coralnet-toolbox 0.0.1__tar.gz

coralnet_toolbox-0.0.1/.gitignore

@@ -0,0 +1,23 @@
+*.hd
+*.hdf5
+*.pt
+*.pth
+*.torchscript
+*.bin
+*.engine
+*.onnx
+*__pycache__/
+*.amltmp
+*.amlignore
+*.ipynb_aml_checkpoints
+
+*egg-info
+*.idea
+*.vscode
+launch.json
+
+build
+dist
+
+Data/
+coralnet_toolbox/QtClustering.py

coralnet_toolbox-0.0.1/LICENSE.txt

@@ -0,0 +1,5 @@
+Software code created by U.S. Government employees is not subject to copyright in the United States (17 U.S.C. §105).
+The United States/Department of Commerce reserve all rights to seek and obtain copyright protection in countries
+other than the United States for Software authored in its entirety by the Department of Commerce. To this end, the
+Department of Commerce hereby grants to Recipient a royalty-free, nonexclusive license to use, copy, and create
+derivative works of the Software outside of the United States.

coralnet_toolbox-0.0.1/MANIFEST.in

@@ -0,0 +1,7 @@
+include LICENSE
+include README.md
+include requirements.txt
+
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+

coralnet_toolbox-0.0.1/PKG-INFO

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+Metadata-Version: 2.1
+Name: coralnet-toolbox
+Version: 0.0.1
+Summary: Tools for annotating and developing ML models for benthic imagery
+Home-page: https://github.com/Jordan-Pierce/CoralNet-Toolbox
+Author: Jordan Pierce
+Author-email: Jordan Pierce <jordan.pierce@noaa.gov>
+License: MIT License
+Project-URL: Homepage, https://github.com/Jordan-Pierce/CoralNet-Toolbox
+Keywords: CoralNet-Toolbox
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3.10
+Requires-Python: >=3.10, <3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: PyQt5>=5.15.11
+Requires-Dist: QtRangeSlider==0.1.5
+Requires-Dist: ultralytics==8.3.0
+Requires-Dist: supervision==0.24.0
+Requires-Dist: pycocotools>=2.0.6
+Requires-Dist: timm==0.9.2
+Requires-Dist: autodistill==0.1.28
+Requires-Dist: autodistill-grounding-dino==0.1.4
+Requires-Dist: roboflow==1.1.48
+Requires-Dist: x-segment-anything
+Requires-Dist: rasterio>=1.4.1
+Requires-Dist: requests
+Requires-Dist: dill
+Provides-Extra: all
+Requires-Dist: coralnet-toolbox[extra]; extra == "all"
+Provides-Extra: extra
+Requires-Dist: pandas; extra == "extra"
+
+# CoralNet-Toolbox
+
+<p align="center">
+  <img src="figures/CoralNet_Toolbox.png" alt="CoralNet-Toolbox">
+</p>
+
+[![image](https://img.shields.io/pypi/v/CoralNet-Toolbox.svg)](https://pypi.python.org/pypi/CoralNet-Toolbox)
+
+
+The `CoralNet-Toolbox` is an unofficial codebase that can be used to augment processes associated with those on
+[CoralNet](https://coralnet.ucsd.edu/).
+
+It uses✨[`Ultralytics`](https://github.com/ultralytics/ultralytics)🚀 as a  base, which is an open-source library for
+computer vision and deep learning built in `PyTorch`. For more information on their `AGPL-3.0` license, see
+[here](https://github.com/ultralytics/ultralytics/blob/main/LICENSE).
+
+The `toolbox` also uses the following to create rectangle and polygon annotations:
+- [`Fast-SAM`]()
+- [`RepViT-SAM`]()
+- [`EdgeSAM`](https://github.com/chongzhou96/EdgeSAM)
+- [`MobileSAM`](https://github.com/ChaoningZhang/MobileSAM)
+- [`SAM`](https://github.com/facebookresearch/segment-anything)
+- [`AutoDistill`](https://github.com/autodistill)
+  - [`GroundingDino`]()
+
+## Quick Start
+
+Running the following command will install the `coralnet-toolbox`, which you can then run from the command line:
+```bash
+# cmd
+
+# Install
+pip install coralnet-toolbox
+
+# Run
+coralnet-toolbox
+```
+
+<p align="center">
+  <img src="figures/SegmentEverything.gif" alt="CoralNet-Toolbox">
