sand-atlas 1.3.1

A python package for processing 3d volumetric data to build meshes for the Sand Atlas data repository

Sand Atlas

Documentation here, or compile it yourself following the details below.

Installation

First, install ffmpeg and blender on your system. Both of these need to be available in your system path (so that running ffmpeg and blender in the command line works).

This package can then be installed via pip install sand-atlas. If installing from github, try cloning and then running:

pip install -e .

If you make any changes to the source code, re-run those two lines to have your changes reflected in your installed package.

Usage

Processing particles

If you are interested in reproducing a dataset that is available in the Sand Atlas, you can use the installed script sand_atlas_process, like so:

sand_atlas_process <path_to_json_file> --label <path_to_labelled_image> --raw <path_to_raw_image>

If you supply only the raw image, the script will attempt to label the image for you. If you supply the labelled image, the script will use that to generate the dataset. The json file contains the metadata for the dataset you are interested in. The json files for the datasets in the Sand Atlas are available here.

VDB files

VDB files are the industry standard for level set data. They can be viewed in recent versions of the open source software blender, via Add -> Volume -> Import OpenVDB. If you would like to use these files in a python environment that doesn't include the pyopenvdb package, you can use the vdb_to_npy script provided by the sand_atlas package to convert the VDB file to a numpy array:

vdb_to_npy <path_to_vdb_file>

This will produce a .npy file in the same directory where you run the script. You can then load this file in python with np.load:

import numpy as np
data = np.load('path_to_npy_file.npy')

Downloading particles from the python API

You can query the server to get a list of all of the available types of particles with

import sand_atlas
particles = sand_atlas.data.list()
print(particles)

If you would like to download all of the particles with a particular mesh quality to the current working directory, you do this via

import sand_atlas
sand_atlas.data.get_all('SAND-NAME', MESH-QUALITY)

If you would like to download a specific particle, you can do this via

import sand_atlas
sand_atlas.data.get_by_id('SAND-NAME', MESH-QUALITY, PARTICLE-ID)