Merge pull request #1089 from thom-dani/critical-point-tracking

Critical point tracking
topology-tool-kit · Feb 8, 2025 · ab0369c · ab0369c
2 parents 7c38d09 + afe3a72
commit ab0369c
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Showing 25 changed files with 1,079 additions and 75 deletions.
diff --git a/core/base/arrayPreconditioning/ArrayPreconditioning.h b/core/base/arrayPreconditioning/ArrayPreconditioning.h
@@ -293,7 +293,9 @@ namespace ttk {
         std::vector<globalOrder::vertexToSort<DT>> verticesToSort;
         verticesToSort.reserve(nVerts);
 #ifdef TTK_ENABLE_OPENMP
-#pragma omp declare reduction (merge : std::vector<globalOrder::vertexToSort<DT>> : omp_out.insert(omp_out.end(), omp_in.begin(), omp_in.end()))
+#pragma omp declare reduction(                                           \
+    merge : std::vector<globalOrder::vertexToSort<DT>> : omp_out.insert( \
+        omp_out.end(), omp_in.begin(), omp_in.end()))
 #pragma omp parallel for reduction(merge : verticesToSort) schedule(static)
 #endif
         for(size_t i = 0; i < nVerts; i++) {

diff --git a/core/base/assignmentSolver/AssignmentAuction.h b/core/base/assignmentSolver/AssignmentAuction.h
@@ -275,6 +275,7 @@ namespace ttk {
     initFirstRound();
     while(not stoppingCriterion(this->costMatrix)) {
       initBiddersAndGoods();
+
       runAuctionRound(this->costMatrix);
 
       dataType cost = getMatchingDistance(this->costMatrix);

diff --git a/core/base/clusteringMetrics/ClusteringMetrics.cpp b/core/base/clusteringMetrics/ClusteringMetrics.cpp
@@ -114,7 +114,8 @@ int ttk::ClusteringMetrics::computeARI(
 
   double sumNChooseContingency = 0;
 #ifdef TTK_ENABLE_OPENMP
-#pragma omp parallel for num_threads(this->threadNumber_) reduction(+:sumNChooseContingency)
+#pragma omp parallel for num_threads(this->threadNumber_) \
+  reduction(+ : sumNChooseContingency)
 #endif // TTK_ENABLE_OPENMP
   for(size_t i1 = 0; i1 < nCluster1; i1++) {
     for(size_t i2 = 0; i2 < nCluster2; i2++)
@@ -165,7 +166,8 @@ int ttk::ClusteringMetrics::computeNMI(
   double mutualInfo = 0;
   bool invalidCell = false;
 #ifdef TTK_ENABLE_OPENMP
-#pragma omp parallel for num_threads(this->threadNumber_) reduction(+:mutualInfo)
+#pragma omp parallel for num_threads(this->threadNumber_) \
+  reduction(+ : mutualInfo)
 #endif // TTK_ENABLE_OPENMP
   for(size_t i1 = 0; i1 < nCluster1; i1++) {
     for(size_t i2 = 0; i2 < nCluster2; i2++) {

diff --git a/core/base/common/Os.h b/core/base/common/Os.h
@@ -25,7 +25,7 @@
 #include <string>
 #include <vector>
 
-//#define SINGLE_PRECISION
+// #define SINGLE_PRECISION
 
 #ifdef SINGLE_PRECISION
 #define REAL_TYPE float

diff --git a/core/base/contourAroundPoint/ContourAroundPoint.hpp b/core/base/contourAroundPoint/ContourAroundPoint.hpp
@@ -251,9 +251,9 @@ int ttk::ContourAroundPoint::execute() const {
 
