ENH: enhancements for edgeMesh mergeEdges(), mergePoints()

- filter out degenerate edges
- remove unused points

STYLE: remove unused mergePoints() parameter

STYLE: doxygen for edgeMesh

src/edgeMesh/edgeMesh.C

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-     \\/     M anipulation  | Copyright (C) 2015 OpenCFD Ltd.
+     \\/     M anipulation  | Copyright (C) 2015-2017 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -29,6 +29,7 @@ License
 #include "addToMemberFunctionSelectionTable.H"
 #include "ListOps.H"
 #include "EdgeMap.H"
+#include "PackedBoolList.H"
 
 // * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
 
@@ -286,16 +287,12 @@ void Foam::edgeMesh::scalePoints(const scalar scaleFactor)
 }
 
 
-void Foam::edgeMesh::mergePoints
+void Foam::edgeMesh::mergePoints(const scalar mergeDist)
-(
-    const scalar mergeDist,
-    labelList& reversePointMap
-)
 {
     pointField newPoints;
     labelList pointMap;
 
-    bool hasMerged = Foam::mergePoints
+    const bool hasMerged = Foam::mergePoints
     (
         points_,
         mergeDist,
@@ -307,92 +304,107 @@ void Foam::edgeMesh::mergePoints
 
     if (hasMerged)
     {
-        pointEdgesPtr_.clear();
+        pointEdgesPtr_.clear();   // connectivity change
 
         points_.transfer(newPoints);
 
-        // connectivity changed
-        pointEdgesPtr_.clear();
-
-        // Renumber and make sure e[0] < e[1] (not really necessary)
         forAll(edges_, edgeI)
         {
             edge& e = edges_[edgeI];
 
-            label p0 = pointMap[e[0]];
+            e[0] = pointMap[e[0]];
-            label p1 = pointMap[e[1]];
+            e[1] = pointMap[e[1]];
-
-            if (p0 < p1)
-            {
-                e[0] = p0;
-                e[1] = p1;
-            }
-            else
-            {
-                e[0] = p1;
-                e[1] = p0;
-            }
-        }
-
-        // Compact using a hashtable and commutative hash of edge.
-        EdgeMap<label> edgeToLabel(2*edges_.size());
-
-        label newEdgeI = 0;
-
-        forAll(edges_, edgeI)
-        {
-            const edge& e = edges_[edgeI];
-
-            if (e[0] != e[1])
-            {
-                if (edgeToLabel.insert(e, newEdgeI))
-                {
-                    newEdgeI++;
-                }
-            }
-        }
-
-        edges_.setSize(newEdgeI);
-
-        forAllConstIter(EdgeMap<label>, edgeToLabel, iter)
-        {
-            edges_[iter()] = iter.key();
         }
     }
+
+    this->mergeEdges();
 }
 
 
 void Foam::edgeMesh::mergeEdges()
 {
-    EdgeMap<label> existingEdges(2*edges_.size());
+    HashSet<edge, Hash<edge>> uniqEdges(2*edges_.size());
+    PackedBoolList pointIsUsed(points_.size());
 
-    label curEdgeI = 0;
+    label nUniqEdges = 0;
+    label nUniqPoints = 0;
     forAll(edges_, edgeI)
     {
         const edge& e = edges_[edgeI];
 
-        if (existingEdges.insert(e, curEdgeI))
+        // Remove degenerate and repeated edges
+        // - reordering (e[0] < e[1]) is not really necessary
+        if (e[0] != e[1] && uniqEdges.insert(e))
         {
-            curEdgeI++;
+            if (nUniqEdges != edgeI)
+            {
+                edges_[nUniqEdges] = e;
+            }
+            edges_[nUniqEdges].sort();
+            ++nUniqEdges;
+
+            if (pointIsUsed.set(e[0], 1))
+            {
+                ++nUniqPoints;
+            }
+            if (pointIsUsed.set(e[1], 1))
+            {
+                ++nUniqPoints;
+            }
         }
     }
 
     if (debug)
     {
         Info<< "Merging duplicate edges: "
-            << edges_.size() - existingEdges.size()
+            << (edges_.size() - nUniqEdges)
-            << " edges will be deleted." << endl;
+            << " edges will be deleted, "
+            << (points_.size() - nUniqPoints)
+            << " unused points will be removed." << endl;
     }
 
