openptv2 1.0.0__tar.gz

openptv2-1.0.0/LICENSE

@@ -0,0 +1,165 @@
+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
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openptv2-1.0.0/MANIFEST.in

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+include README.md
+include LICENSE
+include pyproject.toml
+include setup.py
+
+# Include C source files
+recursive-include lib *.c *.h *.txt
+recursive-include lib/src *.c
+recursive-include lib/include *.h
+
+# Include Cython sources (both .pyx and generated .c)
+recursive-include bindings *.pyx *.pxd *.py *.toml *.c
+recursive-include bindings/optv *.pyx *.pxd *.py *.c
+recursive-include bindings/liboptv *.c *.h
+
+# Include Python packages
+recursive-include openptv2 *.py *.pxd
+recursive-include algorithms *.py
+recursive-include gui *.py *.toml
+
+# Include tests
+recursive-include bindings/tests *.py
+recursive-include algorithms/tests *.py
+recursive-include gui/tests *.py
+recursive-include lib/tests *.c

openptv2-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: openptv2
+Version: 1.0.0
+Summary: Unified OpenPTV: Particle Tracking Velocimetry with dual-engine support
+Author-email: OpenPTV Community <openptv@googlegroups.com>
+License: LGPL-3.0-or-later
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Cython
+Classifier: Programming Language :: C
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Requires-Python: <3.14,>=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=2.0.0
+Requires-Dist: pytest>=9.0.2
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: scipy>=1.10.0
+Provides-Extra: gui
+Requires-Dist: traits>=6.4.0; extra == "gui"
+Requires-Dist: traitsui>=7.4.0; extra == "gui"
+Requires-Dist: enable>=6.1.0; extra == "gui"
+Requires-Dist: chaco>=6.1.0; extra == "gui"
+Requires-Dist: PySide6>=6.0.0; extra == "gui"
+Requires-Dist: scikit-image>=0.20.0; extra == "gui"
+Requires-Dist: pandas>=2.0.0; extra == "gui"
+Requires-Dist: matplotlib>=3.7.0; extra == "gui"
+Requires-Dist: tables>=3.8.0; extra == "gui"
+Requires-Dist: tqdm>=4.65.0; extra == "gui"
+Requires-Dist: imagecodecs>=2023.1.23; extra == "gui"
+Requires-Dist: flowtracks>=0.3.0; extra == "gui"
+Requires-Dist: Pygments>=2.15.0; extra == "gui"
+Requires-Dist: pyparsing>=3.0.0; extra == "gui"
+Requires-Dist: marimo>=0.19.10; extra == "gui"
+Provides-Extra: numba
+Requires-Dist: numba>=0.60.0; extra == "numba"
+Provides-Extra: test
+Requires-Dist: pytest>=8.0.0; extra == "test"
+Requires-Dist: pytest-cov>=5.0.0; extra == "test"
+Provides-Extra: dev
+Requires-Dist: pytest>=8.0.0; extra == "dev"
+Requires-Dist: pytest-cov>=5.0.0; extra == "dev"
+Requires-Dist: mypy>=1.10.0; extra == "dev"
+Requires-Dist: pre-commit>=4.0.0; extra == "dev"
+Requires-Dist: ruff>=0.5.0; extra == "dev"
+Requires-Dist: traits>=6.4.0; extra == "dev"
+Requires-Dist: traitsui>=7.4.0; extra == "dev"
+Requires-Dist: enable>=6.1.0; extra == "dev"
+Requires-Dist: chaco>=6.1.0; extra == "dev"
+Requires-Dist: PySide6>=6.0.0; extra == "dev"
+Requires-Dist: scikit-image>=0.20.0; extra == "dev"
+Requires-Dist: pandas>=2.0.0; extra == "dev"
+Requires-Dist: matplotlib>=3.7.0; extra == "dev"
+Requires-Dist: tables>=3.8.0; extra == "dev"
+Requires-Dist: tqdm>=4.65.0; extra == "dev"
+Requires-Dist: imagecodecs>=2023.1.23; extra == "dev"
+Requires-Dist: flowtracks>=0.3.0; extra == "dev"
+Requires-Dist: Pygments>=2.15.0; extra == "dev"
+Requires-Dist: pyparsing>=3.0.0; extra == "dev"
