dronelytics 1.0.1__tar.gz

dronelytics-1.0.1/LICENSE

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+MIT License
+
+Copyright (c) 2024 Research Development
+
+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.

dronelytics-1.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: dronelytics
+Version: 1.0.1
+Summary: Comprehensive Python package for drone orthomosaic analysis and agricultural field phenotyping
+Author: Lalit BC
+Author-email: Lalit BC <lalitiaas@gmail.com>
+License: MIT
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: rasterio
+Requires-Dist: matplotlib
+Requires-Dist: scipy
+Requires-Dist: pandas
+Provides-Extra: pointcloud
+Requires-Dist: laspy; extra == "pointcloud"
+Requires-Dist: pyvista; extra == "pointcloud"
+Dynamic: author
+Dynamic: license-file
+Dynamic: requires-python
+
+# Dronelytics
+
+Comprehensive Python package for end-to-end drone orthomosaic analysis and agricultural field phenotyping.
+
+## Features
+
+Dronelytics provides a complete workflow for processing multispectral drone imagery and point clouds:
+
+- **Multispectral Orthomosaic Processing**: Load and manage 4-band (RGB+NIR) and 5-band (RGB+NIR+RedEdge) GeoTIFF files
+- **10 Vegetation Indices**: NDVI, NDRE, GNDVI, ExG, SAVI, MSAVI, VARI, ARVI, CVI, OSAVI
+- **Custom Formula Support**: Define your own vegetation index formulas using lambda functions
+- **Plot Segmentation**: Automated detection and boundary extraction of crop plots
+- **Pixel-Level Extraction**: Extract spectral data by plot or region
+- **3D Canopy Modeling**: Generate DTM, DSM, and CHM from point clouds
+- **3D Visualization**: Interactive and static visualization of point clouds, elevation models, and meshes
+- **Data Export**: Save results to CSV and Excel formats
+
+## Installation
+
+Install from PyPI:
+
+```bash
+pip install dronelytics
+```
+
+For point cloud processing support (optional):
+
+```bash
+pip install dronelytics[pointcloud]
+```
+
+This installs additional dependencies for LAS file handling and 3D mesh generation.
+
+## Quick Start
+
+### Load Orthomosaic and Calculate Vegetation Indices
+
+```python
+from dronelytics import Orthomosaic, VegetationIndicesExtended
+
+ortho = Orthomosaic('field.tif', band_config={
+    'red': 1, 'green': 2, 'blue': 3, 'nir': 4
+})
+
+vi = VegetationIndicesExtended(ortho)
+ndvi = vi.ndvi()
+gndvi = vi.gndvi()
+exg = vi.exg()
+
+print(f"NDVI Mean: {ndvi.mean:.4f}")
+print(f"GNDVI Mean: {gndvi.mean:.4f}")
+```
+
+### Process 5-Band Imagery with Red-Edge
+
+```python
+ortho = Orthomosaic('field_5band.tif', band_config={
+    'red': 1, 'green': 2, 'blue': 3, 'nir': 4, 'rededge': 5
+})
+
+vi = VegetationIndicesExtended(ortho)
+ndvi = vi.ndvi()
+ndre = vi.ndre()
+all_indices = vi.calculate_all()
+```
+
+### Detect Plots and Extract Data
+
+```python
+from dronelytics import PlotSegmentation, PixelExtraction
+
+segmentation = PlotSegmentation(ortho)
+seg_result = segmentation.segment_by_ndvi(ndvi.data, threshold=0.3)
+
+extraction = PixelExtraction(ortho)
+extract_result = extraction.extract_spectra()
+df = extraction.to_dataframe()
+```
+
+### Process Point Cloud and Generate CHM
+
+```python
+from dronelytics import PointCloudProcessor
+
+processor = PointCloudProcessor('field.las')
+
+chm, meta = processor.generate_chm(cell_size=1.0)
+dtm, _ = processor.generate_dtm(cell_size=1.0)
+dsm, _ = processor.generate_dsm(cell_size=1.0)
+
+print(f"Mean crop height: {meta['mean_height']:.2f}m")
+```
+
+### Visualize Results
+
+```python
+from dronelytics.visualization import show_chm, show_comparison
+
+show_chm(chm, title="Crop Height Model")
+show_comparison({'DTM': dtm, 'DSM': dsm, 'CHM': chm})
+```
+
+### Custom Vegetation Index
+
+```python
+def my_formula(ortho):
+    nir = ortho.get_band('nir')
+    red = ortho.get_band('red')
+    return (nir - red) / (nir + red + 1e-10)
+
+custom = vi.custom(my_formula, 'MyIndex')
+```
+
+## Band Configuration
+
+Specify how bands are mapped in your GeoTIFF file:
+
+```python
+band_config = {
+    'red': 1,       # Band 1 is red
+    'green': 2,     # Band 2 is green
+    'blue': 3,      # Band 3 is blue
+    'nir': 4,       # Band 4 is NIR
