Merge pull request #54 from Waltham-Data-Science/claude/port-ndi-matlab-changes-9ttly

Add analog event type support with threshold-based detection

Author: stevevanhooser

AGENTS.md

@@ -32,7 +32,58 @@ Every sub-package contains a file named `ndi_matlab_python_bridge.yaml`.
 - **Internal Access:** Use 0-based indexing for internal Python data structures (lists, NumPy arrays).
 - **Formatting:** Code must pass `black` and `ruff check --fix` before completion.
 
-## 5. Directory Mapping Reference
+## 5. CI Lint & Test Commands
+
+Before pushing any changes, you **must** run these commands and ensure they all pass. These are the same checks CI runs.
+
+### Formatting (Black)
+
+```bash
+black --check src/ tests/
+```
+
+To auto-fix formatting issues:
+
+```bash
+black src/ tests/
+```
+
+Configuration is in `pyproject.toml`: line-length = 100, target-version = py310/py311/py312.
+
+### Linting (Ruff)
+
+```bash
+ruff check src/ tests/
+```
+
+To auto-fix what ruff can:
+
+```bash
+ruff check --fix src/ tests/
+```
+
+Configuration is in `pyproject.toml` under `[tool.ruff]` and `[tool.ruff.lint]`.
+
+### Tests
+
+```bash
+pytest tests/ -v --tb=short
+```
+
+Symmetry tests (cross-language MATLAB/Python parity) are excluded from the default run and are invoked separately in CI:
+
+```bash
+pytest tests/symmetry/make_artifacts/ -v --tb=short
+pytest tests/symmetry/read_artifacts/ -v --tb=short
+```
+
+### Quick pre-push checklist
+
+```bash
+black src/ tests/ && ruff check src/ tests/ && pytest tests/ -x -q
+```
+
+## 6. Directory Mapping Reference
 
 - **MATLAB Source:** `VH-ndi_gui_Lab/NDI-matlab` (GitHub)
 - **Python Target:** `src/ndi/[namespace]/` (Mirrors MATLAB `+namespace/`)

pyproject.toml

@@ -36,7 +36,7 @@ classifiers = [
 requires-python = ">=3.10"
 dependencies = [
     "did @ git+https://github.com/VH-Lab/DID-python.git@main",
-    "ndr @ git+https://github.com/VH-lab/NDR-python.git@main",
+    "ndr[formats] @ git+https://github.com/VH-lab/NDR-python.git@main",
     "vhlab-toolbox-python @ git+https://github.com/VH-Lab/vhlab-toolbox-python.git@main",
     "ndi-compress @ git+https://github.com/Waltham-Data-Science/NDI-compress-python.git@main",
     "numpy>=1.20.0",

src/ndi/class_registry.py

@@ -43,6 +43,9 @@ def _build_registry() -> dict[str, type]:
     from .setup.daq.reader.mfdaq.stimulus.nielsenvisintan import (
         ndi_setup_daq_reader_mfdaq_stimulus_nielsenvisintan,
     )
+    from .setup.daq.reader.mfdaq.stimulus.nielsenvisneuropixelsglx import (
+        ndi_setup_daq_reader_mfdaq_stimulus_nielsenvisneuropixelsglx,
+    )
     from .setup.daq.reader.mfdaq.stimulus.vhaudreybpod import (
         ndi_setup_daq_reader_mfdaq_stimulus_VHAudreyBPod,
     )
@@ -71,6 +74,7 @@ def _build_registry() -> dict[str, type]:
         ndi_daq_reader_mfdaq_spikegadgets,
         ndi_setup_daq_reader_mfdaq_stimulus_vhlabvisspike2,
         ndi_setup_daq_reader_mfdaq_stimulus_nielsenvisintan,
+        ndi_setup_daq_reader_mfdaq_stimulus_nielsenvisneuropixelsglx,
         ndi_setup_daq_reader_mfdaq_stimulus_VHAudreyBPod,
     ):
         registry[cls.NDI_DAQREADER_CLASS] = cls
@@ -81,6 +85,8 @@ def _build_registry() -> dict[str, type]:
     # File navigators
     registry[ndi_file_navigator.NDI_FILENAVIGATOR_CLASS] = ndi_file_navigator
     registry[ndi_file_navigator_epochdir.NDI_FILENAVIGATOR_CLASS] = ndi_file_navigator_epochdir
+    # Custom lab-specific navigators mapped to epochdir until dedicated classes exist
+    registry["ndi.setup.file.navigator.vhlab_np_epochdir"] = ndi_file_navigator_epochdir
 
     return registry
 

src/ndi/daq/daqsystemstring.py

@@ -76,7 +76,16 @@ def parse(cls, devstr: str) -> ndi_daq_daqsystemstring:
             channeltype = match.group(1)
             numspec = match.group(2)
 
+            # Check for threshold suffix (e.g., '_t2.5' in 'aep1-3_t2.5')
+            threshold_str = ""
+            t_idx = numspec.find("_t")
+            if t_idx != -1:
+                threshold_str = numspec[t_idx:]
+                numspec = numspec[:t_idx]
+
             channellist = _parse_channel_numbers(numspec)
+            if threshold_str:
+                channeltype = channeltype + threshold_str
             channels.append((channeltype, channellist))
 
         return cls(devicename=devicename, channels=channels)
@@ -96,8 +105,7 @@ def devicestring(self) -> str:
             if not channellist:
                 parts.append(channeltype)
             else:
-                numstr = _format_channel_numbers(channellist)
-                parts.append(f"{channeltype}{numstr}")
+                parts.append(ndi_daq_daqsystemstring.channeltype2str(channeltype, channellist))
 
         return f"{self.devicename}:{';'.join(parts)}"
 
@@ -132,6 +140,51 @@ def __str__(self) -> str:
     def __repr__(self) -> str:
         return f"ndi_daq_daqsystemstring('{self.devicestring()}')"
 
+    @staticmethod
+    def channeltype2str(ct: str, channellist: list[int]) -> str:
+        """
+        Build a device string segment from a channeltype and channel list.
+
+        Handles threshold suffixes (e.g., ``_t2.5``) by placing the channel
+        numbers between the base type and the suffix.
+
+        Args:
+            ct: Channel type string, optionally with threshold suffix
+                (e.g., ``'aep'`` or ``'aep_t2.5'``)
+            channellist: List of channel numbers
+
+        Returns:
+            Device string segment (e.g., ``'aep1-3_t2.5'``)
+        """
+        t_idx = ct.find("_t")
+        if t_idx != -1:
+            base = ct[:t_idx]
+            threshold_str = ct[t_idx:]
+            return f"{base}{_format_channel_numbers(channellist)}{threshold_str}"
+        return f"{ct}{_format_channel_numbers(channellist)}"
+
+    @staticmethod
+    def parse_analog_event_channeltype(ct: str) -> tuple[str, float]:
+        """
+        Extract base type and threshold from a channel type string.
+
+        Given a channel type string like ``'aep_t2.5'``, returns the base
+        type (``'aep'``) and threshold (``2.5``). If no threshold suffix
+        is present, threshold is ``0.0``.
+
+        Args:
+            ct: Channel type string (e.g., ``'aep_t2.5'``, ``'aimp'``)
+
+        Returns:
+            Tuple of (base_type, threshold)
+        """
+        t_idx = ct.find("_t")
+        if t_idx != -1:
+            base_type = ct[:t_idx]
+            threshold = float(ct[t_idx + 2 :])
+            return base_type, threshold
+        return ct, 0.0
+
     def __eq__(self, other) -> bool:
         if not isinstance(other, ndi_daq_daqsystemstring):
             return False