jfernandz/gvtxto-parser

Script to parse txt output files printed by GammaVision spectroscopy software

GammaVision output parser

This script parses output .txt files from GammaVision spectroscopy software, It does convert those files to a long format much more treatable from statistic point of view.

The more appropriate way to treat this output files should be using R, however this script does clean that info and rearrange the values in a long format. Then you are gonna be able to treat those values with any kind of statistical software.

Usage

A general usage would be

$ ./gvtxto-parser.py [-i/--input <filename.txt>] [-o/--output <filename.DAT>] [-ot/--out-type {enhanced|raw|csv}]

In the case you don't provide any option, you will be prompted about input and output files (tab-autocomplete has not been implemented in this prompting mode, so I recommend in-line mode to take advantage of shell native autocomplete) and --out-type is set as raw by default.

• enhanced

  It will parse also GammaVision .txt header. Which consist in info about date, time and a description previously provided by user in GammaVision.

• raw

  It will parse the GammaVision output .txt to generate a file with channels raw data

• csv

  This will produce a .csv file (comma separated values), this is the most appropriate format to treat with R or any spreadsheet. You must use .csv extension to output file name in this case.

Dependencies

Further than python, you will need to install a few extra modules available through pip:

• click to handle/parse command line arguments.
• regex to parse data using regular expresions.

You will be able to install these packages performing the following commands, depending on your OS.

Windows

• Download python from their official website

• Install python

  • Launch python install process (double click in python-<whatever>.exe). you will be asked about some admin password if you choose install launcher for all users (recommended), which is marked by default, and I also recommend to keep that tick enabled.

    • I of course also recommend choose the option Add python <whatever> to PATH, like this picture shows

      

      This will allow you to run the script directly from command line using

      .\gvtxto-parser.py [option1] [option2] ...

      And you will not need explicitly call installed python binary (during previous install process) before type gvtxto-parser.py command.

      ==============

      In other way (if you have not added python to PATH environment variable) you should run something like:

      C:\Users\<whatever>\AppData\Local\programs\Python\Python<whatever> .\gvtxto-parser.py [option1] [option2] ...
      

• Upgrade pip, install click and regex

  • This script does not require admin privileges, it is fully functional at user space. As much, you will be asked for some admin password when performing main python install process, but this is normal, of course; it is related to any kind of software install process in the system. So, open a new cmd window and type the following commands:

    • Upgrade pip

    python -m pip install --upgrade pip
    

    • Install click and regex

    python -m pip install --user click regex
    

You also may want to add python to your PATH environment variable, if you did not when you did start python install process.

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(Optional) To perform a system-wide install you must launch your python-<whatever>.exe installer as admin, and perform the pip upgrade, click and regex install process in a cmd window with elevated privileges.

Linux

• Install python

  I recommend to use the package present at your distro repositories. You will need to perform this operation as root.

• Upgrade pip

  First update your pip module. From your distro repositories for a system-wide install or using pip itself

  $ python -m pip install --user --upgrade pip
  

• Install click and regex. From your distro repos (system-wide) or using pip, as follows.

  $ python -m pip install --user click regex
  

License

This project is licensed under GPLv3. - see the LICENSE.md file for details.