bplusplus 1.2.2__tar.gz → 1.2.4__tar.gz

bplusplus-1.2.4/PKG-INFO

@@ -0,0 +1,207 @@
+Metadata-Version: 2.3
+Name: bplusplus
+Version: 1.2.4
+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 (==1.26.4)
+Requires-Dist: pandas (==2.1.4)
+Requires-Dist: pillow (==11.3.0)
+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 (==1.7.1)
+Requires-Dist: tabulate (==0.9.0)
+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 six 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.  **Download Weights**: Fetch pre-trained weights for the detection model.
+5.  **Test Model**: Evaluate the performance of the trained model.
+6.  **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
+)
+```
+
+#### 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
+    # num_workers=0  # Optional: force single-process loading (most stable)
+)
+```
+
+**Note:** The `num_workers` parameter controls DataLoader multiprocessing (defaults to 0 for stability). You can increase it for potentially faster data loading.
+
+#### Step 4: Download Detection Weights
+The inference pipeline uses a separate, pre-trained YOLO model for initial insect detection. You need to download its weights manually.
+
+You can download the weights file from [this link](https://github.com/Tvenver/Bplusplus/releases/download/v1.2.3/v11small-generic.pt).
+
+Place it in the `trained_model` directory and ensure it is named `yolo_weights.pt`.
+
+#### Step 5: Run Inference on Video
+Process a video file to detect, classify, and track insects. The final output is an annotated video and a CSV file with aggregated results for each tracked insect.
+
+```python
+VIDEO_INPUT_PATH = Path("my_video.mp4")
+VIDEO_OUTPUT_PATH = Path("my_video_annotated.mp4")
+HIERARCHICAL_MODEL_PATH = TRAINED_MODEL_DIR / "best_multitask.pt"
+YOLO_WEIGHTS_PATH = TRAINED_MODEL_DIR / "yolo_weights.pt"
+
+bplusplus.inference(
+    species_list=names,
+    yolo_model_path=YOLO_WEIGHTS_PATH,
+    hierarchical_model_path=HIERARCHICAL_MODEL_PATH,
+    confidence_threshold=0.35,
+    video_path=VIDEO_INPUT_PATH,
+    output_path=VIDEO_OUTPUT_PATH,
+    tracker_max_frames=60,
+    fps=15  # Optional: set processing FPS
+)
+```
+
+### 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.
+- `trained_model/`: Saves the trained model weights (`best_multitask.pt`) and pre-trained detection weights.
+
+# 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.**
+

bplusplus-1.2.4/README.md

@@ -0,0 +1,178 @@
+# 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 six 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.  **Download Weights**: Fetch pre-trained weights for the detection model.
+5.  **Test Model**: Evaluate the performance of the trained model.
+6.  **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
+)
+```
+
+#### 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
+    # num_workers=0  # Optional: force single-process loading (most stable)
+)
+```
+
+**Note:** The `num_workers` parameter controls DataLoader multiprocessing (defaults to 0 for stability). You can increase it for potentially faster data loading.
+
+#### Step 4: Download Detection Weights
+The inference pipeline uses a separate, pre-trained YOLO model for initial insect detection. You need to download its weights manually.
+
+You can download the weights file from [this link](https://github.com/Tvenver/Bplusplus/releases/download/v1.2.3/v11small-generic.pt).
+
+Place it in the `trained_model` directory and ensure it is named `yolo_weights.pt`.
+
+#### Step 5: Run Inference on Video
+Process a video file to detect, classify, and track insects. The final output is an annotated video and a CSV file with aggregated results for each tracked insect.
+
+```python
+VIDEO_INPUT_PATH = Path("my_video.mp4")
+VIDEO_OUTPUT_PATH = Path("my_video_annotated.mp4")
+HIERARCHICAL_MODEL_PATH = TRAINED_MODEL_DIR / "best_multitask.pt"
+YOLO_WEIGHTS_PATH = TRAINED_MODEL_DIR / "yolo_weights.pt"
+
+bplusplus.inference(
+    species_list=names,
+    yolo_model_path=YOLO_WEIGHTS_PATH,
+    hierarchical_model_path=HIERARCHICAL_MODEL_PATH,
+    confidence_threshold=0.35,
+    video_path=VIDEO_INPUT_PATH,
+    output_path=VIDEO_OUTPUT_PATH,
+    tracker_max_frames=60,
+    fps=15  # Optional: set processing FPS
+)
+```
+
+### 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.
+- `trained_model/`: Saves the trained model weights (`best_multitask.pt`) and pre-trained detection weights.
+
+# 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.**

{bplusplus-1.2.2 → bplusplus-1.2.4}/pyproject.toml

@@ -1,21 +1,25 @@
 [tool.poetry]
 name = "bplusplus"
-version = "1.2.2"
+version = "1.2.4"
 description = "A simple method to create AI models for biodiversity, with collect and prepare pipeline"
-authors = ["Titus Venverloo <tvenver@mit.edu>", "Deniz Aydemir <deniz@aydemir.us>", "Orlando Closs <orlando.closs@wur.nl>", "Ase Hatveit <aase@mit.edu>"]
+authors = ["Titus Venverloo <tvenver@mit.edu>", "Deniz Aydemir <deniz@aydemir.us>", "Orlando Closs <orlandocloss@pm.me>", "Ase Hatveit <aase@mit.edu>"]
 license = "MIT"
 readme = "README.md"
 
 [tool.poetry.dependencies]
-python = "^3.9.0"
+python = "^3.10"
 requests = "2.25.1"
-ultralytics = "8.0.195"
-pygbif = "^0.6.4"
-validators = "^0.33.0"
+pandas = "2.1.4"
+ultralytics = "8.3.173"
+pyyaml = "6.0.1"
+tqdm = "4.66.4"
 prettytable = "3.7.0"
-scikit-learn = "^1.6.1"
-tabulate = "^0.9.0"
-torch = "2.5.0"
+pillow = "11.3.0"
+numpy = "1.26.4"
+scikit-learn = "1.7.1"
+pygbif = "0.6.5"
+validators = "0.33.0"
+tabulate = "0.9.0"
 
 [tool.poetry.group.dev.dependencies]
 jupyter = "^1.0.0"

bplusplus-1.2.4/src/bplusplus/__init__.py

@@ -0,0 +1,15 @@
+try:
+    import torch
+    import torchvision
+except ImportError:
+    raise ImportError(
+        "PyTorch and Torchvision are not installed. "
+        "Please install them before using bplusplus by following the instructions "
+        "on the official PyTorch website: https://pytorch.org/get-started/locally/"
+    )
+
+from .collect import Group, collect
+from .prepare import prepare
+from .train import train
+from .test import test
+from .inference import inference