BoundaryPixelTracker plugin keeps a list of boundary pixels for each cell. The
syntax is as follows:
<Plugin Name="BoundaryPixelTracker"> <NeighborOrder>1</NeighborOrder> </Plugin>
This plugin is also used by other plugins as a helper module. Examples use of this plugin is found in Demos/PluginDemos/BoundaryPixelTracker_xxx.
GlobalBoundaryPixelTracker plugin tracks boundary pixels of all
the cells including
Medium. It is used in a
Boundary Walker algorithm
where instead of blindly picking pixel copy candidate we pick it from the set of pixels comprising
boundaries of non frozen cells. In situations when lattice is large and
there are not that many cells it makes sense to use
algorithm to limit number of pixel picks that would not lead to actual pixel copy.
BoundaryWalkerAlgorithm does not really work with OpenMP
version of CC3D which includes all versions starting with
Take a look at the following example:
<Potts> <Dimensions x="100" y="100" z="1"/> <Anneal>10</Anneal> <Steps>10000</Steps> <Temperature>5</Temperature> <Flip2DimRatio>1</Flip2DimRatio> <NeighborOrder>2</NeighborOrder> <MetropolisAlgorithm>BoundaryWalker</MetropolisAlgorithm> <Boundary_x>Periodic</Boundary_x> </Potts> <Plugin Name="GlobalBoundaryPixelTracker"> <NeighborOrder>2</NeighborOrder> </Plugin>
Here we are using
BoundaryWalker algorithm (
Potts section) and
subsequently we list
GlobalBoundaryTracker plugin where we set neighbor
order to match that in the Potts section. The neighbor order determines
how “thick” the overall boundary of cells will be. The higher this
number the more pixels will belong to the boundary.
PixelTracker plugin allows storing list of all pixels belonging to a given cell.
The syntax is as follows:
<Plugin Name="PixelTracker"> <TrackMedium/> </Plugin>
This plugin is also used by other modules (e.g.
Mitosis) as a helper
module. Simple example can be found in Demos/PluginDemos/PixelTrackerExample.
4.1.2, medium pixels can be optionally tracked using
This feature is automatically enabled by attaching a Fluctuation Compensator to a