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fix-indexing-issue
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Signed-off-by: Perminder <[email protected]>
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@perminder-17
perminder-17 committed Nov 12, 2024
1 parent 6afb548 commit ca76e51
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Showing 2 changed files with 62 additions and 85 deletions.
115 changes: 51 additions & 64 deletions avogadro/core/cube.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -24,27 +24,23 @@ Cube::~Cube()
m_lock = nullptr;
}

std::vector<float>::const_iterator Cube::getRowIter(int j, int k) const
{
return m_data.cbegin() + m_points.x() * (k * m_points.y() + j);
}
// std::vector<float>::const_iterator Cube::getRowIter(int j, int k) const
// {
// return m_data.cbegin() + m_points.z() * k * m_points.y() + m_points.z() * j;
// }


bool Cube::setLimits(const Vector3& min_, const Vector3& max_,
const Vector3i& points)
{
// Calculate the maximum dimension
int maxPoints = std::max({points.x(), points.y(), points.z()});
Vector3i equalPoints(maxPoints, maxPoints, maxPoints);

// Recalculate spacing based on equal points
// We can calculate all necessary properties and initialise our data
Vector3 delta = max_ - min_;
m_spacing = Vector3(delta.x() / (equalPoints.x() - 1),
delta.y() / (equalPoints.y() - 1),
delta.z() / (equalPoints.z() - 1));
m_spacing =
Vector3(delta.x() / (points.x() - 1), delta.y() / (points.y() - 1),
delta.z() / (points.z() - 1));
m_min = min_;
m_max = max_;
m_points = equalPoints;
m_points = points;
m_data.resize(m_points.x() * m_points.y() * m_points.z());
return true;
}
Expand Down Expand Up @@ -205,69 +201,58 @@ float Cube::value(int i, int j, int k) const
else
return 0.0;
}

std::array<float, 3> Cube::computeGradient(int i, int j, int k) const
{
int nx = m_points.x();
int ny = m_points.y();
int nz = m_points.z();
int dataIdx = (i * ny * nz) + (j * nz) + k;

std::array<std::array<float, 2>, 3> x;
std::array<float, 3> run;

int dataIdx = i + (j * m_points.x()) + (k * m_points.x() * m_points.y());

// std::cout << m_spacing[0];
if (i == 0)
{
x[0][0] = m_data[dataIdx + 1];
x[0][1] = m_data[dataIdx];
// X-direction
if (i == 0) {
x[0][0] = m_data[dataIdx + ny * nz]; // (i+1, j, k)
x[0][1] = m_data[dataIdx]; // (i, j, k)
run[0] = m_spacing.x();
}
else if (i == (m_points.x() - 1))
{
x[0][0] = m_data[dataIdx];
x[0][1] = m_data[dataIdx - 1];
} else if (i == (nx - 1)) {
x[0][0] = m_data[dataIdx]; // (i, j, k)
x[0][1] = m_data[dataIdx - ny * nz]; // (i-1, j, k)
run[0] = m_spacing.x();
}
else
{
x[0][0] = m_data[dataIdx + 1];
x[0][1] = m_data[dataIdx - 1];
} else {
x[0][0] = m_data[dataIdx + ny * nz]; // (i+1, j, k)
x[0][1] = m_data[dataIdx - ny * nz]; // (i-1, j, k)
run[0] = 2 * m_spacing.x();
}

if (j == 0)
{
x[1][0] = m_data[dataIdx + m_points.x()];
x[1][1] = m_data[dataIdx];
// Y-direction
if (j == 0) {
x[1][0] = m_data[dataIdx + nz]; // (i, j+1, k)
x[1][1] = m_data[dataIdx]; // (i, j, k)
run[1] = m_spacing.y();
}
else if (j == (m_points.y() - 1))
{
x[1][0] = m_data[dataIdx];
x[1][1] = m_data[dataIdx - m_points.x()];
} else if (j == (ny - 1)) {
x[1][0] = m_data[dataIdx]; // (i, j, k)
x[1][1] = m_data[dataIdx - nz]; // (i, j-1, k)
run[1] = m_spacing.y();
}
else
{
x[1][0] = m_data[dataIdx + m_points.x()];
x[1][1] = m_data[dataIdx - m_points.x()];
} else {
x[1][0] = m_data[dataIdx + nz]; // (i, j+1, k)
x[1][1] = m_data[dataIdx - nz]; // (i, j-1, k)
run[1] = 2 * m_spacing.y();
}