   // The following open-mp processing is only relevant for
   // embarrassingly parallel algorithms.
-  //#ifdef TTK_ENABLE_OPENMP
-  //#pragma omp parallel for num_threads(threadNumber_)
-  //#endif
+  // #ifdef TTK_ENABLE_OPENMP
+  // #pragma omp parallel for num_threads(threadNumber_)
+  // #endif
   for(size_t p = 0; p < _inpPtsNum; ++p) {
     handleOneInpPt<scalarT>(
       findInpFldVert(p), _inpPtsIsovals[p], _inpPtsFlags[p], _inpPtsScalars[p]);

diff --git a/core/base/contourTreeAlignment/CTA_contourtree.h b/core/base/contourTreeAlignment/CTA_contourtree.h
@@ -11,8 +11,8 @@ namespace ttk {
 
   namespace cta {
 
-    //#####################################################################################################################
-    // enums and structs for tree data structure
+    // #####################################################################################################################
+    //  enums and structs for tree data structure
 
     //=====================================================================================================================
     // node types of a contour tree
@@ -174,7 +174,7 @@ namespace ttk {
       int segId;
     };
 
-    ///#####################################################################################################################
+    /// #####################################################################################################################
     // class for an unrooted contour tree
 
     /**

diff --git a/core/base/distanceMatrixDistortion/DistanceMatrixDistortion.cpp b/core/base/distanceMatrixDistortion/DistanceMatrixDistortion.cpp
@@ -62,7 +62,8 @@ int ttk::DistanceMatrixDistortion::execute(
   double totalSum = 0;
 
 #ifdef TTK_ENABLE_OPENMP
-#pragma omp parallel for num_threads(this->threadNumber_), reduction(+:totalSum)
+#pragma omp parallel for num_threads(this->threadNumber_), \
+  reduction(+ : totalSum)
 #endif // TTK_ENABLE_OPENMP
   for(size_t i = 0; i < n; i++) {
     double sum = 0;

diff --git a/core/base/integralLines/IntegralLines.h b/core/base/integralLines/IntegralLines.h
@@ -870,7 +870,9 @@ int ttk::IntegralLines::getGlobalIdentifiers(
   ttk::SimplexId intervalSize;
   // Counts vertices and edges number (with and without ghosts)
 #ifdef TTK_ENABLE_OPENMP4
-#pragma omp parallel for reduction(+:outputVertexNumber,outputCellNumber,realCellNumber,realVertexNumber) schedule(static,1) private(intervalSize)
+#pragma omp parallel for reduction(+ : outputVertexNumber, outputCellNumber, \
+                                     realCellNumber, realVertexNumber)       \
+  schedule(static, 1) private(intervalSize)
 #endif
   for(int thread = 0; thread < threadNumber_; thread++) {
     std::list<std::array<ttk::intgl::IntegralLine,

diff --git a/core/base/mergeTreeAutoencoder/MergeTreeAutoencoder.cpp b/core/base/mergeTreeAutoencoder/MergeTreeAutoencoder.cpp
@@ -1280,8 +1280,9 @@ bool ttk::MergeTreeAutoencoder::forwardStep(
   mtu::TorchMergeTree<float> dummyTMT;
   bool reset = false;
 #ifdef TTK_ENABLE_OPENMP
-#pragma omp parallel for schedule(dynamic) num_threads(this->threadNumber_) \
-  if(parallelize_) reduction(||: reset) reduction(+:loss)
+#pragma omp parallel for schedule(dynamic)                                \
+  num_threads(this->threadNumber_) if(parallelize_) reduction(|| : reset) \
+  reduction(+ : loss)
 #endif
   for(unsigned int ind = 0; ind < indexes.size(); ++ind) {
     unsigned int i = indexes[ind];
@@ -1488,8 +1489,8 @@ float ttk::MergeTreeAutoencoder::computeLoss(
   if(useDoubleInput_)
     matchings2.resize(trees2.size());
 #ifdef TTK_ENABLE_OPENMP
-#pragma omp parallel for schedule(dynamic) num_threads(this->threadNumber_) \
-  if(parallelize_) reduction(+:loss)
+#pragma omp parallel for schedule(dynamic) \
+  num_threads(this->threadNumber_) if(parallelize_) reduction(+ : loss)
 #endif
   for(unsigned int ind = 0; ind < indexes.size(); ++ind) {
     unsigned int i = indexes[ind];

