Eiger2Crysalis¶

Purpose:¶

Convert a stack of images acquires with an Eiger detector (HDF5, format eiger or lima) into a CrysalisPro project

CrysalisPro is a single-crystal data reduction program developped by Mathias Meyer and gracefully made available free of charge by Rigaku.

The Crysalis project directory is populated with:

a set of Esperanto files, corresponding to the different frames of the HDF5 file
a set-file, ascii format, with the description of the detector (mostly unused)
a ccd-file, binary format, with the description of the mask of the detector
a par-file, ascii format, with the description of the sample, goniometer, source, …
a run-file, binary format, with the description of the scans (sometimes called sweep in MX)

The directory can directly be opened with CrysalisPro.

Usage:¶

eiger2crysalis [-h] [-V] [-v] [–debug] [-l] [-o OUTPUT] [-O OFFSET] [-D DUMMY] [–dry-run] [–calc-mask] [-e ENERGY] [-w WAVELENGTH] [-d DISTANCE] [-b BEAM BEAM] [-p POLARIZATION] [–alpha ALPHA] [–kappa KAPPA] [–phi PHI] [–omega OMEGA] [–theta THETA] [–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
-l, –list: show the list of available formats and exit

Main arguments:¶

-o OUTPUT, –output OUTPUT: output directory and filename template, for example {basename}/crysalis/scan_1_{index}.esperanto
-O OFFSET, –offset OFFSET: index offset, CrysalisPro likes indexes to start at 1, Python starts at 0. The default is 1
-D DUMMY, –dummy DUMMY: Set masked values to this dummy value

Optional behaviour arguments:¶

–dry-run: do everything except modifying the file system
–calc-mask: Generate a fine mask from pixels marked as invalid. By default, only treats gaps (faster)

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 millimeters
-b BEAM BEAM, –beam BEAM BEAM: Direct beam in pixels x, y
-p POLARIZATION, –polarization POLARIZATION: Polarization factor (0.99 by default on synchrotron)

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
–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
–theta THETA: Goniometer angle theta value (angle of the detector arm) in degrees or formula f(index). -50+5*index

Nota: only one angle can vary during a given scan.

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??. By default 180 deg (flip_up with origin=lower and flip_lr because the image is seen from the sample).
–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 eperanto image differs from the one entered.

$ eiger2crysalis --help
usage: eiger2crysalis [-h] [-V] [-v] [--debug] [-l] [-o OUTPUT] [-O OFFSET]
                      [-D DUMMY] [--dry-run] [--calc-mask] [-e ENERGY]
                      [-w WAVELENGTH] [-d DISTANCE] [-b BEAM BEAM]
                      [-p POLARIZATION] [--alpha ALPHA] [--kappa KAPPA]
                      [--phi PHI] [--omega OMEGA] [--theta THETA]
                      [--rotation ROTATION] [--transpose] [--flip-ud]
                      [--flip-lr]
                      [IMAGE ...]

Portable image converter based on FabIO library to export Eiger frames
(including the one from LImA) to a set of esperanto frames which can be
imported into CrysalisPro.

positional arguments:
  IMAGE                 File with input images

optional arguments:
  -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:
  -l, --list            show the list of available formats and exit
  -o OUTPUT, --output OUTPUT
                        output directory and filename template
  -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

optional behaviour arguments:
  --dry-run             do everything except modifying the file system
  --calc-mask           Generate a fine mask from pixels marked as invalid. By
                        default, only treats gaps

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 millimeters
  -b BEAM BEAM, --beam BEAM BEAM
                        Direct beam in pixels x, y
  -p POLARIZATION, --polarization POLARIZATION
                        Polarization factor (0.99 by default on synchrotron)

Goniometer setup:
  --alpha ALPHA         Goniometer angle alpha value in deg. Constant, angle
                        between kappa/omega.
  --kappa KAPPA         Goniometer angle kappa value in deg or formula
                        f(index).
  --phi PHI             Goniometer angle phi value in deg. or formula
                        f(index). Inner-most rotation.
  --omega OMEGA         Goniometer angle omega value in deg. or formula
                        f(index). Outer-most rotation.
  --theta THETA         Goniometer angle theta value in deg. or formula
                        f(index). Tilt angle of the detector.

Image preprocessing (Important: applied in this order!):
  --rotation ROTATION   Rotate the initial image by this value in degrees.
                        Must be a multiple of 90°. By default 180 deg (flip_up
                        with origin=lower and flip_lr because the image is
                        seen from the sample).
  --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