int addTrainingInstance(std::vector<DataInstance>& training_data, std::vector<int>& labels, const Instance& instance, const VolumePtr<short>& gt)
{
const VolumePtr<unsigned char>& mask = std::get<2>(instance);
int width, height, depth;
std::tie(width, height, depth) = getVolumeDimension<unsigned char>(mask);
const std::array<double, 5> rate = { 0.05, 1.0, 1.0, 1.0, 1.0 };
int n_voxels = 0;
for (int z = 0; z < depth; ++z)
{
for (int y = 0; y < height; ++y)
{
for (int x = 0; x < width; ++x)
{
itk::Index<3> index;
index[0] = x;
index[1] = y;
index[2] = z;
if (mask->GetPixel(index) == 0) continue;
const short label = gt->GetPixel(index);
assert(label <= 4);
const double p = (double)rand() / RAND_MAX;
if (p > rate[label]) continue;
training_data.push_back(DataInstance(instance, x, y, z));
labels.push_back(label);
++n_voxels;
}
}
}
return n_voxels;
}
int addInstance(const fs::path& instance_path, std::vector<VolumeVector<short>>& mrs, VolumeVector<unsigned char>& masks, VolumeVector<short>& gts, std::vector<std::vector<double>>& gmm_data, std::vector<int>& counts)
{
const fs::path flair_path(instance_path / fs::path("VSD.Brain.XX.O.MR_Flair"));
const fs::path t1_path(instance_path / fs::path("VSD.Brain.XX.O.MR_T1"));
const fs::path t1c_path(instance_path / fs::path("VSD.Brain.XX.O.MR_T1c"));
const fs::path t2_path(instance_path / fs::path("VSD.Brain.XX.O.MR_T2"));
const fs::path gt_path(instance_path / fs::path("VSD.Brain_3more.XX.XX.OT"));
const vector<fs::path> volume_paths =
{
flair_path,
t1_path,
t1c_path,
t2_path
};
const VolumePtr<short> gt = readVolume<short>(findMHA(gt_path).string());
gts.push_back(gt);
VolumeVector<short> volumes;
int width, height, depth;
std::tie(width, height, depth) = getVolumeDimension<short>(gt);
for (const fs::path& p : volume_paths)
{
volumes.push_back(readVolume<short>(findMHA(p).string()));
}
mrs.push_back(volumes);
const short lower_thres = 1;
const VolumePtr<unsigned char> mask = createMask<short>(volumes[0], lower_thres);
masks.push_back(mask);
const std::array<double, 5> rate = { 0.01, 0.6, 0.1, 1.0, 0.3 };
int n_voxels = 0;
for (int z = 0; z < depth; ++z)
{
for (int y = 0; y < height; ++y)
{
for (int x = 0; x < width; ++x)
{
itk::Index<3> index;
index[0] = x;
index[1] = y;
index[2] = z;
if (mask->GetPixel(index) == 0) continue;
++n_voxels;
const short label = gt->GetPixel(index);
assert(label <= 4);
++counts[label];
const double p = (double)rand() / RAND_MAX;
if (p > rate[label]) continue;
for (int i = 0; i < 4; ++i)
{
const double v = static_cast<double>(volumes[i]->GetPixel(index));
gmm_data[label].push_back(v);
}
}
}
}
return n_voxels;
}
