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Add additional edges in Dijkstra initialization round #23

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Add additional edges in Dijkstra initialization round #23

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dbbfc6b
Add neighbour edges close to src
fdsteffen Apr 16, 2019
0ad0d49
Add comment for stable sorting in neighbourEdges
fdsteffen Dec 20, 2019
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12 changes: 8 additions & 4 deletions FlexLabel/src/FlexLabel.cxx
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Original file line number Diff line number Diff line change
Expand Up @@ -92,7 +92,7 @@ class Grid3DExt final : public Grid3D
void fillOutsideSphere(const Eigen::Vector4f &xyzR,
const float gridRef);

void setPathLengths(const Eigen::Vector3f &source);
void setPathLengths(const Eigen::Vector3f &source, const float linkerDiameterPlusgridSize);

void setAboveThreshold(const float threshold, const float rho);

Expand Down Expand Up @@ -217,6 +217,8 @@ std::vector<Grid3DExt::edge_t> Grid3DExt::neighbourEdges(const float maxR) const
}
}
idxs.shrink_to_fit();
// change sort to stable_sort to preserve order of equivalent distances (for debugging)
// std::stable_sort(idxs.begin(), idxs.end(),
std::sort(idxs.begin(), idxs.end(),
[](const edge_t &lhs, const edge_t &rhs) {
return lhs.r < rhs.r;
Expand Down Expand Up @@ -392,7 +394,7 @@ void Grid3DExt::fillOutsideSphere(const Eigen::Vector4f &xyzR,
}
}

void Grid3DExt::setPathLengths(const Eigen::Vector3f &source)
void Grid3DExt::setPathLengths(const Eigen::Vector3f &source, const float linkerDiameterPlusgridSize)
{
// perform dijkstra algorithm
// the grid must be padded, i.e. N outermost layers of edges must be set
Expand All @@ -401,7 +403,8 @@ void Grid3DExt::setPathLengths(const Eigen::Vector3f &source)
using Eigen::Array4i;
using Eigen::Vector4f;
using std::vector;
const vector<edge1D_t> &edges = toEdges1D(essentialNeighbours());
const vector<edge1D_t> &edges_ess = toEdges1D(essentialNeighbours());
const vector<edge1D_t> &edges_source = toEdges1D(neighbourEdges(linkerDiameterPlusgridSize));
const Array4i ijk0 = getIjk(Vec4f(source));
const int i0 = index1D(ijk0[0], ijk0[1], ijk0[2]);
grid[i0] = 0.0f;
Expand All @@ -417,6 +420,7 @@ void Grid3DExt::setPathLengths(const Eigen::Vector3f &source)
if (qt.r > grid[qt.idx])
continue;
edge1D_t t;
const vector<edge1D_t> &edges = (qt.idx == i0) ? edges_source : edges_ess;
for (const edge1D_t &e : edges) {
t.idx = qt.idx + e.idx;
const float &val = grid[t.idx];
Expand Down Expand Up @@ -447,7 +451,7 @@ Grid3DExt minLinkerLength(const Eigen::Matrix4Xf &atomsXyzr,
Grid3DExt grid =
Grid3DExt::fromSource(sourceXyz, discStep, linkerLength, 0.0f);
grid.fillSpheres(atomsXyzr, linkerDiameter * 0.5f, -1.0f);
grid.setPathLengths(sourceXyz);
grid.setPathLengths(sourceXyz, linkerDiameter + discStep);
return grid;
}

Expand Down