clang-formatting

topology-tool-kit · Jun 7, 2024 · 1dbee0c · 1dbee0c
1 parent 1461cfe
commit 1dbee0c
Show file tree

Hide file tree

Showing 24 changed files with 101 additions and 77 deletions.
diff --git a/core/base/arrayPreconditioning/ArrayPreconditioning.h b/core/base/arrayPreconditioning/ArrayPreconditioning.h
@@ -290,7 +290,9 @@ 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/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/common/welcomeMsg.inl b/core/base/common/welcomeMsg.inl
@@ -13,31 +13,37 @@ printMsg(
   debug::LineMode::NEW,
   stream);
 printMsg(debug::output::BOLD
-    //+ "|_   _|_   _| |/ /                   / /__\\ \\  |___ \\ / _ " "\\___ \\|___ /"
-    + "|_   _|_   _| |/ /                  / /__\\ \\  |___ \\ / _ \\___ \\| || |"
+           //+ "|_   _|_   _| |/ /                   / /__\\ \\  |___ \\ / _ "
+           //"\\___ \\|___ /"
+           + "|_   _|_   _| |/ /                  / /__\\ \\  |___ \\ / _ "
+             "\\___ \\| || |"
            + debug::output::ENDCOLOR,
          debug::Priority::PERFORMANCE,
          debug::LineMode::NEW,
          stream);
 printMsg(
   debug::output::BOLD
-    //+ "  | |   | | | ' /                   | |/ __| |   __) | | | |__) | |_ \\"
+    //+ "  | |   | | | ' /                   | |/ __| |   __) | | | |__) | |_
+    //\\"
     + "  | |   | | | ' /                  | |/ __| |   __) | | | |__) | || |_"
     + debug::output::ENDCOLOR,
   debug::Priority::PERFORMANCE,
   debug::LineMode::NEW,
   stream);
 printMsg(
   debug::output::BOLD
-//    + "  | |   | | | . \\                   | | (__| |  / __/| |_| / __/ ___) |"
+    //    + "  | |   | | | . \\                   | | (__| |  / __/| |_| / __/
+    //    ___) |"
     + "  | |   | | | . \\                  | | (__| |  / __/| |_| / __/|__   _|"
     + debug::output::ENDCOLOR,
   debug::Priority::PERFORMANCE,
   debug::LineMode::NEW,
   stream);
 printMsg(debug::output::BOLD
-//    + "  |_|   |_| |_|\\_\\                  | |\\___| | " "|_____|\\___/_____|____/"
-    + "  |_|   |_| |_|\\_\\                 | |\\___| | |_____|\\___/_____|  |_|"
+           //    + "  |_|   |_| |_|\\_\\                  | |\\___| | "
+           //    "|_____|\\___/_____|____/"
+           + "  |_|   |_| |_|\\_\\                 | |\\___| | "
+             "|_____|\\___/_____|  |_|"
            + debug::output::ENDCOLOR,
          debug::Priority::PERFORMANCE,
          debug::LineMode::NEW,

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
@@ -41,9 +41,8 @@ int ttk::DistanceMatrixDistortion::execute(
   }
 
 #ifdef TTK_ENABLE_OPENMP
-#pragma omp parallel for num_threads(this->threadNumber_) reduction(max     \
-                                                                    : maxi) \
-  schedule(dynamic)
+#pragma omp parallel for num_threads(this->threadNumber_) \
+  reduction(max : maxi) schedule(dynamic)
 #endif // TTK_ENABLE_OPENMP
   for(size_t i = 0; i < n; i++) {
     for(size_t j = i + 1; j < n; j++) {
@@ -62,7 +61,8 @@ 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/implicitTriangulation/ImplicitTriangulation.cpp b/core/base/implicitTriangulation/ImplicitTriangulation.cpp
@@ -2969,11 +2969,9 @@ int ttk::ImplicitTriangulation::preconditionDistributedCells() {
     localBBox_z_max{this->localGridOffset_[2]};
 
