bplusplus 2.0.4__py3-none-any.whl

bplusplus-2.0.4.dist-info/METADATA

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+Metadata-Version: 2.3
+Name: bplusplus
+Version: 2.0.4
+Summary: A simple method to create AI models for biodiversity, with collect and prepare pipeline
+License: MIT
+Author: Titus Venverloo
+Author-email: tvenver@mit.edu
+Requires-Python: >=3.10,<4.0
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Dist: numpy (>=1.26.0,<1.26.5) ; sys_platform == "win32"
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+Requires-Dist: numpy (>=1.26.0,<1.27.0) ; sys_platform == "linux" and platform_machine == "x86_64"
+Requires-Dist: pandas (==2.1.4)
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+Requires-Dist: pillow (>=10.0.0,<12.0.0) ; sys_platform == "win32"
+Requires-Dist: prettytable (==3.7.0)
+Requires-Dist: pygbif (==0.6.5)
+Requires-Dist: pyyaml (==6.0.1)
+Requires-Dist: requests (==2.25.1)
+Requires-Dist: scikit-learn (>=1.3.0,<1.7.0) ; sys_platform == "linux" and platform_machine == "aarch64"
+Requires-Dist: scikit-learn (>=1.3.0,<1.7.0) ; sys_platform == "win32"
+Requires-Dist: scikit-learn (>=1.4.0,<1.8.0) ; sys_platform == "darwin" and platform_machine == "arm64"
+Requires-Dist: scikit-learn (>=1.4.0,<1.8.0) ; sys_platform == "darwin" and platform_machine == "x86_64"
+Requires-Dist: scikit-learn (>=1.4.0,<1.8.0) ; sys_platform == "linux" and platform_machine == "x86_64"
+Requires-Dist: tabulate (==0.9.0)
+Requires-Dist: torch (>=2.0.0,<2.8.0) ; sys_platform == "darwin" and platform_machine == "arm64"
+Requires-Dist: torch (>=2.0.0,<2.8.0) ; sys_platform == "linux"
+Requires-Dist: torch (>=2.0.0,<2.8.0) ; sys_platform == "win32"
+Requires-Dist: torch (>=2.2.0,<2.3.0) ; sys_platform == "darwin" and platform_machine == "x86_64"
+Requires-Dist: tqdm (==4.66.4)
+Requires-Dist: ultralytics (==8.3.173)
+Requires-Dist: validators (==0.33.0)
+Description-Content-Type: text/markdown
+
+# B++ repository
+
+[![DOI](https://zenodo.org/badge/765250194.svg)](https://zenodo.org/badge/latestdoi/765250194) 
+[![PyPi version](https://img.shields.io/pypi/v/bplusplus.svg)](https://pypi.org/project/bplusplus/)
+[![Python versions](https://img.shields.io/pypi/pyversions/bplusplus.svg)](https://pypi.org/project/bplusplus/)
+[![License](https://img.shields.io/pypi/l/bplusplus.svg)](https://pypi.org/project/bplusplus/)
+[![Downloads](https://static.pepy.tech/badge/bplusplus)](https://pepy.tech/project/bplusplus)
+[![Downloads](https://static.pepy.tech/badge/bplusplus/month)](https://pepy.tech/project/bplusplus)
+[![Downloads](https://static.pepy.tech/badge/bplusplus/week)](https://pepy.tech/project/bplusplus)
+
+This project provides a complete, end-to-end pipeline for building a custom insect classification system. The framework is designed to be **domain-agnostic**, allowing you to train a powerful detection and classification model for **any insect species** by simply providing a list of names.
+
+Using the `Bplusplus` library, this pipeline automates the entire machine learning workflow, from data collection to video inference.
+
+## Key Features
+
+- **Automated Data Collection**: Downloads hundreds of images for any species from the GBIF database.
+- **Intelligent Data Preparation**: Uses a pre-trained model to automatically find, crop, and resize insects from raw images, ensuring high-quality training data.