+    'rededge': 5    # Band 5 is red-edge (optional, 5-band only)
+}
+
+ortho = Orthomosaic('field.tif', band_config=band_config)
+```
+
+## Vegetation Indices
+
+10 vegetation indices are implemented:
+
+| Index | Formula | Use Case |
+|-------|---------|----------|
+| NDVI | (NIR - RED) / (NIR + RED) | Vegetation health, stress detection |
+| NDRE | (NIR - RedEdge) / (NIR + RedEdge) | Nitrogen content (5-band only) |
+| GNDVI | (NIR - GREEN) / (NIR + GREEN) | Chlorophyll content |
+| ExG | 2*GREEN - RED - BLUE | Greenness index for RGB imagery |
+| SAVI | ((NIR - RED) / (NIR + RED + L)) * (1 + L) | Soil adjustment (L=0.5) |
+| MSAVI | Modified SAVI | Improved soil adjustment |
+| VARI | (GREEN - RED) / (GREEN + RED - BLUE) | Visible atmospherically resistant |
+| ARVI | (NIR - (2*RED - BLUE)) / (NIR + (2*RED - BLUE)) | Atmospheric correction |
+| CVI | (NIR / GREEN) * (RED / GREEN) | Chlorophyll |
+| OSAVI | Optimized SAVI with Y=0.16 | Better soil adjustment |
+
+## 3D Visualization Functions
+
+The visualization module (3dVis) provides 5 simple functions:
+
+```python
+from dronelytics.visualization import (
+    show_pointcloud,    # Visualize point cloud with classification
+    show_dem,          # Visualize elevation models (DTM, DSM)
+    show_chm,          # Visualize crop height model
+    show_mesh,         # Visualize 3D surface mesh
+    show_comparison    # Compare multiple elevation models
+)
+```
+
+## File Structure
+
+```
+dronelytics/
+├── core/                      # Core modules
+│   ├── orthomosaic.py        # Orthomosaic loading and management
+│   ├── indices.py            # Standard vegetation indices
+│   ├── vegetation_indices_extended.py  # 10 indices + custom formulas
+│   ├── segmentation.py       # Plot boundary detection
+│   ├── extraction.py         # Pixel-level data extraction
+│   └── pointcloud.py         # Point cloud processing, DTM/DSM/CHM
+│
+├── visualization/            # 3D visualization (3dVis)
+│   └── vis3d.py             # 5 visualization functions
+│
+├── export/                  # Data export
+│   ├── csv_export.py        # CSV export
+│   └── excel_export.py      # Excel export
+│
+├── processing/              # Analysis pipelines
+│   └── pipeline.py          # Orchestrate analysis workflow
+│
+├── data/                    # Data structures
+│   └── structures.py        # VegetationIndexData, SegmentationResult, etc.
+│
+└── utils/                   # Utilities
+    └── logger.py            # Clean logging (no decorative symbols)
+```
+
+## Examples
+
+### Basic Workflow
+
+```bash
+python examples/basic_workflow.py
+```
+
+### Advanced Workflow (5-band, Point Cloud)
+
+```bash
+python examples/advanced_workflow.py
+```
+
+### 3D Visualization
+
+```bash
+python examples/visualization_example.py
+```
+
+## Requirements
+
+- Python 3.7+
+- numpy
+- rasterio (GeoTIFF support)
+- matplotlib (visualization)
+- scipy (segmentation)
+- pandas (data extraction)
+
+Optional dependencies:
+- laspy (LAS/LAZ file support)
+- pyvista (3D mesh and interactive visualization)
+
+## Testing
+
+Run unit tests:
+
+```bash
+python -m pytest tests/test_core.py
+```
+
+Or use the test module directly:
+
+```bash
+python tests/test_core.py
+```
+
+## CHM Calculation
+
+Crop Height Model (CHM) is calculated as:
+
+```
+CHM = DSM - DTM
+```
+
+Where:
+- DSM: Digital Surface Model (top of vegetation)
+- DTM: Digital Terrain Model (ground surface)
+- CHM: Height of vegetation above ground
+
+## Documentation
+
+- `WORKFLOW.md`: Complete analysis workflow guide
+- `VISUALIZATION_GUIDE.md`: 3D visualization usage
+- `5BAND_SUPPORT_GUIDE.md`: Red-edge band support
+- `COMPLETE_FEATURE_SUMMARY.md`: Feature overview
+- `DEPLOYMENT_CHECKLIST.md`: Production deployment guide
+
+## License
+
+MIT License. See LICENSE file for details.
+
+## Citation
+
+If you use Dronelytics in your research, please cite:
+
+```
+Dronelytics v1.0.0 - Comprehensive drone orthomosaic analysis package
+```
+
+## Support
+
+For issues, feature requests, or questions, please refer to the documentation files or create an issue on GitHub.
+
+---
+
+Made for agricultural field phenotyping and precision agriculture research.

