Merge branch 'master' into carpmeshIO

Author: dcwhite

src/Core/Algorithms/Legacy/Fields/MeshDerivatives/GetFieldBoundaryAlgo.cc

@@ -53,15 +53,10 @@ GetFieldBoundaryAlgo::GetFieldBoundaryAlgo()
   addOption(AlgorithmParameterName("mapping"),"auto","auto|node|elem|none");
 }
 
-struct IndexHash {
-  static const size_t bucket_size = 4;
-  static const size_t min_buckets = 8;
-  
+struct IndexHash 
+{
   size_t operator()(const index_type &idx) const
     { return (static_cast<size_t>(idx)); }
-  
-  bool operator()(const index_type &i1, const index_type &i2) const
-    { return (i1 < i2); }
 };
 
 bool 
@@ -70,7 +65,7 @@ GetFieldBoundaryAlgo::run(FieldHandle input, FieldHandle& output, MatrixHandle&
   ScopedAlgorithmStatusReporter asr(this, "GetFieldBoundary");
 
   /// Define types we need for mapping
-  typedef boost::unordered_map<index_type,index_type,IndexHash> hash_map_type;
+  using hash_map_type = boost::unordered_map<index_type,index_type,IndexHash>;
 
   hash_map_type node_map;
   hash_map_type elem_map;
@@ -94,7 +89,7 @@ GetFieldBoundaryAlgo::run(FieldHandle input, FieldHandle& output, MatrixHandle&
   }
 
   /// Figure out which type of field the output is:
-  bool found_method = false;
+  auto found_method = false;
   if (fi.is_hex_element())    { fo.make_quadsurfmesh(); found_method = true; }
   if (fi.is_prism_element())  { fo.make_quadsurfmesh(); found_method = true; }
   if (fi.is_tet_element())    { fo.make_trisurfmesh(); found_method = true; }
@@ -123,13 +118,13 @@ GetFieldBoundaryAlgo::run(FieldHandle input, FieldHandle& output, MatrixHandle&
   }
 
   /// Get the virtual interfaces:
-  VMesh* imesh = input->vmesh();
-  VMesh* omesh = output->vmesh();
-  VField* ifield = input->vfield();
-  VField* ofield = output->vfield();
-  
-  imesh->synchronize(Mesh::DELEMS_E|Mesh::ELEM_NEIGHBORS_E);
-  
+  auto imesh = input->vmesh();
+  auto omesh = output->vmesh();
+  auto ifield = input->vfield();
+  auto ofield = output->vfield();
+
+  imesh->synchronize(Mesh::DELEMS_E | Mesh::ELEM_NEIGHBORS_E);
+
   /// These are all virtual iterators, virtual index_types and array_types
   VMesh::Elem::iterator be, ee;
   VMesh::Elem::index_type nci, ci;
@@ -148,31 +143,31 @@ GetFieldBoundaryAlgo::run(FieldHandle input, FieldHandle& output, MatrixHandle&
   imesh->begin(be); 
   imesh->end(ee);
 
-  while (be != ee) 
+  while (be != ee)
   {
     checkForInterruption();
     ci = *be;
-    imesh->get_delems(delems,ci);
-    for (size_t p =0; p < delems.size(); p++)
+    imesh->get_delems(delems, ci);
+    for (size_t p = 0; p < delems.size(); p++)
     {
-      bool includeface = false;
-      
-      if(!(imesh->get_neighbor(nci,ci,delems[p]))) includeface = true;
+      auto includeface = false;
+
+      if (!(imesh->get_neighbor(nci, ci, delems[p]))) includeface = true;
 
       if (includeface)
       {
-        imesh->get_nodes(inodes,delems[p]);
+        imesh->get_nodes(inodes, delems[p]);
         onodes.resize(inodes.size());
 
-        for (size_t q=0; q<inodes.size(); q++)
+        for (size_t q = 0; q < inodes.size(); q++)
         {
           a = inodes[q];
-          hash_map_type::iterator it = node_map.find(a);
+          auto it = node_map.find(a);
           if (it == node_map.end())
           {
-            imesh->get_center(point,a);
+            imesh->get_center(point, a);
             onodes[q] = omesh->add_node(point);
-            node_map[a] = onodes[q];            
+            node_map[a] = onodes[q];
           }
           else
           {
@@ -184,11 +179,11 @@ GetFieldBoundaryAlgo::run(FieldHandle input, FieldHandle& output, MatrixHandle&
     }
     ++be;
   }
-  
+
   mapping.reset();
-  
+
   ofield->resize_fdata();
-  
+
   if (
     (
     (ifield->basis_order() == 0)
@@ -308,12 +303,12 @@ GetFieldBoundaryAlgo::run(FieldHandle input, FieldHandle& output, MatrixHandle&
 /// project nodes on.
 
 bool 
-GetFieldBoundaryAlgo::run(FieldHandle input, FieldHandle& output)
+GetFieldBoundaryAlgo::run(FieldHandle input, FieldHandle& output) const
 {
   ScopedAlgorithmStatusReporter asr(this, "GetFieldBoundary");
 