-    edges_.setSize(existingEdges.size());
+    if (nUniqEdges < edges_.size())
-
-    forAllConstIter(EdgeMap<label>, existingEdges, iter)
     {
-        edges_[iter()] = iter.key();
+        pointEdgesPtr_.clear(); // connectivity change
+        edges_.setSize(nUniqEdges);  // truncate
+    }
+
+    if (nUniqPoints < points_.size())
+    {
+        pointEdgesPtr_.clear(); // connectivity change
+
+        // build a oldToNew point-map and rewrite the points.
+        // We can do this simultaneously since the point order is unchanged
+        // and we are only effectively eliminating some entries.
+        labelList pointMap(points_.size(), -1);
+
+        label newId = 0;
+        forAll(pointMap, pointi)
+        {
+            if (pointIsUsed[pointi])
+            {
+                pointMap[pointi] = newId;
+
+                if (newId < pointi)
+                {
+                    // copy down
+                    points_[newId] = points_[pointi];
+                }
+                ++newId;
+            }
+        }
+        points_.setSize(newId);
+
+        // Renumber edges - already sorted (above)
+        forAll(edges_, edgeI)
+        {
+            edge& e = edges_[edgeI];
+
+            e[0] = pointMap[e[0]];
+            e[1] = pointMap[e[1]];
+        }
     }
 
-    // connectivity changed
-    pointEdgesPtr_.clear();
 }
 
 

src/edgeMesh/edgeMesh.H

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2014 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2017 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -59,8 +59,8 @@ class Ostream;
 
 // Forward declaration of friend functions and operators
 class edgeMesh;
-Istream& operator>>(Istream&, edgeMesh&);
+Istream& operator>>(Istream& is, edgeMesh& em);
-Ostream& operator<<(Ostream&, const edgeMesh&);
+Ostream& operator<<(Ostream& os, const edgeMesh& em);
 
 
 /*---------------------------------------------------------------------------*\
@@ -108,7 +108,7 @@ public:
     // Static
 
         //- Can we read this file format?
-        static bool canRead(const fileName&, const bool verbose=false);
+        static bool canRead(const fileName& name, const bool verbose=false);
 
         //- Can we read this file format?
         static bool canReadType(const word& ext, const bool verbose=false);
@@ -126,26 +126,23 @@ public:
         edgeMesh();
 
         //- Construct from components
-        edgeMesh(const pointField&, const edgeList&);
+        edgeMesh(const pointField& points, const edgeList& edges);
 
         //- Construct by transferring components (points, edges).
         edgeMesh
         (
-            const Xfer<pointField>&,
+            const Xfer<pointField>& pointLst,
-            const Xfer<edgeList>&
+            const Xfer<edgeList>& edgeLst
         );
 
         //- Construct as copy
-        edgeMesh(const edgeMesh&);
+        edgeMesh(const edgeMesh& em);
 
         //- Construct from file name (uses extension to determine type)
-        edgeMesh(const fileName&);
+        edgeMesh(const fileName& name);
 
         //- Construct from file name (uses extension to determine type)
-        edgeMesh(const fileName&, const word& ext);
+        edgeMesh(const fileName& name, const word& ext);
-
-        //- Construct from Istream
-        edgeMesh(Istream&);
 
 
     // Declare run-time constructor selection table
@@ -167,12 +164,12 @@ public:
         //- Select constructed from filename (explicit extension)
         static autoPtr<edgeMesh> New
         (
-            const fileName&,
+            const fileName& name,
             const word& ext
         );
 
         //- Select constructed from filename (implicit extension)
-        static autoPtr<edgeMesh> New(const fileName&);
+        static autoPtr<edgeMesh> New(const fileName& name);
 
 
     //- Destructor
@@ -195,7 +192,7 @@ public:
         );
 
         //- Write to file
-        static void write(const fileName&, const edgeMesh&);
+        static void write(const fileName& name, const edgeMesh& mesh);
 
 
     // Member Functions
@@ -204,15 +201,15 @@ public:
         void transfer(edgeMesh&);
 
         //- Transfer contents to the Xfer container
-        Xfer<edgeMesh > xfer();
+        Xfer<edgeMesh> xfer();
 
     // Read
 
         //- Read from file. Chooses reader based on explicit extension
-        bool read(const fileName&, const word& ext);
+        bool read(const fileName& name, const word& ext);
 
         //- Read from file. Chooses reader based on detected extension
-        virtual bool read(const fileName&);
+        virtual bool read(const fileName& name);
 
 
     // Access
@@ -245,13 +242,13 @@ public:
         );
 
         //- Scale points. A non-positive factor is ignored
-        virtual void scalePoints(const scalar);
+        virtual void scalePoints(const scalar scaleFactor);
 
-        //- Merge common points (points within mergeDist). Return map from
+        //- Geometric merge points (points within mergeDist) prior to
-        //  old to new points.
+        //  automatically calling mergeEdges().
-        virtual void mergePoints(const scalar mergeDist, labelList&);
+        virtual void mergePoints(const scalar mergeDist);
 
-        //- Merge duplicate edges
+        //- Merge duplicate edges and eliminate unused points.
         virtual void mergeEdges();
 
 
@@ -268,12 +265,12 @@ public:
 
