Support Online LFP calculation by jorblancoa · Pull Request #2118 · neuronsimulator/nrn

jorblancoa · 2022-12-08T15:40:48Z

No description provided.

bbpbuildbot · 2022-12-08T15:54:48Z

Logfiles from GitLab pipeline #89499 (:no_entry:) have been uploaded here!

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azure-pipelines · 2022-12-08T16:54:12Z

✔️ bbef09668eccbafec724f3c4b176c5205efe7356 -> Azure artifacts URL

bbpbuildbot · 2022-12-09T10:26:32Z

Logfiles from GitLab pipeline #89635 (:no_entry:) have been uploaded here!

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codecov-commenter · 2022-12-09T10:57:17Z

Codecov Report

Merging #2118 (985c561) into master (e7e1603) will decrease coverage by 0.02%.
The diff coverage is 0.00%.

@@            Coverage Diff             @@
##           master    #2118      +/-   ##
==========================================
- Coverage   58.93%   58.91%   -0.02%     
==========================================
  Files         619      619              
  Lines      121607   121637      +30     
==========================================
  Hits        71666    71666              
- Misses      49941    49971      +30

Impacted Files	Coverage Δ
src/coreneuron/io/nrn_filehandler.hpp	`55.84% <0.00%> (-10.31%)`	⬇️
src/coreneuron/io/nrn_setup.cpp	`88.36% <0.00%> (ø)`
src/coreneuron/io/nrnsection_mapping.hpp	`0.00% <0.00%> (ø)`
...eneuron/io/reports/report_configuration_parser.cpp	`0.00% <0.00%> (ø)`
src/coreneuron/io/reports/report_handler.cpp	`0.00% <ø> (ø)`
src/coreneuron/io/reports/report_handler.hpp	`0.00% <ø> (ø)`
src/nrniv/nrncore_write/io/nrncore_io.cpp	`76.54% <0.00%> (-0.76%)`	⬇️
src/nrniv/nrncore_write/utils/nrncore_utils.cpp	`54.47% <0.00%> (-2.56%)`	⬇️
src/nrniv/nrnsection_mapping.h	`10.86% <ø> (ø)`
test/coreneuron/unit/lfp/lfp.cpp	`100.00% <ø> (ø)`

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azure-pipelines · 2022-12-09T11:28:42Z

✔️ b4c89d8dad1d3d9b4833c379b654061e9216a0cd -> Azure artifacts URL

bbpbuildbot · 2022-12-09T12:40:20Z

Logfiles from GitLab pipeline #89686 (:no_entry:) have been uploaded here!

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azure-pipelines · 2022-12-09T15:13:30Z

✔️ 479b5adb82cebaf39e0941547da401b5007abc77 -> Azure artifacts URL

bbpbuildbot · 2022-12-09T15:14:43Z

Logfiles from GitLab pipeline #89773 (:no_entry:) have been uploaded here!

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azure-pipelines · 2022-12-09T20:38:06Z

✔️ 4cd7dc7e65a8eb24be3a9d544a579b0e6e25583c -> Azure artifacts URL

bbpbuildbot · 2022-12-09T21:11:26Z

Logfiles from GitLab pipeline #89827 (:no_entry:) have been uploaded here!

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bbpbuildbot · 2022-12-09T21:13:40Z

Logfiles from GitLab pipeline #89828 (:no_entry:) have been uploaded here!

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azure-pipelines · 2022-12-14T17:01:17Z

✔️ fcc7038 -> Azure artifacts URL

bbpbuildbot · 2022-12-14T17:04:10Z

Logfiles from GitLab pipeline #90677 (:no_entry:) have been uploaded here!

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azure-pipelines · 2023-01-13T14:21:19Z

✔️ 5edd04e -> Azure artifacts URL

bbpbuildbot · 2023-01-13T14:27:17Z

Logfiles from GitLab pipeline #94762 (:no_entry:) have been uploaded here!

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pramodk

quickly skimmed and here are few quick comments!

azure-pipelines · 2023-02-20T16:00:41Z

✔️ ed9d91e -> Azure artifacts URL

bbpbuildbot · 2023-02-20T16:12:27Z

bbpbuildbot · 2023-03-17T14:33:30Z

azure-pipelines · 2023-03-17T14:39:33Z

✔️ 76da430 -> Azure artifacts URL

azure-pipelines · 2023-03-20T11:00:32Z

✔️ 36ab094 -> Azure artifacts URL

bbpbuildbot · 2023-03-20T12:06:08Z

pramodk

I have just few minor last nitpicks!

azure-pipelines · 2023-03-23T11:48:25Z

✔️ a6a8ace -> Azure artifacts URL

bbpbuildbot · 2023-03-23T12:47:38Z

- Read lfp factors from neurodamus - Add lfp report type - Record LFP from multiple electrodes

- Record online LFP from multiple electrodes - Avoid writing lfp factors if size is 0

- Make it compatible with older py-neurodamus versions

Small improvements addressing feedback

azure-pipelines · 2023-03-23T13:40:38Z

✔️ 985c561 -> Azure artifacts URL

bbpbuildbot · 2023-03-23T14:44:42Z

jorblancoa closed this Dec 9, 2022

jorblancoa reopened this Dec 9, 2022

jorblancoa force-pushed the jblanco/lfp branch from 4cd7dc7 to fcc7038 Compare December 14, 2022 16:08

jorblancoa force-pushed the jblanco/lfp branch from fcc7038 to 5edd04e Compare January 13, 2023 11:41

jorblancoa marked this pull request as ready for review January 13, 2023 15:49

jorblancoa requested review from iomaganaris and pramodk January 13, 2023 15:49

pramodk reviewed Jan 13, 2023

View reviewed changes

jorblancoa force-pushed the jblanco/lfp branch from 15afbff to ed9d91e Compare February 20, 2023 15:10

jorblancoa force-pushed the jblanco/lfp branch from ed9d91e to 76da430 Compare March 17, 2023 13:25

jorblancoa force-pushed the jblanco/lfp branch from 76da430 to 36ab094 Compare March 20, 2023 10:19

jorblancoa requested a review from pramodk March 20, 2023 11:13

pramodk reviewed Mar 22, 2023

View reviewed changes

Comment thread test/coreneuron/unit/lfp/lfp.cpp

Comment thread src/coreneuron/io/nrnsection_mapping.hpp Outdated

Comment thread src/coreneuron/io/reports/report_event.cpp Outdated

jorblancoa added 11 commits March 23, 2023 13:50

CoreNEURON: Support Online LFP calculation

4fea40d

- Read lfp factors from neurodamus - Add lfp report type - Record LFP from multiple electrodes

NEURON: Support Online LFP calculation

47310f2

- Record online LFP from multiple electrodes - Avoid writing lfp factors if size is 0

Clang-format

386d663

Use intersected gids for lfp reports

a734958

fixup! Use intersected gids for lfp reports

9a6b45b

Read lfp arguments only if present

71382ce

- Make it compatible with older py-neurodamus versions

Move variable out of switch to avid gcc compiler errors

809511e

Add unit test for lfp_calc

270c6c2

Small improvements addressing feedback

Enable unit test when reports enabled only

e6987ee

Remove check for reportinglib

db6144a

Address comments

985c561

jorblancoa force-pushed the jblanco/lfp branch from a6a8ace to 985c561 Compare March 23, 2023 12:51

pramodk approved these changes Mar 24, 2023

View reviewed changes

pramodk merged commit 2ea1c37 into master Mar 24, 2023

pramodk deleted the jblanco/lfp branch March 24, 2023 15:08

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