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py_isx's Introduction

isx: pure-python API to read Inscopix data

This is a pure-python API to read Inscopix ISXD files.

Documentation

Read the documentation

Support

File type Support
ISXD CellSet
ISXD Movie
ISXD Movie (multi-plane)
ISXD Movie (dual-color)
GPIO data
ISXD Events
ISXD VesselSet

Install

Poetry

poetry add isx

pip

pip install isx

Caution

This is a work in progress, and all reading functions in the IDPS Python API are not supported yet.

Testing

This code is tested using GitHub Actions on the following python versions:

  • 3.9
  • 3.10
  • 3.11
  • 3.12

py_isx's People

Contributors

bendichter avatar brunoboivin avatar nosheen-adil avatar sg-s avatar zachary-ip avatar

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Forkers

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py_isx's Issues

Make sure license file is visible on PyPI

problem

setup.py file should contain something like this:

license_files = ('LICENSE.txt',),

but this isn't being created by our automatic generation of the setup.py file

Support dropped/cropped/blank frames

isxd movies can have invalid frames of the following type: dropped, cropped, blank.

They are not stored on disk, the only indication of them is in the json metadata. Currently this api breaks when trying to access the last frame of a movie with dropped frames because it's not correctly recalculating the "true" frame index on disk.

We need to update the Timing class to have these properties and update the read/write functions to support these invalid frames.

Movie frame data type inconsistent between operating systems

For reading "movie_u8.isxd" and "movie_longer_than_3_min.isxd" on unix operating systems, Movie.read(file_path).get_frame_data(0).dtype results in dtype('int64') , however on Windows, the dtype is dtype('int32'). Is this the intended behavior?

get cellset timestamps

I'm not sure if this is a duplicate of #13, but what is the recommended way to get the frame times from a cellset file?

PyPi package name mirrors API package name

Both the API distributed with IDPS and the PyPi package share the package name 'isx'
This can cause ambiguity as to which package is installed when trying to automate package installation and dependency checking using setup tools or another method. Perhaps the API shipped with IDPS should be renamed to isx_api or something similar in future releases.

Cheers!

Upgrades py_isx

support for VesselSets

  • write classes for isx.VesselSet
  • structure VesselSet classes and methods like it is in the original isx (IDPS) implementation
  • use the isx.CellSet in py_isx as a reference

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