agilent-ir-formats

Agilent File Format Handling for Infrared Spectroscopy

Author: Alex Henderson <alex.henderson@manchester.ac.uk>
Version: 1.0.0
Copyright: (c) 2018-2025 Alex Henderson

About

Python package to read hyperspectral image files produced by infrared spectroscopy instrumentation from Agilent Technologies, Inc.

Currently, the code reads single or multi-tile images (*.seq files or *.dmt files)

Help information

``` python Class to open, read and export the contents of an Agilent Fourier Transform Infrared (FTIR) microscopy file.

FTIR instruments from Agilent Technologies Inc., that use a focal plane array detector, can store hyperspectral images in single 'tile' or multi-tile 'mosaic' file formats. This class can read both single and multi-tile images. Files with a filename extension of *.seq or *.dmt are compatible.

The class has properties and methods allowing the user to explore the numeric values in the file. In addition, some metadata values are also accessible.

Properties: wavenumbers x-axis values of the spectral dimension. data spectral intensities of the hyperspectral data as a 3D object (height, width, datapoints). totalspectrum sum of intensity in all pixels, as a function of wavenumber. totalimage sum of intensity in all pixels as a function of position (height, width). metadata simple metadata relating to these data. hdf5_metadata metadata arranged into a hierarchy for use in HDF5 export of these data.

Methods: read() open and parse a file. export_hdf5() create a representation on disc of the file in the HDF5 file format.

Static methods: filetype() string identifying the type of files this class reads. filefilter() string identifying the Windows file extensions for files this class can read. find_files() list of all readable files in a directory structure. isreadable() whether this class is capable of reading a given file. version() the version number of this code. ```

Usage

Example 1

Open a file and display simple metadata.

``` python from pprint import pprint # only for this example

from agilentirformats.agilentirfile import AgilentIRFile

filename = r"C:\mydata\myfile\myfile.dmt"

reader = AgilentIRFile() reader.read(filename)

wavenumbers = reader.wavenumbers intensities = reader.intensities metadata = reader.metadata

print(wavenumbers.shape) print(intensities.shape) pprint(metadata)

output...

(728,) (128, 256, 728) {'acqdatetime': '2023-05-11T14:37:02', 'filename': WindowsPath('C:/mydata/myfile/myfile.dmt'), 'firstwavenumber': 898.6699159145355, 'fpasize': 128, 'lastwavenumber': 3702.674331665039, 'numpts': 728, 'xlabel': 'wavenumbers (cm-1)', 'xpixels': 256, 'xtiles': 2, 'ylabel': 'absorbance', 'ypixels': 128, 'ytiles': 1} ```

Example 2

Convert a file to HDF5 format in the same location.

``` python from agilentirformats.agilentirfile import AgilentIRFile

filename = r"C:\mydata\myfile\myfile.dmt"

AgilentIRFile(filename).export_hdf5() ```

Requirements

• python >= 3.10
  
• h5py
• numpy

Licence conditions

Copyright (c) 2018-2025 Alex Henderson (alex.henderson@manchester.ac.uk)
Licensed under the MIT License. See https://opensource.org/licenses/MIT
SPDX-License-Identifier: MIT
Visit https://github.com/AlexHenderson/agilent-ir-formats/ for the most recent version

See also:

• MATLAB code available here: https://bitbucket.org/AlexHenderson/agilent-file-formats/