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Fix buffer overflow in DWI bootstrapping #2779

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merged 3 commits into from
Apr 18, 2024
Merged

Fix buffer overflow in DWI bootstrapping #2779

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7fa0142
Fix buffer overflow in DWI bootstrapping
Lestropie Jan 16, 2024
fe7505f
Merge remote-tracking branch 'origin/dev' into tckgen_tensorprob_fix
Lestropie Jan 23, 2024
b2fa527
DWI::Bootstrap: Multiple fixes
Lestropie Jan 23, 2024
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32 changes: 16 additions & 16 deletions src/dwi/bootstrap.h
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Original file line number Diff line number Diff line change
Expand Up @@ -46,8 +46,10 @@ class Bootstrap : public Adapter::Base<Bootstrap<ImageType, Functor, NUM_VOX_PER
};

Bootstrap(const ImageType &Image, const Functor &functor)
: base_type(Image), func(functor), next_voxel(nullptr), last_voxel(nullptr) {
: base_type(Image), func(functor), next_voxel(nullptr), last_voxel(nullptr), current_chunk(0) {
assert(ndim() == 4);
voxel_buffer.push_back(std::vector<value_type>(NUM_VOX_PER_CHUNK * size(3)));
clear();
}

value_type value() { return get_voxel()[index(3)]; }
Expand All @@ -65,8 +67,6 @@ class Bootstrap : public Adapter::Base<Bootstrap<ImageType, Functor, NUM_VOX_PER

void clear() {
voxels.clear();
if (voxel_buffer.empty())
voxel_buffer.push_back(std::vector<value_type>(NUM_VOX_PER_CHUNK * size(3)));
next_voxel = &voxel_buffer[0][0];
last_voxel = next_voxel + NUM_VOX_PER_CHUNK * size(3);
current_chunk = 0;
Expand All @@ -82,11 +82,10 @@ class Bootstrap : public Adapter::Base<Bootstrap<ImageType, Functor, NUM_VOX_PER

value_type *allocate_voxel() {
if (next_voxel == last_voxel) {
++current_chunk;
if (current_chunk >= voxel_buffer.size())
if (++current_chunk >= voxel_buffer.size())
voxel_buffer.push_back(std::vector<value_type>(NUM_VOX_PER_CHUNK * size(3)));
assert(current_chunk < voxel_buffer.size());
next_voxel = &voxel_buffer.back()[0];
next_voxel = &voxel_buffer[current_chunk][0];
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@jdtournier Note bug here resolved in b2fa527.

last_voxel = next_voxel + NUM_VOX_PER_CHUNK * size(3);
}
value_type *retval = next_voxel;
Expand All @@ -95,16 +94,17 @@ class Bootstrap : public Adapter::Base<Bootstrap<ImageType, Functor, NUM_VOX_PER
}

value_type *get_voxel() {
value_type *&data(
voxels.insert(std::make_pair(Eigen::Vector3i(index(0), index(1), index(2)), nullptr)).first->second);
if (!data) {
data = allocate_voxel();
ssize_t pos = index(3);
for (auto l = Loop(3)(*this); l; ++l)
data[index(3)] = base_type::value();
index(3) = pos;
func(data);
}
const Eigen::Vector3i voxel(index(0), index(1), index(2));
const typename std::map<Eigen::Vector3i, value_type *, IndexCompare>::const_iterator existing = voxels.find(voxel);
if (existing != voxels.end())
return existing->second;
Comment on lines +99 to +100

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value_type *const data = allocate_voxel();
ssize_t pos = index(3);
for (auto l = Loop(3)(*this); l; ++l)

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data[index(3)] = base_type::value();
Comment on lines +103 to +104

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index(3) = pos;
func(data);
voxels.insert({voxel, data});
return data;
}
};
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