thyra 1.8.4__tar.gz

thyra-1.8.4/LICENSE

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+MIT License
+
+Copyright (c) 2025 Theodoros Visvikis
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

thyra-1.8.4/PKG-INFO

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+Metadata-Version: 2.3
+Name: thyra
+Version: 1.8.4
+Summary: A modern Python library for converting Mass Spectrometry Imaging (MSI) data into SpatialData/Zarr format - your portal to spatial omics
+License: MIT
+Keywords: mass-spectrometry,imaging,spatialdata,zarr,omics,bioinformatics,msi,imzml,bruker,spatial-omics,data-conversion,scientific-computing
+Author: Theodoros Visvikis
+Author-email: t.visvikis@maastrichtuniversity.nl
+Maintainer: Theodoros Visvikis
+Maintainer-email: t.visvikis@maastrichtuniversity.nl
+Requires-Python: >=3.11,<3.13
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT 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 :: 3.10
+Classifier: Topic :: File Formats
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: Typing :: Typed
+Requires-Dist: Shapely (>=1.8.0)
+Requires-Dist: anndata (>=0.11.0)
+Requires-Dist: cryptography (>=45.0.5,<46.0.0)
+Requires-Dist: dask (>=2023.0.0)
+Requires-Dist: geopandas (>=0.9.0)
+Requires-Dist: lxml (>=4.6.0)
+Requires-Dist: matplotlib (>=3.10.6,<4.0.0)
+Requires-Dist: numpy (>=2.0.0)
+Requires-Dist: pandas (>=2.0.0)
+Requires-Dist: pyimzML (>=1.4.0)
+Requires-Dist: scipy (>=1.7.0)
+Requires-Dist: spatialdata (>=0.2.0)
+Requires-Dist: tqdm (>=4.50.0)
+Requires-Dist: zarr (>=3.0.0)
+Project-URL: Bug Tracker, https://github.com/Tomatokeftes/thyra/issues
+Project-URL: Changelog, https://github.com/Tomatokeftes/thyra/blob/main/CHANGELOG.md
+Project-URL: Contributing, https://github.com/Tomatokeftes/thyra/blob/main/CONTRIBUTING.md
+Project-URL: Documentation, https://github.com/Tomatokeftes/thyra#readme
+Project-URL: Discussions, https://github.com/Tomatokeftes/thyra/discussions
+Project-URL: Homepage, https://github.com/Tomatokeftes/thyra
+Project-URL: Repository, https://github.com/Tomatokeftes/thyra
+Description-Content-Type: text/markdown
+
+# Thyra
+
+[![Tests](https://img.shields.io/github/actions/workflow/status/Tomatokeftes/thyra/tests.yml?branch=main&logo=github)](https://github.com/Tomatokeftes/thyra/actions/workflows/tests.yml)
+[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+
+**Thyra** (from Greek θύρα, meaning "door" or "portal") - A modern Python library for converting Mass Spectrometry Imaging (MSI) data into the standardized **SpatialData/Zarr format**, serving as your portal to spatial omics analysis workflows.
+
+## Features
+
+- **Multiple Input Formats**: ImzML, Bruker (.d directories)
+- **SpatialData Output**: Modern, cloud-ready format with Zarr backend
+- **Memory Efficient**: Handles large datasets (100+ GB) through streaming processing
+- **Metadata Preservation**: Extracts and maintains all acquisition parameters
+- **3D Support**: Process volume data or treat as 2D slices
+- **Cross-Platform**: Windows, macOS, and Linux support
+
+## Installation
+
+### Via pip (Recommended)
+```bash
+pip install thyra
+```
+
+### Via conda
+```bash
+conda install -c conda-forge thyra
+```
+
+### From source
+```bash
+git clone https://github.com/Tomatokeftes/thyra.git
+cd thyra
+poetry install
+```
+
+## Quick Start
+
+### Command Line Interface
+
+```bash
+# Basic conversion
+thyra input.imzML output.zarr
+
+# With custom parameters
+thyra data.d output.zarr --pixel-size 50 --dataset-id "experiment_001"
+
+# 3D volume processing
+thyra volume.imzML output.zarr --handle-3d
+```
+
+### Python API
+
+```python
+from thyra import convert_msi
+
+# Simple conversion
+success = convert_msi(
+    input_path="data/sample.imzML",
+    output_path="output/sample.zarr",
+    pixel_size_um=25.0
+)
+
+# Advanced usage with custom parameters
