w2t-bkin 0.0.9__tar.gz

w2t_bkin-0.0.9/LICENSE

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w2t_bkin-0.0.9/PKG-INFO

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+Metadata-Version: 2.4
+Name: w2t_bkin
+Version: 0.0.9
+Summary: Mouse wiskers body kinematics and behaviour
+Author: Larkum Lab
+Requires-Python: ~=3.10.0
+Description-Content-Type: text/markdown
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+License-File: LICENSE
+Requires-Dist: pydantic~=2.12.0
+Requires-Dist: pydantic-settings~=2.11.0
+Requires-Dist: tomli~=2.3.0
+Requires-Dist: facemap~=1.0.0
+Requires-Dist: deeplabcut[tf]~=2.3.0
+Requires-Dist: pynwb~=3.1.0
+Requires-Dist: hdmf~=4.1.0
+Requires-Dist: ndx-pose~=0.2.0
+Requires-Dist: ndx-events~=0.4.0
+Requires-Dist: ndx-structured-behavior~=0.1.0
+Requires-Dist: ffmpeg-python~=0.2.0
+Requires-Dist: scipy~=1.15.0
+Requires-Dist: pandas~=2.3.0
+Requires-Dist: h5py~=3.15.0
+Requires-Dist: tables~=3.8.0
+Requires-Dist: nwbinspector~=0.6.5
+Requires-Dist: typer~=0.20.0
+Requires-Dist: rich~=14.2.0
+Requires-Dist: black~=25.9.0 ; extra == "dev"
+Requires-Dist: isort~=7.0.0 ; extra == "dev"
+Requires-Dist: pytest~=9.0.0 ; extra == "dev"
+Requires-Dist: matplotlib~=3.8.0 ; extra == "dev"
+Requires-Dist: numpy~=1.26.0 ; extra == "dev"
+Provides-Extra: dev
+
+# W2T Body Kinematics Pipeline (w2t-bkin)
+
+A modular, reproducible Python pipeline for processing multi-camera rodent behavior recordings. It integrates synchronization, pose estimation (DeepLabCut/SLEAP), facial metrics, and behavioral events into standardized **NWB (Neurodata Without Borders)** datasets.
+
+## Key Features
+
+- **NWB-First Architecture**: Produces NWB-native data structures directly, eliminating intermediate conversion layers.
+- **Hierarchical Metadata**: Supports cascading configuration from global → subject → session levels for efficient metadata management.
+- **Bpod Integration**: Parses Bpod `.mat` files and converts them to `ndx-structured-behavior` format.
+- **Pose Estimation**: Imports and harmonizes data from DeepLabCut and SLEAP into `ndx-pose`.
+- **Synchronization**: Robust alignment of behavioral data and video frames to a common timebase using TTL pulses.
+- **Modular Design**: Distinct modules for behavior, pose, sync, and session management.
+
+## Installation
+
+The project requires Python ~3.10.
+
+1. **Install `ndx-structured-behavior`** (currently required from source):
+
+   ```bash
+   git clone https://github.com/rly/ndx-structured-behavior.git
+   pip install -U ./ndx-structured-behavior
+   ```
+
+2. **Install `w2t-bkin`**:
+
+   ```bash
+   pip install w2t-bkin
+   ```
+
+## Project Structure
+
+```text
+project/
+├── config.toml              # Pipeline configuration
+├── data/
+│   ├── raw/                 # Raw data organized by subject/session
+│   │   ├── metadata.toml    # Optional: Global metadata (lab-wide defaults)
+│   │   └── subject-001/
+│   │       ├── subject.toml # Optional: Subject-specific metadata
+│   │       └── session-001/
+│   │           ├── session.toml  # Session-specific NWB metadata
+│   │           ├── Video/        # Raw video files
+│   │           ├── TTLs/         # TTL pulse timestamps
+│   │           └── Bpod/         # Bpod behavior files
+│   ├── interim/             # Processed data (pose estimation, etc.)
+│   │   └── subject-001/
+│   │       └── session-001/
+│   │           └── Pose/
+│   └── processed/           # Final NWB output files
+└── models/                  # Pose estimation models (DLC/SLEAP)
+```
+
+## Configuration
+
+The pipeline uses TOML for configuration:
+
+### Pipeline Configuration (`config.toml`)
+
+Defines paths, timebase, and synchronization settings:
+
+```toml
+[project]
+name = "my-experiment"
+
+[paths]
+raw_root = "data/raw"
+intermediate_root = "data/interim"
+output_root = "data/processed"
+models_root = "models"
+root_metadata = "data/raw/metadata.toml"  # Optional global metadata
+
+[synchronization]
+strategy = "hardware_pulse"
+reference_channel = "ttl_camera"
+
+[synchronization.alignment]
+method = "nearest"
+tolerance_s = 0.001
+
+[[bpod.sync.trial_types]]
+trial_type = 1
+sync_signal = "W2T_Audio"
+sync_ttl = "ttl_cue"
+```
+
+### Hierarchical Metadata
+
+Metadata is loaded and merged from multiple levels (later files override earlier ones):
+
+1. **`root_metadata`** (optional): Lab/project-wide defaults
+2. **`raw_root/metadata.toml`** (optional): Experiment-wide settings
+3. **`raw_root/subject_id/subject.toml`** (optional): Subject-specific metadata
+4. **`raw_root/subject_id/session_id/session.toml`**: Session-specific NWB metadata
+
+Example `session.toml`:
+
+```toml
+session_description = "Behavioral training with pose tracking"
+identifier = "session-001"
+session_start_time = "2025-11-21T14:30:00Z"
+experimenter = ["Esteban, Borja"]
+institution = "My Lab"
+lab = "Neuroscience Lab"
+
+[subject]
+subject_id = "subject-001"
+species = "Mus musculus"
+sex = "M"
+age = "P90D"
+
+# Camera configuration
+[[cameras]]
