SPA-file-reader

SPA is the default file type of Thermo Scientific(TM) OMNIC Series Software(TM). These files store infrared (IR) spectral data in a binary format, which makes data analysis and processing unnecessarily difficult without OMNIC Series Software(TM).

As a student without home-access to OMNIC software (and who may or may not have saved all of his IR data in the SPA format), I wanted to find a way to extract my spectral data and save them in an easy-to-process and human-readable format. Thankfully, a Cprogramming user, JonathanS, put together a functional C++ program capable of extracting these data. SPA-file-reader is a continuation of Jonathan's work.

Currently, this program is entirely capable of converting the SPA files found in the 'SPA-Files' folder to CSV files. The spectra were taken using a Nicolet iS10 FT-IR spectrometer. It is unlikely, however, that this program will work as-is for SPA files generated by a different spectrometer; some effort would need to be put forth in order to determine the offset addresses where transmission/absorption data begins and ends, the step-size (in inverse centimeters) between consecutive data, the smallest or largest wavenumber at which transmission/absorption was measured, and the order and format of the data.

How to use this program

Once compiled, you can view the usage statement from the command-line in Windows or Linux by executing the program without any arguments, or with the optional arguments -h, -?, or --help.

Compiling the latest source files (located in src)

This program has been successfully compiled on Linux (Ubuntu 18.04 LTS) using g++ and on Windows using Visual Studio Build Tools 2017 RC. Once the repository has been cloned, users should change directory into the src folder from the command-line. From there, they can execute the following commands to compile the source files into an executable.

On Linux

Using GNU make (recommended)

$ cd src
$ make        # Create the `spa-reader` executable
$ make clean  # (Optional.) Removes .o object files from the directory

Using g++

$ g++ -std=c++11 main-with-new-cla.cpp data-processing.cpp parse-command-line-args.cpp print-usage.cpp read-write.cpp str-to-int.cpp -o spa-reader

On Windows (Developer Command Prompt for VS 2017 RC)

> cl /EHsc main-with-new-cla.cpp data-processing.cpp parse-command-line-args.cpp print-usage.cpp read-write.cpp str-to-int.cpp /link /out:spa-reader.exe

Using the old source files (located in src/old)

Assuming a user has access to the g++ compiler, they may compile and run this program by following the provided steps.

1. Download the get-ir-mwv.cpp source file.
2. From a terminal, change directory to the folder which contains the downloaded source file.
3. Compile the source file into an executable with the following command:g++ get-ir-mwv.cpp -o get-ir-mwv
4. Move the SPA file from which data should be extracted into the directory containing the executable.
5. Run the executable on the SPA file with the following command: ./get-ir-mwv <SPA Filename>

Example:

./get-ir-mwv 0min-1-97C.SPA

If everything works, the user should now have a new file in the current directory named <SPA Filename>.CSV (e.g. 0min-1-97C.SPA.CSV) which contains the extracted transmission or absorption data.

If a user has multiple SPA files in the same directory, they may move the executable into that directory and process all SPA files at once by entering the following into a terminal running bash:

for FILE in *.SPA
  do
    ./get-ir-mwv $FILE
  done