diff --git a/core/base/mergeTreePrincipalGeodesics/MergeTreePrincipalGeodesicsBase.h b/core/base/mergeTreePrincipalGeodesics/MergeTreePrincipalGeodesicsBase.h
@@ -56,7 +56,8 @@ namespace ttk {
       matchings.resize(inputTrees.size());
       dataType reconstructionError = 0.0;
 #ifdef TTK_ENABLE_OPENMP
-#pragma omp parallel for schedule(dynamic) num_threads(this->threadNumber_) reduction(+:reconstructionError)
+#pragma omp parallel for schedule(dynamic) num_threads(this->threadNumber_) \
+  reduction(+ : reconstructionError)
 #endif
       for(unsigned int i = 0; i < inputTrees.size(); ++i) {
         ftm::MergeTree<dataType> reconstructedTree;

diff --git a/core/base/persistenceDiagramClustering/PDBarycenter.cpp b/core/base/persistenceDiagramClustering/PDBarycenter.cpp
@@ -38,7 +38,8 @@ void ttk::PDBarycenter::runMatching(
 
   double local_cost = *total_cost;
 #ifdef TTK_ENABLE_OPENMP
-#pragma omp parallel for num_threads(threadNumber_) schedule(dynamic, 1) reduction(+:local_cost)
+#pragma omp parallel for num_threads(threadNumber_) schedule(dynamic, 1) \
+  reduction(+ : local_cost)
 #endif
   for(int i = 0; i < numberOfInputs_; i++) {
     PersistenceDiagramAuction auction(
@@ -87,7 +88,8 @@ void ttk::PDBarycenter::runMatchingAuction(
   bool actual_distance) {
   double local_cost = *total_cost;
 #ifdef TTK_ENABLE_OPENMP
-#pragma omp parallel for num_threads(threadNumber_) schedule(dynamic, 1) reduction(+:local_cost)
+#pragma omp parallel for num_threads(threadNumber_) schedule(dynamic, 1) \
+  reduction(+ : local_cost)
 #endif
   for(int i = 0; i < numberOfInputs_; i++) {
     PersistenceDiagramAuction auction(

diff --git a/core/base/topologicalCompression/TopologicalCompression.h b/core/base/topologicalCompression/TopologicalCompression.h
@@ -505,16 +505,16 @@ int ttk::TopologicalCompression::ReadFromFile(
   // [fm->] Read data.
   char *buf = reinterpret_cast<char *>(dest);
 
-  //#ifndef _MSC_VER
-  // FILE *fm = fmemopen(buf, destLen, "r+");
-  //#else
+  // #ifndef _MSC_VER
+  //  FILE *fm = fmemopen(buf, destLen, "r+");
+  // #else
   const std::string s = fileName + std::string(".temp");
   const char *ffn = s.c_str();
   FILE *ftemp = fopen(ffn, "wb");
   fwrite(buf, destLen, sizeof(char), ftemp);
   fclose(ftemp);
   FILE *fm = fopen(ffn, "rb");
-  //#endif
+  // #endif
 
   // Do read topology.
   if(!(ZFPOnly)) {

diff --git a/core/base/trackingFromCriticalPoints/CMakeLists.txt b/core/base/trackingFromCriticalPoints/CMakeLists.txt
@@ -0,0 +1,10 @@
+ttk_add_base_library(trackingFromCriticalPoints
+  SOURCES
+		TrackingFromCriticalPoints.cpp
+  HEADERS
+		TrackingFromCriticalPoints.h
+  DEPENDS
+    assignmentSolver
+    persistenceDiagram
+    triangulation
+    )