+id = "camera_0"             # Must match a device name in [[devices]]
+paths = "Video/cam0_*.avi"  # Glob pattern for video files
+fps = 150.0                 # Acquisition frame rate (defaults to 30.0 if omitted)
+ttl_id = "ttl_camera"       # Associated TTL stream for synchronization
+```
+
+## Quick Start
+
+### Using the High-Level Helper
+
+```python
+from pathlib import Path
+from w2t_bkin.config import load_config
+from w2t_bkin.utils import load_session_metadata_and_nwb
+
+# Load configuration
+config = load_config("config.toml")
+
+# Load hierarchical metadata and create NWBFile in one step
+metadata, nwbfile = load_session_metadata_and_nwb(
+    config=config,
+    subject_id="subject-001",
+    session_id="session-001"
+)
+
+# Continue with your pipeline...
+```
+
+### Manual Approach
+
+```python
+from pathlib import Path
+from w2t_bkin import config, sync
+from w2t_bkin.core import session
+from w2t_bkin.ingest import behavior, bpod, ttl
+
+# 1. Load Configuration
+settings = config.load_config("config.toml")
+
+# 2. Build metadata paths and load hierarchically
+metadata_paths = session.build_metadata_paths(
+    raw_root=settings.paths.raw_root,
+    subject_id="subject-001",
+    session_id="session-001",
+    root_metadata=settings.paths.root_metadata
+)
+metadata = session.load_metadata(metadata_paths)
+
+# 3. Create NWBFile
+nwbfile = session.create_nwb_file(metadata)
+
+# 4. Get session directory
+session_dir = settings.paths.raw_root / "subject-001" / "session-001"
+
+# 5. Import TTL Signals
+ttl_patterns = {
+    "ttl_camera": "TTLs/*.xa_7_0*.txt",
+    "ttl_cue": "TTLs/*.xia_3_0*.txt",
+}
+ttl_pulses = ttl.get_ttl_pulses(session_dir, ttl_patterns)
+
+# 6. Parse Bpod Data
+bpod_data = bpod.parse_bpod(
+    session_dir=session_dir,
+    pattern="Bpod/*.mat",
+    order="name_asc"
+)
+
+# 7. Synchronize Bpod to TTL
+trial_offsets, warnings = sync.align_bpod_trials_to_ttl(
+    trial_type_configs=settings.bpod.sync.trial_types,
+    bpod_data=bpod_data,
+    ttl_pulses=ttl_pulses,
+)
+
+# 8. Extract Behavioral Data (NWB objects)
+task, recording, trials = behavior.extract_behavioral_data(
+    bpod_data,
+    trial_offsets
+)
+
+# 9. Add to NWB
+nwbfile.add_lab_meta_data(task)
+nwbfile.add_acquisition(recording.states)
+nwbfile.add_acquisition(recording.events)
+nwbfile.add_acquisition(recording.actions)
+nwbfile.trials = trials
+```
+
+## Examples
+
+The `examples/` directory contains complete working examples:
+
+- **`bpod_camera_sync.py`**: Demonstrates Bpod-camera synchronization with TTL alignment
+- **`pose_camera_nwb.py`**: Shows pose estimation data import and NWB file creation
+- **`sync_recovery_demo.py`**: Robust sync recovery with missing TTL pulses
+
+Run an example:
+
+```bash
+python examples/pose_camera_nwb.py
+```
+
+## Module Overview
+
+| Module                     | Description                                                                                        |
+| :------------------------- | :------------------------------------------------------------------------------------------------- |
+| `w2t_bkin.ingest.behavior` | Converts Bpod data into `ndx-structured-behavior` classes (StatesTable, EventsTable, TrialsTable). |
+| `w2t_bkin.ingest.bpod`     | Low-level parsing and validation of Bpod `.mat` files.                                             |
+| `w2t_bkin.ingest.pose`     | Imports pose estimation data (DLC/SLEAP) and builds `ndx-pose` objects (PoseEstimation, Skeleton). |
+| `w2t_bkin.ingest.ttl`      | Loads hardware TTL pulse timestamps and creates `ndx-events` tables.                               |
+| `w2t_bkin.sync`            | Handles timebase alignment, jitter calculation, and synchronization of video/behavior to TTLs.     |
+| `w2t_bkin.core.session`    | Loads metadata hierarchically and assembles the root `NWBFile`.                                    |
+| `w2t_bkin.core.pipeline`   | High-level orchestration of the entire workflow.                                                   |
+| `w2t_bkin.utils`           | Shared utilities including datetime parsing, dictionary merging, and helper functions.             |
+
+## CLI Utilities
+
+The `scripts/` directory contains useful utilities:
+
+- `mat2json.py`: Converts MATLAB `.mat` files to JSON, handling nested structures and arrays.
+- `pose2ttl.py`: Generates mock TTL signals from DeepLabCut pose data (useful for testing or when hardware sync fails).
+- `trials2df.py`: Converts NWB `TrialsTable` and `TaskRecording` objects into a flat pandas DataFrame for analysis.
+
+## Testing
+
+The project includes synthetic data generation for testing:
+
+```python
+from synthetic import build_raw_folder, build_interim_pose
+
+# Generate synthetic session
+session = build_raw_folder(
+    out_root=Path("output/test/raw"),
+    project_name="test-project",
+    subject_id="subject-001",
+    session_id="session-001",
+    camera_ids=["cam0", "cam1"],
+    ttl_ids=["ttl_camera", "ttl_bpod"],
+    n_frames=300,
+    n_trials=10,
+)
+```
+
+## License
+
+See `LICENSE` file for details.
+