Heatmap Generation

This guide will walk you through setting up your environment, creating heatmaps with QGIS and Python, and visualizing data from our sorghum research field trials. These instructions are designed to be accessible for high school students and will help you explore geospatial data and its applications.

Setting Up Your Project

Download Project Files

• Before you begin, download the project files located here: Project Files.
• Create a folder in a location you’ll remember and place all downloaded files, including the Shapefile folder (plot_boundaries files), in it.

Install Required Software

Install QGIS

• Visit the QGIS Download Page (if you have not done already).
• Choose the Long Term Release (3.34 LTR) version.
• Select your operating system (Windows, macOS, or Linux) and follow the installation instructions.

Install Miniconda

• Visit the Miniconda Installation Page (if you have not done already).
• Choose the version for your operating system (Windows or macOS/Linux) and follow the instructions.

Set Up Python and Dependencies

Create a Working Project Directory

1. Windows Users:

   • Create a new folder and place the env_setup.yml file in it.

   You should know!

   Remember, this file was downloaded from the google drive folder previously provided to you here: Project Files.

   • Create a new folder and place the env_setup.yml file in it.
   • Open the Anaconda command line application (Anaconda PowerShell).
   • Navigate to the folder containing env_setup.yml:

     cd C:\Path\To\Folder\Containing\YML\
     

2. Mac/Linux Users:

   • Create a new folder and place the env_setup.yml file in it.
   • Open a terminal application (e.g., iTerm or Terminal).
   • Navigate to the folder containing env_setup.yml:

     cd \Path\To\Folder\Containing\YML\
     

Activating your environment

Create and Activate Environment

1. While in the same directory (folder) of your env_setup.yml file, run the following command to create the environment:

   conda env create -f env_setup.yml
   

2. When the installation completes:

   • Verify the environment was created:

     conda env list
     

   • Activate the environment:

     conda activate geo_ml_env
     

   • View your environment's packages (that were installed using the env_setup.yml file):

     conda list
     

Install and Setup VS Code

1. Visit the Visual Studio Code webpage (if you have not done so already).

2. Download the installer provided for your Operating System (Mac/Windows).

3. After installing, launch VS Code.

4. In your newly opened Visual Studio code window, navigate to the Extensions tab (View -> Extensions).

5. Search for and install the following extensions:

   'Python'
   'Jupyter'
   

6. You should now have the following in your Extensions list under Installed:

   'Jupyter Slide Show'
   'Jupyter Notebook Renderers'
   'Jupyter Keymap'
   'Jupyter Cell Tags'
   'Jupyter'
   'Python Debugger'
   'Python'
   'Pylance'
   

   You should know!

   Navigating Visual Studio code for the first time can be tricky! If you need help with shortcuts, visit their documentation page, or visit their Getting Started page.

Making the Heatmap

Heatmap creation

Generate a Heatmap Using PyQGIS

1. Within VS Code, select File -> Open Folder and navigate to your project folder created at the beginning of the instructions. Highlight the folder and click Open.

2. Double-click the are_pyqgis.ipynb Python Notebook file in the VS Code Explorer on the left-hand side. If you do not see the Explorer, go to View -> Explorer.

3. At top right, click Select Kernel -> Python Environments -> geo_ml_env.

4. You will now want to provide for the string constants:

   • CSV_IN: Path to the field_sensor_data.csv file.
   • SHP_IN: Path to the plot_boundaries.shp file. Ensure this file is in the same folder as the other plot_boundaries files (this is very important!).
   • PROJECT_OUT: Output the path and filename for the generated QGIS project file (e.g., /path/to/your/qgis_heatmap.qgs), making sure to include the .qgs extension on the filename.

   Important!

   You can right-click a file in the Explorer tab and choose Copy Path to get its file path, to use in the above step. Paste this into the quotes for each.

   Example:

   CSV_IN = r"<paste_path_here>.
   

   If your file path is C:\Code\field_sensor_data.csv then your assignment will look like::

   CSV_IN = r"C:\Code\field_sensor_data.csv"`
   

5. Provide the column/data name (label_name string) for the data you wish to view as a heatmap.

6. Run each cell (by pressing the shift + enter keys, or pressing the play button at the top of the editor).

Troubleshooting tips

1. If any files are not found, check your paths and try again. Use absolute paths if necessary.

2. If the kernel crashes, hit Restart and run again.

Heatmap View

View Heatmap in QGIS

1. Launch QGIS and select Project → Open to load your .qgs file.

2. Add the Google Satellite layer:

   • Right-click XYZ Tiles in the browser pane (on the left) and select New Connection.
   • Enter the following details:
     • Name: Google Satellite
     • URL: http://mt0.google.com/vt/lyrs=s&hl=en&x={x}&y={y}&z={z}
   • Click OK.

3. Drag and drop the newly created Google Satellite entry under XYZ Tiles into your Layers list.

4. Arrange the layers so that the Google Satellite layer is at the bottom.