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.