multiple of 90 degrees.
–transpose: Flip the x/y axis
–flip-ud: Flip the image upside-down
–flip-lr: Flip the image left-right

Return code:

0 means a success.
1 means the conversion contains a failure,
2 means there was an error in the arguments

Nota:

Images are made square, so the beam center found in the CBF-files differs from the one entered.

$ eiger2cbf --help
usage: eiger2cbf [-h] [-V] [-v] [--debug] [-o OUTPUT] [-m MASK] [-O OFFSET]
                 [-D DUMMY] [--pilatus] [--dry-run] [-e ENERGY]
                 [-w WAVELENGTH] [-d DISTANCE] [-b BEAM BEAM] [--alpha ALPHA]
                 [--kappa KAPPA] [--chi CHI] [--phi PHI] [--omega OMEGA]
                 [--rotation ROTATION] [--transpose] [--flip-ud] [--flip-lr]
                 [IMAGE ...]

Portable image converter based on FabIO library to export Eiger frames
(including te one from LIMA) to CBF and mimic the header from Dectris Pilatus.

positional arguments:
  IMAGE                 File with input images

options:
  -h, --help            show this help message and exit
  -V, --version         output version and exit
  -v, --verbose         show information for each conversions
  --debug               show debug information

main arguments:
  -o OUTPUT, --output OUTPUT
                        output directory and filename template:
                        eiger2cbf/frame_{index:04d}.cbf
  -m MASK, --mask MASK  Read masked pixel from this file
  -O OFFSET, --offset OFFSET
                        index offset, CrysalisPro likes indexes to start at 1,
                        Python starts at 0
  -D DUMMY, --dummy DUMMY
                        Set masked values to this dummy value
  --pilatus             Select an image shape similar to Pilatus detectors for
                        compatibiliy with Crysalis

optional behaviour arguments:
  --dry-run             do everything except modifying the file system

Experimental setup options:
  -e ENERGY, --energy ENERGY
                        Energy of the incident beam in keV
  -w WAVELENGTH, --wavelength WAVELENGTH
                        Wavelength of the incident beam in Å
  -d DISTANCE, --distance DISTANCE
                        Detector distance in meters
  -b BEAM BEAM, --beam BEAM BEAM
                        Direct beam in pixels x, y

Goniometer setup:
  --alpha ALPHA         Goniometer angle alpha value in deg.
  --kappa KAPPA         Goniometer angle kappa value in deg.
  --chi CHI             Goniometer angle chi value in deg. or formula f(index)
  --phi PHI             Goniometer angle phi value in deg. or formula f(index)
  --omega OMEGA         Goniometer angle omega value in deg. or formula
                        f(index) like '-180+index*0.1

Image preprocessing (Important: applied in this order!):
  --rotation ROTATION   Rotate the initial image by this value in degrees.
                        Must be a multiple of 90°.
  --transpose           Flip the x/y axis
  --flip-ud             Flip the image upside-down
  --flip-lr             Flip the image left-right

return codes: 0 means a success. 1 means the conversion contains a failure, 2
means there was an error in the arguments