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

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