Merge pull request #17 from VH-Lab/claude/pip-installable-intan-rhd-9sc0o

Add Intan RHD2000 file header reader

Author: stevevanhooser

.github/workflows/ci.yml

@@ -0,0 +1,31 @@
+name: CI
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - run: pip install ruff
+      - run: ruff check vlt/ tests/
+
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - run: pip install -e ".[test]"
+      - run: python -m pytest tests/ -v

.gitignore

@@ -4,3 +4,4 @@ __pycache__/
 venv/
 .pytest_cache/
 test_logs/
+*.egg-info/

pyproject.toml

@@ -0,0 +1,42 @@
+[build-system]
+requires = ["setuptools>=64"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "vhlab-toolbox-python"
+version = "0.1.0"
+description = "Python port of vhlab-toolbox-matlab"
+requires-python = ">=3.9"
+dependencies = [
+    "numpy",
+    "pandas",
+    "scipy",
+    "h5py",
+    "matplotlib",
+]
+
+[project.optional-dependencies]
+test = ["pytest"]
+
+[project.urls]
+Repository = "https://github.com/VH-Lab/vhlab-toolbox-python"
+
+[tool.pytest.ini_options]
+addopts = "--import-mode=importlib"
+
+[tool.ruff.lint]
+select = ["E", "F", "W"]
+ignore = [
+    "E501",   # line too long — existing code
+    "E701",   # multiple statements on one line — existing style
+    "E741",   # ambiguous variable name — existing style
+    "F401",   # unused imports — many in existing code
+    "F841",   # local variable assigned but never used — existing code
+    "E722",   # bare except — existing code
+    "E402",   # module-level import not at top — existing code
+    "W293",   # blank line contains whitespace — existing code
+    "W605",   # invalid escape sequence — existing code
+]
+
+[tool.setuptools.packages.find]
+include = ["vlt*"]