if (k == 0)
{
x[2][0] = m_data[dataIdx + (m_points.x() * m_points.y())];
x[2][1] = m_data[dataIdx];
// Z-direction
if (k == 0) {
x[2][0] = m_data[dataIdx + 1]; // (i, j, k+1)
x[2][1] = m_data[dataIdx]; // (i, j, k)
run[2] = m_spacing.z();
}
else if (k == (m_points.z() - 1))
{
x[2][0] = m_data[dataIdx];
x[2][1] = m_data[dataIdx - (m_points.x() * m_points.y())];
} else if (k == (nz - 1)) {
x[2][0] = m_data[dataIdx]; // (i, j, k)
x[2][1] = m_data[dataIdx - 1]; // (i, j, k-1)
run[2] = m_spacing.z();
}
else
{
x[2][0] = m_data[dataIdx + (m_points.x() * m_points.y())];
x[2][1] = m_data[dataIdx - (m_points.x() * m_points.y())];
} else {
x[2][0] = m_data[dataIdx + 1]; // (i, j, k+1)
x[2][1] = m_data[dataIdx - 1]; // (i, j, k-1)
run[2] = 2 * m_spacing.z();
}

Expand Down Expand Up @@ -314,10 +299,12 @@ std::array<float, 8> Cube::getValsCube(int i, int j, int k) const
}


inline float
Cube::getData(int i, int j, int k) const
inline float Cube::getData(int i, int j, int k) const
{
return m_data[(k * m_points.x() * m_points.y()) + (j * m_points.x()) + i];
int nx = m_points.x();

Check notice on line 304 in avogadro/core/cube.cpp

View check run for this annotation

Codacy Production / Codacy Static Code Analysis

avogadro/core/cube.cpp#L304 

Variable 'nx' is assigned a value that is never used.
int ny = m_points.y();
int nz = m_points.z();
return m_data[(i * ny * nz) + (j * nz) + k];
}


Expand Down Expand Up @@ -366,7 +353,7 @@ std::array<std::array<float, 3>, 8> Cube::getPosCube(int i, int j, int k) const
}

float Cube::value(const Vector3i& pos) const
{
{
unsigned int index =
pos.x() * m_points.y() * m_points.z() + pos.y() * m_points.z() + pos.z();
if (index < m_data.size())
Expand Down Expand Up @@ -465,4 +452,4 @@ bool Cube::fillStripe(
return true;
}

} // End Avogadro namespace
} // End Avogadro namespace
32 changes: 11 additions & 21 deletions avogadro/qtgui/meshgenerator.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -69,29 +69,19 @@ void MeshGenerator::FlyingEdgesAlgorithmPass1()
{
// Loop through z-dimension

for(int k = 0; k != m_dim.z(); ++k) {
for(int j = 0; j != m_dim.y(); ++j)
{

auto curEdgeCases = edgeCases.begin() + (m_dim.x() - 1) * (k * m_dim.y() + j);

auto curPointValues = m_cube->getRowIter(j, k);

// Initialize the isGE array to track isosurface crossings
std::array<bool, 2> isGE;
isGE[0] = (curPointValues[0] >= m_iso); // first element initialization

// loop through x-dimension
for(int i = 1; i != m_dim.x(); ++i)
{
// update isGE for the current point
for (int k = 0; k != m_dim.z(); ++k) {
for (int j = 0; j != m_dim.y(); ++j) {

isGE[i % 2] = (curPointValues[i] >= m_iso);
auto curEdgeCases = edgeCases.begin() + (m_dim.x() - 1) * (k * m_dim.y() + j);
std::array<bool, 2> isGE;
isGE[0] = (m_cube->getData(0, j, k) >= m_iso);

curEdgeCases[i-1] = calcCaseEdge(isGE[(i+1)%2], isGE[i%2]);
for (int i = 1; i != m_dim.x(); ++i) {
isGE[i % 2] = (m_cube->getData(i, j, k) >= m_iso);
curEdgeCases[i - 1] = calcCaseEdge(isGE[(i + 1) % 2], isGE[i % 2]);
}
}
}
}
}

for(int k = 0; k != m_dim.z(); ++k){
for(int j = 0; j != m_dim.y(); ++j)
Expand Down Expand Up @@ -471,6 +461,7 @@ void MeshGenerator::FlyingEdgesAlgorithmPass4()
const char* caseTri = caseTriangles[caseId]; // size 16
for(int idx = 0; caseTri[idx] != -1; idx += 3)
{

tris[triIdx][0] = globalIdxs[caseTri[idx]];
tris[triIdx][1] = globalIdxs[caseTri[idx+1]];
tris[triIdx][2] = globalIdxs[caseTri[idx+2]];
Expand All @@ -488,7 +479,6 @@ void MeshGenerator::run()
qDebug() << "No mesh or cube set - nothing to find isosurface of…";
return;
}

m_mesh->setStable(false);
m_mesh->clear();

Expand Down

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