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API:ENH: Adding raw traces as an output for the functional interface #237

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merged 5 commits into from Jul 20, 2021

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It would be useful for new users to quickly get started with implementing FISSA, and an important part of that is comparing the raw extracted traces to the decontaminated ones. Previously the functional interface did not allow for that, and with this PR I make that a standard behavior. Now with deltaf calculation:

deltaf_result, deltaf_raw = fissa.run_fissa(images_location, rois_location, return_deltaf=True)

and without

result, raw = fissa.run_fissa(images_location, rois_location, return_deltaf=False)

See also #169 for more discussion on this.

For now this is a draft pull request, because #228 should be finished first so that I can implement those changes in the notebook easily, and then update the plotting accordingly.

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codecov bot commented Jul 12, 2021

Codecov Report

Merging #237 (0cba6d8) into master (af2708e) will not change coverage.
The diff coverage is 100.00%.

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@@           Coverage Diff           @@
##           master     #237   +/-   ##
=======================================
  Coverage   94.12%   94.12%           
=======================================
  Files           8        8           
  Lines        1209     1209           
  Branches      302      302           
=======================================
  Hits         1138     1138           
  Misses         36       36           
  Partials       35       35           
Flag Coverage Δ
nbsmoke 59.88% <100.00%> (-0.17%) ⬇️
unittests 93.79% <100.00%> (ø)

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Impacted Files Coverage Δ
fissa/core.py 96.55% <100.00%> (ø)

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@scottclowe scottclowe mentioned this pull request Jul 12, 2021
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I have now updated the notebook to compare both the raw and separated traces. I also added an example to show how to inspect the neuropil region signals.

@swkeemink swkeemink marked this pull request as ready for review July 19, 2021 15:57
@swkeemink swkeemink merged commit 865fb95 into rochefort-lab:master Jul 20, 2021
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2 participants