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InferenceSystem

README.md

Working with the InferenceSystem

The InferenceSystem is an umbrella term for all the code used to stream audio from Orcasound's S3 buckets, perform inference on audio segments using the deep learning model and upload positive detections to Azure. The entrypoint for the InferenceSystem is src/LiveInferenceOrchestrator.py.

This document describes the following steps

  1. How to run the InferenceSystem locally.
  2. Deploying an updated docker build to Azure Container Instances.

Note: We use Python 3, specifically tested with Python 3.7.4

How to run the InferenceSystem locally

Create a virtual environment

  1. In your working directory, run python -m venv inference-venv. This creates a directory inference-venv with relevant files/scripts.

  2. On Mac or Linux, activate this environment with source inference-venv/bin/activate and when you're done, deactivate

    On Windows, activate with .\inference-venv\Scripts\activate.bat and .\inference-venv\Scripts\deactivate.bat when done

  3. In an active environment, cd to /InferenceSystem and run python -m pip install --upgrade pip && pip install -r requirements.txt

Model download

  1. Download the current production model from this link.
  2. Unzip *.zip and extract to InferenceSystem/model using unzip 11-15-20.FastAI.R1-12.zip
  3. Check the contents of InferenceSystem/model. There should be 1 file
    • model.pkl

Get connection string for interface with Azure Storage

To be able to upload detections to Azure, you will need a connection string.

Go to Azure portal and find the "LiveSRKWNotificationSystem" resource group. Within that go to the "livemlaudiospecstorage" storage account. Refer to this page to see how to get the connection string.

Windows

setx AZURE_STORAGE_CONNECTION_STRING "<yourconnectionstring>"

Mac or Linux

export AZURE_STORAGE_CONNECTION_STRING="<copied-connection-string>"

Get primary key for interface with CosmosDB

Go to the Azure portal

Go to the "LiveSRKWNotificationSystem" resource group and within that go to the "aifororcasmetadatastore" CosmosDB account.

Go to "Keys" and look up the primary key

Windows

setx AZURE_COSMOSDB_PRIMARY_KEY "<yourprimarykey>"

Mac or Linux

export AZURE_COSMOSDB_PRIMARY_KEY="<yourprimarykey>"

Get connection string for interface with App Insights

Go to the Azure portal

Go to the "LiveSRKWNotificationSystem" resource group and within that go to the "InferenceSystemInsights" App Insights service

Look up the connection key from 'Essentials'

Windows

setx INFERENCESYSTEM_APPINSIGHTS_CONNECTION_STRING "<yourconnectionstring>"

Mac or Linux

export INFERENCESYSTEM_APPINSIGHTS_CONNECTION_STRING="<yourconnectionstring>"

Run live inference locally

cd InferenceSystem
python src/LiveInferenceOrchestrator.py --config ./config/Test/FastAI_LiveHLS_OrcasoundLab.yml

You should see the following logs in your terminal. Since this is a Test config, no audio is uploaded to Azure and no metadata is written to CosmosDB.

Listening to location https://s3-us-west-2.amazonaws.com/audio-orcasound-net/rpi_orcasound_lab
Downloading live879.ts
live879.ts: 205kB [00:00, 1.17MB/s]                                             
Downloading live880.ts
live880.ts: 205kB [00:00, 1.11MB/s]                                             
Downloading live881.ts
live881.ts: 205kB [00:00, 948kB/s]                                              
Downloading live882.ts
live882.ts: 205kB [00:00, 1.14MB/s]                                             
Downloading live883.ts
live883.ts: 205kB [00:00, 1.07MB/s]                                             
Downloading live884.ts
live884.ts: 205kB [00:00, 1.04MB/s]                                             
rpi_orcasound_lab_2021_10_13_15_11_18_PDT.wav
Length of Audio Clip:60.010666666666665
Preprocessing: Downmixing to Mono
Preprocessing: Resampling to 200009/59 00:00<00:00]

Running inference system in a local docker container

To deploy to production we use Azure Container Instances. To enable deploying to production, you need to first build the docker image for the inference system locally.

Prerequisites

  • Docker: To complete this step, you need Docker installed locally. Docker provides packages that configure the Docker environment on macOS, Windows, and Linux.

  • model.zip: Download model from this link. Rename the *.zip to model.zip and place it in InferenceSystem/model.zip.

