gesengi / landcover

Land Cover Mapping

Land Cover Mapping Tool

This repository holds both the "frontend" web-application and "backend" web API server that make up our "Land Cover Mapping" tool. An instance of this tool may be live, here.

Setup

Azure VM setup instructions

We develop / use the tool on Data Science Virtual Machines for Linux (Ubuntu) images on Azure (see the Azure Portal), so these setup instructions are tailored for that environment, however there is no reason that this project cannot be run on any machine (see "Local setup instructions below").

Initial machine setup

• Create a new VM with the Data Science Virtual Machine for Linux (Ubuntu) image via the Azure Portal
• Open the incoming ports 4040 and 4444 to the VM through the Azure Portal (these ports will be used by the web tool)
• SSH into the VM using a desktop SSH client
• Run the following commands to install the additional necessary Python packages:

sudo apt-get update
sudo apt-get install blobfuse
conda activate py35
conda install rasterio fiona shapely rtree
pip install --user --upgrade bottle mercantile rasterio
conda deactivate

• Log out and log back in
• Visit the Microsoft AI for Earth Azure storage account (your account will need to be given access first)
  • Download the web-tool/mount_remotes_for_deployment.sh and web-tool/web_tool_data_install.sh scripts to the home directory
  • Run the mount_remotes_for_deployment.sh script to mount the necessary blob storage containers (note: you will need to run this script every time you restart the VM)

Repository setup instructions

• SSH into the VM using a desktop SSH client
• git clone [e-mail]:microsoft/landcover.git (clone this repository)
• mv web_tool_data_install.sh landcover/
• cd landcover
• Edit web_tool_data_install.sh as appropriate. This script will copy the necessary data files from the web-tool-data blob container to the project directory, however you probably don't need all the data in web-tool-data/web_tool/tiles/ as these files can be large and are project instance specific.
• ./web_tool_data_install.sh
• rm web_tool_data_install.sh (to keep the project directory clean!)
• Edit web_tool/endpoints.mine.js and replace "msrcalebubuntu.eastus.cloudapp.azure.com" with the address of your VM (find/change your VM's host name or IP address in the Azure portal).

Local setup instructions

The following instructions serve to get a working instance of the web tool running, and were tested on August 1st, 2019 on a vanilla Azure Ubuntu 18.04 LTS Server image. You will probably need to modify these as appropriate (e.g. if you have a GPU you will need to install different packages/drivers).

# Install Anaconda
cd ~
wget https://repo.anaconda.com/archive/Anaconda3-2019.07-Linux-x86_64.sh
bash Anaconda3-2019.07-Linux-x86_64.sh
rm Anaconda3-2019.07-Linux-x86_64.sh

## logout and log back in
exit

# Install unzip and a library that opencv will need
sudo apt update
sudo apt install -y unzip libgl1

# Create a new conda environment for running the web tool
## setting strict channel_priority seems to be a very important step - else all the gdal dependencies are very broken
conda config --set channel_priority strict
conda create -y -n ai4e python=3.6
## make sure `which python` points to the python installation in our new environment
conda deactivate
conda activate ai4e
conda install -y -c conda-forge keras gdal rasterio fiona shapely scikit-learn matplotlib utm mercantile bottle opencv rtree
## the Azure packages are the only ones that don't want to play nice with others
pip install azure


# Get the project and demo project data
git clone https://github.com/microsoft/landcover.git

wget -O landcover.zip "https://www.dropbox.com/s/pb3ucdka4zffpkk/landcover.zip?dl=1"
unzip landcover.zip
rm landcover.zip

# Finally, setup and run the server using the demo model
cd landcover
export PYTHONPATH=.
git checkout dev
cp web_tool/endpoints.js web_tool/endpoints.mine.js
## Edit `web_tool/endpoints.mine.js` and replace "msrcalebubuntu.eastus.cloudapp.azure.com" with the address of your machine
nano web_tool/endpoints.mine.js
python web_tool/server.py --model nips_hr --model_fn web_tool/data/demo_model --fine_tune last_layer --port 4444

Running an instance of the tool

Whether you setup the server in an Azure VM or locally, the following steps should apply to start an instance of the server:

• Open a terminal on the machine that you setup (e.g. SSH into the VM using a desktop SSH client)
• cd landcover
• python web_tool/server.py --model nips_sr --model_fn <path/to/model.h5> --fine_tune last_layer
  • This will start an HTTP server on :4444 that both serves the "frontend" web application and responds to API calls from the "frontend", allowing the web-app to interface with our CNN models (i.e. the "backend").
• You should now be able to visit http://<your machine's address>:4444/index.html and see the "frontend" interface.

Design Overview

• "Frontend"
  • index.html, endpoints.js
  • Whenever an user clicks somewhere on the map, the app will query each server defined in endpoints.js and show the results overlayed on the map.
  • Upon new installation, copy endpoints.js to endpoints.mine.js. This copy allows customizing the back-end server to use, and will be ignored by Git.
  • When changing the host-name and port number, the URL must end with / (eg. http://msrcalebubuntu.eastus.cloudapp.azure.com:4444/).
• "Backend"
  • Consists of server.py, ServerModels*.py, DataLoader.py
  • server.py starts a bottle server to serve the frontend web application and API
    • Can be provided a port via command line argument, must be provided a "model" to serve via command line argument.
    • The "model" that is provided via the command line argument corresponds to one of the ServerModels*.py files. Currently this interface is just an ugly hack.
  • DataLoader.py contains all the code for finding the data assosciated with a given spatial query.

API

The "backend" server provides the following API:

POST /predPatch

Input example:

{
    "extent": { // definition of bounding box to run model on
        "xmax": bottomright.x,
        "xmin": topleft.x,
        "ymax": topleft.y,
        "ymin": bottomright.y,
        "spatialReference": {
            "latestWkid": 3857 // CRS of the coordinates
        }
    },
    "weights": [0.25, 0.25, 0.25, 0.25], // reweighting of the softmax outputs, there should be one number (per class)
}

Output example:

{
    "extent": ..., // copied from input
    "weights": ..., // copied from input
    "model_name": "Full-US-prerun", // name of the model being served
    "input_naip": "..." // base64 encoding of input NAIP imagery used to generate the model output, as PNG
    "output_hard": "..." // base64 encoding of hard class estimates, also as PNG
    "output_soft": "..." // base64 encoding of soft class estimates, see `utils.class_prediction_to_img()` for how image is generated

}

POST /getInput

Input example:

{
    "extent": { // definition of bounding box to run model on
        "xmax": bottomright.x,
        "xmin": topleft.x,
        "ymax": topleft.y,
        "ymin": bottomright.y,
        "spatialReference": {
            "latestWkid": 3857 // CRS of the coordinates
        }
    },
}

Output example:

{
    "extent": ..., // copied from input
    "input_naip": "..." // base64 encoding of input NAIP imagery used to webpagegenerate the model output, as PNG
}

TODO

• Update "Design Overview" section
• Add a tutorial for using the tool
• Update the "API" section
• Explain how different datasets work
• Write section detailing the user study implementation