Merge pull request #2 from VH-Lab/claude/complete-intan-port-9bQeC

Port MATLAB NDR functions to Python and rename base reader class

Author: stevevanhooser

docs/PORT_STATUS.md

@@ -0,0 +1,92 @@
+# NDR-python Port Status
+
+Status of the MATLAB → Python port of [NDR-matlab](https://github.com/VH-Lab/NDR-matlab).
+
+## Naming Convention
+
+Python class names are a mechanical mapping of the fully-qualified MATLAB class name,
+applying the **Mirror Rule**:
+
+1. Periods (`.`) are replaced with single underscores (`_`).
+2. Existing underscores (`_`) in the MATLAB name are replaced with double underscores (`__`).
+
+| MATLAB qualified name | Python module | Python class |
+|---|---|---|
+| `ndr.reader` | `ndr.reader_wrapper` | `ndr_reader` |
+| `ndr.reader.base` | `ndr.reader.base` | `ndr_reader_base` |
+| `ndr.reader.intan_rhd` | `ndr.reader.intan_rhd` | `ndr_reader_intan__rhd` |
+| `ndr.reader.ced_smr` | `ndr.reader.ced_smr` | `ndr_reader_ced__smr` |
+| `ndr.reader.axon_abf` | `ndr.reader.axon_abf` | `ndr_reader_axon__abf` |
+| `ndr.reader.neo` | `ndr.reader.neo` | `ndr_reader_neo` |
+| `ndr.reader.spikegadgets_rec` | `ndr.reader.spikegadgets_rec` | `ndr_reader_spikegadgets__rec` |
+| `ndr.reader.tdt_sev` | `ndr.reader.tdt_sev` | `ndr_reader_tdt__sev` |
+| `ndr.reader.bjg` | `ndr.reader.bjg` | `ndr_reader_bjg` |
+| `ndr.reader.dabrowska` | `ndr.reader.dabrowska` | `ndr_reader_dabrowska` |
+| `ndr.reader.whitematter` | `ndr.reader.whitematter` | `ndr_reader_whitematter` |
+| `ndr.reader.somecompany_someformat` | `ndr.reader.somecompany_someformat` | `ndr_reader_somecompany__someformat` |
+
+## Reader Status
+
+| Reader | getchannelsepoch | t0\_t1 | samplerate | readchannels\_epochsamples | readevents\_epochsamples\_native | read | Tests |
+|---|---|---|---|---|---|---|---|
+| **ndr\_reader\_intan\_\_rhd** | Yes | Yes | Yes | Yes (single-file) | Stub (empty) | Yes | 6 pass |
+| **ndr\_reader\_ced\_\_smr** | Yes | Yes | Yes | Yes | Yes | Yes (via base) | 14 pass |
+| **ndr\_reader\_axon\_\_abf** | Yes | Yes | Yes | Yes | Stub (empty) | Yes (via base) | 6 pass |
+| **ndr\_reader\_neo** | Stub (empty) | Stub | Stub | NotImplementedError | Stub (empty) | No | 24 xfail |
+| **ndr\_reader\_spikegadgets\_\_rec** | Stub (empty) | Stub | Stub | NotImplementedError | Stub (empty) | No | xfail |
+| **ndr\_reader\_tdt\_\_sev** | Stub (empty) | Stub | Stub | NotImplementedError | Stub (empty) | No | skipped |
+| **ndr\_reader\_bjg** | Stub (empty) | Stub | Stub | NotImplementedError | Stub (empty) | No | skipped |
+| **ndr\_reader\_dabrowska** | Stub (empty) | Stub | Stub | NotImplementedError | Stub (empty) | No | skipped |
+| **ndr\_reader\_whitematter** | Stub (empty) | Stub | Stub | NotImplementedError | Stub (empty) | No | skipped |
+
+**Legend:**
+- **Yes** — Fully implemented and tested with example data
+- **Stub (empty)** — Returns empty arrays / default values; no errors raised
+- **NotImplementedError** — Raises an exception; not yet implemented
+- **Stub** — Inherits base class default (empty list, `[[nan,nan]]`, etc.)
+
+## Format Parsers
+
+Low-level format parsers (under `ndr.format.*`) that read binary files:
+
+| Format | Module | Status |
+|---|---|---|
+| Intan RHD | `ndr.format.intan` | Implemented (header + single-file data reader) |
+| CED SMR/SON | `ndr.format.ced` | Implemented (via `neo` library) |
+| Axon ABF | `ndr.format.axon` | Implemented (via `pyabf` library) |
+| SpikeGadgets REC | `ndr.format.spikegadgets` | Implemented (config, analog, digital, trode) |
+| TDT SEV | `ndr.format.tdt` | Implemented (header + channel reader) |
+| BJG | `ndr.format.bjg` | Implemented (header + data reader) |
+| Dabrowska | `ndr.format.dabrowska` | Implemented (header + data reader) |
+| WhiteMatter | `ndr.format.whitematter` | Implemented (header + data reader) |
+| Neo / Blackrock | `ndr.format.neo` | Implemented (utilities) |
+| Binary Matrix | `ndr.format.binarymatrix` | Implemented |
+| Text Signal | `ndr.format.textSignal` | Implemented |
+
+Note: For SpikeGadgets, TDT, BJG, Dabrowska, and WhiteMatter, the format parsers are implemented but the reader classes have not yet been wired up to use them.
+
+## Reader Wrapper
+
+The top-level `ndr_reader` class (`reader_wrapper.py`) wraps any format-specific reader and adds:
+
+| Feature | Status |
+|---|---|
+| `read()` convenience method | Implemented |
+| `readevents_epochsamples()` with derived events (dep, den, dimp, dimn) | Implemented |
+| Delegation to underlying reader | Implemented |
+
+## External Dependencies
+
+| Dependency | Used by | Purpose |
+|---|---|---|
+| `neo` | ndr\_reader\_ced\_\_smr, ndr\_reader\_neo | Read CED SMR/SON and Blackrock files |
+| `pyabf` | ndr\_reader\_axon\_\_abf | Read Axon Binary Format files |
+| `numpy` | All readers | Array operations |
+
+## Test Summary
+
+```
+38 passed, 28 xfailed, 13 skipped, 2 failed (pre-existing spikegadgets format test issues)
+```
+
+Example data files are included in `src/ndr/example_data/` for Intan (.rhd), CED (.smr), Axon (.abf), SpikeGadgets (.rec), and Blackrock (.nev, .ns2).