tests/vlt/hardware/__init__.py

@@ -0,0 +1,218 @@
+"""Tests for vlt.hardware.intan module."""
+
+import os
+import struct
+import tempfile
+
+import pytest
+
+from vlt.hardware.intan import read_Intan_RHD2000_header
+
+
+def _write_qstring(fid, s):
+    """Write a Qt-style QString to a binary file."""
+    if not s:
+        fid.write(struct.pack('<I', 0xFFFFFFFF))
+    else:
+        encoded = s.encode('utf-16-le')
+        fid.write(struct.pack('<I', len(encoded)))
+        fid.write(encoded)
+
+
+def _write_channel(fid, native_name, custom_name, native_order, custom_order,
+                   signal_type, channel_enabled, chip_channel, board_stream):
+    """Write a single channel definition to the binary file."""
+    _write_qstring(fid, native_name)
+    _write_qstring(fid, custom_name)
+    fid.write(struct.pack('<hhhhhh', native_order, custom_order,
+                          signal_type, channel_enabled, chip_channel, board_stream))
+    # Trigger settings
+    fid.write(struct.pack('<hhhh', 0, 0, 0, 0))
+    # Impedance
+    fid.write(struct.pack('<ff', 0.0, 0.0))
+
+
+def create_synthetic_rhd(filepath, sample_rate=20000.0, num_amp_channels=2,
+                         num_aux_channels=3, num_supply_channels=1,
+                         num_adc_channels=0, num_dig_in_channels=0,
+                         num_dig_out_channels=0, num_data_blocks=1000,
+                         version_major=1, version_minor=3):
+    """Create a synthetic .rhd file for testing.
+
+    With version 1.x, each data block contains 60 samples.
+    """
+    num_samples_per_block = 60 if version_major <= 1 else 128
+
+    with open(filepath, 'wb') as fid:
+        # Magic number
+        fid.write(struct.pack('<I', 0xC6912702))
+        # Version
+        fid.write(struct.pack('<hh', version_major, version_minor))
+        # Sample rate
+        fid.write(struct.pack('<f', sample_rate))
+        # Frequency parameters: dsp_enabled(h) + 6 floats
+        fid.write(struct.pack('<hffffff', 1, 1.0, 1.0, 7500.0, 1.0, 1.0, 7500.0))
+        # Notch filter mode
+        fid.write(struct.pack('<h', 2))  # 60 Hz
+        # Impedance test frequencies
+        fid.write(struct.pack('<ff', 1000.0, 1000.0))
+        # Notes
+        _write_qstring(fid, '')
+        _write_qstring(fid, '')
+        _write_qstring(fid, '')
+        # Num temp sensor channels (version >= 1.1)
+        num_temp_channels = 1
+        fid.write(struct.pack('<h', num_temp_channels))
+        # Eval board mode (version >= 1.3)
+        fid.write(struct.pack('<h', 0))
+        # Reference channel (version >= 2.0)
+        if version_major > 1:
+            _write_qstring(fid, '')
+
+        # Signal groups: put all channels in one group
+        total_channels = (num_amp_channels + num_aux_channels +
+                          num_supply_channels + num_adc_channels +
+                          num_dig_in_channels + num_dig_out_channels)
+        fid.write(struct.pack('<h', 1))  # 1 signal group
+
+        _write_qstring(fid, 'Port A')
+        _write_qstring(fid, 'A')
+        fid.write(struct.pack('<hhh', 1, total_channels, 0))
+
+        order = 0
+        for i in range(num_amp_channels):
+            _write_channel(fid, f'A-{i:03d}', f'A-{i:03d}', order, order, 0, 1, i, 0)
+            order += 1
+        for i in range(num_aux_channels):
+            _write_channel(fid, f'AUX-{i}', f'AUX-{i}', order, order, 1, 1, i, 0)
+            order += 1
+        for i in range(num_supply_channels):
+            _write_channel(fid, f'VDD-{i}', f'VDD-{i}', order, order, 2, 1, i, 0)
+            order += 1
+        for i in range(num_adc_channels):
+            _write_channel(fid, f'ADC-{i}', f'ADC-{i}', order, order, 3, 1, i, 0)
+            order += 1
+        for i in range(num_dig_in_channels):
+            _write_channel(fid, f'DIN-{i}', f'DIN-{i}', order, order, 4, 1, i, 0)
+            order += 1
+        for i in range(num_dig_out_channels):
+            _write_channel(fid, f'DOUT-{i}', f'DOUT-{i}', order, order, 5, 1, i, 0)
+            order += 1
+
+        header_size = fid.tell()
+
+        # Compute bytes per data block and write dummy data
+        bytes_per_block = 0
+        bytes_per_block += num_samples_per_block * 4  # timestamps
+        bytes_per_block += num_samples_per_block * num_amp_channels * 2  # amplifier
+        bytes_per_block += (num_samples_per_block // 4) * num_aux_channels * 2  # aux
+        bytes_per_block += 1 * num_supply_channels * 2  # supply voltage