+- **Hierarchical Classification**: Trains a model to identify insects at three taxonomic levels: **family, genus, and species**.
+- **Video Inference & Tracking**: Processes video files to detect, classify, and track individual insects over time, providing aggregated predictions.
+## Pipeline Overview
+
+The process is broken down into five main steps, all detailed in the `full_pipeline.ipynb` notebook:
+
+1.  **Collect Data**: Select your target species and fetch raw insect images from the web.
+2.  **Prepare Data**: Filter, clean, and prepare images for training.
+3.  **Train Model**: Train the hierarchical classification model.
+4.  **Validate Model**: Evaluate the performance of the trained model.
+5.  **Run Inference**: Run the full pipeline on a video file for real-world application.
+
+## How to Use
+
+### Prerequisites
+
+- Python 3.10+
+
+### Setup
+
+1.  **Create and activate a virtual environment:**
+    ```bash
+    python3 -m venv venv
+    source venv/bin/activate
+    ```
+
+2.  **Install the required packages:**
+    ```bash
+    pip install bplusplus
+    ```
+
+### Running the Pipeline
+
+The pipeline can be run step-by-step using the functions from the `bplusplus` library. While the `full_pipeline.ipynb` notebook provides a complete, executable workflow, the core functions are described below.
+
+#### Step 1: Collect Data
+Download images for your target species from the GBIF database. You'll need to provide a list of scientific names.
+
+```python
+import bplusplus
+from pathlib import Path
+
+# Define species and directories
+names = ["Vespa crabro", "Vespula vulgaris", "Dolichovespula media"]
+GBIF_DATA_DIR = Path("./GBIF_data")
+
+# Define search parameters
+search = {"scientificName": names}
+
+# Run collection
+bplusplus.collect(
+    group_by_key=bplusplus.Group.scientificName,
+    search_parameters=search,
+    images_per_group=200,  # Recommended to download more than needed
+    output_directory=GBIF_DATA_DIR,
+    num_threads=5
+)
+```
+
+#### Step 2: Prepare Data
+Process the raw images to extract, crop, and resize insects. This step uses a pre-trained model to ensure only high-quality images are used for training.
+
+```python
+PREPARED_DATA_DIR = Path("./prepared_data")
+
+bplusplus.prepare(
+    input_directory=GBIF_DATA_DIR,
+    output_directory=PREPARED_DATA_DIR,
+    img_size=640,        # Target image size for training
+    conf=0.6,            # Detection confidence threshold (0-1)
+    valid=0.1,           # Validation split ratio (0-1), set to 0 for no validation
+    blur=None,           # Gaussian blur as fraction of image size (0-1), None = disabled
+)
+```
+
+**Note:** The `blur` parameter applies Gaussian blur before resizing, which can help reduce noise. Values are relative to image size (e.g., `blur=0.01` means 1% of the smallest dimension). Supported image formats: JPG, JPEG, and PNG.
+
+#### Step 3: Train Model
+Train the hierarchical classification model on your prepared data. The model learns to identify family, genus, and species.
+
+```python
+TRAINED_MODEL_DIR = Path("./trained_model")
+
+bplusplus.train(
+    batch_size=4,
+    epochs=30,
+    patience=3,
+    img_size=640,
+    data_dir=PREPARED_DATA_DIR,
+    output_dir=TRAINED_MODEL_DIR,
+    species_list=names,
+    backbone="resnet50",  # Choose: "resnet18", "resnet50", or "resnet101"
+    # num_workers=0,      # Optional: force single-process loading (most stable)
+    # train_transforms=custom_transforms,  # Optional: custom torchvision transforms
+)
+```
+
+**Note:** The `num_workers` parameter controls DataLoader multiprocessing (defaults to 0 for stability). The `backbone` parameter allows you to choose between different ResNet architectures—use `resnet18` for faster training or `resnet101` for potentially better accuracy.
+
+#### Step 4: Validate Model
+Evaluate the trained model on a held-out validation set. This calculates precision, recall, and F1-score at all taxonomic levels.
