Metadata-Version: 1.1
Name: thorns
Version: 1
Summary: Spike analysis software
Home-page: https://github.com/mrkrd/thorns
Author: Marek Rudnicki
Author-email: marek.rudnicki@tum.de
License: GPLv3+
Download-URL: https://github.com/mrkrd/thorns/tarball/master
Description: thorns and waves
        ================
        
        ::
        
          __|________|_____|_|_|___|_____|____||_____|_____|_____|____|_____|___||______
          _|_______________________|______|_________|_______|_____|____|__|________|_|__
          _____|___|__|_____|_______|____|_________________________|__|_________|_______
          ___|_______|_____|______|_____|_______|__|___|________|______|___|____________
          __|__|_______|_____|__|___|______|________|______|______|_____|_______THORNS__
        
        
        
        With *thorns* you can analyze and display `spike trains`_ generated by
        neurons.  It can be useful for the analysis of experimental and
        simulation data using Python.  For example, you can easily calculate
        peristimulus time histogram (PSTH), interspike time histogram (ISIH),
        vector strength (VS), entrainment and visualize action potentials with
        raster plot.
        
        *waves* is a submodule with some useful signal processing and
        generation functions, e.g. generate ramped tone, amplitude modulation
        tone, FFT filter, set level (dB_SPL).
        
        The software was originally developed during my PhD in the group of
        `Werner Hemmert`_ at the TUM.  It is oriented towards auditory
        research, but it could be easily extended.
        
        .. _`spike trains`: https://en.wikipedia.org/wiki/Spike_train
        .. _`Werner Hemmert`: https://www.ei.tum.de/en/bai/home/
        
        
        
        Usage
        -----
        
        Don't forget to check our IPython Notebook DEMO_ and scripts in the
        examples_ directory!
        
        Initialize and load spike trains::
        
          import thorns as th
          from thorns.datasets import load_anf_zilany2014
        
          spike_trains = load_anf_zilany2014()
        
        
        
        Calculate vector strength::
        
          th.vector_strength(spike_trains, freq=1000)
        
        
        
        Raster plot::
        
          th.plot_raster(spike_trains)
          th.show()
        
        
        
        Generate and plot AM tone::
        
          import thorns.waves as wv
        
          sound = wv.amplitude_modulated_tone(
              fs=48e3,
              fm=100,
              fc=1e3,
              m=0.7,
              duration=0.1,
          )
        
          wv.plot_signal(sound, fs=48e3)
        
          wv.show()
        
        
        
        You can also browse the API documentation at
        https://pythonhosted.org/thorns/
        
        
        .. _DEMO: https://github.com/mrkrd/thorns/blob/master/examples/thorns_demo.ipynb
        .. _examples: examples
        
        
        
        Features
        --------
        
        - Analyzes and displays spike trains
        - Uses pandas.DataFrame as the main data container (spike trains,
          results)
        - Handy signal processing and generating functions: ``thorns.waves``
        - Map implementation with various backend (also parallel) and caching:
          ``thorns.util.map()``
        - Dumpdb: quickly dump ``map()``'s results in one script and load from
          another one: ``thorns.util.dumpdb()``, ``thorns.util.loaddb()``
        - Pure Python
        
        
        
        
        
        Installation
        ------------
        
        In order to use *thorns*, you'll need to install the following
        dependencies first:
        
        - Python (2.7)
        - Numpy
        - Scipy
        - Pandas
        - PyTables / tables
        - Matplotlib
        
        - py-notify (optional, enables notifications)
        
        
        Next, type in your command line::
        
           pip install thorns
        
        
        
        Contribute
        ----------
        
        - Open tasks: TODO.org_ (best viewed in Emacs org-mode)
        - Issue Tracker: https://github.com/mrkrd/thorns/issues
        - Source Code: https://github.com/mrkrd/thorns
        
        .. _TODO.org: TODO.org
        
        
        
        License
        -------
        
        The project is licensed under the GNU General Public License v3 or
        later (GPLv3+).
        
Platform: Linux
Platform: Windows
Platform: FreeBSD
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: End Users/Desktop
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Operating System :: POSIX
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2.7
