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Port MATLAB NDR functions to Python and rename base reader class#2

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stevevanhooser merged 9 commits intomainfrom
claude/complete-intan-port-9bQeC
Mar 17, 2026
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Port MATLAB NDR functions to Python and rename base reader class#2
stevevanhooser merged 9 commits intomainfrom
claude/complete-intan-port-9bQeC

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@stevevanhooser stevevanhooser commented Mar 17, 2026

Summary

This is a major port of MATLAB functions from NDR-matlab to Python, along with a critical refactoring of the base reader class naming convention. The changes include porting numerous format readers, utility functions, and test suites while establishing consistent naming patterns for the Python implementation.

Key Changes

Base Class Refactoring

  • Renamed Base class to ndr_reader_base in src/ndr/reader/base.py to follow MATLAB naming conventions
  • Updated all reader implementations to inherit from ndr_reader_base:
    • axon_abf.py
    • bjg.py
    • ced_smr.py
    • dabrowska.py
    • neo.py
    • spikegadgets_rec.py
    • tdt_sev.py
    • whitematter.py
  • Updated imports in reader_wrapper.py and reader/__init__.py

Format Readers Ported

  • Intan RHD2000: Enhanced header reading and data file handling
  • CED SOM/SMR: Complete reader implementation with header, sample interval, and data file support
  • SpikeGadgets .rec: Config, analog, digital, and trode channel readers
  • TDT SEV: Header, channel, and log file readers
  • Axon ABF: Header reading and time conversion utilities
  • BJG: Binary format reader with header support
  • WhiteMatter: Binary data file reader with header parsing
  • Dabrowska Lab: MAT file reader with header support
  • Text Signal: Header and data readers for text-based signal format
  • Binary Matrix: Binary matrix format reader
  • Neo: Python-based Neo library integration with utilities

Utility Functions Ported

  • TimeReference class in src/ndr/time/timereference.py
  • Data utilities: assign.py, struct2namevaluepair.py
  • String utilities and format-specific helpers

Test Suite Ported

  • Automated tests for Neo, CED SMR, and Axon ABF readers
  • Format-specific tests for binary matrix, CED, SpikeGadgets, and Intan RHD
  • Reader functionality tests for all major formats
  • Example data files added for testing (.rec, .rhd, .smr, .abf, .nev, .ns2)

Documentation & Configuration

  • Added PORT_STATUS.md documenting the porting progress
  • Updated PYTHON_PORTING_GUIDE.md with additional porting guidelines
  • Added MATLAB-Python bridge YAML configuration files for multiple format modules
  • Updated resource configuration in ndr_reader_types.json

Example Data

  • Added example neurophysiology files for testing readers
  • Added text signal example files with timestamp and numeric variants
  • Comprehensive README documenting example file sources and usage

Notable Implementation Details

  • Maintained strict MATLAB naming conventions in ported functions (e.g., read_Intan_RHD2000_file_var)
  • Preserved function signatures and behavior from MATLAB implementations
  • Added comprehensive docstrings indicating MATLAB source origins
  • Established consistent module structure with __init__.py files for all format packages
  • Updated all reader class registrations and imports to use new base class name

https://claude.ai/code/session_01B7KUYa1gnwsrJHVLsAH3NB

claude added 9 commits March 17, 2026 00:47
@claude
Complete intan port: add missing functions from NDR-matlab
c93158b 
Port the remaining 5 functions from +ndr/+format/+intan/ and all 3
manufacturer utilities that were missing from the initial port:

- fread_QString: public Qt string reader (was only private helper)
- read_Intan_RHD2000_directory: one-file-per-channel directory reader
- cat_Intan_RHD2000_files: concatenate multiple RHD files
- concat_rhd_files: concatenate all RHD files in a directory
- copy_Intan_RHD2000_blocks: copy block ranges between RHD files
- manufacturer/read_Intan_RHD2000_file: full file reader with summary
- manufacturer/read_Intan_RHD2000_file_var: full file reader returning dict
- manufacturer/upsample2x: 2x cubic spline upsampler

Also updates __init__.py exports and bridge YAML to reflect all functions.

https://claude.ai/code/session_01B7KUYa1gnwsrJHVLsAH3NB
@claude
Port all ndr.format.* subpackages from NDR-matlab to Python
d756dad 
Ports the following MATLAB format modules:
- axon: ABF file reading via pyabf (abfTimeToDatetime, read_abf, read_abf_header)
- binarymatrix: Binary matrix file reader with seek optimization
- bjg: BJG binary data reader (header parser + data reader)
- ced: CED SOM/SMR reading via neo (header, datafile, sampleinterval)
- dabrowska: Dabrowska MAT file reader (header + data)
- neo: Neo utility functions (Utils, neo_python)
- spikegadgets: SpikeGadgets .rec file support (config, trode/analog/digital channels, copy)
- tdt: TDT SEV file support (logs, header, channel reader)
- textSignal: Text signal format (about, readHeader, readData)
- whitematter: WhiteMatter binary format (header, reader)