   /// Define types we need for mapping
-  typedef boost::unordered_map<index_type,index_type,IndexHash> hash_map_type;
+  using hash_map_type = boost::unordered_map<index_type,index_type,IndexHash>;
 
   hash_map_type node_map;
   hash_map_type elem_map;
@@ -337,7 +332,7 @@ GetFieldBoundaryAlgo::run(FieldHandle input, FieldHandle& output)
   }
 
   /// Figure out which type of field the output is:
-  bool found_method = false;
+  auto found_method = false;
   if (fi.is_hex_element())    { fo.make_quadsurfmesh(); found_method = true; }
   if (fi.is_prism_element())  { fo.make_quadsurfmesh(); found_method = true; }
   if (fi.is_tet_element())    { fo.make_trisurfmesh(); found_method = true; }
@@ -366,10 +361,10 @@ GetFieldBoundaryAlgo::run(FieldHandle input, FieldHandle& output)
   }
 
   /// Get the virtual interfaces:
-  VMesh* imesh = input->vmesh();
-  VMesh* omesh = output->vmesh();
-  VField* ifield = input->vfield();
-  VField* ofield = output->vfield();
+  auto imesh = input->vmesh();
+  auto omesh = output->vmesh();
+  auto ifield = input->vfield();
+  auto ofield = output->vfield();
 
   imesh->synchronize(Mesh::DELEMS_E|Mesh::ELEM_NEIGHBORS_E);
 
@@ -391,30 +386,30 @@ GetFieldBoundaryAlgo::run(FieldHandle input, FieldHandle& output)
   imesh->begin(be); 
   imesh->end(ee);
 
-  while (be != ee) 
+  while (be != ee)
   {
     checkForInterruption();
     ci = *be;
-    imesh->get_delems(delems,ci);
-    for (size_t p =0; p < delems.size(); p++)
+    imesh->get_delems(delems, ci);
+    for (size_t p = 0; p < delems.size(); p++)
     {
-      bool includeface = false;
-      
-      if(!(imesh->get_neighbor(nci,ci,delems[p]))) includeface = true;
+      auto includeface = false;
+
+      if (!(imesh->get_neighbor(nci, ci, delems[p]))) includeface = true;
 
       if (includeface)
       {
-        imesh->get_nodes(inodes,delems[p]);
+        imesh->get_nodes(inodes, delems[p]);
         if (onodes.size() == 0) onodes.resize(inodes.size());
-        for (size_t q=0; q<onodes.size(); q++)
+        for (size_t q = 0; q < onodes.size(); q++)
         {
           a = inodes[q];
-          hash_map_type::iterator it = node_map.find(a);
+          auto it = node_map.find(a);
           if (it == node_map.end())
           {
-            imesh->get_center(point,a);
+            imesh->get_center(point, a);
             onodes[q] = omesh->add_node(point);
-            node_map[a] = onodes[q];            
+            node_map[a] = onodes[q];
           }
           else
           {

src/Core/Algorithms/Legacy/Fields/MeshDerivatives/GetFieldBoundaryAlgo.h

@@ -52,7 +52,7 @@ class SCISHARE GetFieldBoundaryAlgo : public AlgorithmBase, public Thread::Inter
   /// With mapping
   bool run(FieldHandle input, FieldHandle& output, Datatypes::MatrixHandle& mapping) const;
   /// Without mapping
-  bool run(FieldHandle input, FieldHandle& output);
+  bool run(FieldHandle input, FieldHandle& output) const;
 
   AlgorithmOutput run(const AlgorithmInput& input) const;
 };

src/Core/Application/Preferences/CMakeLists.txt

@@ -46,6 +46,12 @@ TARGET_LINK_LIBRARIES(Core_Application_Preferences
   ${SCI_BOOST_LIBRARY}
 )
 
+IF(BUILD_WITH_PYTHON)
+TARGET_LINK_LIBRARIES(Core_Application_Preferences
+  Core_Python
+)
+ENDIF()
+
 IF(BUILD_SHARED_LIBS)
   ADD_DEFINITIONS(-DBUILD_Core_Application_Preferences)
 ENDIF(BUILD_SHARED_LIBS)

src/Core/Application/Preferences/Preferences.cc

@@ -33,6 +33,9 @@
 #include <boost/algorithm/string/predicate.hpp>
 #include <boost/algorithm/string/split.hpp>
 #include <boost/algorithm/string/classification.hpp>
+#ifdef BUILD_WITH_PYTHON
+#include <Core/Python/PythonInterpreter.h>
+#endif
 
 using namespace SCIRun::Core;
 using namespace SCIRun::Core::Logging;
@@ -80,6 +83,11 @@ void Preferences::setDataDirectory(const boost::filesystem::path& path)
 
