Torch Traps is python package for lighting ⚡ fast wildlife camera trap image annotation based on PyTorch. 🔥
- Documentation: https://torchtraps.readthedocs.io.
- GitHub: https://github.com/winzurk/torchtraps
- PyPI: https://pypi.python.org/pypi/torchtraps
- MIT License
Photo Credit: Northern Jaguar Project
Over the past several decades, biologists all over the world have widely adopted camera traps as a standard tool for monitoring biodiversity, resulting in backlogs often on the order of millions of images waiting to be manually reviewed by humans to assess wildlife population densities. The application of modern computer vision and deep learning methods to accelerate the processing of wildlife camera trap data has the potential to alleviate existing bottlenecks for large scale biodiversity monitoring, thus dramatically increasing the speed at which researchers can obtain data-driven insights about ecosystems, and ultimately leading to more efficient resource allocation and better informed policy making by NGOs and government agencies.
Torch Traps aims to provide a simple tool (as little as 1 line of python code) to bring state-of-the-art computer vision models into the hands of biologists to accelerate the speed at which they can review camera trap imagery.
$ pip install torchtrapsClassify an entire folder of camera trap images in one line of code by simply passing the relative path to the folder containing images. Outputs are automatically saved to a csv file which can be further processed opened in an application like Excel.
import torchtraps.lightning import kachow
kachow('path/to/image/folder')| image | prediction | confidence |
|---|---|---|
| image1.jpg | jaguar | 0.99 |
| image2.jpg | empty | 0.98 |
| image3.jpg | agouti | 0.91 |
| image4.jpg | empty | 0.95 |
| image5.jpg | ocelot | 0.87 |
- Training and fine-tune classification models on your own images. (Coming soon)
- Animal and Species Detection. (Coming soon)
- Visualize embeddings with t-SNE. (Coming soon)
This is a full tutorial on how to install and get up and running with Torch Traps. Zero programming knowledge is assumed in the attempt to make Torch Traps as accessible as possible. If you do run into any problems, please email me at zwinzurk@asu.edu
Step 1: Install Anaconda
Go to https://www.anaconda.com/distribution/
Download Anaconda Python 3.7 version for the operating system you are using (Windows, MacOS, or Linux).
Click on 64-Bit Graphical Installer (442 MB) to download the version with a Graphical User Interface.
Why do I need Anaconda?
Torch Traps is a module written in Python (a programming language), so we first need to have Python installed on our computer. There are several ways to install python, but Anaconda allows us to install Python and it comes pre-installed with many of the common modules used for Data Science, and optionally comes with a GUI which can be used to open notebooks.
After download is complete, double-click to install and follow installation instructions.
Step 2: Open Anaconda Navigator
After installing Anaconda, open the Anaconda Navigator application on your computer.
Step 3: Launch Jupyter Lab
We will then launch a Jupyter Lab. Your web browser will open but the Jupyter server is running locally as you can see the url should be http://localhost:8889/lab
Step 4: Navigate to Working Folder on Left
By clicking on the folder icon in the upper-left corner we can navigate the file system.
Navigate to the directory on your computer where your camera trap image folder is located.
Step 5: Open Python3 Notebook
Now that we are working in the right directory, we can launch a new Python notebook. This will create a new file in our working directory called Untitled.ipynb. We can right-click on the file name to re-name it.
Step 6: Install Torch Traps
Jupyter notebooks allow us to run python code one 'cell' at a time. So the first thing we need to do is install torch traps, if we have not before. Copy the code below into the first cell, and then run the cell by either clicking the play button or hitting SHIFT+ENTER at the same.
!pip install torch traps
Step 7: Run Torch Traps on Folder of Images
Now that the Torch Traps is installed, you can copy the code below into a new code cell.
Change the 'path/to/image/folder' to the name of your folder containing camera trap images (ex. 'camera_trap_images')
Run the cell. (SHIFT + ENTER)
Note: If running for the first time, an internet connection will be required to download the model file.
When complete an output.csv file will appear in the directory you are working in. You can double-click csv files to view in Jupyter Lab or open with another application like Excel.
from torchtraps.lightning import kachow kachow('path/to/image/folder')
- Step 8: Open CSV File To See Classification Results
- Step 9: Parameters
- Step 10: View Images of Particular Class (Coming Soon)
This project is a part of an undergraduate capstone project in the Biomedical Informatics department at Arizona State University, and was advised by Dr. Jianming Liang
License: MIT