biosigio 1.0.0__tar.gz

biosigio-1.0.0/LICENSE

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2024, Swartz Center for Computational Neuroscience
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

biosigio-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: biosigio
+Version: 1.0.0
+Summary: A Python package for EMG data import/export and manipulation with unified interface for various EMG systems
+Author-email: Seyed Yahya Shirazi <shirazi@ieee.org>
+Maintainer-email: Seyed Yahya Shirazi <shirazi@ieee.org>
+License: BSD 3-Clause License
+        
+        Copyright (c) 2024, Swartz Center for Computational Neuroscience
+        All rights reserved.
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        1. Redistributions of source code must retain the above copyright notice, this
+           list of conditions and the following disclaimer.
+        
+        2. Redistributions in binary form must reproduce the above copyright notice,
+           this list of conditions and the following disclaimer in the documentation
+           and/or other materials provided with the distribution.
+        
+        3. Neither the name of the copyright holder nor the names of its
+           contributors may be used to endorse or promote products derived from
+           this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+        
+Project-URL: Homepage, https://github.com/neuromechanist/biosigio
+Project-URL: Documentation, https://neuromechanist.github.io/biosigio/
+Project-URL: Repository, https://github.com/neuromechanist/biosigio
+Project-URL: Issues, https://github.com/neuromechanist/biosigio/issues
+Project-URL: Changelog, https://github.com/neuromechanist/biosigio/releases
+Keywords: emg,electromyography,biosignal,edf,bdf,wfdb,trigno,delsys,neuroscience,signal-processing
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.20.0
+Requires-Dist: pandas>=1.3.0
+Requires-Dist: scipy>=1.7.0
+Requires-Dist: matplotlib>=3.4.0
+Requires-Dist: pyedflib>=0.1.30
+Requires-Dist: wfdb>=4.0.0
+Requires-Dist: pyxdf>=1.16.0
+Provides-Extra: meg
+Requires-Dist: mne>=1.6; extra == "meg"
+Provides-Extra: arrow
+Requires-Dist: pyarrow>=14; extra == "arrow"
+Provides-Extra: neo
+Requires-Dist: neo>=0.13; extra == "neo"
+Provides-Extra: zarr
+Requires-Dist: zarr>=3; extra == "zarr"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
+Requires-Dist: ruff>=0.14; extra == "dev"
+Requires-Dist: ty; extra == "dev"
+Requires-Dist: mne>=1.6; extra == "dev"
+Requires-Dist: pyarrow>=14; extra == "dev"
+Requires-Dist: neo>=0.13; extra == "dev"
+Requires-Dist: zarr>=3; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: mkdocs>=1.6.0; extra == "docs"
+Requires-Dist: mkdocs-material>=9.5.0; extra == "docs"
+Requires-Dist: mkdocstrings[python]>=1.0.0; extra == "docs"
+Requires-Dist: pymdown-extensions>=10.10.0; extra == "docs"
+Requires-Dist: mkdocs-jupyter>=0.25.0; extra == "docs"
+Requires-Dist: mike>=2.1.0; extra == "docs"
+Provides-Extra: all
+Requires-Dist: biosigio[arrow,dev,docs,meg,neo,zarr]; extra == "all"
+Dynamic: license-file
+
+# biosigIO
+
+[![PyPI version](https://badge.fury.io/py/biosigio.svg)](https://badge.fury.io/py/biosigio)
+[![Tests](https://github.com/neuromechanist/biosigio/actions/workflows/tests.yml/badge.svg)](https://github.com/neuromechanist/biosigio/actions/workflows/tests.yml)
+[![codecov](https://codecov.io/gh/neuromechanist/biosigio/branch/main/graph/badge.svg?token=63EDIA9TWD)](https://codecov.io/gh/neuromechanist/biosigio)
+
+A Python package for biosignal import/export and manipulation across modalities (EEG, EMG, iEEG, MEG, and behavioral/marker streams). biosigIO provides a unified `Recording` interface for loading data from many acquisition systems and archives (EEGLAB, Delsys Trigno, OTB, EDF/BDF, WFDB, XDF, MEG/CTF and BrainVision via MNE, and proprietary electrophysiology such as Intan/Blackrock via python-neo) and exporting it to standardized and serving formats (EDF/BDF, Parquet, Arrow, Zarr) with harmonized metadata.
+
+The determination of the EDF/BDF format is based on the dynamic range of the data. If the data is within the range of 16-bit integers (~90dB), the EDF format is used. Otherwise, the BDF format is used. This is to ensure that the data is stored in the most efficient format possible. This determination is made automatically using SVD decomposition and/or FFT to determine the dynamic range of the data. (Alternatively, the user can override the format selection by explicitly indicating their desired format).
