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Package for processing spectroscopy data

Project description

Introduction

specdal is a Python package for loading and manipulating field spectroscopy data. It currently supports readers for ASD, SVC, and PSR spectremeters. specdal provides useful functions and command line scripts for processing and aggregating the data.

Features

  1. Command line interface

    • specdal_info: lightweight script to read and display content of spectral files

    • specdal_pipeline: default script to convert spectral files into datasets and figures

  2. Python interface

    • readers for .asd, .sig, .sed spectral files - Pico files (WIP)

    • spectral functions that operate on pandas objects

      • interpolation

      • jump_correction

      • joining proximal measurements (WIP)

    • Spectrum and Collection classes which wrap around pandas objects to provide simpler interface

Tutorials

See the Jupyter notebooks in (PROVIDE A LINK HERE).

Installation

Prerequisite

  1. Setup virtualenv (recommended)

    $ pip install --user virtualenv
    $ mkdir ~/venv
    $ virtualenv -p python3 ~/venv/specdal
    $ source ~/venv/specdal/bin/activate
    
    $ ... # install/use specdal
    
    $ deactivate

Via pip

  1. Install Python 3

    $ pip3 install specdal --upgrade

Development version

  1. Open terminal or Git-bash and navigate to the desired directory using cd <directory>.

  2. The following command will create a directory SpecDAL containing SpecDAL:

    $ git clone https://github.com/EnSpec/SpecDAL.git
    $ cd SpecDAL
  3. To update the package, go to SpecDAL directory and run the following command:

    $ git pull origin master
  4. To install specdal in development mode

    $ source ~/venv/specdal/bin/activate # recommended (see virtualenv section)
    $ pip3 install -r requirements.txt
    $ python setup.py develop
    
    $ ... # edit and test specdal
    
    $ python setup.py develop --uninstall

Project details


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