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Initial implementation of MiV HDF5-based data format #90

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merged 21 commits into from
Aug 21, 2022

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iraikov
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@iraikov iraikov commented Aug 8, 2022

This pull request contains an initial implementation of an HDF5-based data format for experimental data.
It makes the following additions:

  • module miv.io.file which contains the principal read and write routines
  • script scripts/convert_open_ephys.py which can convert data in OpenEphys format to MiV h5
  • script examples/io/file_analysis.py which illustrates how to read data in the HDF5 format and analyze it
  • tests tests/io/test_file_{read|write}.py which contain basic tests of the read/write functionality

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skim0119 commented Aug 9, 2022

@iraikov Thank you. I'll go over the code.

@skim0119 skim0119 mentioned this pull request Aug 9, 2022
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@skim0119 skim0119 changed the base branch from update-0.2.0 to update-0.2.1 August 9, 2022 09:39
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skim0119 commented Aug 9, 2022

I'll merge it in the next version update v0.2.1.

@skim0119 skim0119 added this to the Version 0.2.1 milestone Aug 9, 2022
@skim0119 skim0119 added enhancement New feature or request prio:high High-priority issue labels Aug 9, 2022
@skim0119 skim0119 self-requested a review August 21, 2022 21:33
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Codecov Report

Base: 82.13% // Head: 76.48% // Decreases project coverage by -5.64% ⚠️

Coverage data is based on head (9430043) compared to base (764b691).
Patch coverage: 52.16% of modified lines in pull request are covered.

Additional details and impacted files
@@               Coverage Diff                @@
##           update-0.2.1      #90      +/-   ##
================================================
- Coverage         82.13%   76.48%   -5.65%     
================================================
  Files                40       46       +6     
  Lines              1097     1646     +549     
  Branches            117      253     +136     
================================================
+ Hits                901     1259     +358     
- Misses              174      314     +140     
- Partials             22       73      +51     
Flag Coverage Δ
unittests 76.48% <52.16%> (-5.65%) ⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
miv/io/binary.py 96.22% <ø> (-0.14%) ⬇️
miv/io/serial/__init__.py 0.00% <0.00%> (ø)
miv/io/serial/arduino.py 0.00% <0.00%> (ø)
miv/io/serial/stimjim.py 0.00% <0.00%> (ø)
miv/io/file/read.py 59.13% <59.13%> (ø)
miv/io/file/write.py 66.95% <66.95%> (ø)
miv/io/file/__init__.py 100.00% <100.00%> (ø)
miv/statistics/spiketrain_statistics.py 88.67% <100.00%> (+0.92%) ⬆️
miv/visualization/connectivity.py 97.05% <100.00%> (+66.17%) ⬆️
miv/statistics/info_theory.py 100.00% <0.00%> (+58.00%) ⬆️
... and 1 more

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Thank you!

@skim0119 skim0119 merged commit 333332f into GazzolaLab:update-0.2.1 Aug 21, 2022
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3 participants