March 15, 2017 Software Open Access

Agilent FTIR Mosaic Image File Reader

Henderson, Alex

This MATLAB source code will read an Agilent FTIR hyperspectral mosaicked image file set.

Version 6. Release_1.0

Source code and further information is available here: https://bitbucket.org/AlexHenderson/agilent-file-formats/ Please check before use to see whether there is an updated version.

The Agilent (formerly Varian) file format consists of a number of files with extensions: .dms, .dmt, .drd, .dmd. This function will import that data into MATLAB.

The source code is licenced under the GPL v3 licence. This means if you change it, and release your new version, you MUST release the source code too. If you would like to use the code under different licensing conditions, please contact the author.

If you find this code fails for whatever reason, please let the author know using the issues section of the BitBucket website: https://bitbucket.org/AlexHenderson/agilent-file-formats/issues

If you make use of this file in your work, please consider citing this repository deposition: DOI:10.5281/zenodo.399238

Alex Henderson <alex.henderson@manchester.ac.uk>

Usage Information 

% Function: agilentMosaic
% Usage: 
%   [wavenumbers, data, width, height, filename, acqdate] = agilentMosaic();
%   [wavenumbers, data, width, height, filename, acqdate] = agilentMosaic(filename);
%   [wavenumbers, data, width, height, filename, acqdate] = agilentMosaic(filename, keepme);
%
% Purpose:
%   Extracts the spectra from an Agilent (formerly Varian) .dmt/.dms/.dmd
%   file combination. Plots an image of the total signal.
%
%  input:
%   'filename' string containing the full path to the .dms file (optional)
%   'keepme' vector of wavenumber values in pairs indicating the limits of regions to retain (optional)
% 
%  output:
%   'wavenumbers' is a list of the wavenumbers related to the data
%   'data' is a 3D cube of the data in the file ((fpaSize x X) x (fpaSize x Y) x wavenumbers)
%   'width' is width in pixels of the entire mosaic
%   'height' is height in pixels of the entire mosaic
%   'filename' is a string containing the full path to the .dms file
%   'acqdate' is a string containing the date and time of acquisition
%
%                     *******Caution******* 
%   This code is a hack of the Agilent format and the location of the data
%   within the file may vary. Always check the output to make sure it is
%   sensible. If you have a file that doesn't work, please contact Alex.
%
%   Copyright (c) 2011 - 2017, Alex Henderson 
%   Contact email: alex.henderson@manchester.ac.uk
%   Licenced under the GNU General Public License (GPL) version 3
%   http://www.gnu.org/copyleft/gpl.html
%   Other licensing options are available, please contact Alex for details
%   If you use this file in your work, please acknowledge the author(s) in
%   your publications. 
%
%       version 6 March 2017