docs/developer_notes/PYTHON_PORTING_GUIDE.md

@@ -17,6 +17,21 @@ Function and class names must match MATLAB exactly.
 - **Case Preservation:** Use `readchannels_epochsamples`, not `read_channels_epoch_samples`.
 - **Directory Parity:** Python file paths must mirror MATLAB `+namespace` paths
   (e.g., `+ndr/+reader` -> `src/ndr/reader/`).
+- **Class Name Mirror Rule:** Python class names are derived from the fully-qualified
+  MATLAB class name by applying two substitutions:
+  1. Periods (`.`) are replaced with single underscores (`_`).
+  2. Existing underscores (`_`) in the MATLAB name are replaced with double
+     underscores (`__`).
+
+  Examples:
+  | MATLAB qualified name               | Python class name                      |
+  |--------------------------------------|----------------------------------------|
+  | `ndr.reader`                         | `ndr_reader`                           |
+  | `ndr.reader.base`                    | `ndr_reader_base`                      |
+  | `ndr.reader.intan_rhd`              | `ndr_reader_intan__rhd`               |
+  | `ndr.reader.ced_smr`                | `ndr_reader_ced__smr`                 |
+  | `ndr.reader.axon_abf`               | `ndr_reader_axon__abf`                |
+  | `ndr.reader.somecompany_someformat` | `ndr_reader_somecompany__someformat`  |
 
 ## 3. The Porting Workflow (The Bridge Protocol)
 1. **Check the Bridge:** Open the `ndr_matlab_python_bridge.yaml` in the target package.

src/ndr/__init__.py

@@ -3,6 +3,6 @@
 A Python port of NDR-matlab (https://github.com/VH-Lab/NDR-matlab).
 """
 
-from ndr.reader_wrapper import Reader as reader
+from ndr.reader_wrapper import ndr_reader as reader
 
 __version__ = "0.1.0"

src/ndr/data/__init__.py

@@ -3,5 +3,7 @@
 Port of +ndr/+data/
 """
 