+success = convert_msi(
+    input_path="data/experiment.d",
+    output_path="output/experiment.zarr",
+    dataset_id="exp_001",
+    pixel_size_um=10.0,
+    handle_3d=True
+)
+```
+
+## Supported Formats
+
+### Input Formats
+| Format | Extension | Description | Status |
+|--------|-----------|-------------|--------|
+| ImzML | `.imzML` | Open standard for MS imaging | ✅ Full support |
+| Bruker | `.d` | Bruker proprietary format | ✅ Full support |
+
+### Output Formats
+| Format | Description | Benefits |
+|--------|-------------|----------|
+| SpatialData/Zarr | Modern spatial omics standard | Cloud-ready, efficient, standardized |
+
+## Advanced Usage
+
+### Configuration Options
+
+```bash
+# All available options
+thyra input.imzML output.zarr \
+    --pixel-size 25 \
+    --dataset-id "my_experiment" \
+    --handle-3d \
+    --optimize-chunks \
+    --log-level DEBUG \
+    --log-file conversion.log
+```
+
+### Batch Processing
+
+```python
+import glob
+from thyra import convert_msi
+
+# Process multiple files
+for input_file in glob.glob("data/*.imzML"):
+    output_file = input_file.replace(".imzML", ".zarr")
+    convert_msi(input_file, output_file)
+```
+
+### Working with SpatialData
+
+```python
+import spatialdata as sd
+
+# Load converted data
+sdata = sd.read_zarr("output/sample.zarr")
+
+# Access the MSI data
+msi_data = sdata.tables["msi_dataset"]
+print(f"Shape: {msi_data.shape}")
+print(f"Mass channels: {msi_data.var.index}")
+```
+
+## Development
+
+### Setup Development Environment
+
+```bash
+# Clone repository
+git clone https://github.com/Tomatokeftes/thyra.git
+cd thyra
+
+# Install with development dependencies
+poetry install
+
+# Install pre-commit hooks
+poetry run pre-commit install
+```
+
+### Running Tests
+
+```bash
+# Unit tests only
+poetry run pytest -m "not integration"
+
+# All tests
+poetry run pytest
+
+# With coverage
+poetry run pytest --cov=thyra
+```
+
+### Code Quality
+
+```bash
+# Format code
+poetry run black .
+poetry run isort .
+
+# Run linting
+poetry run flake8
+
+# Run all checks
+poetry run pre-commit run --all-files
+```
+
+## Documentation
+
+- **API Documentation**: [Auto-generated docs](https://github.com/Tomatokeftes/thyra#readme)
+- **Contributing Guide**: [CONTRIBUTING.md](CONTRIBUTING.md)
+- **Architecture Overview**: [docs/architecture.md](docs/architecture.md)
+- **Changelog**: [CHANGELOG.md](CHANGELOG.md)
+
+## Contributing
+
+We welcome contributions! Please see our [Contributing Guidelines](CONTRIBUTING.md) for details.
+
+### Quick Contribution Steps
+
+1. Fork the repository
+2. Create a feature branch (`git checkout -b feature/amazing-feature`)
+3. Make your changes and add tests
+4. Run the test suite (`poetry run pytest`)
+5. Commit your changes (`git commit -m 'Add amazing feature'`)
+6. Push to your branch (`git push origin feature/amazing-feature`)
+7. Open a Pull Request
+
+## License
+
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
+
+## Support
+
+- **Issues**: [GitHub Issues](https://github.com/Tomatokeftes/thyra/issues)
+- **Discussions**: [GitHub Discussions](https://github.com/Tomatokeftes/thyra/discussions)
+- **Email**: t.visvikis@maastrichtuniversity.nl
+
+## Citation
+
+If you use Thyra in your research, please cite:
+
+```bibtex
+@software{thyra2024,
+  title = {Thyra: Modern Mass Spectrometry Imaging Data Conversion - Portal to Spatial Omics},
+  author = {Visvikis, Theodoros},
+  year = {2024},
+  url = {https://github.com/Tomatokeftes/thyra}
+}
+```
+
+## Acknowledgments
+
+- Built with [SpatialData](https://spatialdata.scverse.org/) ecosystem
+- Powered by [Zarr](https://zarr.readthedocs.io/) for efficient storage
+- Uses [pyimzML](https://github.com/alexandrovteam/pyimzML) for ImzML parsing
+
+---
+
+**Thyra** - Your portal from traditional MSI formats to modern spatial omics workflows
+

