Specification of snapshot images

Locating images

nXDS adopts two ways for specifying snapshot images for processing.

1. Image directory and list of file names

Starting from the processing directory - where nXDS will be invoked - the data images are found in directory ../images. Here, 'images' abbreviates a long path name using the command
ln -s path_to_image_directory images. After moving to the image directory the names of the wanted snapshots are collected in a file called Liste1 in the example, using the command
ls -1 *.cbf >Liste1. Liste1 is moved subsequently to the processing directory where nXDS will be invoked. In the example these images are recorded by the CBF format (see below) which is automatically recognized by nXDS and could have been omitted.

2. Generic file name template and image numbers

NAME_TEMPLATE_OF_DATA_FRAMES= ../data_images_??????.h5  GENERIC
The question marks in the file name template serve as placeholders for a specific snapshot number to be analyzed. If necessary nXDS will extended the snapshot number by leading zeros to exactly match the number of question marks of the template. The numbers are listed, each in a single line, in a file with the fixed name SHOTNUMBERS, accessible from the processing directory.

This way of specifying snapshot images by a template is also adopted for reading images by an external library routine whose full path name is provided by the input parameter LIB=. Use of such a dynamically linked library routine is indicated by the optional keyword GENERIC following the name template. In case of EIGER detector images the Neggia library from DECTRIS would be used which can retrieve images stored in a container structure.
If no external image reading routine is provided by the LIB= input parameter, nXDS relies on its internal routines denoted by the format keywords below.

Initially, on the first call of nXDS, a file named SHOTNUMBERS may not be available. In this case it will be generated from user input parameters like, for example,
DATA_RANGE=1 100000
In the example here, each line of the file SHOTNUMBERS has one number from the allowed ranges 1...6489, 6557...100000. An arbitrary number of EXCLUDE_DATA_RANGE parameters can be specified. If a file named SHOTNUMBERS is already available it will be used and any DATA_RANGE and EXCLUDE_DATA_RANGE parameters are ignored.

Image formats

For many of the detectors presently used the image format is recognized automatically by nXDS. A format keyword, like MAR or GENERIC is not needed. However, if the format is explicitly named, nXDS will attempt to read the snapshot images in the specified way. The format KEYWORD can be:

The actual reading of the image data is done by the external, dynamically linked library specified by the parameter LIB=name_of_external_library. This special software must be provided by the detector manufacturer and is independent from nXDS. The software is only supposed to somehow retrieve requested image data using the information from the given name template and the image number. The great flexibility of this method uncouples nXDS from new detector developments and image data representation.
Byte offset variant of the Crystallographic Binary Files format ( CBFlib );
PILATUS pixel detector format
MAR555 and MAR345 image format
Compressed images by Jan Pieter Abrahams algorithm with number representation used at MRC
TIFF-format used by CCDCHESS and MARCCD detectors
ADSC CCD-detector image data format;
R-AXIS4 and SATURN92 CCD-detector format;
NOIR-1 detector format;
CCD-detector (1024 X 1024) at Brandeis & Brookhaven;
old marresearch detector; BRANDEIS_B4 CCD detector
IPDS image data format (Stoe & Cie GmbH, D-Darmstadt)
Bruker AXS image data format for the SMART6000 CCD detector
SIEMENS multiwire detector

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page last updated: Feb 14, 2019