+
+## Documentation
+
+The documentation including installation instructions, examples, and API reference is available at [https://neuromechanist.github.io/biosigio/](https://neuromechanist.github.io/biosigio/).
+
+## Features
+
+- Import biosignal recordings from many systems and archives:
+  - EEGLAB set files (supported)
+  - Delsys Trigno (supported)
+  - OTB Systems (supported)
+  - EDF/BDF(+) (supported, including annotations)
+  - WFDB (supported, including annotations)
+  - XDF/Lab Streaming Layer (supported, multi-stream)
+  - MEG: `.fif` and CTF `.ds` via MNE (supported; `meg` extra)
+  - BrainVision `.vhdr` via MNE (supported; `meg` extra)
+  - Proprietary electrophysiology via python-neo: Intan, Blackrock, Spike2, Plexon, Micromed, Neuralynx (supported; `neo` extra)
+  - Generic CSV (supported with auto-detection)
+  - Noraxon (planned)
+  
+- Smart import:
+  - Automatic file format detection based on extension
+  - Specialized format detection for CSV files
+  - Custom importers for system-specific formats
+  - Automatic annotation loading (WFDB, planned for EDF+/BDF+ and EEGLAB's .set files)
+  - LSL timestamp preservation for XDF files (for synchronization)
+  
+- Export to standardized formats:
+  - EDF/BDF(+) with channels.tsv metadata (automatically selects format based on signal properties, preserves annotations)
+
+- Serialization & serving (see [docs](https://neuromechanist.github.io/biosigio/formats/serialization/)):
+  - Parquet and Arrow/Feather: lossless columnar round-trip (analytics, fast IPC); requires the `arrow` extra
+  - Zarr: cloud-native serving store (one store serves viewing, inference, and training), a derived downsampled copy; requires the `zarr` extra
+  
+- Data manipulation:
+  - Channel selection
+  - Metadata handling
+  - Event/Annotation handling (access, add)
+  - Basic signal visualization
+  - Raw data access and modification
+
+## Installation
+
+biosigIO uses [UV](https://docs.astral.sh/uv/) for Python environment and package management.
+
+### From PyPI (recommended)
+
+```bash
+uv pip install biosigio
+```
+
+(If your own project is uv-managed, use `uv add biosigio` to track it as a dependency.)
+
+### From source
+
+```bash
+git clone https://github.com/neuromechanist/biosigio.git
+cd biosigio
+uv pip install .
+```
+
+## Usage
+
+### Basic Example
+
+```python
+from biosigio import Recording
+
+# Load data with automatic format detection
+emg = Recording.from_file('data.csv')  # Format detected from file extension
+
+# Load data with explicit importer
+emg = Recording.from_file('data.csv', importer='trigno')
+
+# Plot specific channels
+emg.plot_signals(['EMG1', 'EMG2'])
+
+# Export to EDF or BDF (format automatically determined)
+emg.to_edf('output.edf')
+```
+
+### Generic CSV Import
+
+```python
+# Import a generic CSV file
+emg = Recording.from_file('data.csv', importer='csv',
+                   sample_frequency=1000,  # Required if no time column
+                   has_header=True,        # Whether file has header row
+                   channel_names=['EMG_L', 'EMG_R', 'ACC_X'])
+```
+
+### Channel Selection
+
+```python
+# Select specific channels
+subset_emg = emg.select_channels(['EMG1', 'EMG2', 'ACC1'])
+
+# Select all channels of a specific type
+emg_only = emg.select_channels(channel_type='EMG')
+
+# Plot selected channels
+subset_emg.plot_signals()
+```
+
+### Metadata Handling
+
+```python
+# Set metadata
+emg.set_metadata('subject', 'S001')
+emg.set_metadata('condition', 'resting')
+
+# Get metadata
+subject = emg.get_metadata('subject')
+```
+
+## Development
+
+### Setup
+
+1. Clone the repository:
+```bash
+git clone https://github.com/neuromechanist/biosigio.git
+cd biosigio
+```
+
+2. Install for development (editable install with dev dependencies):
+```bash
+uv sync --extra dev
+```
+
+### Running Tests
+
+```bash
+uv run pytest
+```
+
+## Contributing
+
+Contributions are welcome! Please feel free to submit a Pull Request.
+
+## License
+
+This project is licensed under the BSD 3-Clause License - see the LICENSE file for details.
+
+## Acknowledgment
+This project is partially supported by a Meta Reality Labs gift to @sccn and NIH 5R01NS047293.

