napari-nifti-viewer 0.1.0__tar.gz

napari_nifti_viewer-0.1.0/PKG-INFO

@@ -0,0 +1,248 @@
+Metadata-Version: 2.4
+Name: napari-nifti-viewer
+Version: 0.1.0
+Summary: A comprehensive napari plugin for NIfTI file analysis and visualization
+Home-page: https://github.com/yohanchiu/napari-nifti-viewer
+Author: Yohanchiu
+Author-email: Your Name <your.email@example.com>
+Maintainer-email: Your Name <your.email@example.com>
+License: MIT
+Project-URL: Homepage, https://github.com/yohanchiu/napari-nifti-viewer
+Project-URL: Bug Tracker, https://github.com/yohanchiu/napari-nifti-viewer/issues
+Project-URL: Documentation, https://github.com/yohanchiu/napari-nifti-viewer/wiki
+Project-URL: Source Code, https://github.com/yohanchiu/napari-nifti-viewer
+Project-URL: Changelog, https://github.com/yohanchiu/napari-nifti-viewer/blob/main/CHANGELOG.md
+Keywords: napari,nifti,neuroimaging,medical imaging,visualization,plugin
+Classifier: Development Status :: 4 - Beta
+Classifier: Framework :: napari
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+Requires-Dist: napari>=0.4.18
+Requires-Dist: numpy>=1.21.0
+Requires-Dist: nibabel>=5.2.1
+Requires-Dist: qtpy>=2.0.0
+Requires-Dist: magicgui>=0.7.0
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: black; extra == "dev"
+Requires-Dist: isort; extra == "dev"
+Requires-Dist: flake8; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Provides-Extra: test
+Requires-Dist: pytest>=7.0; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Dynamic: author
+Dynamic: home-page
+Dynamic: requires-python
+
+# napari-nifti-viewer
+
+A powerful napari plugin for comprehensive NIfTI file analysis and visualization.
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Python](https://img.shields.io/badge/python-3.8+-blue.svg)](https://www.python.org/downloads/)
+[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-nifti-viewer)](https://napari-hub.org/plugins/napari-nifti-viewer)
+
+## Overview
+
+napari-nifti-viewer is a comprehensive napari plugin specifically designed for reading, analyzing, and visualizing NIfTI (.nii/.nii.gz) files. It provides detailed metadata extraction, intelligent label detection, and seamless integration with napari's visualization capabilities.
+
+## Features
+
+### 🔍 **Complete NIfTI Support**
+- Read .nii and .nii.gz format files
+- Support for NIfTI-1 standard
+- Compatible with both image and label data
+
+### 📊 **Comprehensive Metadata Analysis**
+- Extract complete NIfTI header information (40+ fields)
+- Display affine transformation matrices
+- Show coordinate system information
+- Analyze voxel spacing and orientation
+
+### 🏷️ **Intelligent Label Detection**
+- Automatic label image detection
+- Statistical analysis of label distributions
+- Label value counting and percentage calculations
+
+### 📈 **Data Statistics**
+- Complete data shape and type information
+- Statistical measures (min, max, mean, std)
+- Non-zero voxel counting
+- Unique value analysis
+
+### 💾 **Export Capabilities**
+- Export complete metadata as JSON
+- Preserve all numerical precision
+- Human-readable format
+
+### 🎨 **User-Friendly Interface**
+- Clean, organized tabbed interface
+- Real-time data loading
+- Seamless napari integration
+
+## Interface
+
+The plugin provides a clean, organized interface with three main tabs:
+
+### 📋 File Overview Tab
+Displays basic file information and data statistics including file size, format, data shape, and statistical measures.
+
+### 📊 Detailed Information Tab  
+Shows complete NIfTI header fields and metadata in an organized table format, alongside full JSON metadata export.
+
+### 🏷️ Label Analysis Tab