dronelytics-1.0.1/README.md

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+# Dronelytics
+
+Comprehensive Python package for end-to-end drone orthomosaic analysis and agricultural field phenotyping.
+
+## Features
+
+Dronelytics provides a complete workflow for processing multispectral drone imagery and point clouds:
+
+- **Multispectral Orthomosaic Processing**: Load and manage 4-band (RGB+NIR) and 5-band (RGB+NIR+RedEdge) GeoTIFF files
+- **10 Vegetation Indices**: NDVI, NDRE, GNDVI, ExG, SAVI, MSAVI, VARI, ARVI, CVI, OSAVI
+- **Custom Formula Support**: Define your own vegetation index formulas using lambda functions
+- **Plot Segmentation**: Automated detection and boundary extraction of crop plots
+- **Pixel-Level Extraction**: Extract spectral data by plot or region
+- **3D Canopy Modeling**: Generate DTM, DSM, and CHM from point clouds
+- **3D Visualization**: Interactive and static visualization of point clouds, elevation models, and meshes
+- **Data Export**: Save results to CSV and Excel formats
+
+## Installation
+
+Install from PyPI:
+
+```bash
+pip install dronelytics
+```
+
+For point cloud processing support (optional):
+
+```bash
+pip install dronelytics[pointcloud]
+```
+
+This installs additional dependencies for LAS file handling and 3D mesh generation.
+
+## Quick Start
+
+### Load Orthomosaic and Calculate Vegetation Indices
+
+```python
+from dronelytics import Orthomosaic, VegetationIndicesExtended
+
+ortho = Orthomosaic('field.tif', band_config={
+    'red': 1, 'green': 2, 'blue': 3, 'nir': 4
+})
+
+vi = VegetationIndicesExtended(ortho)
+ndvi = vi.ndvi()
+gndvi = vi.gndvi()
+exg = vi.exg()
+
+print(f"NDVI Mean: {ndvi.mean:.4f}")
+print(f"GNDVI Mean: {gndvi.mean:.4f}")
+```
+
+### Process 5-Band Imagery with Red-Edge
+
+```python
+ortho = Orthomosaic('field_5band.tif', band_config={
+    'red': 1, 'green': 2, 'blue': 3, 'nir': 4, 'rededge': 5
+})
+
+vi = VegetationIndicesExtended(ortho)
+ndvi = vi.ndvi()
+ndre = vi.ndre()
+all_indices = vi.calculate_all()
+```
+
+### Detect Plots and Extract Data
+
+```python
+from dronelytics import PlotSegmentation, PixelExtraction
+
+segmentation = PlotSegmentation(ortho)
+seg_result = segmentation.segment_by_ndvi(ndvi.data, threshold=0.3)
+
+extraction = PixelExtraction(ortho)
+extract_result = extraction.extract_spectra()
+df = extraction.to_dataframe()
+```
+
+### Process Point Cloud and Generate CHM
+
+```python
+from dronelytics import PointCloudProcessor
+
+processor = PointCloudProcessor('field.las')
+
+chm, meta = processor.generate_chm(cell_size=1.0)
+dtm, _ = processor.generate_dtm(cell_size=1.0)
+dsm, _ = processor.generate_dsm(cell_size=1.0)
+
+print(f"Mean crop height: {meta['mean_height']:.2f}m")
+```
+
+### Visualize Results
+
+```python
+from dronelytics.visualization import show_chm, show_comparison
+
+show_chm(chm, title="Crop Height Model")
+show_comparison({'DTM': dtm, 'DSM': dsm, 'CHM': chm})
+```
+
+### Custom Vegetation Index
+
+```python
+def my_formula(ortho):
+    nir = ortho.get_band('nir')
+    red = ortho.get_band('red')
+    return (nir - red) / (nir + red + 1e-10)
+
+custom = vi.custom(my_formula, 'MyIndex')
+```
+
+## Band Configuration
+
+Specify how bands are mapped in your GeoTIFF file:
+
+```python
+band_config = {
+    'red': 1,       # Band 1 is red
+    'green': 2,     # Band 2 is green
+    'blue': 3,      # Band 3 is blue
+    'nir': 4,       # Band 4 is NIR
+    'rededge': 5    # Band 5 is red-edge (optional, 5-band only)
+}
+
+ortho = Orthomosaic('field.tif', band_config=band_config)
+```
+
+## Vegetation Indices
+
+10 vegetation indices are implemented:
+
+| Index | Formula | Use Case |
+|-------|---------|----------|
+| NDVI | (NIR - RED) / (NIR + RED) | Vegetation health, stress detection |
+| NDRE | (NIR - RedEdge) / (NIR + RedEdge) | Nitrogen content (5-band only) |
