Metadata-Version: 2.1
Name: treem
Version: 1.0.0a1
Summary: Tree-like morphology data processing
Home-page: https://gitr.sys.kth.se/akozlov/treem
Author: Alexander Kozlov
Author-email: akozlov@kth.se
License: UNKNOWN
Keywords: neuron,morphology,reconstruction,processing,morphometry,modification,repair
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.7
Description-Content-Type: text/markdown
Requires-Dist: numpy
Requires-Dist: matplotlib


treem - neuron morphology processing tool
=========================================

Module provides data structure and command-line tools for accessing and
manipulating the digital reconstructions of the neuron morphology in
Stockley-Wheal-Cannon format (SWC).


Main classes
------------

Access to morphological data from the source code is supported by the
classes ``Tree``, ``Node``, ``Morph`` and ``SWC``.

=========  =========================================================
``Tree``   Recursive tree data structure
``Node``   Morphology data storage
``Morph``  Neuron morphology representation
``SWC``    Definitions of the data format
=========  =========================================================


Commands
--------

Common operations with SWC files are possible via the ``swc`` command-line
tool::

    swc <command> [options] file

List of ``swc`` commands:

=========  =========================================================
`check`    Test morphology reconstruction for structural consistency
`convert`  Convert morphology to compliant SWC format
`find`     Locate single nodes in the reconstruction
`measure`  Calculate morphometric features
`modify`   Manipulate morphology reconstruction
`repair`   Correct reconstruction errors
`view`     Show morphology structure
=========  =========================================================


Installation
------------

Basic installation
~~~~~~~~~~~~~~~~~~

Install the latest stable release::

    pip3 install treem

Install a development version::

    pip3 install git+git://github.com/a1eko/treem

See ``pip3`` documentation for installation alternatives.


Dependencies
~~~~~~~~~~~~

Module ``treem`` has minimal runtime dependencies:

* ``python`` >= 3.7
* ``matplotlib``
* ``numpy``

For testing and documentation, ``treem`` needs development packages with
third-party extensions:

* ``sphinx`` with ``napoleon`` and ``programoutput``
* ``pytest`` with ``pytest-cov``
* ``coverage``


Documentation
-------------

Documentation is available online at `Read the Docs <https://readthedocs.org/>`_.



