Animl ML

Machine Learning resources for camera trap data processing

Note

This needs updating

Intro

We are using AWS Sagemaker to host our model endpoints. The initial models we will run inference on are Microsoft's Megadetector, a model to detect animals, people, and vehicles in camera trap images, and MIRA, a pair of species classifiers trained on labeled images from Santa Cruz Island.

This repo contains:

• Python Notebooks to facilitate loading and deploying models as endpoints on AWS Sagemaker
• Resources for running & debugging model endpoints locally
• A Serverless API for submitting images & bounding boxes to the MIRA endpoints for real-time inference
• A notebook with code examples for invoking the APIs and testing the inference pipeline end-to-end

Test the inference pipeline - TODO, update for new pipeline.

The most fun place to start is the notebooks/test-inference-pipeline.ipynb. Fire it up and step though the notebook to test submitting images to the Megadetector API for object detection and then to MIRA API for species classification.

Deploy a model endpoint using AWS Sagemaker Notebook

When you deploy model endpoints to Sagemaker, AWS starts an EC2 instance and starts a docker container with in it optimized for serving particular model's architecture. You can find Python Notebooks to facilitate the deployment of models in the notebooks/ directory of this repo.

To deploy a model endpoint, start up a Sagemaker notebook instance in AWS, associate this repo with it, and step through one of the deployment notebooks in the notebooks/ directory to get started.

Local endpoint development and debugging

If you want to launch a TensorFlow serving container locally to debug and test endpoints on your computer before deploying, this repo contains a script to clone AWS's Sagemaker TensorFlow Serving Container repo and Microsoft's CameraTraps repo and instructions below to help you run the container, load models, dependencies, and pre/postprocessing scripts into it, and submit requests to the local endpoints for inference.

NOTE: be sure that you have the following installed:

• aws-vault
• docker
• virtualenv

1. Clone the repo and set up the virtual env

$ mkdir animl-ml
$ git clone https://github.com/tnc-ca-geo/animl-ml.git
$ virtualenv env -p python3
$ source env/bin/activate
$ cd animl-ml
$ pip3 install -r requirements.txt

2. Get the CameraTrap and Sagemaker container repos

After cloning this repo, from the animl-ml/animl-ml/ project directory, run the script to clone the necessary external repos:

$ bash ./scripts/get-libs.sh

3. Get the MIRA models

The MIRA models we use in this app are available in Tensorflow ProtoBuf format at s3://animl-model-zoo. To download and unzip them, run the following from the same animl-ml project directory:

$ aws-vault exec <vault_profile> -- bash ./scripts/get-models.sh

NOTE: If you're on a mac, make sure there aren't any stray .DS_store files in animl-ml/models/. The sagemaker-tensorflow-serving-container build scripts will mistake them for models and try to load them into the container. A quick way to recursively remove all .DS_store files is to cd to the animl-ml/models/ directory and run:

$ find . -name '*.DS_Store' -type f -delete

4. Building the container

And finally, to build the docker container in which the model will be run locally, execute:

$ aws-vault exec <vault_profile> -- bash ./scripts/build-container.sh

5. Running the container

To run the container, run the start-container.sh script

$ aws-vault exec <vault_profile> -- bash ./scripts/start-container.sh

Check that it was successful and the container is running with:

$ docker ps

Alternatively, you can also start the container in interactive mode with:

$ aws-vault exec <vault_profile> -- bash ./scripts/start-container-interactive.sh

To stop the container, run:

$ aws-vault exec <vault_profile> -- bash ./scripts/stop-container.sh

All output from the container will be piped into log.txt.

6. Run inference on the local endpoint

To test the endpoint, pass the make-request.py script a path to an local image file:

$ aws-vault exec <vault_profile> -- python ./scripts/make-request.py input/sample-img.jpg

Megadetector V5a endpoint

See [api/megadetectorv5/README.md] for instructions on setting up a local endpoint and deploying a serverless endpoint of the new Megadetector v5 model. Instructions above are based on the old Megadetector v4 model written in Tensorflow and need to be updated.

Related repos

Animl is comprised of a number of microservices, most of which are managed in their own repositories.

Core services

Services necessary to run Animl:

• Animl Ingest
• Animl API
• Animl Frontend
• EXIF API

Wireless camera services

Services related to ingesting and processing wireless camera trap data:

• Animl Base
• Animl Email Relay
• Animl Ingest API

Misc. services

• Animl ML
• Animl Analytics