+Requires-Dist: marimo>=0.19.10; extra == "dev"
+Requires-Dist: numba>=0.60.0; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx>=8.0.0; extra == "docs"
+Requires-Dist: sphinx-autoapi>=3.0.0; extra == "docs"
+Requires-Dist: pydata-sphinx-theme>=0.16.0; extra == "docs"
+Requires-Dist: myst-parser>=5.0.0; extra == "docs"
+Dynamic: license-file
+
+# openptv2
+
+**Unified OpenPTV**: Particle Tracking Velocimetry with dual-engine support
+
+[![Python](https://img.shields.io/pypi/pyversions/openptv2.svg)](https://pypi.org/project/openptv2/)
+[![License](https://img.shields.io/badge/License-LGPL%20v3-blue.svg)](LICENSE)
+
+## Overview
+
+openptv2 combines the best of three repositories into a single, maintainable package:
+
+- **C core library** (`lib/`) - High-performance particle tracking algorithms
+- **Cython bindings** (`bindings/`) - Python interface to C library
+- **Python/Numba fallback** (`algorithms/`) - Pure Python implementation for debugging
+- **TraitsUI GUI** (`gui/`) - Full-featured graphical interface
+
+## Key Features
+
+- **Dual-engine architecture**: Use fast C/Cython (`optv`) or debuggable Python/Numba (`python`)
+- **Identical results**: Both engines produce the same output (within floating-point tolerance)
+- **Backward compatible**: Works with existing `optv` and `pyptv` code
+- **Easy installation**: Pre-built wheels for Linux, Windows, macOS
+
+---
+
+## Installation
+
+### For End Users (Pre-built Wheels)
+
+**Prerequisites:**
+- Python 3.11, 3.12, or 3.13
+- pip or uv package manager
+
+#### Option 1: Using pip
+
+```bash
+pip install openptv2
+```
+
+#### Option 2: Using uv (recommended)
+
+```bash
+# Install uv if you haven't already
+curl -LsSf https://astral.sh/uv/install.sh | sh
+
+# Install openptv2
+uv add openptv2
+```
+
+#### Verify Installation
+
+```bash
+python -c "import openptv2; print(f'openptv2 version: {openptv2.__version__}')"
+python -c "from openptv2 import Tracker; print('Tracker imported successfully')"
+```
+
+---
+
+### For Developers (Build from Source)
+
+**Prerequisites:**
+- Python 3.11, 3.12, or 3.13
+- CMake 3.15+
+- C compiler (gcc on Linux, clang on macOS, MSVC on Windows)
+- Cython 3.0+
+- NumPy 2.0+
+- uv (recommended) or pip
+
+#### System Dependencies
+
+**Linux (Debian/Ubuntu):**
+```bash
+sudo apt-get update
+sudo apt-get install -y cmake build-essential python3-dev
+```
+
+**Linux (Fedora/RHEL):**
+```bash
+sudo dnf install -y cmake gcc gcc-c++ python3-devel
+```
+
+**macOS:**
+```bash
+# Install Xcode Command Line Tools
+xcode-select --install
+
+# Install cmake via Homebrew (optional, if not using system cmake)
+brew install cmake
+```
+
+**Windows:**
+- Install [Microsoft Visual C++ Build Tools](https://visualstudio.microsoft.com/visual-cpp-build-tools/)
+- Install [CMake](https://cmake.org/download/)
+
+#### Step 1: Clone the Repository
+
+```bash
+git clone https://github.com/openptv/openptv2.git
+cd openptv2
+```
+
+#### Step 2: Install Dependencies and Build
+
+**Using uv (recommended):**
+```bash
+# Sync all dependencies and build the package
+uv sync --extra dev
+```
+
+**Using pip:**
+```bash
+# Create virtual environment
+python -m venv .venv
+source .venv/bin/activate  # On Windows: .venv\Scripts\activate
+
+# Install build dependencies
+pip install scikit-build-core cython numpy
+
+# Install in development mode
+pip install -e ".[dev]"
+```
+
