tree-detection-framework 0.1.0

Framework for detecting trees in remote sensing data

tree-detection-framework

This project has three main goals:

• Enable tree detection on realistic-scale raster data with minimal boilerplate
• Facilitate direct comparison of multiple algorithms
• Rely on modern libraries and software best practice for a robust, performant, and modular tool

We use the torchgeo package to perform data loading and standardization using standard geospatial input formats. This library allows us to generate chips on the fly of a given size, stride, and spatial resolution. Training and inference is done with modular detectors that can be based on existing models and algorithms. We have preliminary support for using PyTorch Lightning to minimize boilerplate around model training and prediction. Region-level nonmax-suppression (NMS) is done using the PolyGoneNMS library which is efficient for large images. Visualization and saving of the predictions is done using geopandas, a common library for geospatial data.

This project is under active development by the Open Forest Observatory. We welcome contributions and suggestions for improvement.

Other resources

There are a variety of projects for tree detection that you may find useful. This list is incomplete, so feel free to suggest additions.

DeepForest

• Github
• Implements various preprocessing, postprocessing, visualization, and evaluation tasks.
• Used for RGB data with rectangular bounding box predictions.
• Provides a RetinaNet model trained on a large number of semi-supervised tree crown annotations and a smaller set of manual annotations.
• Training data is from the US only but represents diverse regions the model has been applied on data from outside the US successfully.
• Supports model fine-tuning with optional support for species/type classification
• Implemented in this framework.

DetectTree2

• Github
• Implements various preprocessing, postprocessing, visualization, and evaluation tasks.
• Used for RGB data with polygon boundaries.
• Provides a Mask R-CNN model train on a manually labeled tree crowns from four sites.
• Trained using data from tropical forests.
• Planned support within this framework

Install

Some of the dependencies are managed by a tool called Poetry. I've found easiest to install this using the "official installer" option as follows. Note that this should be run in the base conda environment or with no environment active.

curl -sSL https://install.python-poetry.org | python3 -

Now create and activate a conda environment for the dependencies of this project.

conda create -n tree-detection-framework python=3.10 -y
conda activate tree-detection-framework

Now, from the root directory of the project, run the following command. Note that on Jetstream2, you may need to run this in a graphical session and respond to a keyring popup menu.

poetry install

Finally, choose to either install the Detectron2 or SAM2 detection framework.

Detectron2: The Detectron2 library is not compatible with poetry so must be installed directly with pip

# https://detectron2.readthedocs.io/en/latest/tutorials/install.html#build-detectron2-from-source
pip install git+https://github.com/facebookresearch/detectron2.git

SAM2: Clone the SAM2 repository and install the necessary config files

git clone https://github.com/facebookresearch/sam2.git && cd sam2

pip install -e .

And download the associated checkpoints

cd checkpoints && \
./download_ckpts.sh && \
cd ..

And move into this repo

mv checkpoints ../tree-detection-framework 

Use

The module code is in the tree_detection_framework folder. Once installed using the poetry command above, this code can be imported into scripts or notebooks under the name tree_detection_framework the same as you would for any other library.

Examples

To begin with, you can access example geospatial data here, which should be downloaded and placed in the data folder at the top level of this project. Our goal is to have high-quality, up-to-date examples in the examples folder. We also have work-in-progress or one-off code in sandbox, which still may provide some insight but is not guaranteed to be current or generalizable. Finally, the tree_detection_framework/entrypoints folder has command line scripts that can be run to complete tasks.