Python package for numerical analysis of spectroscopic data
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README.md

spectroscopy

Version 2.0

Created by Alex Pronschinske (email: ampron@gmail.com)

Introduction

The purpose of this package is to enable python-based numerical analysis of spectroscopic data. This version has been primarily written to deal with scanning tunneling spectroscopy (STS) data that has been generated by Omicron MATRIX software and saved in ASCII-encoded text files by SPIP. Currently there are some generalization included to read in other typical column-formated text file data as well.

Software Requirements

This package has the following dependencies: * python 2.7 * numpy >= 1.5.1 (lower versions are untested) * scipy >= 0.9.0 (lower versions are untested) * matplotlib >= 1.1.0

Installation

You may install this package directly into your python distribution, but it is recommended that you instead install a .pth (path) file point to a custom installation location.

Instructions:

1. Open python in the terminal and look up site-packages folder.
   >>> import sys
   >>> for p in sys.path:
   >>>     print repr(p)
   >>> 
2. Typical paths

    * Windows 7:     "C:\Python2.7\site-packages\"
    * Linux:         "/usr/lib/python2.7/dist-packages"
    * Linux (local): "/home/user_name/.local/lib/python2.7/site-packages/"

3. Copy the "spectroscopy" folder into the desired folder
4. Or, make a ".pth" file in the site-packages folder with one line that is
  the location of the "spectroscopy" folder

Script Use

There are some common use script installed in the "specroscopy/scripts" folder that can be run from the terminal. The command is expected to have the following form:

$ python -m spectroscopy script_name -f arg1 arg2

In this command the "-m" flag tells python that the spectroscopy package is to be run as a script. The "script_name" will be the name of the python module installed in the scripts folder. We see as an example "-f" is how one includes any flags and "arg1 arg2" is how one includes any input arguments (note they are space separated, a text space within an argument should be preceded with a backslash, ""). The user should refer to the individual script documentation to see what flags and arguments are optional and required.

================= Importing package

All modules in the "spectroscopy/" directory will be *-imported into the spectroscopy module when it is imported, so that the command:

   >>> import spectroscopy

will yield an object containing all functions and classes in all submodules, but not modules in the subpackages (such as scripts or importers). Although, if the user desires they can import individual submodules.