Agglomerate an exact copy of a reference segmentation

Set the agglomerate threshold to 0, but reject any merger below the input threshold unless the two parts have the same semantic id, which is specified by the reference segmentation.
seung-lab · Sep 30, 2024 · 7852296 · 7852296
1 parent 0094286
commit 7852296
Showing 1 changed file with 23 additions and 22 deletions.
diff --git a/src/agg/mean_aggl.cpp b/src/agg/mean_aggl.cpp
@@ -692,36 +692,36 @@ inline agglomeration_output_t<T> agglomerate_cc(agglomeration_data_t<T, Compare>
                 continue;
             }
 
-            if (!comp(e.edge->w, sem_aff_threshold)) {
-                if (!sem_counts.empty()){
-                    if (!sem_can_merge(sem_counts[v0],sem_counts[v1],sem_params)) {
-                        output.sem_rg_vector.push_back(*(e.edge));
-                        e.edge->w = Limits::min();
-                        continue;
-                    }
-                }
-            }
-
-            if (!comp(e.edge->w, size_aff_threshold)) {
-                size_t size0 = seg_size[v0];
-                size_t size1 = seg_size[v1];
-                auto p = std::minmax({size0, size1});
-                if (p.first > size_params.small_voxel_threshold and (size0+size1) > size_params.large_voxel_threshold) {
-                    output.rej_rg_vector.push_back(*(e.edge));
+            if (!sem_counts.empty()){
+                if ((!comp(e.edge->w, sem_aff_threshold) and (sem_counts[v0][0] == 0 or sem_counts[v1][0] == 0)) or (sem_counts[v0][0] != sem_counts[v1][0])) {
+                    output.sem_rg_vector.push_back(*(e.edge));
                     e.edge->w = Limits::min();
                     continue;
                 }
             }
 
-            if (!comp(e.edge->w, backbone_threshold)){
+            if (sem_counts.empty() or sem_counts[v0][0] == 0 or sem_counts[v1][0] == 0) {
                 size_t size0 = seg_size[v0];
                 size_t size1 = seg_size[v1];
                 auto p = std::minmax({size0, size1});
-                if ((p.first > twig_params.voxel_threshold) or (e.edge->w.num > twig_params.area_threshold)) {
-                    e.edge->w = Limits::min();
-                    continue;
+                if (!comp(e.edge->w, size_aff_threshold)) {
+                    if (p.first > size_params.small_voxel_threshold and (size0+size1) > size_params.large_voxel_threshold) {
+                        output.rej_rg_vector.push_back(*(e.edge));
+                        e.edge->w = Limits::min();
+                        continue;
+                    }
+                }
+
+                if (!comp(e.edge->w, backbone_threshold)){
+                    size_t size0 = seg_size[v0];
+                    size_t size1 = seg_size[v1];
+                    auto p = std::minmax({size0, size1});
+                    if ((p.first > twig_params.voxel_threshold) or (e.edge->w.num > twig_params.area_threshold)) {
+                        e.edge->w = Limits::min();
+                        continue;
+                    }
+                    output.twig_rg_vector.push_back(*(e.edge));
                 }
-                output.twig_rg_vector.push_back(*(e.edge));
             }
 #ifdef FINAL
             if (incident[v0].size() < incident[v1].size()) {
@@ -918,7 +918,8 @@ inline void agglomerate(const char * rg_filename, const char * fs_filename, cons
 {
     Compare comp;
 
-    auto th = params.input_aff_threshold - params.twig_params.aff_threshold_delta;
+    params.sem_params.aff_threshold = params.input_aff_threshold;
+    auto th = 0.0;
 
     T const final_threshold = T(th,1);