biosigio-1.0.0/README.md

@@ -0,0 +1,155 @@
+# biosigIO
+
+[![PyPI version](https://badge.fury.io/py/biosigio.svg)](https://badge.fury.io/py/biosigio)
+[![Tests](https://github.com/neuromechanist/biosigio/actions/workflows/tests.yml/badge.svg)](https://github.com/neuromechanist/biosigio/actions/workflows/tests.yml)
+[![codecov](https://codecov.io/gh/neuromechanist/biosigio/branch/main/graph/badge.svg?token=63EDIA9TWD)](https://codecov.io/gh/neuromechanist/biosigio)
+
+A Python package for biosignal import/export and manipulation across modalities (EEG, EMG, iEEG, MEG, and behavioral/marker streams). biosigIO provides a unified `Recording` interface for loading data from many acquisition systems and archives (EEGLAB, Delsys Trigno, OTB, EDF/BDF, WFDB, XDF, MEG/CTF and BrainVision via MNE, and proprietary electrophysiology such as Intan/Blackrock via python-neo) and exporting it to standardized and serving formats (EDF/BDF, Parquet, Arrow, Zarr) with harmonized metadata.
+
+The determination of the EDF/BDF format is based on the dynamic range of the data. If the data is within the range of 16-bit integers (~90dB), the EDF format is used. Otherwise, the BDF format is used. This is to ensure that the data is stored in the most efficient format possible. This determination is made automatically using SVD decomposition and/or FFT to determine the dynamic range of the data. (Alternatively, the user can override the format selection by explicitly indicating their desired format).
+
+## Documentation
+
+The documentation including installation instructions, examples, and API reference is available at [https://neuromechanist.github.io/biosigio/](https://neuromechanist.github.io/biosigio/).
+
+## Features
+
+- Import biosignal recordings from many systems and archives:
+  - EEGLAB set files (supported)
+  - Delsys Trigno (supported)
+  - OTB Systems (supported)
+  - EDF/BDF(+) (supported, including annotations)
+  - WFDB (supported, including annotations)
+  - XDF/Lab Streaming Layer (supported, multi-stream)
+  - MEG: `.fif` and CTF `.ds` via MNE (supported; `meg` extra)
+  - BrainVision `.vhdr` via MNE (supported; `meg` extra)
+  - Proprietary electrophysiology via python-neo: Intan, Blackrock, Spike2, Plexon, Micromed, Neuralynx (supported; `neo` extra)
+  - Generic CSV (supported with auto-detection)
+  - Noraxon (planned)
+  
+- Smart import:
+  - Automatic file format detection based on extension
+  - Specialized format detection for CSV files
+  - Custom importers for system-specific formats
+  - Automatic annotation loading (WFDB, planned for EDF+/BDF+ and EEGLAB's .set files)
+  - LSL timestamp preservation for XDF files (for synchronization)
+  
+- Export to standardized formats:
+  - EDF/BDF(+) with channels.tsv metadata (automatically selects format based on signal properties, preserves annotations)
+
+- Serialization & serving (see [docs](https://neuromechanist.github.io/biosigio/formats/serialization/)):
+  - Parquet and Arrow/Feather: lossless columnar round-trip (analytics, fast IPC); requires the `arrow` extra
+  - Zarr: cloud-native serving store (one store serves viewing, inference, and training), a derived downsampled copy; requires the `zarr` extra
+  
+- Data manipulation:
+  - Channel selection
+  - Metadata handling
+  - Event/Annotation handling (access, add)
+  - Basic signal visualization
