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

Two small improvements to `BrukerTiffMultiPlaneImagingExtractor` #268

Closed h-mayorquin closed 11 months ago

h-mayorquin commented 12 months ago

1) Avoid calculating calling determine_imaging_is_volumetric which parses the whole xml file twice. The code to get the streams already calculates this and if returns sucesfully the streams have plane_streams:

https://github.com/catalystneuro/roiextractors/blob/467bbb00c20d79ecdd383b39aa1ced2734fcb33e/src/roiextractors/extractors/tiffimagingextractors/brukertiffimagingextractor.py#L114-L116

2) When stream_name is not passed and there are multiple channels we can make the life of the user easier by already displaying the options which we have already available.

CodyCBakerPhD commented 12 months ago

Leaving this one to @alessandratrapani as well

codecov[bot] commented 11 months ago

Codecov Report

Merging #268 (b17b2b1) into main (518baca) will increase coverage by 0.03%. Report is 1 commits behind head on main. The diff coverage is 100.00%.

Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/catalystneuro/roiextractors/pull/268/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/268?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=catalystneuro) ```diff @@ Coverage Diff @@ ## main #268 +/- ## ========================================== + Coverage 79.13% 79.17% +0.03% ========================================== Files 39 39 Lines 3053 3054 +1 ========================================== + Hits 2416 2418 +2 + Misses 637 636 -1 ``` | [Flag](https://app.codecov.io/gh/catalystneuro/roiextractors/pull/268/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/268/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=catalystneuro) | `79.17% <100.00%> (+0.03%)` | :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/268?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=catalystneuro) | Coverage Δ | | |---|---|---| | [...iffimagingextractors/brukertiffimagingextractor.py](https://app.codecov.io/gh/catalystneuro/roiextractors/pull/268?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=catalystneuro#diff-c3JjL3JvaWV4dHJhY3RvcnMvZXh0cmFjdG9ycy90aWZmaW1hZ2luZ2V4dHJhY3RvcnMvYnJ1a2VydGlmZmltYWdpbmdleHRyYWN0b3IucHk=) | `96.10% <100.00%> (+0.40%)` | :arrow_up: |