+#### Step 3: Verify Build
+
+```bash
+# Test imports
+python -c "import openptv2; print(f'openptv2 version: {openptv2.__version__}')"
+python -c "from openptv2 import Tracker; print('Tracker imported successfully')"
+
+# Run tests
+pytest tests/ -v --tb=short
+```
+
+---
+
+### Installation with GUI Dependencies
+
+The GUI requires additional dependencies:
+
+```bash
+# Using uv
+uv sync --all-extras
+
+# Using pip
+pip install -e ".[gui,dev]"
+```
+
+**GUI dependencies include:**
+- traits, traitsui (Enthought framework)
+- enable, chaco (visualization)
+- PySide6 (Qt bindings)
+- scikit-image, pandas, matplotlib (analysis)
+
+---
+
+### Installing from Binary Wheels
+
+Pre-built manylinux wheels are available for Linux:
+
+```bash
+# Using pip
+pip install openptv2
+
+# Using uv
+uv pip install openptv2
+```
+
+The wheels are compatible with glibc 2.17+ (CentOS 7, Ubuntu 14.04, Debian 8, etc.)
+
+---
+
+### Building Binary Wheels from Source
+
+See [BUILDING_BINARY_WHEELS.md](BUILDING_BINARY_WHEELS.md) for detailed instructions on building portable binary wheels using cibuildwheel.
+
+---
+
+### Troubleshooting Installation
+
+#### Common Issues
+
+**1. "CMake not found"**
+```bash
+# Install CMake
+# Linux: sudo apt-get install cmake
+# macOS: brew install cmake
+# Windows: Download from https://cmake.org/download/
+```
+
+**2. "C compiler not found"**
+```bash
+# Linux: sudo apt-get install build-essential
+# macOS: xcode-select --install
+# Windows: Install MSVC Build Tools
+```
+
+**3. "Cython not found"**
+```bash
+pip install cython>=3.0.0
+```
+
+**4. "NumPy version mismatch"**
+```bash
+pip install numpy>=2.0.0
+```
+
+**5. "optv module not found" (after cloning)**
+```bash
+# The optv package is built by CMake - you need to build the package
+uv sync --extra dev
+# or
+pip install -e ".[dev]"
+```
+
+---
+
+## Usage
+
+### Basic Tracking
+
+```python
+import openptv2
+from openptv2 import Tracker, detect_targets
+
+# Load images
+from skimage import io
+images = [io.imread(f"cam1_{i:04d}.tif") for i in range(100)]
+
+# Detect particles
+targets = [detect_targets(img) for img in images]
+
+# Track particles
+tracker = Tracker()
+tracks = tracker.track([t.coordinates for t in targets])
+
+print(f"Found {len(tracks)} tracks")
+```
+
+### Engine Selection
+
+```python
+import openptv2
+
+# Use default (fastest) engine
+openptv2.set_engine("optv")
+
+# Use Python engine for debugging
+openptv2.set_engine("python")
+
+# Per-call engine selection
+from openptv2 import track_particles
+result = track_particles(images, engine="python")
+```
+
+### GUI
+
+```bash
+# Launch the GUI
+openptv2-gui
+
+# Or with specific engine
+openptv2-gui --engine python
+```
+
+### Batch Processing
+
+```bash
+# Serial batch
+openptv2-batch parameters.yaml 1 100
+
+# Parallel batch
+python -m openptv2.gui.pyptv_batch_parallel parameters.yaml 1 100 4
+```
+
+---
+
+## Documentation
+
+- [Installation Guide](docs/developer_guide/building.md)
+- [Quick Start](docs/tutorials/)
+- [API Reference](docs/sphinx/)
+- [Algorithm Documentation](docs/algorithms/)
+- [Developer Guide](docs/developer_guide/)
+
+---
+
+## Repository Structure
+
+```
+openptv2/
+├── algorithms/        # Python/Numba fallback engine
+│   ├── calibration.py
+│   ├── correspondences.py
+│   ├── image_processing.py
+│   ├── orientation.py
+│   ├── parameters.py
+│   ├── segmentation.py
+│   ├── track.py
+│   └── ...
