public class MeshSubstrate extends Substrate
a, border, factor, intersectsBoundary, spatialOptInitialised, voxToObjects
Constructor and Description |
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MeshSubstrate(SimulationParams simParams)
read a substrate from the named PLY file and scale it to the
specified length.
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Modifier and Type | Method and Description |
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boolean |
crossesMembrane(Walker walker,
double[] offset,
double[] stepVector,
double[] normal,
double[] d,
boolean skipCurrent,
double origLength,
boolean[] in,
double[] p)
checks if a step will cross a barrier or not
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double |
getPeakCoord()
return peak coord, used as the ncentre of the object
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double[] |
getSubstrateSize()
returns the size of the unit cell
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void |
init()
not used, does nothing.
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boolean |
intracellular(Walker walker)
performs the ray test to check if a point is inside the
object or not.
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static void |
main(java.lang.String[] args)
test ply substrate reading and intra cellular routine
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boolean |
voxelContains(double[] pos)
check is a given walker is in the voxel.
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amend, getBottomLeft, getDiffusivityAt, getLogMagnetisationChange, getN, getSubsObj, getSubstrateCoords, getSubVoxelIndex, getUpperRight, initBoundaryIntersectionArrays, initCandidates, initialiseSpatialOptimisation, mapStepIntoSubstrate, moreCandidates, nextCandidate, testAmendment, testStepAmendment, unmapStepFromSubstrate
public MeshSubstrate(SimulationParams simParams)
fname
- name of PLY file to readscale
- length to scale object topublic boolean crossesMembrane(Walker walker, double[] offset, double[] stepVector, double[] normal, double[] d, boolean skipCurrent, double origLength, boolean[] in, double[] p)
Substrate
crossesMembrane
in class Substrate
walker
- the walkerstepVector
- the step vectornormal
- container for the normalskipCurrent
- flag saying whether
to ignore the current
normal and distance
or notpublic double getPeakCoord()
getPeakCoord
in class Substrate
public double[] getSubstrateSize()
getSubstrateSize
in class Substrate
public boolean intracellular(Walker walker)
intracellular
in class Substrate
walker
- the walker whose position to test.public boolean voxelContains(double[] pos)
voxelContains
in class Substrate
pos
- walker pos in global coordspublic static void main(java.lang.String[] args)
args
-