+Provides intelligent label detection and statistical analysis with automatic identification of label images and distribution analysis.
+
+## Installation
+
+### From PyPI (Recommended)
+```bash
+pip install napari-nifti-viewer
+```
+
+### From Source
+```bash
+git clone https://github.com/yohanchiu/napari-nifti-viewer.git
+cd napari-nifti-viewer
+pip install -e .
+```
+
+## Quick Start
+
+1. **Launch napari** with the plugin installed
+2. **Open the plugin** from the Plugins menu → napari-nifti-viewer
+3. **Load a file** by clicking "Browse..." and selecting a .nii/.nii.gz file
+4. **Explore the data** across three informative tabs:
+   - **File Overview**: Basic information and statistics
+   - **Detailed Info**: Complete NIfTI headers and metadata
+   - **Label Analysis**: Label detection and analysis
+5. **Visualize in napari** by clicking "Load to Napari"
+
+## Usage Examples
+
+### Loading a Medical Image
+```python
+import napari
+from napari_nifti_viewer import NiftiViewerWidget
+
+# Create napari viewer
+viewer = napari.Viewer()
+
+# The plugin will be available in the Plugins menu
+# Or you can add it programmatically:
+widget = NiftiViewerWidget(viewer)
+viewer.window.add_dock_widget(widget, name="NIfTI Viewer")
+```
+
+### Exporting Metadata
+The plugin allows you to export complete metadata including:
+- File information (size, format, version)
+- NIfTI header fields (all 40+ standard fields)
+- Data statistics (shape, type, value ranges)
+- Coordinate system information
+- Affine transformation matrices
+
+## Requirements
+
+- **napari** >= 0.4.18
+- **nibabel** >= 5.2.1
+- **numpy** >= 1.21.0
+- **qtpy** >= 2.0.0
+- **magicgui** >= 0.7.0
+- **Python** >= 3.8
+
+## Supported File Formats
+
+- `.nii` - Uncompressed NIfTI files
+- `.nii.gz` - Compressed NIfTI files
+- Compatible with NIfTI-1 standard
+- Support for both neuroimaging and medical imaging data
+
+## Development
+
+### Setting up Development Environment
+
+```bash
+# Clone the repository
+git clone https://github.com/yohanchiu/napari-nifti-viewer.git
+cd napari-nifti-viewer
+
+# Create virtual environment
+python -m venv venv
+source venv/bin/activate  # On Windows: venv\Scripts\activate
+
+# Install in development mode
+pip install -e ".[dev]"
+
+# Run tests
+python -m pytest
+```
+
+### Running Tests
+
+```bash
+# Basic functionality test
+python test_plugin.py
+
+# Test with napari interface
+python test_plugin.py --napari
+```
+
+## Contributing
+
+We welcome contributions! Please see our [Contributing Guidelines](CONTRIBUTING.md) for details.
+
+### Ways to Contribute
+- 🐛 Report bugs
+- 💡 Suggest new features
+- 📝 Improve documentation
+- 🔧 Submit pull requests
+
+## License
+
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
+
+## Citation
+
+If you use this plugin in your research, please consider citing:
+
+```bibtex
+@software{napari_nifti_viewer,
+  title={napari-nifti-viewer: Comprehensive NIfTI Analysis for napari},
+  author={Qiu Yuheng},
+  year={2024},
+  url={https://github.com/yohanchiu/napari-nifti-viewer}
+}
+```
+
+## Acknowledgments
+
+- Built with [napari](https://napari.org/) - a fast, interactive, multi-dimensional image viewer
+- Uses [nibabel](https://nipy.org/nibabel/) for NIfTI file handling
+- Inspired by the neuroimaging and medical imaging communities
+
+## Support
+
+- 📖 [Documentation](https://github.com/yohanchiu/napari-nifti-viewer/wiki)
+- 🐛 [Issue Tracker](https://github.com/yohanchiu/napari-nifti-viewer/issues)
+- 💬 [Discussions](https://github.com/yohanchiu/napari-nifti-viewer/discussions)
+
+---
+
+Made with ❤️ for the napari and neuroimaging communities 

