Port NDR reader framework from MATLAB to Python#1
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stevevanhooser merged 2 commits intomainfrom Mar 17, 2026
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- Create repo structure mirroring MATLAB +namespace paths - Port ndr.reader.base abstract base class with all method signatures - Port ndr.reader wrapper (reader_wrapper.py) with read(), delegation - Implement Intan RHD format reader with binary file parsing - Implement Axon ABF reader (pyabf backend) - Implement CED SMR reader (neo backend) - Add stub readers: BJG, Dabrowska, Neo, SpikeGadgets, TDT, WhiteMatter - Port utility packages: time (clocktype, samples2times, times2samples), data (colvec, rowvec), string (channelstring2channels, str2intseq), file (textfile2char), fun (ndrpath, ndrresource, bitDepth) - Port globals, known_readers with ndr_reader_types.json resource - Create bridge YAML files for reader and format/intan packages - Create developer notes: porting guide, xlang principles, bridge spec, symmetry test docs - Create symmetry test framework (make_artifacts, read_artifacts) - Add 50 unit tests covering base class, Intan static methods, channel strings, time functions, known readers, and wrapper - All tests pass, black formatted, ruff clean https://claude.ai/code/session_01QGdJXLDUuQGSiDw8ZggEMU
- Lint job: black --check and ruff check - Test job: pytest across Python 3.10, 3.11, 3.12 with fail-fast disabled https://claude.ai/code/session_01QGdJXLDUuQGSiDw8ZggEMU
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Summary
This PR implements a comprehensive Python port of the NDR (Neuroscience Data Reader) MATLAB library, establishing the core reader framework and format-specific handlers for reading neural data files.
Key Changes
Core Reader Framework
ndr/reader/base.py: Abstract base class for all format-specific readers with concrete utility methods for channel validation, type conversion, and time/sample conversionsndr/reader_wrapper.py: High-levelReaderclass providing unified interface to format-specific readers with dynamic loader based on data format typeFormat-Specific Readers
ndr/reader/intan_rhd.py: Complete reader for Intan RHD2000 format with channel mapping, header parsing, and data block handlingndr/reader/axon_abf.py: Reader for Axon ABF format (pyabf-based)ndr/reader/ced_smr.py: Reader for CED Spike2 SMR format (neo-based)ndr/reader/neo.py: Generic neo library wrapper for multiple formatstdt_sev.py,bjg.py,dabrowska.py,spikegadgets_rec.py,whitematter.pyfor future implementationIntan RHD Format Handler
ndr/format/intan/read_Intan_RHD2000_header.py: Binary header parsing with Qt QString supportndr/format/intan/read_Intan_RHD2000_datafile.py: Data block structure calculation and file I/OUtility Modules
ndr/time/clocktype.py,ndr/time/fun/samples2times.py,ndr/time/fun/times2samples.pyfor time/sample conversionsndr/string/channelstring2channels.py,ndr/string/str2intseq.py,ndr/string/intseq2str.pyfor channel specification parsingndr/data/colvec.py,ndr/data/rowvec.pyfor array reshapingndr/fun/ndrpath.py,ndr/fun/ndrresource.py,ndr/fun/bitDepth.py,ndr/fun/getDataTypeString.pyndr/file/textfile2char.pyConfiguration & Resources
ndr/resource/ndr_reader_types.json: Registry mapping format identifiers to reader class implementationsndr/globals.py: Global path and configuration managementndr/known_readers.py: Public API for discovering available readersTesting & Documentation
tests/test_reader_base.py,tests/test_readers.pywith comprehensive coverage of static methods and channel type conversionstests/symmetry/with artifact generation and validation for MATLAB/Python parityndr_matlab_python_bridge.yamlfiles documenting MATLAB-to-Python mapping contractsPYTHON_PORTING_GUIDE.md,ndr_xlang_principles.md,symmetry_tests.mdfor cross-language developmentProject Configuration
pyproject.toml: Package metadata, dependencies (numpy, pydantic, vhlab-toolbox-python), and optional dev dependenciesREADME.md: Updated with comprehensive overview of NDR architecture and capabilitiesImplementation Details
https://claude.ai/code/session_01QGdJXLDUuQGSiDw8ZggEMU