From 7852296260ac30d1bfcde29b07da37403384001a Mon Sep 17 00:00:00 2001
From: Ran Lu <ranl@princeton.edu>
Date: Sun, 29 Sep 2024 23:59:01 -0400
Subject: [PATCH] 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.
---
 src/agg/mean_aggl.cpp | 45 ++++++++++++++++++++++---------------------
 1 file changed, 23 insertions(+), 22 deletions(-)

diff --git a/src/agg/mean_aggl.cpp b/src/agg/mean_aggl.cpp
index 962bc37..843256e 100644
--- 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);