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catalystneuro / roiextractors

Python-based module for extracting from, converting between, and handling optical imaging data from several file formats. Inspired by SpikeInterface.
https://roiextractors.readthedocs.io/en/latest/index.html
BSD 3-Clause "New" or "Revised" License
12 stars 7 forks source link

add inscopix imaging extractor #276

Closed bendichter closed 5 months ago

bendichter commented 9 months ago

blocked by https://github.com/inscopix/py_isx/issues/48

pauladkisson commented 6 months ago

Looks like this is unblocked as of v1.0.4 (https://github.com/inscopix/py_isx/issues/48#issuecomment-2033057806)

CodyCBakerPhD commented 6 months ago

Looks like the test cases just need to be updated now - also a CHANGELOG entry

bendichter commented 6 months ago

This is finally working. Though I think dropping 3.8 should probably be a different PR

CodyCBakerPhD commented 6 months ago

I'll defer to @pauladkisson for PR review but mostly looks good to me

Though I think dropping 3.8 should probably be a different PR

For the global drop of 3.8 I would agree, and then we can do it synchronously throughout the ecosystem across the next few weeks (I think we have a couple of months still)

However, you would still need various skips of isx stuff for 3.8 (such as in the CI installation step too) for this PR so maybe too much bother here?

Could do the 3.8 drop in separate PR, give that PR precedence, then come back to this?

pauladkisson commented 5 months ago

Happy to review, but will have to wait until 5/20

h-mayorquin commented 5 months ago

https://github.com/catalystneuro/neuroconv/pull/853

bendichter commented 5 months ago

depends on https://github.com/catalystneuro/roiextractors/pull/325

bendichter commented 5 months ago

@h-mayorquin I added a method as you suggested. I also added a test to ensure that the dtype of the data indeed matches this dtype extacted from the metadata (this did not match in a previous version of the isx package)

codecov[bot] commented 5 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 79.57%. Comparing base (7aa2a63) to head (6f2f8d4). Report is 21 commits behind head on main.

:exclamation: Current head 6f2f8d4 differs from pull request most recent head a41d30c. Consider uploading reports for the commit a41d30c to get more accurate results

Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/catalystneuro/roiextractors/pull/276/graphs/tree.svg?width=650&height=150&src=pr&token=UA958XVSZP&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=catalystneuro)](https://app.codecov.io/gh/catalystneuro/roiextractors/pull/276?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=catalystneuro) ```diff @@ Coverage Diff @@ ## main #276 +/- ## ========================================== + Coverage 79.37% 79.57% +0.19% ========================================== Files 39 41 +2 Lines 3069 3099 +30 ========================================== + Hits 2436 2466 +30 Misses 633 633 ``` | [Flag](https://app.codecov.io/gh/catalystneuro/roiextractors/pull/276/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=catalystneuro) | Coverage Δ | | |---|---|---| | [unittests](https://app.codecov.io/gh/catalystneuro/roiextractors/pull/276/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=catalystneuro) | `79.57% <100.00%> (+0.19%)` | :arrow_up: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=catalystneuro#carryforward-flags-in-the-pull-request-comment) to find out more. | [Files](https://app.codecov.io/gh/catalystneuro/roiextractors/pull/276?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=catalystneuro) | Coverage Δ | | |---|---|---| | [src/roiextractors/extractorlist.py](https://app.codecov.io/gh/catalystneuro/roiextractors/pull/276?src=pr&el=tree&filepath=src%2Froiextractors%2Fextractorlist.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=catalystneuro#diff-c3JjL3JvaWV4dHJhY3RvcnMvZXh0cmFjdG9ybGlzdC5weQ==) | `100.00% <100.00%> (ø)` | | | [...tractors/extractors/inscopixextractors/\_\_init\_\_.py](https://app.codecov.io/gh/catalystneuro/roiextractors/pull/276?src=pr&el=tree&filepath=src%2Froiextractors%2Fextractors%2Finscopixextractors%2F__init__.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=catalystneuro#diff-c3JjL3JvaWV4dHJhY3RvcnMvZXh0cmFjdG9ycy9pbnNjb3BpeGV4dHJhY3RvcnMvX19pbml0X18ucHk=) | `100.00% <100.00%> (ø)` | | | [...ors/inscopixextractors/inscopiximagingextractor.py](https://app.codecov.io/gh/catalystneuro/roiextractors/pull/276?src=pr&el=tree&filepath=src%2Froiextractors%2Fextractors%2Finscopixextractors%2Finscopiximagingextractor.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=catalystneuro#diff-c3JjL3JvaWV4dHJhY3RvcnMvZXh0cmFjdG9ycy9pbnNjb3BpeGV4dHJhY3RvcnMvaW5zY29waXhpbWFnaW5nZXh0cmFjdG9yLnB5) | `100.00% <100.00%> (ø)` | |