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.