+</p>
+
+
+For further instructions, see [How to Install](); for information on how to use, check out the [docs](./docs).
+
+## Tools
+
+Enhance your CoralNet experience with these tools:
+- ✏️ Annotate: Create annotations freely
+- 👁️ Visualize: See CoralNet and CPCe annotations superimposed on images
+- 🔬 Sample: Sample patches using various methods (Uniform, Random, Stratified)
+- 🧩 Patches: Create patches (points)
+- 🔳 Rectangles: Create rectangles (bounding boxes)
+- 🟣 Polygons: Create polygons (instance masks)
+- 🦾 SAM: Use [`FastSAM`](), [`RepViT-SAM`](), [`EdgeSAM`](), [`MobileSAM`](), and [`SAM`]() to create polygons
+- 🧪 AutoDistill: Use [`AutoDistill`](https://github.com/autodistill) to access `GroundingDINO` for creating rectangles
+- 🧠 Train: Build local patch-based classifiers, object detection, and instance segmentation models
+- 🔮 Deploy: Use trained models for predictions
+- 📊 Evaluation: Evaluate model performance
+- 🚀 Optimize: Productionize models for faster inferencing
+- ⚙️ Batch Inference: Perform predictions on multiple images, automatically
+- ↔️ I/O: Import and Export annotations from / to CoralNet, Viscore, and TagLab
+- 📸 YOLO: Import and Export YOLO datasets for machine learning
+
+### TODO
+- 🔍 API: Get predictions from any CoralNet source model
+- 📥 Download: Retrieve source data from CoralNet
+- 📤 Upload: Add images and annotations to CoralNet
+- 📦 Toolshed: Access tools from the old repository
+
+
+<details open>
+  <summary><h2><b>Watch the Video Demos</b></h2></summary>
+  <p align="center">
+    <a href="https://youtube.com/playlist?list=PLG5z9IbwhS5NQT3B2jrg3hxQgilDeZak9&feature=shared">
+      <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/toolbox_qt.PNG" alt="Video Title" width="50%">
+    </a>
+  </p>
+</details>
+
+## **How to Install**
+
+### Anaconda
+
+It's recommended to use `Anaconda` to create an environment for the `toolbox`:
+```bash
+# cmd
+
+# Create and activate an environment
+conda create --name coralnet-toolbox python=3.10 -y
+conda activate coralnet-toolbox
+```
+
+### Install
+
+Once this has finished, install the `toolbox`:
+```bash
+# cmd
+
+# Install
+pip install coralnet-toolbox
+```
+
+### CUDA
+
+If you have `CUDA`, you should install the versions of `cuda-nvcc` and `cudatoolkit` that you
+need, and then install the corresponding versions of `torch` and `torchvision`. Below is an example of how that can be
+done using `CUDA` version 11.8:
+```bash
+# cmd
+
+# Example for CUDA 11.8
+conda install nvidia/label/cuda-11.8.0::cuda-nvcc -y
+conda install nvidia/label/cuda-11.8.0::cuda-toolkit -y
+
+# Example for torch w/ CUDA 11.8
+pip install torch torchvision --index-url https://download.pytorch.org/whl/cu118 --upgrade
+```
+
+If `CUDA` is installed on your computer, and `torch` was built with it properly, you should see a `🐇` icon in the
+`toolbox` instead of a `🐢`; if you have multiple `CUDA` devices available, you should see a `🚀` icon,
+and if you're using a Mac with `Metal`, you should see an `🍎` icon (click on the icon to see the device information).
+
+See here for more details on [`cuda-nvcc`](https://anaconda.org/nvidia/cuda-nvcc),
+[`cudatoolkit`](https://anaconda.org/nvidia/cuda-toolkit), and [`torch`](https://pytorch.org/get-started/locally/)
+versions.
+
+### Run
+Finally, you can run the `toolbox` from the command line:
+```bash
+# cmd
+
+# Run
+coralnet-toolbox
+```
+
+## GitHub Repository
+
+If you prefer to clone the repository and run the `toolbox` from the source code, you can do so with the following:
+
+```bash
+# cmd
+
+# Create and activate an environment
