Merge pull request #379 from microsoft/PyTorchWildlife_Dev_0.0.1.1.2

PyTorchWildlife 0.0.1.1.2

.gitignore

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-################################################################################
-# This .gitignore file was automatically created by Microsoft(R) Visual Studio.
-################################################################################
-
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# mypy
-.mypy_cache/
-.dmypy.json
-dmypy.json
-
-# Apple directory 
-*.DS_Store
-
-# IDEs
-*.idea/
-*.project
-.spyderproject
-.spyproject
-.vscode
-
-# Demo files
-demo/aadconfig.py
-demo/apiconfig.py
-demo/CameraTrapAssets
-demo/static/uploads
-demo/static/results
-.webassets-cache/
-
-# CameraTrapJsonFileProcessingApp
-api/batch_processing/postprocessing/CameraTrapJsonFileProcessingApp/.vs/
-api/batch_processing/postprocessing/CameraTrapJsonFileProcessingApp/bin/
-api/batch_processing/postprocessing/CameraTrapJsonFileProcessingApp/obj/
-api/batch_processing/postprocessing/CameraTrapJsonFileProcessingApp/packages/
-
-# TF and PyTorch model files
-*.pb
-*.pt
-
-# batch processing API config files
-api_config*.py
-
-# Other
-*.pth
-*.o
-debug.log
-*.swp
-
-# Things created when building the sync API
-yolov5
-api/synchronous/api_core/animal_detection_api/detection
-
+__pycache__
+*weights*
+*processed.*
+*output*
+*flagged*
+*temp*
+PytorchWildlife.egg-info/
+*dev*
+*test*
+*setup/*
+*dist/*

.readthedocs.yaml

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+version: "2"
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.8"
+
+python:
+  install:
+    - requirements: docs/requirements.txt
+
+sphinx:
+  configuration: docs/conf.py

INSTALLATION.md

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+# PyTorch Wildlife: A Collaborative Deep Learning Framework for Conservation
+
+## Welcome to Version 0.0.1.1.2
+
+The Pytorch-wildlife library allows users to directly load the MegadetectorV5 model weights for animal detection. We've fully refactored our codebase, prioritizing ease of use in model deployment and expansion. In addition to `MegadetectorV5`, `Pytorch-wildlife` also accommodates a range of classification weights, such as those derived from the Amazon Rainforest dataset and the Opossum classification dataset. Explore the codebase and functionalities of `Pytorch-wildlife` through our interactive `Gradio` web app and detailed Jupyter notebooks, designed to showcase the practical applications of our enhancements. You can find more information in our [documentation](https://cameratraps.readthedocs.io/en/latest/).
+
+## Table of Contents
+1. [Prerequisites](#prerequisites)
+2. [Installation](#installation) 
+3. [Running the Demo](#running-the-demo)
+4. [License](#license)
+
+## Prerequisites
+
+1. Python 3.8 
+2. NVIDIA GPU (for CUDA support, although the demo can run on CPU)
+
+If you have conda/mamba installed, you can create a new environment with the following command:
+```bash
+conda create -n pytorch-wildlife python=3.8 -y
+conda activate pytorch-wildlife
+```
+
+## Installation
+### 1. Install through pip:
+```bash
+pip install PytorchWildlife
+```
+## Running the Demo
+Here is a brief example on how to perform detection and classification on a single image using `PyTorch-wildlife`:
+```python
+import torch
+from PytorchWildlife.models import detection as pw_detection
+from PytorchWildlife.models import classification as pw_classification
+img = torch.randn((3, 1280, 1280))
+# Detection
+detection_model = pw_detection.MegaDetectorV5()
+detection_result = detection_model.single_image_detection(img)
+#Classification
+classification_model = pw_classification.AI4GAmazonRainforest()
+classification_results = classification_model.single_image_classification(img)
+```
+
+#### Version 0.0.1.1.2 does not currently have video detection support, you can use the Gradio app for single image and batch image detection \& classification.
+If you want to use our Gradio demo for a user-friendly interface. Please run the following code inside the current repo. You can also find Jupyter Notebooks with an image and video tutorial:
+```bash
+git clone -b PytorchWildlife_Dev --single-branch https://github.com/microsoft/CameraTraps.git
+cd CameraTraps
+cd demo
+# For the image demo
+python image_demo.py
+# For the video demo
+python video_demo.py
+# For the gradio app
+python demo_gradio.py
+```
+The `demo_gradio.py` will launch a Gradio interface where you can:
+- Perform Single Image Detection: Upload an image and set a confidence threshold to get detections.
+- Perform Batch Image Detection: Upload a zip file containing multiple images to get detections in a JSON format.
+- Perform Video Detection: Upload a video and get a processed video with detected animals (Not supported in version 0.0.1.1.2).
+
+## License
+This project is licensed under the MIT License. Refer to the LICENSE file for more details.
+## Copyright
+Copyright (c) Microsoft Corporation. All rights reserved.

