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.