+
+```python
+HIERARCHICAL_MODEL_PATH = TRAINED_MODEL_DIR / "best_multitask.pt"
+
+results = bplusplus.validate(
+    species_list=names,
+    validation_dir=PREPARED_DATA_DIR / "valid",
+    hierarchical_weights=HIERARCHICAL_MODEL_PATH,
+    img_size=640,           # Must match training
+    batch_size=32,
+    backbone="resnet50",    # Must match training
+)
+```
+
+#### Step 5: Run Inference on Video
+Process a video file to detect, classify, and track insects using motion-based detection. The pipeline uses background subtraction (GMM) to detect moving insects, tracks them across frames, and classifies confirmed tracks.
+
+**Output files generated in `output_dir`:**
+- `{video}_annotated.mp4` - Video showing confirmed tracks with classifications
+- `{video}_debug.mp4` - Debug video with motion mask and all detections
+- `{video}_results.csv` - Aggregated results per confirmed track
+- `{video}_detections.csv` - Frame-by-frame detection data
+
+```python
+VIDEO_INPUT_PATH = Path("my_video.mp4")
+OUTPUT_DIR = Path("./output")
+HIERARCHICAL_MODEL_PATH = TRAINED_MODEL_DIR / "best_multitask.pt"
+
+results = bplusplus.inference(
+    species_list=names,
+    hierarchical_model_path=HIERARCHICAL_MODEL_PATH,
+    video_path=VIDEO_INPUT_PATH,
+    output_dir=OUTPUT_DIR,
+    fps=None,               # None = process all frames
+    backbone="resnet50",    # Must match training
+    save_video=True,        # Set to False to skip video rendering (only CSV output)
+    img_size=60,            # Must match training
+)
+
+print(f"Detected {results['tracks']} tracks ({results['confirmed_tracks']} confirmed)")
+```
+
+**Note:** Set `save_video=False` to skip generating the annotated and debug videos, which speeds up processing when you only need the CSV detection data.
+
+**Custom Detection Configuration:**
+
+For advanced control over detection parameters, provide a YAML config file:
+
+```python
+results = bplusplus.inference(
+    ...,
+    config="detection_config.yaml"
+)
+```
+
+Download a template config from the [releases page](https://github.com/Tvenver/Bplusplus/releases). Parameters control cohesiveness filtering, shape filtering, tracking behavior, and path topology analysis for confirming insect-like movement.
+
+### Customization
+
+To train the model on your own set of insect species, you only need to change the `names` list in **Step 1**. The pipeline will automatically handle the rest.
+
+```python
+# To use your own species, change the names in this list
+names = [
+    "Vespa crabro",
+    "Vespula vulgaris",
+    "Dolichovespula media",
+    # Add your species here
+]
+```
+
+#### Handling an "Unknown" Class
+To train a model that can recognize an "unknown" class for insects that don't belong to your target species, add `"unknown"` to your `species_list`. You must also provide a corresponding `unknown` folder containing images of various other insects in your data directories (e.g., `prepared_data/train/unknown`).
+
+```python
+# Example with an unknown class
+names_with_unknown = [
+    "Vespa crabro",
+    "Vespula vulgaris",
+    "unknown"
+]
+```
+
+## Directory Structure
+
+The pipeline will create the following directories to store artifacts:
+
+- `GBIF_data/`: Stores the raw images downloaded from GBIF.
+- `prepared_data/`: Contains the cleaned, cropped, and resized images ready for training (`train/` and optionally `valid/` subdirectories).
+- `trained_model/`: Saves the trained model weights (`best_multitask.pt`).
+- `output/`: Inference results including annotated videos and CSV files.
+
+# Citation
+
+All information in this GitHub is available under MIT license, as long as credit is given to the authors.
+
+**Venverloo, T., Duarte, F., B++: Towards Real-Time Monitoring of Insect Species. MIT Senseable City Laboratory, AMS Institute.**
+

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