Dynamic::~Dynamic()
{
INFO ("Dynamic seeeding required " + str (total_samples) + " samples to draw " + str (total_seeds) + " seeds");
#ifdef DYNAMIC_SEED_DEBUGGING
const double final_mu = mu();
// Output seeding probabilites at end of execution
Image::Header H;
H.info() = info();
H.datatype() = DataType::Float32;
Image::Buffer<float> prob_mean_data ("seed_prob_mean.mif", H), prob_sum_data ("seed_prob_sum.mif", H);
Image::Buffer<float>::voxel_type prob_mean (prob_mean_data), prob_sum (prob_sum_data);
VoxelAccessor v (accessor);
Image::Loop loop;
for (loop.start (v, prob_mean, prob_sum); loop.ok(); loop.next (v, prob_mean, prob_sum)) {
if (v.value()) {
float sum = 0.0;
size_t count = 0;
for (Fixel_map<Fixel_TD_seed>::ConstIterator i = begin (v); i; ++i) {
sum += i().get_seed_prob (final_mu);
++count;
}
prob_mean.value() = sum / float(count);
prob_sum .value() = sum;
}
}
#endif
}
void run ()
{
Image::Header input_header (argument[0]);
Image::Buffer<float> input_data (input_header);
auto input_voxel = input_data.voxel();
int bounds[3][2] = { {0, input_header.dim (0) - 1},
{0, input_header.dim (1) - 1},
{0, input_header.dim (2) - 1} };
int padding[3][2] = { {0, 0}, {0, 0}, {0, 0} };
Options opt = get_options ("uniform");
if (opt.size()) {
int pad = opt[0][0];
for (int axis = 0; axis < 3; axis++) {
padding[axis][0] = pad;
padding[axis][1] = pad;
}
}
opt = get_options ("axis");
for (size_t i = 0; i != opt.size(); ++i) {
// Manual padding of axis overrides uniform padding
const int axis = opt[i][0];
padding[axis][0] = opt[i][1];
padding[axis][1] = opt[i][2];
}
Image::Header output_header (input_header);
Math::Matrix<float> output_transform (input_header.transform());
for (int axis = 0; axis < 3; ++axis) {
output_header.dim (axis) = output_header.dim(axis) + padding[axis][0] + padding[axis][1];
output_transform (axis, 3) += (output_transform (axis, 0) * (bounds[0][0] - padding[0][0]) * input_header.vox (0))
+ (output_transform (axis, 1) * (bounds[1][0] - padding[0][0]) * input_header.vox (1))
+ (output_transform (axis, 2) * (bounds[2][0] - padding[0][0]) * input_header.vox (2));
}
output_header.transform() = output_transform;
Image::Buffer<float> output_data (argument[1], output_header);
auto output_voxel = output_data.voxel();
Image::Loop loop ("padding image...");
for (loop.start (output_voxel); loop.ok(); loop.next (output_voxel)) {
bool in_bounds = true;
for (int axis = 0; axis < 3; ++axis) {
input_voxel[axis] = output_voxel[axis] - padding[axis][0];
if (input_voxel[axis] < 0 || input_voxel[axis] >= input_header.dim (axis))
in_bounds = false;
}
if (input_voxel.ndim() > 3)
input_voxel[3] = output_voxel[3];
if (in_bounds)
output_voxel.value() = input_voxel.value();
else
output_voxel.value() = 0;
}
}