     // Member Operators
 
-        inline void operator=(const edgeMesh&);
+        inline void operator=(const edgeMesh& rhs);
 
         // Ostream Operator
 
-            friend Ostream& operator<<(Ostream&, const edgeMesh&);
+            friend Ostream& operator<<(Ostream& os, const edgeMesh& em);
-            friend Istream& operator>>(Istream&, edgeMesh&);
+            friend Istream& operator>>(Istream& is, edgeMesh& em);
 
 };
 

src/edgeMesh/extendedEdgeMesh/extendedEdgeMesh.C

@@ -454,6 +454,34 @@ Foam::extendedEdgeMesh::extendedEdgeMesh(Istream& is)
 }
 
 
+Foam::extendedEdgeMesh::extendedEdgeMesh
+(
+    const pointField& points,
+    const edgeList& edges
+)
+:
+    edgeMesh(points, edges),
+    concaveStart_(0),
+    mixedStart_(0),
+    nonFeatureStart_(0),
+    internalStart_(0),
+    flatStart_(0),
+    openStart_(0),
+    multipleStart_(0),
+    normals_(0),
+    normalVolumeTypes_(0),
+    edgeDirections_(0),
+    normalDirections_(0),
+    edgeNormals_(0),
+    featurePointNormals_(0),
+    featurePointEdges_(0),
+    regionEdges_(0),
+    pointTree_(),
+    edgeTree_(),
+    edgeTreesByType_()
+{}
+
+
 Foam::extendedEdgeMesh::extendedEdgeMesh
 (
     const Xfer<pointField>& pointLst,

src/edgeMesh/extendedEdgeMesh/extendedEdgeMesh.H

@@ -250,7 +250,7 @@ public:
         static label nEdgeTypes;
 
         //- Can we read this file format?
-        static bool canRead(const fileName&, const bool verbose=false);
+        static bool canRead(const fileName& name, const bool verbose=false);
 
         //- Can we read this file format?
         static bool canReadType(const word& ext, const bool verbose=false);
@@ -268,7 +268,7 @@ public:
         extendedEdgeMesh();
 
         //- Construct as copy
-        explicit extendedEdgeMesh(const extendedEdgeMesh&);
+        explicit extendedEdgeMesh(const extendedEdgeMesh& fem);
 
         //- Construct from file name (uses extension to determine type)
         extendedEdgeMesh(const fileName&);
@@ -277,13 +277,16 @@ public:
         extendedEdgeMesh(const fileName&, const word& ext);
 
         //- Construct from Istream
-        extendedEdgeMesh(Istream&);
+        extendedEdgeMesh(Istream& is);
+
+        //- Construct from components
+        extendedEdgeMesh(const pointField& points, const edgeList& edges);
 
         //- Construct by transferring components (points, edges)
         extendedEdgeMesh
         (
-            const Xfer<pointField>&,
+            const Xfer<pointField>& pointLst,
-            const Xfer<edgeList>&
+            const Xfer<edgeList>& edgeLst
         );
 
         //- Construct given a surface with selected edges,points
@@ -346,12 +349,12 @@ public:
         //- Select constructed from filename (explicit extension)
         static autoPtr<extendedEdgeMesh> New
         (
-            const fileName&,
+            const fileName& name,
             const word& ext
         );
 
         //- Select constructed from filename (implicit extension)
-        static autoPtr<extendedEdgeMesh> New(const fileName&);
+        static autoPtr<extendedEdgeMesh> New(const fileName& name);
 
 
     //- Destructor
@@ -509,16 +512,16 @@ public:
         // Edit
 
             //- Transfer the contents of the argument and annul the argument
-            void transfer(extendedEdgeMesh&);
+            void transfer(extendedEdgeMesh& mesh);
 
             //- Transfer contents to the Xfer container
-            Xfer<extendedEdgeMesh > xfer();
+            Xfer<extendedEdgeMesh> xfer();
 
             //- Clear all storage
             virtual void clear();
 
             //- Add extendedEdgeMesh. No filtering of duplicates.
-            void add(const extendedEdgeMesh&);
+            void add(const extendedEdgeMesh& fem);
 
             //- Flip normals. All concave become convex, all internal external
             //  etc.
@@ -527,8 +530,8 @@ public:
             //- Update with derived geometry
             void autoMap
             (
-                const pointField&,
+                const pointField& subPoints,
-                const edgeList&,
+                const edgeList& subEdges,
                 const labelList& pointMap,
                 const labelList& edgeMap
             );
@@ -565,10 +568,10 @@ public:
         // Read
 
             //- Read from file. Chooses reader based on explicit extension
-            bool read(const fileName&, const word& ext);
+            bool read(const fileName& name, const word& ext);
 
             //- Read from file. Chooses reader based on detected extension
-            virtual bool read(const fileName&);
+            virtual bool read(const fileName& name);
 
 
         // Write