 #ifdef TTK_ENABLE_OPENMP
-#pragma omp parallel for reduction(                    \
-  min                                                  \
-  : localBBox_x_min, localBBox_y_min, localBBox_z_min) \
-  reduction(max                                        \
-            : localBBox_x_max, localBBox_y_max, localBBox_z_max)
+#pragma omp parallel for reduction(                          \
+    min : localBBox_x_min, localBBox_y_min, localBBox_z_min) \
+  reduction(max : localBBox_x_max, localBBox_y_max, localBBox_z_max)
 #endif
   for(SimplexId lcid = 0; lcid < nLocCells; ++lcid) {
     // only keep non-ghost cells

diff --git a/core/base/implicitTriangulation/ImplicitTriangulation.h b/core/base/implicitTriangulation/ImplicitTriangulation.h
@@ -110,29 +110,33 @@ namespace ttk {
 
     virtual int getTetrahedronEdge(const SimplexId &tetId,
                                    const int &id,
-                                   SimplexId &edgeId) const = 0;
+                                   SimplexId &edgeId) const
+      = 0;
 
     int getTetrahedronEdges(std::vector<std::vector<SimplexId>> &edges) const;
 
     virtual int getTetrahedronTriangle(const SimplexId &tetId,
                                        const int &id,
-                                       SimplexId &triangleId) const = 0;
+                                       SimplexId &triangleId) const
+      = 0;
 
     int getTetrahedronTriangles(
       std::vector<std::vector<SimplexId>> &triangles) const;
 
     virtual int getTetrahedronNeighbor(const SimplexId &tetId,
                                        const int &localNeighborId,
-                                       SimplexId &neighborId) const = 0;
+                                       SimplexId &neighborId) const
+      = 0;
 
-    virtual SimplexId
-      getTetrahedronNeighborNumber(const SimplexId &tetId) const = 0;
+    virtual SimplexId getTetrahedronNeighborNumber(const SimplexId &tetId) const
+      = 0;
 
     int getTetrahedronNeighbors(std::vector<std::vector<SimplexId>> &neighbors);
 
     virtual int getTetrahedronVertex(const SimplexId &tetId,
                                      const int &localVertexId,
-                                     SimplexId &vertexId) const = 0;
+                                     SimplexId &vertexId) const
+      = 0;
 
     SimplexId getTriangleEdgeNumberInternal(
       const SimplexId & /*triangleId*/) const override {
@@ -155,10 +159,12 @@ namespace ttk {
 
     virtual int getTriangleNeighbor(const SimplexId &triangleId,
                                     const int &localNeighborId,
-                                    SimplexId &neighborId) const = 0;
+                                    SimplexId &neighborId) const
+      = 0;
 
     virtual SimplexId
-      getTriangleNeighborNumber(const SimplexId &triangleId) const = 0;
+      getTriangleNeighborNumber(const SimplexId &triangleId) const
+      = 0;
 
     int getTriangleNeighbors(std::vector<std::vector<SimplexId>> &neighbors);
 

diff --git a/core/base/integralLines/IntegralLines.h b/core/base/integralLines/IntegralLines.h
@@ -708,8 +708,8 @@ int ttk::IntegralLines::execute(triangulationType *triangulation) {
   int const taskNumber = (int)seedNumber_ / chunkSize_;
 #ifdef TTK_ENABLE_OPENMP4
 #ifdef TTK_ENABLE_MPI
-#pragma omp parallel shared(                                        \
-  ttk::intgl::finishedElement_, toSend_, ttk::intgl::addedElement_) \
+#pragma omp parallel shared(                                          \
+    ttk::intgl::finishedElement_, toSend_, ttk::intgl::addedElement_) \
   num_threads(threadNumber_)
   {
 #else
@@ -865,7 +865,9 @@ 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/localizedTopologicalSimplification/LocalizedTopologicalSimplification.h b/core/base/localizedTopologicalSimplification/LocalizedTopologicalSimplification.h
@@ -143,7 +143,7 @@ namespace ttk {
         const IT nVertices = triangulation->getNumberOfVertices();
 #ifdef TTK_ENABLE_OPENMP
 #pragma omp parallel for num_threads( \
-  this->threadNumber_) if(nAuthorizedExtremaIndices > 1000)
+    this->threadNumber_) if(nAuthorizedExtremaIndices > 1000)
 #endif // TTK_ENABLE_OPENMP
         for(IT i = 0; i < nAuthorizedExtremaIndices; i++)
           authorizationMask[authorizedExtremaIndices[i]] = -2;

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/mergeTreeClustering/MergeTreeClustering.h b/core/base/mergeTreeClustering/MergeTreeClustering.h
@@ -25,7 +25,6 @@
 ///   href="https://topology-tool-kit.github.io/examples/mergeTreeWAE/">Merge
 ///   Tree Wasserstein Auto-Encoder example</a> \n
 
