coralnet-toolbox 0.0.73__py2.py3-none-any.whl → 0.0.74__py2.py3-none-any.whl

coralnet_toolbox-0.0.73.dist-info/METADATA

@@ -1,341 +0,0 @@
-Metadata-Version: 2.4
-Name: coralnet-toolbox
-Version: 0.0.73
-Summary: Tools for annotating and developing ML models for benthic imagery
-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: <3.11,>=3.10
-Description-Content-Type: text/markdown
-License-File: LICENSE.txt
-Requires-Dist: PyQt5>=5.15.11
-Requires-Dist: pyqtdarktheme
-Requires-Dist: pyqtgraph
-Requires-Dist: ultralytics>=8.3.152
-Requires-Dist: lap>=0.5.12
-Requires-Dist: open-clip-torch>=2.20.0
-Requires-Dist: supervision>=0.24.0
-Requires-Dist: scikit-learn
-Requires-Dist: umap-learn
-Requires-Dist: faiss-cpu
-Requires-Dist: pycocotools
-Requires-Dist: ujson
-Requires-Dist: timm==0.9.2
-Requires-Dist: autodistill
-Requires-Dist: transformers>=4.5.0
-Requires-Dist: x-segment-anything>=0.0.8
-Requires-Dist: yolo-tiling>=0.0.19
-Requires-Dist: roboflow
-Requires-Dist: rasterio
-Requires-Dist: requests
-Requires-Dist: selenium>=4.15.2
-Requires-Dist: beautifulsoup4>=4.12.2
-Requires-Dist: webdriver_manager
-Requires-Dist: dill
-Requires-Dist: seaborn
-Provides-Extra: all
-Requires-Dist: coralnet-toolbox[extra]; extra == "all"
-Dynamic: license-file
-
-# CoralNet-Toolbox 🪸🧰
-
-<div align="center">
-  <p>
-    <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/CoralNet_Toolbox.png" alt="CoralNet-Toolbox">
-  </p>
-</div>
-
-<div align="center">
-
-[![python-version](https://img.shields.io/pypi/pyversions/CoralNet-Toolbox.svg)](https://pypi.org/project/CoralNet-Toolbox)
-[![version](https://img.shields.io/pypi/v/CoralNet-Toolbox.svg)](https://pypi.python.org/pypi/CoralNet-Toolbox)
-[![pypi-passing](https://github.com/Jordan-Pierce/CoralNet-Toolbox/actions/workflows/pypi.yml/badge.svg)](https://pypi.org/project/CoralNet-Toolbox)
-[![windows](https://github.com/Jordan-Pierce/CoralNet-Toolbox/actions/workflows/windows.yml/badge.svg)](https://pypi.org/project/CoralNet-Toolbox)
-[![macos](https://github.com/Jordan-Pierce/CoralNet-Toolbox/actions/workflows/macos.yml/badge.svg)](https://pypi.org/project/CoralNet-Toolbox)
-[![ubuntu](https://github.com/Jordan-Pierce/CoralNet-Toolbox/actions/workflows/ubuntu.yml/badge.svg)](https://pypi.org/project/CoralNet-Toolbox)
-</div>
-
-<div align="center">
-  <table>
-    <tr>
-      <td align="center" width="33%">
-        <h3>🔍 Annotation</h3>
-        <p>Create patches, rectangles, and polygons with AI assistance</p>
-      </td>
-      <td align="center" width="33%">
-        <h3>🧠 AI-Powered</h3>
-        <p>Leverage SAM, YOLOE, and various foundation models</p>
-      </td>
-      <td align="center" width="33%">
-        <h3>🚀 Complete Workflow</h3>
-        <p>From data collection to model training and deployment</p>
-      </td>
-    </tr>
-  </table>
-</div>
-
-## 🚦 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
-```
-
-## 📚 Guides
-
-For further information and instructions, please see the following guides:
-- [Overview](https://jordan-pierce.github.io/CoralNet-Toolbox/overview)
-- [Installation](https://jordan-pierce.github.io/CoralNet-Toolbox/installation)
-- [Usage](https://jordan-pierce.github.io/CoralNet-Toolbox/usage)
-- Community Provided:
-  - [Patch-based Image Classifier](https://jordan-pierce.github.io/CoralNet-Toolbox/classify)
-
-<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="90%">
-    </a>
-  </p>
-</details>
-
-## ⏩ TL;Dr
-
-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).