napari_nifti_viewer-0.1.0/README.md

@@ -0,0 +1,196 @@
+# napari-nifti-viewer
+
+A powerful napari plugin for comprehensive NIfTI file analysis and visualization.
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Python](https://img.shields.io/badge/python-3.8+-blue.svg)](https://www.python.org/downloads/)
+[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-nifti-viewer)](https://napari-hub.org/plugins/napari-nifti-viewer)
+
+## Overview
+
+napari-nifti-viewer is a comprehensive napari plugin specifically designed for reading, analyzing, and visualizing NIfTI (.nii/.nii.gz) files. It provides detailed metadata extraction, intelligent label detection, and seamless integration with napari's visualization capabilities.
+
+## Features
+
+### 🔍 **Complete NIfTI Support**
+- Read .nii and .nii.gz format files
+- Support for NIfTI-1 standard
+- Compatible with both image and label data
+
+### 📊 **Comprehensive Metadata Analysis**
+- Extract complete NIfTI header information (40+ fields)
+- Display affine transformation matrices
+- Show coordinate system information
+- Analyze voxel spacing and orientation
+
+### 🏷️ **Intelligent Label Detection**
+- Automatic label image detection
+- Statistical analysis of label distributions
+- Label value counting and percentage calculations
+
+### 📈 **Data Statistics**
+- Complete data shape and type information
+- Statistical measures (min, max, mean, std)
+- Non-zero voxel counting
+- Unique value analysis
+
+### 💾 **Export Capabilities**
+- Export complete metadata as JSON
+- Preserve all numerical precision
+- Human-readable format
+
+### 🎨 **User-Friendly Interface**
+- Clean, organized tabbed interface
+- Real-time data loading
+- Seamless napari integration
+
+## Interface
+
+The plugin provides a clean, organized interface with three main tabs:
+
+### 📋 File Overview Tab
+Displays basic file information and data statistics including file size, format, data shape, and statistical measures.
+
+### 📊 Detailed Information Tab  
+Shows complete NIfTI header fields and metadata in an organized table format, alongside full JSON metadata export.
+
+### 🏷️ Label Analysis Tab
+Provides intelligent label detection and statistical analysis with automatic identification of label images and distribution analysis.
+
+## Installation
+
+### From PyPI (Recommended)
+```bash
+pip install napari-nifti-viewer
+```
+
+### From Source
+```bash
+git clone https://github.com/yohanchiu/napari-nifti-viewer.git
+cd napari-nifti-viewer
+pip install -e .
+```
+
+## Quick Start
+
+1. **Launch napari** with the plugin installed
+2. **Open the plugin** from the Plugins menu → napari-nifti-viewer
+3. **Load a file** by clicking "Browse..." and selecting a .nii/.nii.gz file
+4. **Explore the data** across three informative tabs:
+   - **File Overview**: Basic information and statistics
+   - **Detailed Info**: Complete NIfTI headers and metadata
+   - **Label Analysis**: Label detection and analysis
+5. **Visualize in napari** by clicking "Load to Napari"
+
+## Usage Examples
+
+### Loading a Medical Image
+```python
+import napari
+from napari_nifti_viewer import NiftiViewerWidget
+
+# Create napari viewer
+viewer = napari.Viewer()
+
+# The plugin will be available in the Plugins menu
+# Or you can add it programmatically:
+widget = NiftiViewerWidget(viewer)
+viewer.window.add_dock_widget(widget, name="NIfTI Viewer")
+```
+
+### Exporting Metadata
+The plugin allows you to export complete metadata including:
+- File information (size, format, version)
+- NIfTI header fields (all 40+ standard fields)
+- Data statistics (shape, type, value ranges)
+- Coordinate system information
+- Affine transformation matrices
+
+## Requirements
+
+- **napari** >= 0.4.18
+- **nibabel** >= 5.2.1
+- **numpy** >= 1.21.0
+- **qtpy** >= 2.0.0
+- **magicgui** >= 0.7.0
+- **Python** >= 3.8
+
+## Supported File Formats
+
+- `.nii` - Uncompressed NIfTI files
+- `.nii.gz` - Compressed NIfTI files
+- Compatible with NIfTI-1 standard
+- Support for both neuroimaging and medical imaging data
+
+## Development
+
+### Setting up Development Environment
+
+```bash
+# Clone the repository
+git clone https://github.com/yohanchiu/napari-nifti-viewer.git
+cd napari-nifti-viewer
+
+# Create virtual environment
+python -m venv venv
+source venv/bin/activate  # On Windows: venv\Scripts\activate
+
+# Install in development mode
+pip install -e ".[dev]"
+
+# Run tests
+python -m pytest
+```
+
+### Running Tests
+
+```bash
+# Basic functionality test
+python test_plugin.py
+
+# Test with napari interface
+python test_plugin.py --napari
+```
+
+## Contributing
+
+We welcome contributions! Please see our [Contributing Guidelines](CONTRIBUTING.md) for details.
+
+### Ways to Contribute
+- 🐛 Report bugs
+- 💡 Suggest new features
+- 📝 Improve documentation
+- 🔧 Submit pull requests
+
+## License
+
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
+
+## Citation
+
+If you use this plugin in your research, please consider citing:
+
+```bibtex
+@software{napari_nifti_viewer,
+  title={napari-nifti-viewer: Comprehensive NIfTI Analysis for napari},
+  author={Qiu Yuheng},
+  year={2024},
+  url={https://github.com/yohanchiu/napari-nifti-viewer}
+}
+```
+
+## Acknowledgments
+
+- Built with [napari](https://napari.org/) - a fast, interactive, multi-dimensional image viewer
+- Uses [nibabel](https://nipy.org/nibabel/) for NIfTI file handling
+- Inspired by the neuroimaging and medical imaging communities
+
+## Support
+
+- 📖 [Documentation](https://github.com/yohanchiu/napari-nifti-viewer/wiki)
+- 🐛 [Issue Tracker](https://github.com/yohanchiu/napari-nifti-viewer/issues)
+- 💬 [Discussions](https://github.com/yohanchiu/napari-nifti-viewer/discussions)
+
+---
+
+Made with ❤️ for the napari and neuroimaging communities 

napari_nifti_viewer-0.1.0/napari_nifti_viewer/__init__.py

@@ -0,0 +1,22 @@
+import os
+import sys
+import logging
+from pathlib import Path
+
+
+if sys.platform == 'darwin':
+    os.environ['QT_MAC_WANTS_LAYER'] = '1'
+   
+    class QtWarningFilter(logging.Filter):
+        def filter(self, record):
+            return not (record.getMessage().find("Layer-backing is always enabled") >= 0)
+    
+    logging.getLogger().addFilter(QtWarningFilter())
+    
+    import warnings
+    warnings.filterwarnings("ignore", message="Layer-backing is always enabled")
+
+from napari_nifti_viewer._version import __version__
+from napari_nifti_viewer._widget import NiftiViewerWidget
+
+__all__ = ["NiftiViewerWidget", "__version__"]