Densify_Bragg#

densify_Bragg is a tool to decompress the sparse data-format used at the ESRF-ID29 beamline with the Jungfrau detector.

Each file stores the information for a few thousands frames, each frame is composed of:

a background profile with the associated uncertainties
a list of pixel values and positions.

The decompression is called densification since only sparse pixel positions were recorded. The background can be made more realistic by regenerating some natural looking noise. Depending on the data reduction software used later-on, noise is needed (XDS) or detrimental (Crysalis) for subsequent analysis.

Usage#

densify_Bragg [-h] [-V] [-v] [--debug] [-l] [-o OUTPUT] [-O FORMAT] [-D DUMMY] [--dry-run] [-N NOISY] [IMAGE …]

Positional arguments:#

IMAGE: File with sparse images stored in them

Pptions:#

-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 output formats and exit
-o OUTPUT, --output OUTPUT: output filename, by default {baseame}_densify.h5
-O FORMAT, --output-format FORMAT: output format among lima, eiger …
-D DUMMY, --dummy DUMMY: Set masked values to this dummy value

optional behaviour arguments:#

--dry-run: do everything except modifying the file system
-N NOISY, --noise NOISY: Noise scaling factor, from 0 to 1, set to 0 to disable the noise reconstruction

Return code:#

0 means a success.
1 means the conversion contains a failure,
2 means there was an error in the arguments

$ densify_Bragg --help
usage: densify [-h] [-V] [-v] [--debug] [-l] [-o OUTPUT] [-O FORMAT]
               [-D DUMMY] [--dry-run] [-N NOISY]
               [IMAGE ...]

Convert a sparse fileformat (Generated by sparsify-Bragg from pyFAI) to a
dense stack of frames in Eiger, Lima ... images.

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:
  -l, --list            show the list of available output formats and exit
  -o OUTPUT, --output OUTPUT
                        output filename, by default {basename}_densify.h5
  -O FORMAT, --output-format FORMAT
                        output format among 'lima', 'eiger' ...
  -D DUMMY, --dummy DUMMY
                        Set masked values to this dummy value

optional behaviour arguments:
  --dry-run             do everything except modifying the file system
  -N NOISY, --noise NOISY
                        Noise scaling factor, from 0 to 1, set to 0 to disable
                        the noise reconstruction

return codes: 0 means a success. 1 means the conversion contains a failure, 2
means there was an error in the arguments