-
-### 🚀 Supported Models
-
-The `toolbox` integrates a variety of state-of-the-art models to help you create rectangle and polygon annotations efficiently. Below is a categorized overview of the supported models and frameworks:
-
-<div align="center">
-
-| Category                | Models                                                                                       |
-|-------------------------|---------------------------------------------------------------------------------------------------------|
-| **Trainable**           | - 🦾 [YOLOv3](https://docs.ultralytics.com/models/) <br> - 🦈 [YOLOv4](https://docs.ultralytics.com/models/) <br> - 🦅 [YOLOv5](https://docs.ultralytics.com/models/) <br> - 🐬 [YOLOv6](https://docs.ultralytics.com/models/) <br> - 🐢 [YOLOv7](https://docs.ultralytics.com/models/) <br> - 🐙 [YOLOv8](https://docs.ultralytics.com/models/) <br> - 🐠 [YOLOv9](https://docs.ultralytics.com/models/) <br> - 🦑 [YOLOv10](https://docs.ultralytics.com/models/) <br> - 🚀 [YOLO11](https://docs.ultralytics.com/models/) <br> - 🐳 [YOLO12](https://docs.ultralytics.com/models/) |
-| **Segment Anything**    | - 🪸 [SAM](https://github.com/facebookresearch/segment-anything) <br> - 🌊 [CoralSCOP](https://github.com/zhengziqiang/CoralSCOP) <br> - ⚡ [FastSAM](https://github.com/CASIA-IVA-Lab/FastSAM) <br> - 🔁 [RepViT-SAM](https://github.com/THU-MIG/RepViT) <br> - ✂️ [EdgeSAM](https://github.com/chongzhou96/EdgeSAM) <br> - 📱 [MobileSAM](https://github.com/ChaoningZhang/MobileSAM) |
-| **Visual Prompting**    | - 👁️ [YOLOE](https://github.com/THU-MIG/yoloe) <br> - 🤖 [AutoDistill](https://github.com/autodistill): <br> &nbsp;&nbsp;&nbsp;• 🦒 Grounding DINO <br> &nbsp;&nbsp;&nbsp;• 🦉 OWLViT <br> &nbsp;&nbsp;&nbsp;• ⚡ OmDetTurbo |
-
-</div>
-
-These models enable fast, accurate, and flexible annotation workflows for a wide range of use cases for patch-based image classification, object detection, instance segmentation.
-
-## 🛠️ Toolbox Features
-
-<div align="center">
-
-| <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Patches.gif" alt="Patch Annotation Tool" width="256" height="256"/><br><sub>**Patch Annotation**</sub> | <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Rectangles.gif" alt="Rectangle Annotation Tool" width="256" height="256"/><br><sub>**Rectangle Annotation**</sub> | <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Polygons.gif" alt="Polygon Annotation Tool" width="256" height="256"/><br><sub>**(Multi) Polygon Annotation**</sub> |
-|:--:|:--:|:--:|
-| <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Classification.gif" alt="Patch-based Image Classification" width="256" height="256"/><br><sub>**Image Classification**</sub> | <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Object_Detection.gif" alt="Object Detection" width="256" height="256"/><br><sub>**Object Detection**</sub> | <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Instance_Segmentation.gif" alt="Instance Segmentation" width="256" height="256"/><br><sub>**Instance Segmentation**</sub> |
-| <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Segment_Anything.gif" alt="Segment Anything Model (SAM)" width="256" height="256"/><br><sub>**Segment Anything (SAM)**</sub> | <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Classifying_Polygons.gif" alt="Polygon Classification" width="256" height="256"/><br><sub>**Polygon Classification**</sub> | <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Work_Areas.gif" alt="Region-based Detection" width="256" height="256"/><br><sub>**Region-based Detection**</sub> |
-| <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Cut.gif" alt="Cut" width="256" height="256"/><br><sub>**Cut**</sub> | <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Combine.gif" alt="Combine" width="256" height="256"/><br><sub>**Combine**</sub> | <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Simplify.gif" alt="Simplify" width="256" height="256"/><br><sub>**Simplify**</sub> |
