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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.
.. command-output:: eiger2crysalis --help
:nostderr:
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