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Fix #2426 - Groom: Alignment should be performed on groomed surfaces, not original #2427

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Merged
akenmorris merged 1 commit into from
Sep 24, 2025
+7 −8
Merged

Fix #2426 - Groom: Alignment should be performed on groomed surfaces, not original #2427

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13 changes: 6 additions & 7 deletions Libs/Groom/Groom.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -216,7 +216,6 @@ bool Groom::image_pipeline(std::shared_ptr<Subject> subject, size_t domain) {

//---------------------------------------------------------------------------
bool Groom::run_image_pipeline(Image& image, GroomParameters params) {

// ensure axis aligned
image.toAxisAligned();

Expand Down Expand Up @@ -572,9 +571,9 @@ bool Groom::run_alignment() {
std::vector<Mesh> meshes;

for (size_t i = 0; i < subjects.size(); i++) {
Mesh mesh = get_mesh(i, 0, true);
Mesh mesh = get_mesh(i, 0, true /* combine */, MeshSource::Groomed);
for (size_t domain = 1; domain < num_domains; domain++) {
mesh += get_mesh(i, domain, true); // combine
mesh += get_mesh(i, domain, true /* combine */, MeshSource::Groomed);
}

// grab the first domain's initial transform (e.g. potentially reflect) and use before ICP
Expand Down Expand Up @@ -607,9 +606,9 @@ bool Groom::run_alignment() {
}
reference_mesh = reference_meshes[reference_index];
} else {
reference_mesh = get_mesh(reference_index, 0, true);
reference_mesh = get_mesh(reference_index, 0, true /* combine */, MeshSource::Groomed);
for (size_t domain = 1; domain < num_domains; domain++) {
reference_mesh += get_mesh(reference_index, domain, true); // combine
reference_mesh += get_mesh(reference_index, domain, true /* combine */, MeshSource::Groomed);
}
}
auto transforms = Groom::get_icp_transforms(meshes, reference_mesh);
Expand Down Expand Up @@ -656,7 +655,7 @@ bool Groom::run_alignment() {
std::vector<Mesh> meshes;
for (size_t i = 0; i < subjects.size(); i++) {
if (!subjects[i]->is_excluded()) {
Mesh mesh = get_mesh(i, domain, true);
Mesh mesh = get_mesh(i, domain, true /* combine */, MeshSource::Groomed);
// if fixed subjects are present, only add the fixed subjects
if (subjects[i]->is_fixed() || !project_->get_fixed_subjects_present()) {
reference_meshes.push_back(mesh);
Expand All @@ -678,7 +677,7 @@ bool Groom::run_alignment() {
reference_index = MeshUtils::findReferenceMesh(reference_meshes, subset_size);
reference_index = reference_meshes[reference_index].get_id();
}
reference_mesh = get_mesh(reference_index, domain, true);
reference_mesh = get_mesh(reference_index, domain, true /* combine */, MeshSource::Groomed);

params.set_alignment_reference_chosen(reference_index);
params.save_to_project();
Expand Down
2 changes: 1 addition & 1 deletion Libs/Groom/Groom.h
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Expand Up @@ -85,7 +85,7 @@ class Groom {

std::vector<vtkSmartPointer<vtkPoints>> get_combined_points();

Mesh get_mesh(int subject, int domain, bool transformed = false, MeshSource source = MeshSource::Original);
Mesh get_mesh(int subject, int domain, bool transformed = false, MeshSource source = MeshSource::Groomed);


vtkSmartPointer<vtkPoints> get_landmarks(int subject, int domain);
Expand Down
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