Metadata-Version: 2.1
Name: treem
Version: 1.1.0.dev3
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
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
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).

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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

or sometimes more convenient as

    swc <command> file [file ...] [options] 

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+https://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/).


Funding
-------

Horizon 2020 Framework Programme (785907, HBP SGA2); Horizon 2020 Framework Programme (945539, HBP SGA3); Vetenskapsrådet (VR-M-2017-02806, VR-M-2020-01652); Swedish e-science Research Center (SeRC); KTH Digital Futures.

We acknowledge the use of Fenix Infrastructure resources, which are partially funded from the European Union's Horizon 2020 research and innovation programme through the ICEI project under the grant agreement No. 800858.

The computations and testing were enabled by resources provided by the Swedish National Infrastructure for Computing (SNIC) at PDC KTH partially funded by the Swedish Research Council through grant agreement no. 2018-05973.