  • Environment Variable File: Create/get an environment variable file. This should be a file called inference-system/.env. This can be completed in two ways.

    1. Ask an existing contributor for their .env file.

    2. Create one of your own. This .env file should be created in the format below.

      <key> and <string> should be filled in with the Azure Storage Connection String and the Azure CosmosDB Primary Key above.

      AZURE_COSMOSDB_PRIMARY_KEY=<key>
AZURE_STORAGE_CONNECTION_STRING=<string>
INFERENCESYSTEM_APPINSIGHTS_CONNECTION_STRING=<string>

Adding a new hydrophone

  1. Create a new config file under the config folder

  2. Update the last line of the Dockerfile to point to the new config file

  3. Create a new deployment YAML under the deploy folder

  4. Update src/LiveInferenceOrchestrator.py and src/globals.py to add variables for the new hydrophone location

  5. Follow all other steps below until you update the kubernetes cluster with the new namespace

Building the docker container for production

From the InferenceSystem directory, run the following command. It will take a while (~2-3 minutes on macOS or Linux, ~10-20 minutes on Windows) the first time, but builds are cached, and it should take a much shorter time in future builds.

docker build . -t live-inference-system -f ./Dockerfile

Note: the config used in the Dockerfile is a Production config.

TODO: fix. For now, you will have to manually create a different docker container for each hydrophone location. Each time you will need to edit the Dockerfile and replace the config for each hydrophone location.

Running the docker container

From the InferenceSystem directory, run the following command.

docker run --rm -it --env-file .env live-inference-system

In addition, you should see something similar to the following in your console.

Listening to location https://s3-us-west-2.amazonaws.com/audio-orcasound-net/rpi_orcasound_lab
Downloading live879.ts
live879.ts: 205kB [00:00, 1.17MB/s]                                             
Downloading live880.ts
live880.ts: 205kB [00:00, 1.11MB/s]                                             
Downloading live881.ts
live881.ts: 205kB [00:00, 948kB/s]                                              
Downloading live882.ts
live882.ts: 205kB [00:00, 1.14MB/s]                                             
Downloading live883.ts
live883.ts: 205kB [00:00, 1.07MB/s]                                             
Downloading live884.ts
live884.ts: 205kB [00:00, 1.04MB/s]                                             
rpi_orcasound_lab_2021_10_13_15_11_18_PDT.wav
Length of Audio Clip:60.010666666666665
Preprocessing: Downmixing to Mono
Preprocessing: Resampling to 200009/59 00:00<00:00]

Pushing your image to Azure Container Registry

This step pushes your local container to the Azure Container Registry (ACR). If you would like more information, this documentation is adapted from this tutorial.

  1. Login to the shared azure directory from the Azure CLI.
az login --tenant adminorcasound.onmicrosoft.com
  1. We will be using the orcaconservancycr ACR in the LiveSRKWNotificationSystem Resource Group. Log in to the container registry.
az acr login --name orcaconservancycr

You should receive something similar to Login succeeded.

  1. Tag your docker container with the version number. We use the following versioning scheme.
docker tag live-inference-system orcaconservancycr.azurecr.io/live-inference-system:<date-of-deployment>.<model-type>.<Rounds-trained-on>.<hydrophone-location>.v<Major>

So, for example your command may look like

docker tag live-inference-system orcaconservancycr.azurecr.io/live-inference-system:11-15-20.FastAI.R1-12.OrcasoundLab.v0

Look at deploy-aci.yaml for examples of how previous models were tagged.

  1. Lastly, push your image to Azure Container Registry for each Orcasound Hydrophone Location.
docker push orcaconservancycr.azurecr.io/live-inference-system:<date-of-deployment>.<model-type>.<Rounds-trained-on>.<hydrophone-location>.v<Major>

Deploying an updated docker build to Azure Kubernetes Service

We are deploying one hydrophone per namespace. To deploy a hydrophone, the following Kubernetes resources need to be created:

  1. Namespace: used to group resources
  2. Secret: holds connection strings used by inference system
  3. Deployment: forces one instance of inference system to remain running at all times