+conda create --name coralnet-toolbox python=3.10 -y
+conda activate coralnet-toolbox
+
+# Clone and enter the repository
+git clone https://github.com/Jordan-Pierce/CoralNet-Toolbox.git
+cd CoralNet-Toolbox
+
+# Install the latest
+pip install -e .
+
+# Install CUDA requirements (if applicable)
+conda install nvidia/label/cuda-11.8.0::cuda-nvcc -y
+conda install nvidia/label/cuda-11.8.0::cuda-toolkit -y
+
+# Example for torch w/ CUDA 11.8
+pip install torch torchvision --index-url https://download.pytorch.org/whl/cu118 --upgrade
+
+# Run
+coralnet-toolbox
+```
+
+## [**About CoralNet**](https://coralnet.ucsd.edu/source/)
+Coral reefs are vital ecosystems that support a wide range of marine life and provide numerous
+benefits to humans. However, they are under threat due to climate change, pollution, overfishing,
+and other factors. CoralNet is a platform designed to aid researchers and scientists in studying
+these important ecosystems and their inhabitants.
+
+CoralNet allows users to upload photos of coral reefs and annotate them with detailed information
+about the coral species and other features present in the images. The platform also provides tools
+for analyzing the annotated images, and create patch-based image classifiers.
+
+The CoralNet-Toolbox is an unofficial tool developed to augment processes associated with analyses that
+use CoralNet and Coral Point Count (CPCe).
+
+
+## **Conclusion**
+In summary, this repository provides a range of tools that can assist with interacting with
+CoralNet and performing various tasks related to analyzing annotated images. These tools can be
+useful for researchers and scientists working with coral reefs, as well as for students and
+hobbyists interested in learning more about these important ecosystems.
+
+
+## Citation
+
+If used in project or publication, please attribute your use of this repository with the following:
+
+```
+@misc{CoralNet-Toolbox,
+  author = {Pierce, Jordan and Edwards, Clinton and Rojano, Sarah and Cook, Sophie and Sweeney, Edward and Costa, Bryan and Vieham, Shay and Battista, Tim},
+  title = {CoralNet-Toolbox},
+  year = {2023},
+  howpublished = {\url{https://github.com/Jordan-Pierce/CoralNet-Toolbox}},
+  note = {GitHub repository}
+}
+```
+
+---
+
+## Disclaimer
+
+This repository is a scientific product and is not official communication of the National
+Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA
+GitHub project code is provided on an 'as is' basis and the user assumes responsibility for its
+use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from
+the use of this GitHub project will be governed by all applicable Federal law. Any reference to
+specific commercial products, processes, or services by service mark, trademark, manufacturer, or
+otherwise, does not constitute or imply their endorsement, recommendation or favoring by the
+Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC
+bureau, shall not be used in any manner to imply endorsement of any commercial product or activity
+by DOC or the United States Government.
+
+
+## License
+
+Software code created by U.S. Government employees is not subject to copyright in the United States
+(17 U.S.C. §105). The United States/Department of Commerce reserve all rights to seek and obtain
+copyright protection in countries other than the United States for Software authored in its
+entirety by the Department of Commerce. To this end, the Department of Commerce hereby grants to
+Recipient a royalty-free, nonexclusive license to use, copy, and create derivative works of the
+Software outside of the United States.

