3D visualization of a Microscale Microbial Ecology Model

This repository contains scripts to produce a 3D visualization of a Microscale Microbial Ecology Model in Blender.

Producing a Movie

The video below is a tutorial on how to create a movie using the scripts.

bachelor-thesis-tutorial-1.mp4

The scripts need to be run in Blender. They have to be copied to Blender's scripts tab. The dataset needs to be placed into the data folder. An example dataset can be found under data/example. All scripts have to be run with the DATA_LOCATION environment variable set to the data folder location. From a bash shell you can simply run DATA_LOCATION=/path/to/data/folder blender

Updating the thresholds for coloring regions with increased DOM

For different datasets the distribution of DOM concentrations will vary and so the thresholds for coloring regions with increased DOM concentrations need to be adjusted. The video below is a tutorial on how to adjust these thresholds.

bachelor-thesis-tutorial-2.mp4

Overview of the Scripts

Blender settings

The script blender-settings.py is used to change a few render settings in Blender and remove unused objects.

Csv to OpenVDB

The script src/grid/csv-to-openvdb.py is used to transform the grid data to the openVDB data format.

Import OpenVDB

The script src/grid/import-openvdb.py is used to import the openVDB data into Blender.

Create Particles

The script src/particles/create-particles.py is used to create spheres in Blender representing the particles in the dataset.

Update Particles

The script src/particles/update-particles.py is used to update the particles position and color in each timestep.

Camera Scripts

The scripts in src/camera/ are used to update the camera type and location of the scene.

Shell Scripts

The scripts in src/scripts/ are basic shellscripts to convert the output format from the model to the format required by the scripts.