-
 #define treesMatchingVector \
   std::vector<std::vector<std::tuple<ftm::idNode, ftm::idNode, double>>>
 #define matchingVectorType std::vector<treesMatchingVector>
@@ -275,7 +274,7 @@ namespace ttk {
 #ifdef TTK_ENABLE_OPENMP4
 #pragma omp parallel for schedule(dynamic)                     \
   shared(centroids, centroids2, oldCentroids_, oldCentroids2_) \
-    num_threads(this->threadNumber_) if(parallelize_)
+  num_threads(this->threadNumber_) if(parallelize_)
 #endif
         for(unsigned int i = 0; i < centroids.size(); ++i) {
           std::vector<std::tuple<ftm::idNode, ftm::idNode, double>> matching,

diff --git a/core/base/mergeTreeClustering/MergeTreeDistance.h b/core/base/mergeTreeClustering/MergeTreeDistance.h
@@ -930,7 +930,7 @@ namespace ttk {
 #ifdef TTK_ENABLE_OPENMP4
 #pragma omp task firstprivate(taskQueue, nodeT) UNTIED()         \
   shared(treeTable, forestTable, treeBackTable, forestBackTable, \
-         treeChildDone, treeNodeDone) if(isTree1)
+           treeChildDone, treeNodeDone) if(isTree1)
         {
 #endif
           ftm::FTMTree_MT *treeT = (isTree1) ? tree1 : tree2;
@@ -1084,7 +1084,7 @@ namespace ttk {
 #ifdef TTK_ENABLE_OPENMP4
 #pragma omp task firstprivate(nodeT) UNTIED()                    \
   shared(treeTable, forestTable, treeBackTable, forestBackTable, \
-         treeChildDone, treeNodeDone)
+           treeChildDone, treeNodeDone)
         {
 #endif
           while((int)nodeT != -1) {

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/periodicImplicitTriangulation/PeriodicImplicitTriangulation.cpp b/core/base/periodicImplicitTriangulation/PeriodicImplicitTriangulation.cpp
@@ -677,11 +677,9 @@ int PeriodicImplicitTriangulation::preconditionDistributedCells() {
     localBBox_z_max{this->localGridOffset_[2]};
   const auto &dims{this->metaGrid_->getGridDimensions()};
 #ifdef TTK_ENABLE_OPENMP
-#pragma omp parallel for reduction(                    \
-  min                                                  \
-  : localBBox_x_min, localBBox_y_min, localBBox_z_min) \
-  reduction(max                                        \
-            : localBBox_x_max, localBBox_y_max, localBBox_z_max)
+#pragma omp parallel for reduction(                          \
+    min : localBBox_x_min, localBBox_y_min, localBBox_z_min) \
+  reduction(max : localBBox_x_max, localBBox_y_max, localBBox_z_max)
 #endif
   for(SimplexId lcid = 0; lcid < nLocCells; ++lcid) {
     // only keep non-ghost cells

diff --git a/core/base/periodicImplicitTriangulation/PeriodicImplicitTriangulation.h b/core/base/periodicImplicitTriangulation/PeriodicImplicitTriangulation.h
@@ -113,28 +113,32 @@ namespace ttk {
 
     virtual int getTetrahedronEdge(const SimplexId &tetId,
                                    const int &id,
-                                   SimplexId &edgeId) const = 0;
+                                   SimplexId &edgeId) const
+      = 0;
 
     int getTetrahedronEdges(std::vector<std::vector<SimplexId>> &edges) const;
 
     virtual int getTetrahedronTriangle(const SimplexId &tetId,
                                        const int &id,
-                                       SimplexId &triangleId) const = 0;
+                                       SimplexId &triangleId) const
+      = 0;
 
     int getTetrahedronTriangles(
       std::vector<std::vector<SimplexId>> &triangles) const;
 
     virtual int getTetrahedronNeighbor(const SimplexId &tetId,
                                        const int &localNeighborId,
-                                       SimplexId &neighborId) const = 0;
+                                       SimplexId &neighborId) const
+      = 0;
 
     SimplexId getTetrahedronNeighborNumber(const SimplexId &tetId) const;
 
     int getTetrahedronNeighbors(std::vector<std::vector<SimplexId>> &neighbors);
 
     virtual int getTetrahedronVertex(const SimplexId &tetId,
                                      const int &localVertexId,
-                                     SimplexId &vertexId) const = 0;
+                                     SimplexId &vertexId) const
+      = 0;
 
     SimplexId getTriangleEdgeNumberInternal(
       const SimplexId &ttkNotUsed(triangleId)) const override {
@@ -157,7 +161,8 @@ namespace ttk {
 
     virtual int getTriangleNeighbor(const SimplexId &triangleId,
                                     const int &localNeighborId,
-                                    SimplexId &neighborId) const = 0;
+                                    SimplexId &neighborId) const
+      = 0;
 
     SimplexId getTriangleNeighborNumber(const SimplexId &triangleId) const;
 

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++) {
     double const delta_lim = delta_lim_;
@@ -88,7 +89,8 @@ 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(