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Resolve integer overflow when running on a large 3D image #249

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merged 1 commit into from
Sep 12, 2023
Merged

Resolve integer overflow when running on a large 3D image #249

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4 changes: 2 additions & 2 deletions stardist/lib/stardist2d.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -550,7 +550,7 @@ static PyObject* c_non_max_suppression_inds(PyObject *self, PyObject *args) {
results, params);
else{
results.resize(n_polys-i);
for (int n = 0; n < results.size(); ++n)
for (size_t n = 0; n < results.size(); ++n)
results[n].first = i+n;
}

Expand All @@ -563,7 +563,7 @@ static PyObject* c_non_max_suppression_inds(PyObject *self, PyObject *args) {
#pragma omp parallel for schedule(dynamic) reduction(+:count_suppressed) shared(suppressed)
#endif

for (int neigh=0; neigh<results.size(); neigh++) {
for (size_t neigh=0; neigh<results.size(); neigh++) {
// for (int j=i+1; j<n_polys; j++) {

long j = results[neigh].first;
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13 changes: 6 additions & 7 deletions stardist/lib/stardist3d_impl.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1171,7 +1171,7 @@ void _COMMON_non_maximum_suppression_sparse(
results, params);
else{
results.resize(n_polys-i);
for (int n = 0; n < results.size(); ++n)
for (size_t n = 0; n < results.size(); ++n)
results[n].first = i+n;
}
// inner loop
Expand All @@ -1192,7 +1192,7 @@ void _COMMON_non_maximum_suppression_sparse(
// if (suppressed[j])
// continue;

for (int neigh=0; neigh<results.size(); neigh++) {
for (size_t neigh=0; neigh<results.size(); neigh++) {

long j = results[neigh].first;

Expand Down Expand Up @@ -1458,13 +1458,12 @@ void _COMMON_polyhedron_to_label(const float* dist, const float* points,

// loop over bounding box and label pixel if inside of the polyhedron
#pragma omp parallel for schedule(dynamic)
for (int z = std::max(0,bbox[0]); z <= std::min(nz-1,bbox[1]); ++z) {
for (int y = std::max(0,bbox[2]); y <= std::min(ny-1,bbox[3]); ++y) {
for (int x = std::max(0,bbox[4]); x <= std::min(nx-1,bbox[5]); ++x) {
for (uint64_t z = std::max(0,bbox[0]); z <= (uint64_t) std::min(nz-1,bbox[1]); ++z) {
for (uint64_t y = std::max(0,bbox[2]); y <= (uint64_t) std::min(ny-1,bbox[3]); ++y) {
for (uint64_t x = std::max(0,bbox[4]); x <= (uint64_t) std::min(nx-1,bbox[5]); ++x) {


bool inside = false;
long offset = x+y*nx+z*(nx*ny);
uint64_t offset = x+y*nx+z*(nx*ny);

switch(render_mode){
case 0:
Expand Down