isx 2.0.1

A python package for interacting with Inscopix data.

pyisx

isx is a python package for interacting with Inscopix data. This package encapsulates the following I/O functionality:

• Reading Inscopix files (.isxd, .isxb, .gpio, .imu)
• Writing Inscopix files (.isxd)
• Exporting Inscopix files to third-party formats (.mp4, .tiff, .csv)

The isx package is built from the pyisx project, a python binding for isxcore, a C++ API for interacting with Inscopix data.

Documentation

For help, please refer to the documentation.

Install

Pre-built binaries of this API can be installed from PyPi.

pip install isx

Note: For Apple Silicon (i.e., macOS arm64 architecture), the package is currently not natively supported. However, it's possible to use anaconda to configure an x86 environment and use the project.

CONDA_SUBDIR=osx-64 conda create -n <name> python=<python>
conda activate <name>
conda config --env --set subdir osx-64
pip install isx

Replace <name> with a name for the conda environment, and <python> with the python version to use.

Supported Platforms

This library has been built and tested on the following operating systems, for python versions 3.9 - 3.12.

OS	Version	Architecture
macOS	13	x86_64
Ubuntu (Linux)	20.04	x86_64
Windows	11	amd64

Development Guide

This guide documents how to build the python package wheel locally.

1. Clone the repo

Setup the repo and initialize its submodule:

git clone [e-mail]:inscopix/pyisx.git
git submodule update --init

1. Setup isxcore Follow the setup instructions for the C++ isxcore repo.

2. Setup python virtual environment

Create a python virtual environment, specifying the desired python version. This guide uses anaconda for demonstration, but other tools like virtualenv or poetry can also be used.

conda create -n <name> python=<python>
conda activate <name>

Replace <name> with a name for the conda environment, and <python> with the python version to use.

Note: On macOS systems with Apple Silicon, the conda environment is configured differently, since isxcore is currently only built for x86 architectures.

CONDA_SUBDIR=osx-64 conda create -n <name> python=<python>
conda activate <name>
conda config --env --set subdir osx-64

Replace <name> with a name for the conda environment, and <python> with the python version to use.

3. Install build & test dependencies

Inside the virtual environment install the following dependencies:

conda install -y build pytest

Note: For python 3.12 the build package must be installed used pip instead.

4. Build the package

make build THIRD_PARTY_DIR=/path/to/third/party/dir

5. Run the unit tests

make test THIRD_PARTY_DIR=/path/to/third/party/dir TEST_DATA_DIR=/path/to/test/data/dir

Support

For any questions or bug reports, please open an issue in our issue tracker.