+from ndr.data.assign import assign
 from ndr.data.colvec import colvec
 from ndr.data.rowvec import rowvec
+from ndr.data.struct2namevaluepair import struct2namevaluepair

src/ndr/data/assign.py

@@ -0,0 +1,65 @@
+"""Assign name/value pairs into a target namespace (dict).
+
+Port of +ndr/+data/assign.m
+"""
+
+from __future__ import annotations
+
+from typing import Any
+
+from ndr.data.struct2namevaluepair import struct2namevaluepair
+
+
+def assign(target: dict[str, Any], *args: Any) -> dict[str, Any]:
+    """Apply a list of name/value pair assignments to *target*.
+
+    In MATLAB ``ndr.data.assign`` uses ``assignin('caller', ...)`` to inject
+    variables into the caller's workspace.  In Python the idiomatic
+    equivalent is to update a dictionary (typically ``locals()`` or an
+    options dict) and return it.
+
+    Parameters
+    ----------
+    target : dict
+        The dictionary to update with the supplied name/value pairs.
+    *args
+        Either a single ``dict`` (struct equivalent), a single ``list``
+        of alternating name/value items, or inline alternating
+        ``name, value, name, value, ...`` arguments.
+
+    Returns
+    -------
+    dict
+        The updated *target* dictionary (same object, mutated in-place).
+
+    Examples
+    --------
+    >>> opts = {'z': 0}
+    >>> assign(opts, 'z', 4)
+    {'z': 4}
+
+    >>> assign({}, {'a': 1, 'b': 2})
+    {'a': 1, 'b': 2}
+
+    >>> assign({}, ['x', 10, 'y', 20])
+    {'x': 10, 'y': 20}
+    """
+    # Normalise a single-argument form (dict or list) into a flat sequence
+    if len(args) == 1:
+        arg = args[0]
+        if isinstance(arg, dict):
+            flat: list[Any] = struct2namevaluepair(arg)
+        elif isinstance(arg, (list, tuple)):
+            flat = list(arg)
+        else:
+            raise TypeError("A single argument must be a dict or a list of name/value pairs.")
+    else:
+        flat = list(args)
+
+    names = flat[0::2]
+    values = flat[1::2]
+
+    for name, value in zip(names, values):
+        target[name] = value
+
+    return target

src/ndr/data/ndr_matlab_python_bridge.yaml

@@ -0,0 +1,47 @@
+project_metadata:
+  bridge_version: "1.1"
+  naming_policy: "Strict MATLAB Mirror"
+  indexing_policy: "Semantic Parity (1-based for user concepts, 0-based for internal data)"
+
+functions:
+  - name: assign
+    matlab_path: "+ndr/+data/assign.m"
+    python_path: "ndr/data/assign.py"
+    input_arguments:
+      - name: target
+        type_python: "dict[str, Any]"
+      - name: args
+        type_python: "*Any"
+    output_arguments:
+      - name: target
+        type_python: "dict[str, Any]"
+
+  - name: colvec
+    matlab_path: "+ndr/+data/colvec.m"
+    python_path: "ndr/data/colvec.py"
+    input_arguments:
+      - name: x
+        type_python: "numpy.ndarray"
+    output_arguments:
+      - name: y
+        type_python: "numpy.ndarray"
+
+  - name: rowvec
+    matlab_path: "+ndr/+data/rowvec.m"
+    python_path: "ndr/data/rowvec.py"
+    input_arguments:
+      - name: x
+        type_python: "numpy.ndarray"
+    output_arguments:
+      - name: y
+        type_python: "numpy.ndarray"
+
+  - name: struct2namevaluepair
+    matlab_path: "+ndr/+data/struct2namevaluepair.m"
+    python_path: "ndr/data/struct2namevaluepair.py"
+    input_arguments:
+      - name: thestruct
+        type_python: "dict[str, Any]"
+    output_arguments:
+      - name: nv
+        type_python: "list[Any]"

src/ndr/data/struct2namevaluepair.py

@@ -0,0 +1,41 @@
+"""Convert a dict to a flat list of name/value pairs.
+
+Port of +ndr/+data/struct2namevaluepair.m
+"""
+
+from __future__ import annotations
+
+from typing import Any
+
+
+def struct2namevaluepair(thestruct: dict[str, Any]) -> list[Any]:
+    """Convert a dictionary to a flat list of name/value pairs.
+
+    This is useful for passing name/value pairs to functions that accept
+    them as extra keyword arguments. Each key of the dictionary is used as
+    the 'name', and the corresponding value is used as the 'value'.
+
+    Parameters
+    ----------
+    thestruct : dict
+        Input dictionary mapping parameter names to values.
+
+    Returns
+    -------
+    list
+        Flat list alternating between keys and values,
+        e.g. ``['param1', 1, 'param2', 2]``.
+
+    Examples
+    --------
+    >>> struct2namevaluepair({'param1': 1, 'param2': 2})
+    ['param1', 1, 'param2', 2]
+    """
+    if not thestruct:
+        return []
+
+    nv: list[Any] = []
+    for key, value in thestruct.items():
+        nv.append(key)
+        nv.append(value)
+    return nv