+├── bindings/          # Cython bindings source
+│   ├── optv/          # Cython .pyx, .pxd files
+│   ├── tests/         # Binding tests
+│   └── pyproject.toml # scikit-build-core config
+├── gui/               # TraitsUI GUI application
+│   ├── pyptv/         # Main GUI package
+│   ├── plugins/       # GUI plugins
+│   └── tests/         # GUI tests
+├── lib/               # C core library
+│   ├── include/       # C headers
+│   ├── src/           # C source files
+│   ├── tests/         # C library tests
+│   └── CMakeLists.txt
+├── openptv2/          # Main Python package
+│   ├── __init__.py
+│   ├── calibration.py
+│   ├── correspondence.py
+│   ├── engine.py      # Engine selector
+│   ├── tracker.py
+│   └── ...
+├── tests/             # Integration tests
+│   ├── engine_comparison/
+│   ├── fixtures/
+│   └── integration/
+├── docs/              # Documentation
+│   ├── algorithms/
+│   ├── developer_guide/
+│   ├── sphinx/
+│   └── tutorials/
+├── scripts/           # Build helpers
+├── CMakeLists.txt     # Root CMake build config
+├── pyproject.toml     # Python project config
+└── README.md
+```
+
+---
+
+## Engine Comparison
+
+| Feature | optv (C/Cython) | python (Numba) |
+|---------|-----------------|----------------|
+| Speed | Fastest | Fast (JIT compiled) |
+| Debugging | Harder | Easy |
+| Visualization | Limited | Full |
+| Use case | Production | Development |
+
+---
+
+## Testing
+
+```bash
+# All tests
+pytest
+
+# C library tests
+cd lib && mkdir build && cd build && cmake .. && ctest
+
+# Engine comparison
+pytest tests/engine_comparison/ --validate-engine
+
+# GUI tests (headless)
+pytest gui/tests/ --headless
+
+# Integration tests
+pytest tests/integration/ -v
+```
+
+---
+
+## Migration from optv/pyptv
+
+openptv2 maintains backward compatibility:
+
+```python
+# Old optv code (still works after installation)
+from optv.tracking_framebuf import Target
+from optv.tracker import Tracker
+
+# New openptv2 code
+from openptv2 import Target, Tracker
+
+# Both work identically
+```
+
+---
+
+## Contributing
+
+1. Fork the repository
+2. Create a feature branch
+3. Make your changes
+4. Run tests: `pytest`
+5. Submit a pull request
+
+### Development Workflow
+
+```bash
+# Set up development environment
+uv sync --extra dev
+
+# Make changes to source code
+
+# Run tests
+pytest tests/ -v
+
+# Build documentation (optional)
+cd docs && make html
+```
+
+---
+
+## License
+
+LGPL-3.0 or later. See [LICENSE](LICENSE) for details.
+
+---
+
+## Acknowledgments
+
+openptv2 combines work from:
+- [openptv](https://github.com/openptv/openptv) - C library and bindings
+- [pyptv](https://github.com/alexlib/pyptv) - Python GUI
+- [openptv-python](https://github.com/openptv/openptv-python) - Python/Numba engine
+
+---
+
+## Contact
+
+- Mailing list: openptv@googlegroups.com
+- GitHub: https://github.com/openptv/openptv2
+- Issues: https://github.com/openptv/openptv2/issues
+
+---
+
+## Helper Scripts
+
+The project includes scripts for building and testing:
+
+| Script | Purpose |
+|--------|---------|
+| `scripts/build_wheel.sh` | Build binary wheel from source |
+| `scripts/install_wheel.sh` | Install wheel in clean test environment |
+| `scripts/run_tests.sh` | Run test suite in test environment |
+| `scripts/Dockerfile.slim` | Slim Docker image for testing |
+
+See [BUILDING_BINARY_WHEELS.md](BUILDING_BINARY_WHEELS.md) for detailed usage.