coralnet_toolbox-0.0.1/README.md

@@ -0,0 +1,224 @@
+# CoralNet-Toolbox
+
+<p align="center">
+  <img src="figures/CoralNet_Toolbox.png" alt="CoralNet-Toolbox">
+</p>
+
+[![image](https://img.shields.io/pypi/v/CoralNet-Toolbox.svg)](https://pypi.python.org/pypi/CoralNet-Toolbox)
+
+
+The `CoralNet-Toolbox` is an unofficial codebase that can be used to augment processes associated with those on
+[CoralNet](https://coralnet.ucsd.edu/).
+
+It uses✨[`Ultralytics`](https://github.com/ultralytics/ultralytics)🚀 as a  base, which is an open-source library for
+computer vision and deep learning built in `PyTorch`. For more information on their `AGPL-3.0` license, see
+[here](https://github.com/ultralytics/ultralytics/blob/main/LICENSE).
+
+The `toolbox` also uses the following to create rectangle and polygon annotations:
+- [`Fast-SAM`]()
+- [`RepViT-SAM`]()
+- [`EdgeSAM`](https://github.com/chongzhou96/EdgeSAM)
+- [`MobileSAM`](https://github.com/ChaoningZhang/MobileSAM)
+- [`SAM`](https://github.com/facebookresearch/segment-anything)
+- [`AutoDistill`](https://github.com/autodistill)
+  - [`GroundingDino`]()
+
+## Quick Start
+
+Running the following command will install the `coralnet-toolbox`, which you can then run from the command line:
+```bash
+# cmd
+
+# Install
+pip install coralnet-toolbox
+
+# Run
+coralnet-toolbox
+```
+
+<p align="center">
+  <img src="figures/SegmentEverything.gif" alt="CoralNet-Toolbox">
+</p>
+
+
+For further instructions, see [How to Install](); for information on how to use, check out the [docs](./docs).
+
+## Tools
+
+Enhance your CoralNet experience with these tools:
+- ✏️ Annotate: Create annotations freely
+- 👁️ Visualize: See CoralNet and CPCe annotations superimposed on images
+- 🔬 Sample: Sample patches using various methods (Uniform, Random, Stratified)
+- 🧩 Patches: Create patches (points)
+- 🔳 Rectangles: Create rectangles (bounding boxes)
+- 🟣 Polygons: Create polygons (instance masks)
+- 🦾 SAM: Use [`FastSAM`](), [`RepViT-SAM`](), [`EdgeSAM`](), [`MobileSAM`](), and [`SAM`]() to create polygons
+- 🧪 AutoDistill: Use [`AutoDistill`](https://github.com/autodistill) to access `GroundingDINO` for creating rectangles
+- 🧠 Train: Build local patch-based classifiers, object detection, and instance segmentation models
+- 🔮 Deploy: Use trained models for predictions
+- 📊 Evaluation: Evaluate model performance
+- 🚀 Optimize: Productionize models for faster inferencing
+- ⚙️ Batch Inference: Perform predictions on multiple images, automatically
+- ↔️ I/O: Import and Export annotations from / to CoralNet, Viscore, and TagLab
+- 📸 YOLO: Import and Export YOLO datasets for machine learning
+
+### TODO
+- 🔍 API: Get predictions from any CoralNet source model
+- 📥 Download: Retrieve source data from CoralNet
+- 📤 Upload: Add images and annotations to CoralNet
+- 📦 Toolshed: Access tools from the old repository
+
+
+<details open>
+  <summary><h2><b>Watch the Video Demos</b></h2></summary>
+  <p align="center">
+    <a href="https://youtube.com/playlist?list=PLG5z9IbwhS5NQT3B2jrg3hxQgilDeZak9&feature=shared">
+      <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/toolbox_qt.PNG" alt="Video Title" width="50%">
+    </a>
+  </p>
+</details>
+
+## **How to Install**
+
+### Anaconda
+
+It's recommended to use `Anaconda` to create an environment for the `toolbox`:
+```bash
+# cmd
+
+# Create and activate an environment
+conda create --name coralnet-toolbox python=3.10 -y
+conda activate coralnet-toolbox
+```
+
+### Install
+
+Once this has finished, install the `toolbox`:
+```bash
+# cmd
+
+# Install
+pip install coralnet-toolbox
+```
+
+### CUDA
+
+If you have `CUDA`, you should install the versions of `cuda-nvcc` and `cudatoolkit` that you
+need, and then install the corresponding versions of `torch` and `torchvision`. Below is an example of how that can be
+done using `CUDA` version 11.8:
+```bash
+# cmd
+
+# Example for CUDA 11.8
+conda install nvidia/label/cuda-11.8.0::cuda-nvcc -y
+conda install nvidia/label/cuda-11.8.0::cuda-toolkit -y
+
+# Example for torch w/ CUDA 11.8
+pip install torch torchvision --index-url https://download.pytorch.org/whl/cu118 --upgrade
+```
+
+If `CUDA` is installed on your computer, and `torch` was built with it properly, you should see a `🐇` icon in the