LICENSE

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-    MIT License
+MIT License
 
-    Copyright (c) Microsoft Corporation. All rights reserved.
+Copyright (c) [2023] [Microsoft]
 
-    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:
+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 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
+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.

PytorchWildlife/__init__.py

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+from .data import *
+from .models import *
+from .utils import *

PytorchWildlife/data/__init__.py

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+from .datasets import *
+from .transforms import *

PytorchWildlife/data/datasets.py

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+# Copyright (c) Microsoft Corporation. All rights reserved.
+# Licensed under the MIT License.
+
+import os
+from PIL import Image
+import numpy as np
+import supervision as sv
+from torch.utils.data import Dataset
+
+# Making the DetectionImageFolder class available for import from this module
+__all__ = [
+    "DetectionImageFolder",
+    ]
+
+
+class DetectionImageFolder(Dataset):
+    """
+    A PyTorch Dataset for loading images from a specified directory.
+    Each item in the dataset is a tuple containing the image data, 
+    the image's path, and the original size of the image.
+    """
+
+    def __init__(self, image_dir, transform=None):
+        """
+        Initializes the dataset.
+
+        Parameters:
+            image_dir (str): Path to the directory containing the images.
+            transform (callable, optional): Optional transform to be applied on the image.
+        """
+        self.image_dir = image_dir
+        # Listing and sorting all image files in the specified directory
+        self.images = sorted(os.listdir(self.image_dir))
+        self.transform = transform
+
+    def __getitem__(self, idx):
+        """
+        Retrieves an image from the dataset.
+
+        Parameters:
+            idx (int): Index of the image to retrieve.
+
+        Returns:
+            tuple: Contains the image data, the image's path, and its original size.
+        """
+        # Get image filename and path
+        img = self.images[idx]
+        img_path = os.path.join(self.image_dir, img)
+
+        # Load and convert image to RGB
+        img = Image.open(img_path).convert("RGB")
+        img = np.asarray(img)
+        img_size_ori = img.shape
+
+        # Apply transformation if specified
+        if self.transform:
+            img = self.transform(img)
+
+        return img, img_path, np.array(img_size_ori)
+
+    def __len__(self):
+        """
+        Returns the total number of images in the dataset.
+
+        Returns:
+            int: Total number of images.
+        """
+        return len(self.images)
+
+
+class DetectionCrops(Dataset):
+
+    def __init__(self, detection_results, transform=None, path_head=None, animal_cls_id=0):
+
+        self.detection_results = detection_results
+        self.transform = transform
+        self.path_head = path_head
+        self.animal_cls_id = animal_cls_id # This determins which detection class id represents animals.
+        self.img_ids = []
+        self.xyxys = []
+
+        self.load_detection_results()
+
+    def load_detection_results(self):
+        for det in self.detection_results:
+            for xyxy, det_id in zip(det["detections"].xyxy, det["detections"].class_id):
+                # Only run recognition on animal detections
+                if det_id == self.animal_cls_id:
+                    self.img_ids.append(det["img_id"])
+                    self.xyxys.append(xyxy)
+
+    def __getitem__(self, idx):
+        """
+        Retrieves an image from the dataset.
+
+        Parameters:
+            idx (int): Index of the image to retrieve.
+
+        Returns:
+            tuple: Contains the image data and the image's path.
+        """
+
+        # Get image path and corresponding bbox xyxy for cropping
+        img_id = self.img_ids[idx]
+        xyxy = self.xyxys[idx]
+
+        img_path = os.path.join(self.path_head, img_id) if self.path_head else img_id
+
+        # Load and crop image with supervision
+        img = sv.crop_image(np.array(Image.open(img_path).convert("RGB")),
+                            xyxy=xyxy)
+
+        # Apply transformation if specified
+        if self.transform:
+            img = self.transform(Image.fromarray(img))
+
+        return img, img_path
+
+    def __len__(self):
+        return len(self.img_ids)