Metadata-Version: 2.1
Name: treem
Version: 1.0.0
Summary: Tree-like morphology data processing
Home-page: https://github.com/a1eko/treem
Author: Alexander Kozlov
Author-email: akozlov@kth.se
License: MIT
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
License-File: LICENSE


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).

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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
* ``render``   - Display 3D model of the reconstruction
* ``repair``   - Correct reconstruction errors
* ``view``     - Show morphology structure


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

Install the latest stable release:

    pip3 install treem

Install a development version:

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

See also ``pip3`` documentation for installation alternatives.


Dependencies
------------

Module ``treem`` has minimal runtime dependencies:

* ``python`` >= 3.7
* ``matplotlib``
* ``numpy``
* ``PyOpenGL`` (optional) enables ``swc render`` command

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://treem.readthedocs.io/en/latest/).



