Read agglomeration threshold directly from the parameter file

seung-lab · Jun 1, 2024 · 21cad7a · 21cad7a
1 parent de122b7
commit 21cad7a
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Showing 4 changed files with 13 additions and 8 deletions.
diff --git a/scripts/atomic_chunk_me.sh b/scripts/atomic_chunk_me.sh
@@ -36,9 +36,9 @@ try touch ns.data
 try touch ongoing_semantic_labels.data
 
 if [ "$OVERLAP" = "1" ]; then
-    try taskset -c $cpuid $BIN_PATH/agg_nonoverlap $AGG_THRESHOLD input_rg.data frozen.data ns.data
+    try taskset -c $cpuid $BIN_PATH/agg_nonoverlap $PARAM_JSON input_rg.data frozen.data ns.data
 else
-    try taskset -c $cpuid $BIN_PATH/agg $AGG_THRESHOLD input_rg.data frozen.data ns.data
+    try taskset -c $cpuid $BIN_PATH/agg $PARAM_JSON input_rg.data frozen.data ns.data
 fi
 
 try cat remap.data >> localmap.data

diff --git a/scripts/composite_chunk_me.sh b/scripts/composite_chunk_me.sh
@@ -61,11 +61,11 @@ do
 done
 
 if [ "$OVERLAP" = "2" ]; then
-    try $BIN_PATH/agg_overlap $AGG_THRESHOLD input_rg.data frozen.data ongoing_supervoxel_counts.data
+    try $BIN_PATH/agg_overlap $PARAM_JSON input_rg.data frozen.data ongoing_supervoxel_counts.data
 elif [ "$OVERLAP" = "1" ]; then
-    try $BIN_PATH/agg_nonoverlap $AGG_THRESHOLD input_rg.data frozen.data ongoing_supervoxel_counts.data
+    try $BIN_PATH/agg_nonoverlap $PARAM_JSON input_rg.data frozen.data ongoing_supervoxel_counts.data
 else
-    try $BIN_PATH/agg $AGG_THRESHOLD input_rg.data frozen.data ongoing_supervoxel_counts.data
+    try $BIN_PATH/agg $PARAM_JSON input_rg.data frozen.data ongoing_supervoxel_counts.data
 fi
 
 try cat remap.data >> localmap.data

diff --git a/scripts/overlap_chunk_me.sh b/scripts/overlap_chunk_me.sh
@@ -26,7 +26,7 @@ do
     cat boundary_"$i"_"$output_chunk".data >> frozen.data
 done
 
-try $BIN_PATH/agg_extra $AGG_THRESHOLD input_rg.data frozen.data ongoing_supervoxel_counts.data
+try $BIN_PATH/agg_extra $PARAM_JSON input_rg.data frozen.data ongoing_supervoxel_counts.data
 
 try rm boundary_*.data
 try rm incomplete_*.data

diff --git a/src/agg/mean_aggl.cpp b/src/agg/mean_aggl.cpp
@@ -31,12 +31,15 @@
 #include <future>
 #include <omp.h>
 #include <sys/stat.h>
+#include <nlohmann/json.hpp>
 
 #include "../seg/SemExtractor.hpp"
 #include "../seg/RemapTable.hpp"
 
 #include "edges.h"
 
+using json = nlohmann::json;
+
 static const size_t frozen = (1UL<<(std::numeric_limits<std::size_t>::digits-2));
 static const size_t boundary = (1UL<<(std::numeric_limits<std::size_t>::digits-1))|frozen;
 
@@ -1145,8 +1148,10 @@ inline void agglomerate(const char * rg_filename, const char * fs_filename, cons
 int main(int argc, char *argv[])
 {
     agglomeration_param_t params;
-    aff_t th = atof(argv[1]);
-    params.input_aff_threshold = th;
+    std::ifstream f(argv[1]);
+    json conf = json::parse(f);
+    f.close();
+    params.input_aff_threshold = atof(conf["AGG_THRESHOLD"]);
 
     std::cout << "agglomerate" << std::endl;
 #ifdef MST_EDGE