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New plotting functions #163

Merged
merged 24 commits into from
Aug 13, 2024
Merged

New plotting functions #163

merged 24 commits into from
Aug 13, 2024

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AurelienJaquier
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@AurelienJaquier AurelienJaquier commented Jul 26, 2024 •
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  • new utility function to get extraction output pickle file paths
  • adding new plotting functions:
    • IV curve
    • FI curve
    • phase plot
    • sinespec / impedance (does not depend on responses, run its own hard-coded protocol)
  • allow new plotting functions in luigi task
  • refactored plotting function with new file: plotting_utils
    in order to shorten a little bit the plotting.py file
  • adds the current trace to efel (for impedance). it is the user responsibility to add a recording with type FixedDtRecordingStimulus or LooseDtRecordingStimulus and name {protocol_name}.iclamp.i for it to work as expected
  • added tests for most of the plotting_utils functions
  • merged test_plotting.py into new plotting_utils.py
  • linted tests/ folder (sorry, that adds a bunch of line changes)

Jaquier Aurélien Tristan added 4 commits July 25, 2024 15:44
new function: plot_IV_curves
7725867 
Change-Id: I5fc800ce7b50f85f35ef232d87450432c8f80d43
new function: phase_plot()
1cb4ef7 
Change-Id: I94067d4f6133e78a5137e9629988293f59a539df
adding plot_IF_curves_comparison and plot_trace_comparison functions
8df2beb 
Change-Id: I6f39334d37a6eaadfe928fa31e0c3ebf6bfedb90
small improvements
447b1b1 
Change-Id: I7abaf2ed0ffd53e2644a5c3ad52eec6b44ff6b69
@AurelienJaquier AurelienJaquier self-assigned this Jul 26, 2024
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codecov-commenter commented Jul 26, 2024 •
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Codecov Report

Attention: Patch coverage is 41.30719% with 449 lines in your changes missing coverage. Please review.

Project coverage is 52.42%. Comparing base (8d5b0ab) to head (9771ee2).
Report is 53 commits behind head on main.

Files Patch % Lines
bluepyemodel/emodel_pipeline/plotting.py 9.74% 250 Missing ⚠️
bluepyemodel/emodel_pipeline/plotting_utils.py 50.90% 135 Missing ⚠️
bluepyemodel/evaluation/recordings.py 25.00% 15 Missing ⚠️
...model/efeatures_extraction/efeatures_extraction.py 27.77% 13 Missing ⚠️
bluepyemodel/evaluation/protocols.py 7.14% 13 Missing ⚠️
bluepyemodel/tasks/emodel_creation/optimisation.py 0.00% 9 Missing ⚠️
bluepyemodel/tools/utils.py 16.66% 5 Missing ⚠️
bluepyemodel/evaluation/evaluator.py 55.55% 4 Missing ⚠️
bluepyemodel/emodel_pipeline/emodel_pipeline.py 0.00% 2 Missing ⚠️
bluepyemodel/emodel_pipeline/emodel_settings.py 94.73% 1 Missing ⚠️
... and 2 more
Additional details and impacted files 
@@            Coverage Diff             @@
##             main     #163      +/-   ##
==========================================
- Coverage   60.07%   52.42%   -7.66%     
==========================================
  Files         109      124      +15     
  Lines        7838    10299    +2461     
==========================================
+ Hits         4709     5399     +690     
- Misses       3129     4900    +1771

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

@AurelienJaquier AurelienJaquier marked this pull request as draft July 26, 2024 15:02
Jaquier Aurélien Tristan added 12 commits July 29, 2024 10:57
rename IF into FI
faa0f67 
Change-Id: Ieb348192e397f5cf7072b91b3e1b1236eb9eee86
improve plotting functions
826ee57 
Change-Id: I4562d27d5a6a4644a4a6765af14e8ef0c7f8af23
use holding current in absolute amplitude computation in IV/FI curve …
29e4062 
…plotting functions

Change-Id: Id8187b27ac1a170a42c140a9345dc5cdaf3a788e
Call plot_trace_comparison from plot_models
72a19da 
Change-Id: I32a9309341c4940e5750a80cd38776cfb6d89049
New file: plotting_utils to refactor plotting
bfbb4b2 
Change-Id: I5ed3d4573dc01c4c6558d272f73d9e269378706a
add tests for plotting utils
9217817 
Change-Id: Ica49bb1d5fa2655a185a4bfdac2f004f58dac7a8
update plot_models call in luigi task
25257ad 
Change-Id: I463dca3e2d6c872d81eff325c17b486e6477e74e
new plotting functions
6e8c396 
Change-Id: I7c59e356db623239c461a8e4edca184fed0b68e7
remove unuseful comment
547fd39 
Change-Id: I56e0c829db6edb4b231d5a5b39b920afae78377c
revert line used during tests
0f1602a 
Change-Id: I894a0658af15731ce8be8f528d5bc8f74edd12a1
fix bluepyefe functions tests
915acb1 
Change-Id: I75f01e37eb2d6b50309f3caa92ad3f65c964c1cd
Fix non soma voltage response edge case for phase plot
0b97b8a 
Change-Id: I8956d44314d6750c2b1aa9332d9298f69e72faa8
@AurelienJaquier AurelienJaquier marked this pull request as ready for review August 7, 2024 14:33
Jaquier Aurélien Tristan added 4 commits August 7, 2024 17:44
fix for new recoding type in configuration
0f7f9ff 
Change-Id: Idb40795269a9ef6c580f2175e5354d38e61766e5
black fix
58b37bb 
Change-Id: Icc0fae8ce116b4f61b2430519e320403583caef1
adding custom file path in emodel settings for BPE output
1c3e1e6 
Change-Id: I03bb06fa572aa0771d4fec9d3cb63f3e26773ae1
replaceing filepath by pklpath in variable names
6b64ddd 
Change-Id: I41716436518ee376bce909855a1a01bc2f30902a
small fixes
d3ce8d6 
Change-Id: I701eb9002dd8d759811622eb10bcc4ec91b5dbab
Jaquier Aurélien Tristan added 2 commits August 13, 2024 09:18
some more small fixes
540eed0 
Change-Id: Idf667560c64e3fcba83114f9e14d5549c33fbeea
improve emodel settings docstring
8c06717 
Change-Id: Iac654f81c66a7401a77fa181dd43618e499d4573
removed comment in recordings
9771ee2 
Change-Id: Idb85dcf3b0f9fc3a3777f5fd16a5d252ec70e614
ilkilic
ilkilic approved these changes Aug 13, 2024
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Great work, thank you! looks good to me

@AurelienJaquier AurelienJaquier merged commit 8387c4d into main Aug 13, 2024
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@AurelienJaquier AurelienJaquier deleted the iv-curve-plot branch August 13, 2024 08:20
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@darshanmandge darshanmandge darshanmandge left review comments

@ilkilic ilkilic ilkilic approved these changes

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@AurelienJaquier @codecov-commenter @darshanmandge @ilkilic