Also adds bridge YAML files for all subpackages and fixes lint issues.

https://claude.ai/code/session_01B7KUYa1gnwsrJHVLsAH3NB
@claude
Port remaining ndr modules and add test suite
d26c401 
New modules:
- ndr.data: assign, struct2namevaluepair (data utility functions)
- ndr.time: timereference (TimeReference class for clock-relative times)
- ndr.reader: somecompany_someformat (template reader class)

Test suite (ndr.test):
- format tests: binarymatrix, ced, intan_rhd, spikegadgets
- reader tests: axon_abf, bjg, ced_smr, intan_rhd, neo, spikegadgets_rec, tdt_sev

Also adds bridge YAML files for data, fun, string, and updates
existing bridge YAMLs for time and reader packages.

https://claude.ai/code/session_01B7KUYa1gnwsrJHVLsAH3NB
@claude
Add remaining reader test ports (readertest.m and automatedTest.m)
cf282cc 
Ports the readertest.m files for axon_abf, bjg, ced_smr, intan_rhd,
spikegadgets_rec, tdt_sev and automatedTest.m files for ced_smr and neo.

https://claude.ai/code/session_01B7KUYa1gnwsrJHVLsAH3NB
@claude
Fix reader implementations, add example data, and make tests functional
bea9396 
- Fix Intan RHD header parser: correct version checks, field sizes (int16
  not int32), remove phantom fields that don't exist in v1.4 format
- Fix Intan RHD datafile _get_header_size with matching corrections
- Rewrite CED SMR reader to use CED native channel numbers instead of
  sequential Neo signal indices
- Add read() convenience method to Base class and IntanRHD override
- Fix reader_wrapper overflow with infinity defaults for t0/t1
- Add example data files (rhd, smr, abf, rec, nev, ns2) for testing
- Remove skip markers from all reader tests, making them functional
- Fix CED automated test expectations for Neo string labels vs MATLAB uint8
- Fix Neo test fixtures (example_1.nev not .ns2) and add xfail markers
- Update channel count assertions to match actual reader output

36 tests pass, 24 xfail (Neo reader not yet implemented), 19 skipped.

https://claude.ai/code/session_01B7KUYa1gnwsrJHVLsAH3NB
@claude
Add PORT_STATUS.md documenting current state of MATLAB-to-Python port
7f6226b 
https://claude.ai/code/session_01B7KUYa1gnwsrJHVLsAH3NB
@claude
Rename all classes to follow MATLAB mirror rule naming convention
1aa945e 
Apply the class naming mirror rule: periods become single underscores,
existing underscores become double underscores. This matches the MATLAB
fully-qualified class names exactly.

Renames:
  Base -> ndr_reader_base
  Reader -> ndr_reader
  IntanRHD -> ndr_reader_intan__rhd
  CedSMR -> ndr_reader_ced__smr
  AxonABF -> ndr_reader_axon__abf
  NeoReader -> ndr_reader_neo
  SpikeGadgetsRec -> ndr_reader_spikegadgets__rec
  TdtSev -> ndr_reader_tdt__sev
  BJG -> ndr_reader_bjg
  Dabrowska -> ndr_reader_dabrowska
  WhiteMatter -> ndr_reader_whitematter
  SomecompanySomeformat -> ndr_reader_somecompany__someformat

Also documents the mirror rule in PYTHON_PORTING_GUIDE.md and updates
the bridge YAML, reader types JSON, and all test imports.

https://claude.ai/code/session_01B7KUYa1gnwsrJHVLsAH3NB
@claude
Fix top-level tests/ to use new mirror rule class names
90c22cd 
Missed tests/test_reader_base.py and tests/test_readers.py which
import from the renamed classes.

https://claude.ai/code/session_01B7KUYa1gnwsrJHVLsAH3NB
@claude
Apply black formatting
cf3a4ce 
https://claude.ai/code/session_01B7KUYa1gnwsrJHVLsAH3NB
@stevevanhooser stevevanhooser merged commit 5534d9e into main Mar 17, 2026
4 checks passed
@stevevanhooser stevevanhooser deleted the claude/complete-intan-port-9bQeC branch March 17, 2026 13:57
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2 participants

@stevevanhooser @claude