thyra-1.8.4/README.md

@@ -0,0 +1,224 @@
+# Thyra
+
+[![Tests](https://img.shields.io/github/actions/workflow/status/Tomatokeftes/thyra/tests.yml?branch=main&logo=github)](https://github.com/Tomatokeftes/thyra/actions/workflows/tests.yml)
+[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+
+**Thyra** (from Greek θύρα, meaning "door" or "portal") - A modern Python library for converting Mass Spectrometry Imaging (MSI) data into the standardized **SpatialData/Zarr format**, serving as your portal to spatial omics analysis workflows.
+
+## Features
+
+- **Multiple Input Formats**: ImzML, Bruker (.d directories)
+- **SpatialData Output**: Modern, cloud-ready format with Zarr backend
+- **Memory Efficient**: Handles large datasets (100+ GB) through streaming processing
+- **Metadata Preservation**: Extracts and maintains all acquisition parameters
+- **3D Support**: Process volume data or treat as 2D slices
+- **Cross-Platform**: Windows, macOS, and Linux support
+
+## Installation
+
+### Via pip (Recommended)
+```bash
+pip install thyra
+```
+
+### Via conda
+```bash
+conda install -c conda-forge thyra
+```
+
+### From source
+```bash
+git clone https://github.com/Tomatokeftes/thyra.git
+cd thyra
+poetry install
+```
+
+## Quick Start
+
+### Command Line Interface
+
+```bash
+# Basic conversion
+thyra input.imzML output.zarr
+
+# With custom parameters
+thyra data.d output.zarr --pixel-size 50 --dataset-id "experiment_001"
+
+# 3D volume processing
+thyra volume.imzML output.zarr --handle-3d
+```
+
+### Python API
+
+```python
+from thyra import convert_msi
+
+# Simple conversion
+success = convert_msi(
+    input_path="data/sample.imzML",
+    output_path="output/sample.zarr",
+    pixel_size_um=25.0
+)
+
+# Advanced usage with custom parameters
+success = convert_msi(
+    input_path="data/experiment.d",
+    output_path="output/experiment.zarr",
+    dataset_id="exp_001",
+    pixel_size_um=10.0,
+    handle_3d=True
+)
+```
+
+## Supported Formats
+
+### Input Formats
+| Format | Extension | Description | Status |
+|--------|-----------|-------------|--------|
+| ImzML | `.imzML` | Open standard for MS imaging | ✅ Full support |
+| Bruker | `.d` | Bruker proprietary format | ✅ Full support |
+
+### Output Formats
+| Format | Description | Benefits |
+|--------|-------------|----------|
+| SpatialData/Zarr | Modern spatial omics standard | Cloud-ready, efficient, standardized |
+
+## Advanced Usage
+
+### Configuration Options
+
+```bash
+# All available options
+thyra input.imzML output.zarr \
+    --pixel-size 25 \
+    --dataset-id "my_experiment" \
+    --handle-3d \
+    --optimize-chunks \
+    --log-level DEBUG \
+    --log-file conversion.log
+```
+
+### Batch Processing
+
+```python
+import glob
+from thyra import convert_msi
+
+# Process multiple files
+for input_file in glob.glob("data/*.imzML"):
+    output_file = input_file.replace(".imzML", ".zarr")
+    convert_msi(input_file, output_file)
+```
+
+### Working with SpatialData
+
+```python
+import spatialdata as sd
+
+# Load converted data
+sdata = sd.read_zarr("output/sample.zarr")
+
+# Access the MSI data
+msi_data = sdata.tables["msi_dataset"]
+print(f"Shape: {msi_data.shape}")
+print(f"Mass channels: {msi_data.var.index}")
+```
+
+## Development
+
+### Setup Development Environment
+
+```bash
+# Clone repository
+git clone https://github.com/Tomatokeftes/thyra.git
+cd thyra
+
+# Install with development dependencies
+poetry install
+
+# Install pre-commit hooks
+poetry run pre-commit install
+```
+
+### Running Tests
+
+```bash
+# Unit tests only
+poetry run pytest -m "not integration"
+
+# All tests
+poetry run pytest
+
+# With coverage
+poetry run pytest --cov=thyra
+```
+
+### Code Quality
+
+```bash
+# Format code
+poetry run black .
+poetry run isort .
+
+# Run linting
+poetry run flake8
+
+# Run all checks
+poetry run pre-commit run --all-files
+```
+
+## Documentation
+
+- **API Documentation**: [Auto-generated docs](https://github.com/Tomatokeftes/thyra#readme)
+- **Contributing Guide**: [CONTRIBUTING.md](CONTRIBUTING.md)
+- **Architecture Overview**: [docs/architecture.md](docs/architecture.md)
+- **Changelog**: [CHANGELOG.md](CHANGELOG.md)
+
+## Contributing
+
+We welcome contributions! Please see our [Contributing Guidelines](CONTRIBUTING.md) for details.
+
+### Quick Contribution Steps
+
+1. Fork the repository
+2. Create a feature branch (`git checkout -b feature/amazing-feature`)
+3. Make your changes and add tests
+4. Run the test suite (`poetry run pytest`)
+5. Commit your changes (`git commit -m 'Add amazing feature'`)
+6. Push to your branch (`git push origin feature/amazing-feature`)
+7. Open a Pull Request
+
+## License
+
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
+
+## Support
+
+- **Issues**: [GitHub Issues](https://github.com/Tomatokeftes/thyra/issues)
+- **Discussions**: [GitHub Discussions](https://github.com/Tomatokeftes/thyra/discussions)
+- **Email**: t.visvikis@maastrichtuniversity.nl
+
+## Citation
+
+If you use Thyra in your research, please cite:
+
+```bibtex
+@software{thyra2024,
+  title = {Thyra: Modern Mass Spectrometry Imaging Data Conversion - Portal to Spatial Omics},
+  author = {Visvikis, Theodoros},
+  year = {2024},
+  url = {https://github.com/Tomatokeftes/thyra}
+}
+```
+
+## Acknowledgments
+
+- Built with [SpatialData](https://spatialdata.scverse.org/) ecosystem
+- Powered by [Zarr](https://zarr.readthedocs.io/) for efficient storage
+- Uses [pyimzML](https://github.com/alexandrovteam/pyimzML) for ImzML parsing
+
+---
+
+**Thyra** - Your portal from traditional MSI formats to modern spatial omics workflows