inscopix/py_isx

Experimentlal pure-python API to read Inscopix data

py_isx's Issues

Support for Movie.get_frame_timestamp

Use pytest fixtrures to handle downloading of test data

update readme on PyPI

Build and provide wheels

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

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!

docs: get_cell_image_data

It looks like the CellSet.get_cell_image_data method is missing from the docs.

Set up PyPI publishing

Switch tests to downloading from test data on this repo

Simplify github actions and tests similar to ideas-python-utils

Merge the small tests into a single action

add license

Support for Movie.get_acquisition_info

remove some extra cruft

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?

new wheels should be pushed to PyPI based on tags

• indicate in pyproject.toml that the version number is always "dev"
• version number in setup.py should be read dynamically from tag
• action should only run when we make a tag/release

Add Movie Support

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.

Separate code from __init__.py into submodules

It's atypical for a Python package to have all of it's relevant code specified in the __init__.py file: https://github.com/inscopix/py_isx/blob/main/isx/__init__.py

Would it be possible to break this into submodules?

sklearn is usually a good reference for how to structure a Python package

clicking on logo should go to main page, not github page

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?

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

Support the data_type attribute in the Movie class

Support for multiplane movies

should support reading mulit-plane movies

improvements to docs

a deploy make target and set up github pages for docs

fix for 2nd sed step

Support for multicolor movies