Metadata-Version: 2.1
Name: TraceAnalyser
Version: 0.0.2
Summary: Time Series Analysis Software
Author: Piers Turner
Author-email: piers.turner@physics.ox.ac.uk
License: 
        The MIT License (MIT)
        
        Copyright (c) 2023 Piers Turner
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in
        all copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
        THE SOFTWARE.
        
Project-URL: Bug Tracker, https://github.com/piedrro/TraceAnalyser/issues
Project-URL: Documentation, https://github.com/piedrro/TraceAnalyser#README.md
Project-URL: Source Code, https://github.com/piedrro/TraceAnalyser
Project-URL: User Support, https://github.com/piedrro/TraceAnalyser/issues
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Framework :: napari
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Image Processing
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: qtpy
Requires-Dist: scipy
Requires-Dist: scikit-learn
Requires-Dist: pymatreader
Requires-Dist: pyqtgraph
Requires-Dist: pomegranate ==0.14.8
Requires-Dist: pandas
Requires-Dist: matplotlib
Requires-Dist: tqdm
Requires-Dist: hmmlearn
Requires-Dist: originpro
Requires-Dist: tensorflow[and-cuda]
Requires-Dist: mat4py
Requires-Dist: tsaug
Requires-Dist: tensorboard
Requires-Dist: parmap
Requires-Dist: openpyxl
Requires-Dist: retrying
Requires-Dist: glob2
Requires-Dist: pyqt5-tools
Requires-Dist: torch
Requires-Dist: tsai
Requires-Dist: ipykernel
Provides-Extra: testing
Requires-Dist: tox ; extra == 'testing'
Requires-Dist: pytest ; extra == 'testing'
Requires-Dist: pytest-cov ; extra == 'testing'
Requires-Dist: pytest-qt ; extra == 'testing'
Requires-Dist: napari ; extra == 'testing'
Requires-Dist: pyqt5 ; extra == 'testing'

# TraceAnalyser

[![License MIT](https://img.shields.io/pypi/l/TraceAnalyser.svg?color=green)](https://github.com/piedrro/TraceAnalyser/raw/main/LICENSE)
[![PyPI](https://img.shields.io/pypi/v/TraceAnalyser.svg?color=green)](https://pypi.org/project/TraceAnalyser)
[![Python Version](https://img.shields.io/pypi/pyversions/TraceAnalyser.svg?color=green)](https://python.org)
[![tests](https://github.com/piedrro/TraceAnalyser/workflows/tests/badge.svg)](https://github.com/piedrro/TraceAnalyser/actions)
[![codecov](https://codecov.io/gh/piedrro/TraceAnalyser/branch/main/graph/badge.svg)](https://codecov.io/gh/piedrro/TraceAnalyser)

A standalone application for analysing time series data, which includes features for processing/labelling/filtering traces and facilitates the detection of hidden states using **Hidden Markov Modelling** (HMM). 
It also includes embdedded pre-trained Deep Learning (InceptionTime) models for classifying/labelling traces.

This is still undergoing development, so some features may not work as expected.

This was built by Dr Piers Turner from the Kapanidis Lab, University of Oxford.

----------------------------------

<!--
Don't miss the full getting started guide to set up your new package:
https://github.com/napari/cookiecutter-napari-plugin#getting-started

and review the napari docs for plugin developers:
https://napari.org/stable/plugins/index.html
-->

## Installation

You can install `TraceAnalyser` via [PyPI]:

    conda create –-name TraceAnalyser python==3.9
    conda activate TraceAnalyser

    pip install TraceAnalyser

You can install `TraceAnalyser` via [GitHub]:

    conda create –-name TraceAnalyser python==3.9
    conda activate TraceAnalyser
    conda install -c anaconda git
    conda update --all

    pip install git+https://github.com/piedrro/TraceAnalyser.git

## To install **MATLAB** engine (Windows):

python 3.9 requires MATLAB >= 2021b

MATLAB compatibility: https://uk.mathworks.com/support/requirements/python-compatibility.html

    pip install matlabengine

This will likely fail due to a MATLAB version issue. 
Read the traceback, and install the recomended verison. 
Then try again:

    pip install matlabengine==XXXX

## Terminal Commands

To launch the Trace Analyser App:

    analysis

To launch an ebFRET instance (requires matlab engine installation):
    
    ebFRET

## Contributing

Contributions are very welcome. Tests can be run with [tox], please ensure
the coverage at least stays the same before you submit a pull request.

## License

Distributed under the terms of the [MIT] license,
"TraceAnalyser" is free and open source software

## Issues

If you encounter any problems, please [file an issue] along with a detailed description.

[napari]: https://github.com/napari/napari
[Cookiecutter]: https://github.com/audreyr/cookiecutter
[@napari]: https://github.com/napari
[MIT]: http://opensource.org/licenses/MIT
[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin

[file an issue]: https://github.com/piedrro/TraceAnalyser/issues

[napari]: https://github.com/napari/napari
[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
[PyPI]: https://pypi.org/