+`toolbox` instead of a `🐢`; if you have multiple `CUDA` devices available, you should see a `🚀` icon,
+and if you're using a Mac with `Metal`, you should see an `🍎` icon (click on the icon to see the device information).
+
+See here for more details on [`cuda-nvcc`](https://anaconda.org/nvidia/cuda-nvcc),
+[`cudatoolkit`](https://anaconda.org/nvidia/cuda-toolkit), and [`torch`](https://pytorch.org/get-started/locally/)
+versions.
+
+### Run
+Finally, you can run the `toolbox` from the command line:
+```bash
+# cmd
+
+# Run
+coralnet-toolbox
+```
+
+## GitHub Repository
+
+If you prefer to clone the repository and run the `toolbox` from the source code, you can do so with the following:
+
+```bash
+# cmd
+
+# Create and activate an environment
+conda create --name coralnet-toolbox python=3.10 -y
+conda activate coralnet-toolbox
+
+# Clone and enter the repository
+git clone https://github.com/Jordan-Pierce/CoralNet-Toolbox.git
+cd CoralNet-Toolbox
+
+# Install the latest
+pip install -e .
+
+# Install CUDA requirements (if applicable)
+conda install nvidia/label/cuda-11.8.0::cuda-nvcc -y
+conda install nvidia/label/cuda-11.8.0::cuda-toolkit -y
+
+# Example for torch w/ CUDA 11.8
+pip install torch torchvision --index-url https://download.pytorch.org/whl/cu118 --upgrade
+
+# Run
+coralnet-toolbox
+```
+
+## [**About CoralNet**](https://coralnet.ucsd.edu/source/)
+Coral reefs are vital ecosystems that support a wide range of marine life and provide numerous
+benefits to humans. However, they are under threat due to climate change, pollution, overfishing,
+and other factors. CoralNet is a platform designed to aid researchers and scientists in studying
+these important ecosystems and their inhabitants.
+
+CoralNet allows users to upload photos of coral reefs and annotate them with detailed information
+about the coral species and other features present in the images. The platform also provides tools
+for analyzing the annotated images, and create patch-based image classifiers.
+
+The CoralNet-Toolbox is an unofficial tool developed to augment processes associated with analyses that
+use CoralNet and Coral Point Count (CPCe).
+
+
+## **Conclusion**
+In summary, this repository provides a range of tools that can assist with interacting with
+CoralNet and performing various tasks related to analyzing annotated images. These tools can be
+useful for researchers and scientists working with coral reefs, as well as for students and
+hobbyists interested in learning more about these important ecosystems.
+
+
+## Citation
+
+If used in project or publication, please attribute your use of this repository with the following:
+
+```
+@misc{CoralNet-Toolbox,
+  author = {Pierce, Jordan and Edwards, Clinton and Rojano, Sarah and Cook, Sophie and Sweeney, Edward and Costa, Bryan and Vieham, Shay and Battista, Tim},
+  title = {CoralNet-Toolbox},
+  year = {2023},
+  howpublished = {\url{https://github.com/Jordan-Pierce/CoralNet-Toolbox}},
+  note = {GitHub repository}
+}
+```
+
+---
+
+## Disclaimer
+
+This repository is a scientific product and is not official communication of the National
+Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA
+GitHub project code is provided on an 'as is' basis and the user assumes responsibility for its
+use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from
+the use of this GitHub project will be governed by all applicable Federal law. Any reference to
+specific commercial products, processes, or services by service mark, trademark, manufacturer, or
+otherwise, does not constitute or imply their endorsement, recommendation or favoring by the
+Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC
+bureau, shall not be used in any manner to imply endorsement of any commercial product or activity
+by DOC or the United States Government.
+
+
+## License
+
+Software code created by U.S. Government employees is not subject to copyright in the United States
+(17 U.S.C. §105). The United States/Department of Commerce reserve all rights to seek and obtain
+copyright protection in countries other than the United States for Software authored in its
+entirety by the Department of Commerce. To this end, the Department of Commerce hereby grants to
+Recipient a royalty-free, nonexclusive license to use, copy, and create derivative works of the
+Software outside of the United States.