+  - Raw data access and modification
+
+## Installation
+
+biosigIO uses [UV](https://docs.astral.sh/uv/) for Python environment and package management.
+
+### From PyPI (recommended)
+
+```bash
+uv pip install biosigio
+```
+
+(If your own project is uv-managed, use `uv add biosigio` to track it as a dependency.)
+
+### From source
+
+```bash
+git clone https://github.com/neuromechanist/biosigio.git
+cd biosigio
+uv pip install .
+```
+
+## Usage
+
+### Basic Example
+
+```python
+from biosigio import Recording
+
+# Load data with automatic format detection
+emg = Recording.from_file('data.csv')  # Format detected from file extension
+
+# Load data with explicit importer
+emg = Recording.from_file('data.csv', importer='trigno')
+
+# Plot specific channels
+emg.plot_signals(['EMG1', 'EMG2'])
+
+# Export to EDF or BDF (format automatically determined)
+emg.to_edf('output.edf')
+```
+
+### Generic CSV Import
+
+```python
+# Import a generic CSV file
+emg = Recording.from_file('data.csv', importer='csv',
+                   sample_frequency=1000,  # Required if no time column
+                   has_header=True,        # Whether file has header row
+                   channel_names=['EMG_L', 'EMG_R', 'ACC_X'])
+```
+
+### Channel Selection
+
+```python
+# Select specific channels
+subset_emg = emg.select_channels(['EMG1', 'EMG2', 'ACC1'])
+
+# Select all channels of a specific type
+emg_only = emg.select_channels(channel_type='EMG')
+
+# Plot selected channels
+subset_emg.plot_signals()
+```
+
+### Metadata Handling
+
+```python
+# Set metadata
+emg.set_metadata('subject', 'S001')
+emg.set_metadata('condition', 'resting')
+
+# Get metadata
+subject = emg.get_metadata('subject')
+```
+
+## Development
+
+### Setup
+
+1. Clone the repository:
+```bash
+git clone https://github.com/neuromechanist/biosigio.git
+cd biosigio
+```
+
+2. Install for development (editable install with dev dependencies):
+```bash
+uv sync --extra dev
+```
+
+### Running Tests
+
+```bash
+uv run pytest
+```
+
+## Contributing
+
+Contributions are welcome! Please feel free to submit a Pull Request.
+
+## License
+
+This project is licensed under the BSD 3-Clause License - see the LICENSE file for details.
+
+## Acknowledgment
+This project is partially supported by a Meta Reality Labs gift to @sccn and NIH 5R01NS047293.

biosigio-1.0.0/biosigio/__init__.py

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+"""biosigIO: import/export biosignal recordings across formats.
+
+The core class is :class:`Recording` (modality-agnostic: EEG/EMG/iEEG/MEG/...).
+"""
+
+from .core.emg import Recording
+from .exporters.edf import EDFExporter
+from .importers.trigno import TrignoImporter
+from .version import __version__, __version_info__
+
+__all__ = [
+    "Recording",
+    "TrignoImporter",
+    "EDFExporter",
+    "__version__",
+    "__version_info__",
+]

biosigio-1.0.0/biosigio/analysis/__init__.py

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+# Signal analysis module
+
+from .signal import (
+    analyze_signal,
+    determine_format_suitability,
+    quantization_analysis,
+    # Add other signal analysis functions if needed
+)
+from .verification import compare_signals
+
+__all__ = [
+    "analyze_signal",
+    "determine_format_suitability",
+    "quantization_analysis",
+    "compare_signals",  # Add to __all__
+]