+| GNDVI | (NIR - GREEN) / (NIR + GREEN) | Chlorophyll content |
+| ExG | 2*GREEN - RED - BLUE | Greenness index for RGB imagery |
+| SAVI | ((NIR - RED) / (NIR + RED + L)) * (1 + L) | Soil adjustment (L=0.5) |
+| MSAVI | Modified SAVI | Improved soil adjustment |
+| VARI | (GREEN - RED) / (GREEN + RED - BLUE) | Visible atmospherically resistant |
+| ARVI | (NIR - (2*RED - BLUE)) / (NIR + (2*RED - BLUE)) | Atmospheric correction |
+| CVI | (NIR / GREEN) * (RED / GREEN) | Chlorophyll |
+| OSAVI | Optimized SAVI with Y=0.16 | Better soil adjustment |
+
+## 3D Visualization Functions
+
+The visualization module (3dVis) provides 5 simple functions:
+
+```python
+from dronelytics.visualization import (
+    show_pointcloud,    # Visualize point cloud with classification
+    show_dem,          # Visualize elevation models (DTM, DSM)
+    show_chm,          # Visualize crop height model
+    show_mesh,         # Visualize 3D surface mesh
+    show_comparison    # Compare multiple elevation models
+)
+```
+
+## File Structure
+
+```
+dronelytics/
+├── core/                      # Core modules
+│   ├── orthomosaic.py        # Orthomosaic loading and management
+│   ├── indices.py            # Standard vegetation indices
+│   ├── vegetation_indices_extended.py  # 10 indices + custom formulas
+│   ├── segmentation.py       # Plot boundary detection
+│   ├── extraction.py         # Pixel-level data extraction
+│   └── pointcloud.py         # Point cloud processing, DTM/DSM/CHM
+│
+├── visualization/            # 3D visualization (3dVis)
+│   └── vis3d.py             # 5 visualization functions
+│
+├── export/                  # Data export
+│   ├── csv_export.py        # CSV export
+│   └── excel_export.py      # Excel export
+│
+├── processing/              # Analysis pipelines
+│   └── pipeline.py          # Orchestrate analysis workflow
+│
+├── data/                    # Data structures
+│   └── structures.py        # VegetationIndexData, SegmentationResult, etc.
+│
+└── utils/                   # Utilities
+    └── logger.py            # Clean logging (no decorative symbols)
+```
+
+## Examples
+
+### Basic Workflow
+
+```bash
+python examples/basic_workflow.py
+```
+
+### Advanced Workflow (5-band, Point Cloud)
+
+```bash
+python examples/advanced_workflow.py
+```
+
+### 3D Visualization
+
+```bash
+python examples/visualization_example.py
+```
+
+## Requirements
+
+- Python 3.7+
+- numpy
+- rasterio (GeoTIFF support)
+- matplotlib (visualization)
+- scipy (segmentation)
+- pandas (data extraction)
+
+Optional dependencies:
+- laspy (LAS/LAZ file support)
+- pyvista (3D mesh and interactive visualization)
+
+## Testing
+
+Run unit tests:
+
+```bash
+python -m pytest tests/test_core.py
+```
+
+Or use the test module directly:
+
+```bash
+python tests/test_core.py
+```
+
+## CHM Calculation
+
+Crop Height Model (CHM) is calculated as:
+
+```
+CHM = DSM - DTM
+```
+
+Where:
+- DSM: Digital Surface Model (top of vegetation)
+- DTM: Digital Terrain Model (ground surface)
+- CHM: Height of vegetation above ground
+
+## Documentation
+
+- `WORKFLOW.md`: Complete analysis workflow guide
+- `VISUALIZATION_GUIDE.md`: 3D visualization usage
+- `5BAND_SUPPORT_GUIDE.md`: Red-edge band support
+- `COMPLETE_FEATURE_SUMMARY.md`: Feature overview
+- `DEPLOYMENT_CHECKLIST.md`: Production deployment guide
+
+## License
+
+MIT License. See LICENSE file for details.
+
+## Citation
+
+If you use Dronelytics in your research, please cite:
+
+```
+Dronelytics v1.0.0 - Comprehensive drone orthomosaic analysis package
+```
+
+## Support
+
+For issues, feature requests, or questions, please refer to the documentation files or create an issue on GitHub.
+
+---
+
+Made for agricultural field phenotyping and precision agriculture research.

