freesiemens / ft-ir-spectrum-analyser- Goto Github PK

A simple python app I wrote to get myself acquainted with the python programming language. The app illustrates the application of a discrete real Fourier transform algorithm to process raw interferograms produced by a Michelson interferometers (such as the ones found in many commercial I.R. spectrometers) into chemically interpretable I.R. spectra.

The GUI and plotting components of the application are based on the pyQt4 and pyqtgraph tool kits. All of the numerical processing functions have been coded from scratch on purpose and don't use built in libraries, this was done for purely educational reasons.

Some future functionality and changes that I'm planning to add to the application:

1. Clean up the code - addition of well functioning init methods to all classes to make the modules more generic and easily modified.
2. The addition of more control over processing parameters which includes dialogues for setting instrumental parameters such as resolution and various apodization functions to play with.
3. Peak width/integration and multiplicity detection in the peak picking component of the app.
4. Better mouse pointer integration in the peak picking tool.
5. Automatic functional group identification based on a machine learning model - Still have to figure out exactly how I'm going to go about this feature.

The application has been tested using the following dependencies installed on a new blank anaconda environment: python 2.7.13 qt=4.8.7 pyqt=4.11.4 pyqtgraph=0.10.0

The JCAMP-Reader folder contains a prototype script for opening certain JCAMP I.R. spectra files. The script is still under development and will be integrated into the main application once support for all JCAMP files have been added.

An excellent introduction to the theory behind the processing of inteferograms generated by FT-I.R. spectrometers can be found at the link below http://www.ccmr.cornell.edu/wp-content/uploads/sites/2/2015/11/Understanding_FTIR.pdf .I do not own this material or the server that it is hosted on and merely came across this link with a Google search.

Instructions for running the application using an anaconda environment: Installing and setting up conda environment:

1)Download and install miniconda with python 2:

Windows -> https://repo.continuum.io/miniconda/Miniconda2-latest-Windows-x86_64.exe Ubuntu -> https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh Platform specific installation instructions https://conda.io/docs/install/quick.html

2)type the following into the command line to install dependencies: $conda create --name test1 $conda install qt=4.8.7 $conda install pyqt=4.11.4 $conda install pyqtgraph

3)activate the environment(bash/cmd): Windows: $activate test1 Linux: $source activate test1 *to verify that environment has been installed successfully : $conda list -> should display required dependencies

4)Running and testing the app python Start.py *An example file containing raw instrumental(interferogram) is provided in the sample folder for testing purposes. The application can also convert processed spectra back to theoretical interferograms to simulate instrumental raw data.

*Removing miniconda from Linux -> 1)delete miniconda folder 2)remove "path=/usr/miniconda/bin" line from ./usr/home/.bashrc file :)