Metadata-Version: 2.1
Name: FlowIO
Version: 1.3.0
Summary: FlowIO is a Python library for reading / writing Flow Cytometry Standard (FCS) files
Author-email: Scott White <whitews@gmail.com>
License: BSD 3-Clause License
        
        Copyright (c) 2019, Scott White
        All rights reserved.
        
        Redistribution and use in source and binary forms, with or without
        modification, are permitted provided that the following conditions are met:
        
        * Redistributions of source code must retain the above copyright notice, this
          list of conditions and the following disclaimer.
        
        * Redistributions in binary form must reproduce the above copyright notice,
          this list of conditions and the following disclaimer in the documentation
          and/or other materials provided with the distribution.
        
        * Neither the name of the copyright holder nor the names of its
          contributors may be used to endorse or promote products derived from
          this software without specific prior written permission.
        
        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
        
Project-URL: Homepage, https://github.com/whitews/flowio
Project-URL: Documentation, https://flowio.readthedocs.io/en/latest/
Project-URL: Repository, https://github.com/whitews/flowio
Project-URL: Issues, https://github.com/whitews/FlowIO/issues
Project-URL: Changelog, https://github.com/whitews/FlowIO/releases
Classifier: Development Status :: 5 - Production/Stable
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.7
Description-Content-Type: text/markdown
License-File: LICENSE
Provides-Extra: test
Requires-Dist: numpy>=1.17; extra == "test"

# FlowIO

[![PyPI license](https://img.shields.io/pypi/l/flowio.svg?colorB=dodgerblue)](https://pypi.python.org/pypi/flowio/)
[![PyPI pyversions](https://img.shields.io/pypi/pyversions/flowio.svg)](https://pypi.python.org/pypi/flowio/)
[![PyPI version](https://img.shields.io/pypi/v/flowio.svg?colorB=blue)](https://pypi.python.org/pypi/flowio/)
[![DOI](https://zenodo.org/badge/14634514.svg)](https://zenodo.org/badge/latestdoi/14634514)


[![Test (master)](https://github.com/whitews/FlowIO/actions/workflows/tests_master.yml/badge.svg)](https://github.com/whitews/FlowIO/actions/workflows/tests_master.yml)
[![Test (develop)](https://github.com/whitews/FlowIO/actions/workflows/tests_develop.yml/badge.svg)](https://github.com/whitews/FlowIO/actions/workflows/tests_develop.yml)
[![Coverage](https://codecov.io/gh/whitews/FlowIO/branch/master/graph/badge.svg)](https://codecov.io/gh/whitews/flowio)
[![Documentation Status](https://readthedocs.org/projects/flowio/badge/?version=latest)](https://flowio.readthedocs.io/en/latest/?badge=latest)
![PyPI - Downloads](https://img.shields.io/pypi/dm/flowio)

## Overview

FlowIO is a Python library for reading / writing Flow Cytometry Standard (FCS) 
files, with zero external dependencies and is compatible with Python 3.7+.

FlowIO retrieves event data exactly as it is encoded in the FCS file: as a 
1-dimensional list without separating the events into channels or performing 
any preprocessing (e.g. applying gain). Metadata stored in the FCS file is 
available as a dictionary via the 'text' attribute. Basic attributes are also 
available for commonly accessed properties. For example, the channel count 
can be used to easily convert the event data to a multi-column NumPy array:

```
import flowio
import numpy

fcs_data = flowio.FlowData('example.fcs')
npy_data = numpy.reshape(fcs_data.events, (-1, fcs_data.channel_count))
```

For higher level interaction with flow cytometry data, including GatingML and FlowJo 10 support, 
see the related [FlowKit](https://github.com/whitews/FlowKit) project.

## Installation

The recommended way to install FlowIO is via the `pip` command:

```
pip install flowio
```

Or, if you prefer, you can install from the GitHub source:

```
git clone https://github.com/whitews/flowio
cd flowio
pip install .
```

## Documentation

The FlowIO API documentation is available [on ReadTheDocs here](https://flowio.readthedocs.io/en/latest/?badge=latest). If you have any questions about FlowIO or find any bugs [please submit an issue to the GitHub repository here](https://github.com/whitews/FlowIO/issues/new/).

### Changelogs

[Changelogs for versions are available here](https://github.com/whitews/FlowIO/releases)