dronelytics-1.0.1/dronelytics/__init__.py

@@ -0,0 +1,45 @@
+"""
+Dronelytics: Comprehensive package for end-to-end drone orthomosaic analysis
+and agricultural field phenotyping.
+
+Features:
+- Load and process multispectral orthomosaics (4-band and 5-band)
+- Calculate 10 vegetation indices with custom formula support
+- Automated plot boundary detection
+- Pixel-level data extraction
+- 3D canopy modeling from point clouds (DTM, DSM, CHM)
+- 3D visualization of point clouds, elevation models, and mesh surfaces
+- CSV/Excel data export
+"""
+
+__version__ = "1.0.0"
+__author__ = "Research Development"
+__license__ = "MIT"
+
+from .core.orthomosaic import Orthomosaic
+from .core.indices import VegetationIndices
+from .core.vegetation_indices_extended import VegetationIndicesExtended
+from .core.segmentation import PlotSegmentation
+from .core.extraction import PixelExtraction
+from .core.pointcloud import PointCloudProcessor
+from .processing.pipeline import AnalysisPipeline
+from .export.csv_export import CSVExporter
+from .export.excel_export import ExcelExporter
+from .utils.logger import setup_logger
+from . import visualization
+
+logger = setup_logger(__name__)
+
+__all__ = [
+    'Orthomosaic',
+    'VegetationIndices',
+    'VegetationIndicesExtended',
+    'PlotSegmentation',
+    'PixelExtraction',
+    'PointCloudProcessor',
+    'AnalysisPipeline',
+    'CSVExporter',
+    'ExcelExporter',
+    'setup_logger',
+    'visualization',
+]

dronelytics-1.0.1/dronelytics/core/__init__.py

@@ -0,0 +1,17 @@
+"""Core modules for dronelytics package."""
+
+from .orthomosaic import Orthomosaic
+from .indices import VegetationIndices
+from .vegetation_indices_extended import VegetationIndicesExtended
+from .segmentation import PlotSegmentation
+from .extraction import PixelExtraction
+from .pointcloud import PointCloudProcessor
+
+__all__ = [
+    'Orthomosaic',
+    'VegetationIndices',
+    'VegetationIndicesExtended',
+    'PlotSegmentation',
+    'PixelExtraction',
+    'PointCloudProcessor',
+]