-| <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/See_Anything.gif" alt="See Anything (YOLOE)" width="256" height="256"/><br><sub>**See Anything (YOLOE)**</sub> | <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Classifying_Orthomosaics.gif" alt="Patch-based LAI Classification" width="256" height="256"/><br><sub>**LAI Classification**</sub> |  |
-
-<br>
-
-| <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Analytics.gif" alt="Video Inference" width="450"/><br><sub>**Video Inference**</sub> | <img src="https://raw.githubusercontent.com/Jordan-Pierce/CoralNet-Toolbox/refs/heads/main/figures/tools/Explorer.gif" alt="Explorer" width="450"/><br><sub>**Explorer**</sub> |
-|:--:|:--:|
-
-</div>
-
-</div>
-
-Enhance your CoralNet experience with these tools:
-- 📥 [Download](https://www.youtube.com/watch?v=Ds9JZATmCmw): Retrieve Source data (images and annotations) from CoralNet
-- 🎬 Rasters: Import images, or extract frames directly from video files
-- ✏️ 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)
-  - 👨‍👩‍👧‍👦 MultiPolygons: Combine multiple, non-overlapping polygons (i.e, genets)
-- ✍️ Edit: Cut and Combine polygons and rectangles
-- 🦾 SAM: Use `FastSAM`, `CoralSCOP`, `RepViT-SAM`, `EdgeSAM`, `MobileSAM`, and `SAM` to create polygons
-  - Uses [`xSAM`](https://github.com/Jordan-Pierce/xSAM)
-- 👷‍♂️ Work areas: Perform region-specific detections / segmentations with any model
-- 👀 YOLOE (See Anything): Detect similar appearing objects using visual prompts automatically
-- 🧪 AutoDistill: Use `AutoDistill` to access the following for creating rectangles and polygons:
-  - Uses `Grounding DINO`, `OWLViT`, `OmDetTurbo`
-- 📻 Tune: Tune hyperparameters to identify ideal training conditions
-- 🧠 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
-- 🎞️ Video Inference: Perform predictions on a video in real-time, record the output and analytics
-- 🔮 [Explorer](https://youtu.be/68eZt5l_7nA): Cluster, view, and re-label annotations using embeddings, mapped from feature-space
-- ↔️ I/O: Import and Export annotations from / to CoralNet, Viscore, and TagLab
-  - Export annotations as [GeoJSONs](https://datatracker.ietf.org/doc/html/rfc7946), segmentation masks
-- 📸 YOLO: Import and Export YOLO datasets for machine learning
-- 🧱 Tile Dataset: Tile existing Detection / Segmentation datasets
-  - Uses [`yolo-tiling`](https://github.com/Jordan-Pierce/yolo-tiling)
-- 🏗️ Tile Inference: Pre-compute multiple work areas for an entire image
-
-### 📝 TODO
-- 🤗 Model Zoo: Download `Ultralytics` models from `HuggingFace` for use in `toolbox`
-- 🦊 BioCLIP, MobileCLIP (AutoDistill): Automatically classify annotations
-- 📦 [Toolshed: Access tools from the old repository](https://github.com/Jordan-Pierce/CoralNet-Toolshed)
-
-## 💾 **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 coralnet10 python=3.10 -y
-conda activate coralnet10
-```
-
-### 📦 Install
-
-Once this has finished, install the `toolbox` using `uv`: 
-
-```bash
-# cmd
-
-# Install uv first
-pip install uv
-
-# Install with uv
-uv pip install coralnet-toolbox
-```
-
-Although fast, `uv` is still relatively new; if this fails, simply fall back to using `pip`:
-
-```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
-uv 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 versions for the following:
-- [`cuda-nvcc`](https://anaconda.org/nvidia/cuda-nvcc)
-- [`cudatoolkit`](https://anaconda.org/nvidia/cuda-toolkit)
-- [`torch`](https://pytorch.org/get-started/locally/)
-
-### ▶️ Run
-
-Finally, you can run the `toolbox` from the command line:
-
-```bash
-# cmd
-
-# Run
-coralnet-toolbox
-```
-
-### **How to Upgrade**
-
-When opening the `toolbox`, you will be notified if there is an update available, and you have the _option_ to do so, 
-if you so choose. To upgrade, run the following command from your terminal:
-
-```bash
-# cmd
-
-uv pip install -U coralnet-toolbox==[enter_newest_version_here]
-```
-
-Again, fall back to using just `pip` and not `uv` if this fails.
-
-## 🌊 Success Stories
-
-Using the `toolbox`? Share your successes and we can feature your work to help others learn!
-
-## 🐠 [**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.