+        bytes_per_block += 1 * num_temp_channels * 2  # temp sensors
+        bytes_per_block += num_samples_per_block * num_adc_channels * 2  # ADC
+        if num_dig_in_channels > 0:
+            bytes_per_block += num_samples_per_block * 2  # digital in
+        if num_dig_out_channels > 0:
+            bytes_per_block += num_samples_per_block * 2  # digital out
+
+        # Write dummy data blocks
+        fid.write(b'\x00' * (bytes_per_block * num_data_blocks))
+
+    return header_size
+
+
+class TestReadIntanRHD2000Header:
+    """Tests for read_Intan_RHD2000_header."""
+
+    def test_basic_header_reading(self, tmp_path):
+        """Test reading a synthetic RHD file with known parameters."""
+        filepath = str(tmp_path / 'test.rhd')
+        create_synthetic_rhd(filepath, sample_rate=20000.0,
+                             num_amp_channels=2, num_data_blocks=1000)
+
+        header = read_Intan_RHD2000_header(filepath)
+
+        assert header['sample_rate'] == 20000.0
+        assert header['num_amplifier_channels'] == 2
+        assert header['num_aux_input_channels'] == 3
+        assert header['num_supply_voltage_channels'] == 1
+        # 1000 blocks * 60 samples/block = 60000 samples
+        assert header['num_samples'] == 60000
+
+    def test_sample_rate_and_num_samples(self, tmp_path):
+        """Test that sample_rate and num_samples are correct for t0_t1 computation.
+
+        With 1000 data blocks at 60 samples/block = 60000 samples,
+        t0 = 0, t1 = (60000 - 1) / 20000 = 2.99995
+        """
+        filepath = str(tmp_path / 'test.rhd')
+        create_synthetic_rhd(filepath, sample_rate=20000.0, num_data_blocks=1000)
+
+        header = read_Intan_RHD2000_header(filepath)
+
+        t0 = 0
+        t1 = (header['num_samples'] - 1) / header['sample_rate']
+        assert t0 == 0
+        assert abs(t1 - 2.99995) < 1e-10
+
+    def test_channel_info_populated(self, tmp_path):
+        """Test that channel info dicts contain expected fields."""
+        filepath = str(tmp_path / 'test.rhd')
+        create_synthetic_rhd(filepath, num_amp_channels=4)
+
+        header = read_Intan_RHD2000_header(filepath)
+
+        assert len(header['amplifier_channels']) == 4
+        ch = header['amplifier_channels'][0]
+        assert 'native_channel_name' in ch
+        assert 'custom_channel_name' in ch
+        assert 'chip_channel' in ch
+        assert ch['signal_type'] == 0
+
+    def test_frequency_parameters(self, tmp_path):
+        """Test that frequency parameters are read correctly."""
+        filepath = str(tmp_path / 'test.rhd')
+        create_synthetic_rhd(filepath, sample_rate=20000.0)
+
+        header = read_Intan_RHD2000_header(filepath)
+
+        freq = header['frequency_parameters']
+        assert freq['amplifier_sample_rate'] == 20000.0
+        assert freq['aux_input_sample_rate'] == 5000.0
+        assert freq['notch_filter_frequency'] == 60
+        assert freq['dsp_enabled'] == 1
+
+    def test_invalid_magic_number(self, tmp_path):
+        """Test that an invalid magic number raises ValueError."""
+        filepath = str(tmp_path / 'bad.rhd')
+        with open(filepath, 'wb') as f:
+            f.write(struct.pack('<I', 0xDEADBEEF))
+            f.write(b'\x00' * 100)
+
+        with pytest.raises(ValueError, match='Not a valid Intan RHD file'):
+            read_Intan_RHD2000_header(filepath)
+
+    def test_version_2(self, tmp_path):
+        """Test reading a version 2.x file (128 samples per block)."""
+        filepath = str(tmp_path / 'test_v2.rhd')
+        create_synthetic_rhd(filepath, sample_rate=30000.0,
+                             num_amp_channels=1, num_aux_channels=1,
+                             num_supply_channels=1, num_data_blocks=100,
+                             version_major=2, version_minor=0)
+
+        header = read_Intan_RHD2000_header(filepath)
+
+        assert header['sample_rate'] == 30000.0
+        assert header['num_amplifier_channels'] == 1
+        # 100 blocks * 128 samples/block = 12800 samples
+        assert header['num_samples'] == 12800
+        assert header['num_samples_per_data_block'] == 128
+
+    def test_no_data_blocks(self, tmp_path):
+        """Test reading a file with header only (no data)."""
+        filepath = str(tmp_path / 'header_only.rhd')
+        create_synthetic_rhd(filepath, num_data_blocks=0)
+
+        header = read_Intan_RHD2000_header(filepath)
+
+        assert header['num_samples'] == 0
+        assert header['sample_rate'] == 20000.0