cabana 0.0.2__tar.gz

cabana-0.0.2/LICENSE

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+MIT License
+
+Copyright (c) 2025 Gavin Lin
+
+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.

cabana-0.0.2/PKG-INFO

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+Metadata-Version: 2.2
+Name: cabana
+Version: 0.0.2
+Summary: Collagen fibre analyser for quantifying collagen fibre architecture in IHC and fluorescence microscopy images.
+Home-page: https://github.com/lxfhfut/cabana.git
+Author: Gavin Lin
+Author-email: x.lin@garvan.org.au
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: colorlog
+Requires-Dist: gitpython
+Requires-Dist: imutils
+Requires-Dist: jaraco.collections
+Requires-Dist: numba
+Requires-Dist: opencv-python
+Requires-Dist: pip-chill
+Requires-Dist: pyqt5
+Requires-Dist: pyyaml
+Requires-Dist: scikit-learn
+Requires-Dist: seaborn
+Requires-Dist: seaborn-image
+Requires-Dist: send2trash
+Requires-Dist: tomli
+Requires-Dist: torch
+Requires-Dist: tqdm
+Requires-Dist: twine
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: requires-dist
+Dynamic: summary
+
+[//]: # (# CABANA - Collagen Fibre Analyzer)
+![image](cabana.png)
+[![PyPI version](https://badge.fury.io/py/cabana.svg)](https://pypi.org/project/cabana/1.0.1/)
+[![Documentation Status](https://readthedocs.org/projects/cabana/badge/?version=latest)](https://cabana.readthedocs.io/en/latest/?badge=latest)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+CABANA (CollAgen FiBre ANAlyzer) is a comprehensive toolkit for analyzing collagen fibre architecture in immunohistochemistry (IHC) and fluorescence microscopy images. It provides:
+
+- Automated detection and quantification of collagen fibres
+- Analysis of fibre orientation, length, and thickness
+- Gap analysis for inter-fibre and intra-fibre spaces
+- Interactive parameter optimization interface
+- Batch processing for large datasets
+
+CABANA combines advanced computer vision algorithms with an intuitive user interface, making it accessible to researchers without extensive programming experience while providing detailed quantitative data for comprehensive analysis of collagen architecture.
+
+## System Requirements
+
+- **Processor (CPU):** Intel Core i7, AMD Ryzen 7, or higher recommended
+- **Memory (RAM):** Minimum 16 GB, 32 GB recommended
+- **GPU:** NVIDIA GeForce GTX/RTX series with at least 10 GB VRAM recommended
+- **Python:** 3.8 or newer
+
+
+## Quick Installation
+
+Install CABANA using pip:
+
+```bash
+pip install -U cabana
+```
+or install the latest version on GitHub:
+
+```bash
+pip install git+https://github.com/lxfhfut/Cabana.git
+```
+
+After installation, you can launch the CABANA GUI by running:
+
+```bash
+python -m cabana
+```
+
+Alternatively, you can import CABANA in your Python code for customized analysis (**see examples in Tutorials**):
+
+```python
+import cabana
+```
+
+## Documentation
+
+Comprehensive documentation is available at:
+[https://cabana.readthedocs.io/en/latest/](https://cabana.readthedocs.io/en/latest/)
+
+## Tutorials
+
+We provide an interactive Jupyter notebook tutorial to help you get started:
+[CABANA Tutorial](https://cabana.readthedocs.io/en/latest/_static/tutorial.ipynb)
+
+## Citation
+
+If you use CABANA in your research, please cite:
+<!--
+```
+Magenau A, et al. (2025). CABANA: A comprehensive toolkit for collagen fibre analysis in biomedical imaging. Journal of XYZ. DOI: XYZ
+```-->
+
+## License
+
+CABANA is released under the MIT License.
+
+## Contact
+
+For questions and support, please contact:
+- Xufeng Lin - <x.lin@garvan.org.au>
+- Astrid Magenau - <a.magenau@garvan.org.au>