Prerequisites

  • You must have completed all of the steps above and should have a working container image pushed to ACR.
  • az cli: installation instructions here
  • kubectl cli: if you don't have this, you can run az aks install-cli or install it using instructions here
  1. Log into az cli
az login
  1. Log into Kubernetes cluster. The current cluster is called inference-system-AKS in the LiveSRKWNotificationSystem resource group.
# replace "inference-system-AKS" with cluster name and "LiveSRKWNotificationSystem" with resource group
az aks get-credentials -g LiveSRKWNotificationSystem -n inference-system-AKS

Verify it is successful. You should see a list of VM names and no error message.

kubectl get nodes
  1. If deploying a new hydrophone, create a new namespace and secret. Skip this step if not bringing up a new hydrophone.
# replace "bush-point" with hydrophone identifier
kubectl create namespace bush-point

kubectl create secret generic inference-system -n bush-point \
    --from-literal=AZURE_COSMOSDB_PRIMARY_KEY='<cosmos_primary_key>' \
    --from-literal=AZURE_STORAGE_CONNECTION_STRING='<storage_connection_string>`' \
    --from-literal=INFERENCESYSTEM_APPINSIGHTS_CONNECTION_STRING='<appinsights_connection_string>'
  1. Create or update deployment. Use file for hydrophone under deploy folder, or create and commit a new one.
kubectl apply -f deploy/bush-point.yaml
  1. To verify that the container is running, check logs:
# get pod name
kubectl get pods -n bush-point

# replace pod name (likely will have different alphanumeric string at the end)
kubectl logs -n bush-point inference-system-6d4845c5bc-tfsbw
Deployment to Azure Container Instances (deprecated) # Deploying an updated docker build to Azure Container Instances # This method has been deprecated

Prerequisites

  • You must have completed all of the steps above and should have a container that is working locally that you wish to deploy live to production.

  • Azure CLI: You must have Azure CLI version 2.0.29 or later installed on your local computer. Run az --version to find the version. If you need to install or upgrade, see Install the Azure CLI.

Deploying your updated container to Azure Container Instances

Ask an existing maintainer for the file deploy-aci-with-creds.yaml or change strings in deploy-aci.yaml. There are three sensitive strings that must be filled in before deployment can happen.

NOTE - Make sure you change these back after running the build - don't commit them to the repository!

  1. <cosmos_primary_key> - Replace this with the AZURE_COSMOSDB_PRIMARY_KEY from your .env file (or found above).
  2. <storage_connection_string> - Replace this with the AZURE_STORAGE_CONNECTION_STRING from your .env file (or found above).
  3. <appinsights_connection_string> - Replace this with the INFERENCESYSTEM_APPINSIGHTS_CONNECTION_STRING from your .env file (or found above).
  4. <image_registry_password> - Replace this with the password for the orcaconservancycr container registry. It can be found at this link under the name password.

Then, run this command from the InferenceSystem directory. It will take a while to complete. Once complete, make sure to check your work below.

az container create -g LiveSRKWNotificationSystem -f .\deploy-aci.yaml

Checking your work

View the container logs with the following command. The logs should be similar to the logs created when you run the container locally (above).

az container attach --resource-group LiveSRKWNotificationSystem --name live-inference-system-aci-3gb-new

No changes made to deploy-aci.yaml?

I purposefully told git to ignore all futher changes to the file with this command: git update-index --assume-unchanged deploy-aci.yaml. This is to prevent people from checking in their credentials into the repository. If you want a change to be tracked, you can turn off this feature with git update-index --no-assume-unchanged deploy-aci.yaml

Running the automatic annotation data upload script PrepareDataForPredictionExplorer.py

This script processes audio from a segment of data and uploads it to the annotation website https://aifororcas-podcast.azurewebsites.net/.

To run the script, find the connection string for blob storage account "mldevdatastorage" and run the following

Windows

setx PODCAST_AZURE_STORAGE_CONNECTION_STRING "<yourconnectionstring>"

Mac or Linux

export PODCAST_AZURE_STORAGE_CONNECTION_STRING="<copied-connection-string>"

Call the script as follows, substituting appropriate values.

python PrepareDataForPredictionExplorer.py --start_time "2020-07-25 19:15" --end_time "2020-07-25 20:15" --s3_stream https://s3-us-west-2.amazonaws.com/audio-orcasound-net/rpi_orcasound_lab --model_path <folder> --annotation_threshold 0.4 --round_id round5 --dataset_folder <path-to-folder>