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Resolve ephys pipeline output differences between nwb1 and nwb2 #321

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5 tasks done
sgratiy opened this issue Feb 5, 2020 · 0 comments · Fixed by #382
Closed
5 tasks done

Resolve ephys pipeline output differences between nwb1 and nwb2 #321

sgratiy opened this issue Feb 5, 2020 · 0 comments · Fixed by #382
Milestone
Marmot 2020-02-25

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@sgratiy
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sgratiy commented Feb 5, 2020 •
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When running pipeline for the same experiment saved in nwb1 vs nwb2 there are some differenced in the metadata produced by the pipeline:
e.g.: nwb2 vs nwb1
"stimulus_code_ext": "X6SP_Rheo_DA_0" vs stimulus_code_ext": "X6SP_Rheo[9]
"bridge_balance_mohm": [ 12.942612648010254 ] vs "bridge_balance_mohm": 12.942613,
same for leak_pa
stimulus_scale_factor value is different between the two:

  • use get_scalar_value function when reading data from nwb2
  • read stimulus_scale_factor from the labnotebook for the MIES nwb2
  • resolve value difference in stimulus_scale factor
  • Review/revise and possibly redesign the nwb reading classes. Related to the issue Refactor nwb_reader #286
  • Add test to compare pipeline outputs for nwb2 and nwb1
@sgratiy sgratiy mentioned this issue Feb 5, 2020
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4 tasks
@wbwakeman wbwakeman added this to the Marmot 2020-02-25 milestone Feb 12, 2020
@sgratiy sgratiy mentioned this issue Feb 15, 2020
Merged
NileGraddis added a commit that referenced this issue Feb 17, 2020
@NileGraddis
#321 tests for mies data set
51c02b5
NileGraddis added a commit that referenced this issue Feb 17, 2020
@NileGraddis
#321 update minimum h5py (some mies datasets cannot be read prior to …
b941783 
…2.10)
NileGraddis added a commit that referenced this issue Feb 17, 2020
@NileGraddis
#321 ensure that aibs fs-requiring tests are skipped if the aibs fs i…
5e39cc3 
…s not available
sgratiy pushed a commit that referenced this issue Feb 19, 2020
@NileGraddis @sgratiy
#321 tests for mies data set
d562802
sgratiy pushed a commit that referenced this issue Feb 19, 2020
@NileGraddis @sgratiy
#321 update minimum h5py (some mies datasets cannot be read prior to …
cae55df 
…2.10)
sgratiy pushed a commit that referenced this issue Feb 19, 2020
@NileGraddis @sgratiy
#321 ensure that aibs fs-requiring tests are skipped if the aibs fs i…
0a239df 
…s not available
sgratiy pushed a commit that referenced this issue Feb 27, 2020
@NileGraddis @sgratiy
#321 tests for mies data set
6ee232c
sgratiy pushed a commit that referenced this issue Feb 27, 2020
@NileGraddis @sgratiy
#321 update minimum h5py (some mies datasets cannot be read prior to …
ddf31b1 
…2.10)
sgratiy pushed a commit that referenced this issue Feb 27, 2020
@NileGraddis @sgratiy
#321 ensure that aibs fs-requiring tests are skipped if the aibs fs i…
563a9a6 
…s not available
@t-b t-b mentioned this issue Feb 28, 2020
Closed
@sgratiy sgratiy mentioned this issue Mar 26, 2020
Merged
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Run pipeline from nwb AllenInstitute/ipfx
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@wbwakeman @MatthewAitken @sgratiy