cabana-0.0.2/README.md

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+[//]: # (# CABANA - Collagen Fibre Analyzer)
+![image](cabana.png)
+[![PyPI version](https://badge.fury.io/py/cabana.svg)](https://pypi.org/project/cabana/1.0.1/)
+[![Documentation Status](https://readthedocs.org/projects/cabana/badge/?version=latest)](https://cabana.readthedocs.io/en/latest/?badge=latest)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+CABANA (CollAgen FiBre ANAlyzer) is a comprehensive toolkit for analyzing collagen fibre architecture in immunohistochemistry (IHC) and fluorescence microscopy images. It provides:
+
+- Automated detection and quantification of collagen fibres
+- Analysis of fibre orientation, length, and thickness
+- Gap analysis for inter-fibre and intra-fibre spaces
+- Interactive parameter optimization interface
+- Batch processing for large datasets
+
+CABANA combines advanced computer vision algorithms with an intuitive user interface, making it accessible to researchers without extensive programming experience while providing detailed quantitative data for comprehensive analysis of collagen architecture.
+
+## System Requirements
+
+- **Processor (CPU):** Intel Core i7, AMD Ryzen 7, or higher recommended
+- **Memory (RAM):** Minimum 16 GB, 32 GB recommended
+- **GPU:** NVIDIA GeForce GTX/RTX series with at least 10 GB VRAM recommended
+- **Python:** 3.8 or newer
+
+
+## Quick Installation
+
+Install CABANA using pip:
+
+```bash
+pip install -U cabana
+```
+or install the latest version on GitHub:
+
+```bash
+pip install git+https://github.com/lxfhfut/Cabana.git
+```
+
+After installation, you can launch the CABANA GUI by running:
+
+```bash
+python -m cabana
+```
+
+Alternatively, you can import CABANA in your Python code for customized analysis (**see examples in Tutorials**):
+
+```python
+import cabana
+```
+
+## Documentation
+
+Comprehensive documentation is available at:
+[https://cabana.readthedocs.io/en/latest/](https://cabana.readthedocs.io/en/latest/)
+
+## Tutorials
+
+We provide an interactive Jupyter notebook tutorial to help you get started:
+[CABANA Tutorial](https://cabana.readthedocs.io/en/latest/_static/tutorial.ipynb)
+
+## Citation
+
+If you use CABANA in your research, please cite:
+<!--
+```
+Magenau A, et al. (2025). CABANA: A comprehensive toolkit for collagen fibre analysis in biomedical imaging. Journal of XYZ. DOI: XYZ
+```-->
+
+## License
+
+CABANA is released under the MIT License.
+
+## Contact
+
+For questions and support, please contact:
+- Xufeng Lin - <x.lin@garvan.org.au>
+- Astrid Magenau - <a.magenau@garvan.org.au>

cabana-0.0.2/cabana/__init__.py

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+name = "cabana"
+
+from .batch_processor import BatchProcessor
+from .cabana import Cabana

cabana-0.0.2/cabana/__main__.py

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+from PyQt5.QtWidgets import QApplication
+from PyQt5.QtGui import QIcon
+from PyQt5.QtCore import Qt
+import sys
+from pathlib import Path
+from .cabana_gui import MainWindow
+
+def main():
+    # Enable High DPI display before creating QApplication
+    QApplication.setAttribute(Qt.AA_EnableHighDpiScaling, True)
+    QApplication.setAttribute(Qt.AA_UseHighDpiPixmaps, True)
+
+    app = QApplication(sys.argv)
+    window = MainWindow()
+    icon_path = Path(__file__).parent.parent / "cabana-logo.ico"
+    app.setWindowIcon(QIcon(str(icon_path)))
+    window.show()
+    sys.exit(app.exec_())
+
+if __name__ == "__main__":
+    main()