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Modularize Analysis #190

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@pauladkisson pauladkisson commented Dec 15, 2025 •
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Fixes #172

This PR modularizes the analysis steps in the GuPPy pipeline by

  • Splitting each operation into logical modules (ex. z_score.py)
  • Separating visualization from analysis code
  • Separating read and write operations from purely functional analysis steps
  • Refactoring analysis code into pure functions with inputs and outputs and without any side effects

Progress

Step 4

  • timestamp correction
  • split up artifact removal from z score
  • z score
  • artifact removal
  • data combination

Step 5

  • PSTH

@pauladkisson
Moved readtsq to tdt_step2.py.
aa4340d
@pauladkisson
Moved import_np_doric_csv to np_doric_csv_step2.py.
c868823
@pauladkisson
Split import_csv out from import_np_doric_csv
a06cae4
@pauladkisson
Fixed TDT
66d60e2
@pauladkisson
Split import_doric out from import_np_doric_csv
4f4e1c9
@pauladkisson
Removed unnecessary imports
341d77d
@pauladkisson
Split import_npm out from import_np_doric_csv
0bcd4fe
@pauladkisson
Added modality selector to the GUI.
7b36f64
@pauladkisson
Added modality selector to the GUI.
100ad14
@pauladkisson
Added modality option to the api and tests
ef978ec
@pauladkisson
Removed intermediate np_doric_csv_step2 module.
6589139
@pauladkisson
Split tdt_step3.py off from read_raw_data.py.
e7ac4d8
@pauladkisson
Hard-coded modality to simplify read.
2f57867
@pauladkisson
Split doric_step3.py off from read_raw_data.py.
092e1b7
@pauladkisson
Added check_doric to doric_step3.py.
7abb8e0
@pauladkisson
Split csv_step3.py off from read_raw_data.py.
b653538
@pauladkisson
Added modality to Step 3.
6d661c2
@pauladkisson
Added tdtRecordingExtractor
a4f6583
@pauladkisson
Adapted parallel execute function to use new extractor.
882556e
@pauladkisson
Added CsvRecordingExtractor for step 2
df7b9e1
@pauladkisson
Installed pre-commit.
bcb78a5
@pauladkisson
Added CsvRecordingExtractor for step 3
1c8ee07
@pauladkisson
Added DoricRecordingExtractor for step 2
9262a5a
@pauladkisson
Added DoricRecordingExtractor for step 2
9c5afce
@pauladkisson
Added DoricRecordingExtractor for step 3
914f23f
@pauladkisson
streamlined inputs
cd966ae
@pauladkisson
Added NpmRecordingExtractor for step 2
ac158de
@pauladkisson
Added NpmRecordingExtractor for step 3
6a470a1
@pauladkisson
Merge branch 'modularization' into extractor
4903817
@pauladkisson
Add a tdt_check_data example session to the tests.
9b88cad
Base automatically changed from extractor to dev December 17, 2025 00:12
@pauladkisson
Merge branch 'dev' into analysis
7e25db9
@pauladkisson
fixed data read bug
a87c507
@pauladkisson
Refactored write operations out of addingNaNtoChunksWithArtifacts
b1cbc83
@pauladkisson
Refactored filepath out of addingNaNtoChunksWithArtifacts
393d3aa
@pauladkisson
Renamed some variables in processTimestampsForArtifacts
22f4f18
@pauladkisson
Refactored read out of processTimestampsForArtifacts
a4a162f
@pauladkisson
Refactored read out of processTimestampsForArtifacts
a25e7ac
@pauladkisson
Reorganized processTimestampsForArtifacts
3c70579
@pauladkisson
Removed write from processTimestampsForArtifacts
b7d0549
@pauladkisson
Removed write from processTimestampsForArtifacts
61b2712
@pauladkisson
Refactored filepath out of processTimestampsForArtifacts
2dc18cc
@pauladkisson
Consolidated write operations
bfb18e0
@pauladkisson
Consolidated into single remove_artifacts fn
d4f3de4
@pauladkisson
fixed bug with read_control_and_signal
c23aa1d
@pauladkisson
fixed naming bug in timestampCorrection
1cda972
@pauladkisson
Fixed combinedata bug
19986c8
@pauladkisson
Fixed combinedata bug
995b1e2
@pauladkisson
Reorganized into execute_combined_data and combine_data.
d4ac68c
@pauladkisson
Renamed some variables for clarity.
042fb33
@pauladkisson
Refactored read operations out of eliminateData.
9db15aa
@pauladkisson
Cleaned up some indentation in combine_data.
0109f83
@pauladkisson
Refactored read operations out of eliminateTs.
d3a8fbc
@pauladkisson
Refactored read operations out of eliminateTs.
c481d95
@pauladkisson
Refactored read operations out of eliminateTs.
ebe24b6
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@pauladkisson