Skip to content

Add additional edges in Dijkstra initialization round #23

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 2 commits into
base: master
Choose a base branch
from
+8 −4
Open

Add additional edges in Dijkstra initialization round #23

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
dbbfc6b
Add neighbour edges close to src
fdsteffen Apr 16, 2019
0ad0d49
Add comment for stable sorting in neighbourEdges
fdsteffen Dec 20, 2019
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 8 additions & 4 deletions FlexLabel/src/FlexLabel.cxx
View file
Original file line number Diff line number Diff line change
@@ -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);

@@ -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;
@@ -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
@@ -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;
@@ -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];
@@ -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;
}