   AlgorithmParameterHelper::setDataDir(dataDir_);
   AlgorithmParameterHelper::setDataDirPlaceholder(dataDirectoryPlaceholder());
+
+#ifdef BUILD_WITH_PYTHON
+  auto setDataDir = "import os; os.environ[\"SCIRUNDATADIR\"] = \"" + dataDir_.string() + "\"";
+  PythonInterpreter::Instance().run_string(setDataDir);
+#endif
 }
 
 /// @todo: not sure where this should go.

src/Core/Datatypes/Legacy/Field/HexVolMesh.h

@@ -60,6 +60,7 @@
 
 #include <Core/Thread/Mutex.h>
 #include <Core/Thread/ConditionVariable.h>
+#include <boost/unordered_map.hpp>
 #include <boost/thread.hpp>
 
 #include <set>
@@ -2732,29 +2733,10 @@ class HexVolMesh : public Mesh
     }
   };
 
-/// Define the hash_map type, as this is not yet an approved type under Windows
-/// it is located in stdext
-
-#ifdef HAVE_HASH_MAP
-  #if defined(_WIN32)
-    /// hash_map is in stdext namespace
-    typedef stdext::hash_map<PFace, typename Face::index_type, FaceHash> face_ht;
-    typedef stdext::hash_map<PFaceNode, typename Face::index_type, FaceHash> face_nt;
-    typedef stdext::hash_map<PEdge, typename Edge::index_type, EdgeHash> edge_ht;
-    typedef stdext::hash_map<PEdgeNode, typename Edge::index_type, EdgeHash> edge_nt;
-  #else
-    /// hash_map is in std namespace
-    typedef hash_map<PFace, typename Face::index_type, FaceHash> face_ht;
-    typedef hash_map<PFaceNode, typename Face::index_type, FaceHash> face_nt;
-    typedef hash_map<PEdge, typename Edge::index_type, EdgeHash> edge_ht;
-    typedef hash_map<PEdgeNode, typename Edge::index_type, EdgeHash> edge_nt;
-  #endif
-#else
-  typedef std::map<PFace, typename Face::index_type, FaceHash> face_ht;
-  typedef std::map<PFaceNode, typename Face::index_type, FaceHash> face_nt;
-  typedef std::map<PEdge, typename Edge::index_type, EdgeHash> edge_ht;
-  typedef std::map<PEdgeNode, typename Edge::index_type, EdgeHash> edge_nt;
-#endif
+  using face_ht = boost::unordered_map<PFace, typename Face::index_type, FaceHash>;
+  using face_nt = boost::unordered_map<PFaceNode, typename Face::index_type, FaceHash>;
+  using edge_ht = boost::unordered_map<PEdge, typename Edge::index_type, EdgeHash>;
+  using edge_nt = boost::unordered_map<PEdgeNode, typename Edge::index_type, EdgeHash>;
 
   typedef std::vector<PFaceCell> face_ct;
   typedef std::vector<PEdgeCell> edge_ct;

src/Core/Datatypes/Legacy/Field/PrismVolMesh.h

@@ -41,7 +41,6 @@
 #include <Core/GeometryPrimitives/BBox.h>
 #include <Core/GeometryPrimitives/CompGeom.h>
 #include <Core/GeometryPrimitives/Point.h>
-#include <Core/GeometryPrimitives/Plane.h>
 #include <Core/GeometryPrimitives/Transform.h>
 #include <Core/GeometryPrimitives/Vector.h>
 
@@ -58,6 +57,7 @@
 #include <Core/Utils/Legacy/CheckSum.h>
 
 #include <boost/thread.hpp>
+#include <boost/unordered_map.hpp>
 #include <Core/Thread/Mutex.h>
 #include <Core/Thread/ConditionVariable.h>
 
@@ -2468,23 +2468,8 @@ class PrismVolMesh : public Mesh
     }
   };
 
-/// Define the hash_map type, as this is not yet an approved type under Windows
-/// it is located in stdext
-
-#ifdef HAVE_HASH_MAP
-  #if defined(_WIN32)
-    /// hash_map is in stdext namespace
-    typedef stdext::hash_map<PFace, typename Face::index_type, FaceHash> face_ht;
-    typedef stdext::hash_map<PEdge, typename Edge::index_type, EdgeHash> edge_ht;
-  #else
-    /// hash_map is in std namespace
-    typedef hash_map<PFace, typename Face::index_type, FaceHash> face_ht;
-    typedef hash_map<PEdge, typename Edge::index_type, EdgeHash> edge_ht;
-  #endif
-#else
-  typedef std::map<PFace, typename Face::index_type, FaceHash> face_ht;
-  typedef std::map<PEdge, typename Edge::index_type, EdgeHash> edge_ht;
-#endif
+  using face_ht = boost::unordered_map<PFace, typename Face::index_type, FaceHash>;
+  using edge_ht = boost::unordered_map<PEdge, typename Edge::index_type, EdgeHash>;
 
   /// container for face storage. Must be computed each time
   ///  nodes or cells change.