ImgCIFHandler.jl

Routines for handling imgCIF files containing raw data pointers
Author jamesrhester
Popularity
0 Stars
Updated Last
12 Months Ago
Started In
February 2022

Testing

ImgCIFHandler

This Julia package provides functions for working with ImgCIF files. imgCIF is a raw data standard developed by the International Union of Crystallography, and recently enhanced with data pointers so that the raw data can be preserved outside of the imgCIF file itself.

Installation

Prerequisites

For some functions, the programs tar, curl and awk must be available in the environment, as well as gzip and bunzip2. This requirement may be removed in the future.

Installation

To install this package, at the Julia package prompt (reached by typing ] at the Julia prompt) type add ImgCIFHandler. See also additional instructions in the tools directory for installing and updating the imgCIF checking tool.

Use

After installation, typing 'using ImgCIFHandler' will import the package. The following functions will be in scope:

  1. imgload. This function can be used to access raw data stored using pointers within imgCIF files. The example file b4_master.cif contains such pointers. For example, to read the raw data array labelled ext1 in b4_master.cif the following call is used:
x = imgload("b4_master.cif","ext1")

Note that this command will only work if the images referred to in b4_master.cif actually exist. To create those files locally, unpack the b4_mini.tar.bz2 contents into location test/testfiles/test_cbf_unzipped.

  1. get_beam_centre(filename). This will calculate the beam centre in pixel and detector coordinates with all axes at zero. get_beam_centre(filename,scan_name,frameno) will calculate the beam centre for the given frame number of the scan.

Supported external formats

This release supports HDF5, CBF, and SMV (ADSC) formats, as well as Tar archives (optionally compressed using Bzip2, Gzip or Xzip) or Zip archives containing files in those formats. In all cases the format stated by the imgCIF file is used.

Contributions

Contributions are welcome. You may raise an issue using the tab above, or clone the repository and create a pull request with your changes.