YTEP-0009: AMRKDTree for Data Sources


Created: February 28, 2012 Author: Sam Skillman

This proposal outlines the changes (functional and API) necessary for the ability to render volumes using arbitrary data sources. This will still operate with the idea of grids and masks. However, this should lead as a stepping stone to non-grid-based rendering.


Status should be one of the following:

  1. Implemented in yt-3.0 PR77

YTEPs do not need to pass through every stage.

Detailed Description

Functional Background:

The volume rendering has long operated on either the entire domain or (at best) a sub-rectangular-prism using left and right edges. This is fairly limiting in that a user may not need (or want) to render the entire volume, and may want to restrict the volume shown by something other than a single box. A majority of the reasoning behind the recent AMRKDTree was to allow for more generic adding of grids/data to the homogenized volume.

The primary problem with attempting to do this is that the volume rendering acts on a rectangular brick of data, and the traversal of this brick is fairly far removed from a AMR3DData object. Therefore, we either need to modify the traversal, or somehow mask out the data being handed to the traversal.

The latter approach can be accomplished using the following code:

def _source_mask(field, data):
    return 1.0*self.source._get_cut_mask(data)'source_mask', function=_source_mask, take_log=False)

then when creating the vertex centered data:

mask = grid.get_vertex_centered_data('source_mask',smoothed=False,no_ghost=self.no_ghost).astype('float64')
mask = np.clip(mask, 0.0, 1.0)
mask[mask<1.0] = np.inf
for i,field in enumerate(self.fields):
    vcd = grid.get_vertex_centered_data(field,smoothed=True,no_ghost=self.no_ghost).astype('float64')
    vcd = vcd*mask

However, this approach is full of quirks since what we really want is to mask out an entire cell, and not some set of vertices. Therefore, we propose to modify the PartitionedGrid object to include an integer mask that is used during traversal to mask out the individual cells.

API Background:

The method for specifying a data source in a volume rendering has not been suggested. Currently, the rectangular volume that is used for rendering uses a le and re pair of keywords to specify the left and right edges. When moving to a data source, we should simplify the volume selection by simply supplying a data_source= keyword.

Changes to the Camera interfaces suggested in YTEP-0010 will handle the move to using a data_source.

In my working solution, I have set the AMRKDTree __init__ function to have the following form:

class AMRKDTree(ParallelAnalysisInterface)
    def __init__(self, pf, min_level=None, max_level=None, data_source=None):

Backwards Compatibility

This YTEP breaks the following backwards compatibility:


It will additionally break internal uses of the API for the Camera, other cameras inheriting the __init__ of Camera, and the AMRKDTree.


  • Do nothing
  • Add more keyword arguments to everything
  • Wait until rendering is ready in yt-3.0, which will also likely demand a breakage of API.

After discussion, it was found to be easiest to only implement in yt-3.0, as it is increasingly difficult to manage the two versions and how they handle grids. Since in yt-3.0 there are explicit mask objects in the pf.h.blocks generator, it was significantly easier than expected to implement the mask on the PartitionedGrid object. I’m also hopeful that this simplification is along the same lines of the idea of a simplified volume rendering scene object, as outlined in YTEP-0010.