Replace vtkTheshold with VtkUtils_ThresholdSurface() VtkUtils_Thresho…

…ldUgrid() functions.

Code/Source/sv/Geometry/sv_sys_geom.cxx

@@ -4126,32 +4126,40 @@ int sys_geom_set_ids_for_caps( cvPolyData *pd,cvPolyData **outpd,int **doublecap
  for (int i = 0; i < facemax; i++)
  {
  double facecaprange[2];
- vtkNew(vtkThreshold,threshold1);
+ auto threshold_surface = VtkUtils_ThresholdSurface(i+1.0, i+1.0, "ModelFaceID", geom);
+ /* dp
+ vtkNew(vtkThreshold, threshold1);
  threshold1->SetInputData(geom);
  threshold1->SetInputArrayToProcess(0,0,0,1,"ModelFaceID");
- //dp threshold1->ThresholdBetween(i+1,i+1);
+ threshold1->ThresholdBetween(i+1,i+1);
  threshold1->Update();
 
  vtkNew(vtkDataSetSurfaceFilter,surfacer);
  surfacer->SetInputData(threshold1->GetOutput());
  surfacer->Update();
+ */
 
- vtkNew(vtkIntArray,modelfacecaps);
+ vtkNew(vtkIntArray, modelfacecaps);
 
- if (VtkUtils_PDCheckArrayName(surfacer->GetOutput(),1,"CapID") != SV_OK)
+ if (VtkUtils_PDCheckArrayName(threshold_surface, 1, "CapID") != SV_OK)
+ //dp if (VtkUtils_PDCheckArrayName(surfacer->GetOutput(),1,"CapID") != SV_OK)
  {
  fprintf(stderr,"Second\n");
  fprintf(stderr,"CapID Array is not on the surface\n");
  delete [] capone;
  delete [] captwo;
  return SV_ERROR;
  }
- modelfacecaps = vtkIntArray::SafeDownCast(surfacer->GetOutput()->
- GetCellData()->GetArray("CapID"));
+
+ modelfacecaps = vtkIntArray::SafeDownCast(threshold_surface->GetCellData()->GetArray("CapID"));
+ //dp modelfacecaps = vtkIntArray::SafeDownCast(surfacer->GetOutput()->GetCellData()->GetArray("CapID"));
+
  capone[i] = 0;
  captwo[i] = 0;
  (*doublecaps)[i] = 0;
- for (int j = 0; j < surfacer->GetOutput()->GetNumberOfCells();j++)
+
+ for (int j = 0; j < threshold_surface->GetNumberOfCells();j++)
+ //dp for (int j = 0; j < surfacer->GetOutput()->GetNumberOfCells();j++)
  {
  if (modelfacecaps->GetValue(j) == 1)
  capone[i] = 1;

Code/Source/sv/Mesh/VMTKUtils/sv_vmtk_utils.cxx

@@ -40,6 +40,7 @@
  */
 
 #include "sv_vmtk_utils.h"
+#include "sv_vtk_utils.h"
 
 #include "SimVascular.h"
 #include "sv_tetgenmesh_utils.h"
@@ -1612,38 +1613,47 @@ int VMTKUtils_CreateBoundaryLayerSurfaceAndCaps(vtkUnstructuredGrid* boundaryMes
 
  // Create boundary layer surface mesh from cells with 'isSurface' array value 1. 
  //
+ /* dp
  auto thresholder = vtkSmartPointer<vtkThreshold>::New();
  thresholder->SetInputData(boundaryMesh);
  thresholder->SetInputArrayToProcess(0, 0, 0, 1, "isSurface");
- //dp thresholder->ThresholdBetween(1, 1);
+ thresholder->ThresholdBetween(1, 1);
  thresholder->Update();
 
  auto surfacer = vtkSmartPointer<vtkDataSetSurfaceFilter>::New();
  surfacer->SetInputData(thresholder->GetOutput());
  surfacer->Update();
 
  boundaryMeshSurface->DeepCopy(surfacer->GetOutput());
+ */
+ auto threshold_surface = VtkUtils_ThresholdSurface(1.0, 1.0, "isSurface", boundaryMesh);
+ boundaryMeshSurface->DeepCopy(threshold_surface);
 
  // Create boundary layer volume mesh from cells with 'isSurface' array value 0. 
  //
+ /* dp
  thresholder->SetInputData(boundaryMesh);
  thresholder->SetInputArrayToProcess(0, 0, 0, 1, "isSurface");
- //dp thresholder->ThresholdBetween(0, 0);
+ thresholder->ThresholdBetween(0, 0);
  thresholder->Update();
-
  boundaryMeshVolume->DeepCopy(thresholder->GetOutput());
+ */
+ auto threshold_volume = VtkUtils_ThresholdUgrid(0.0, 0.0, "isSurface", boundaryMesh);
+ boundaryMeshVolume->DeepCopy(threshold_volume);
 
  // Create boundary layer mesh caps from cells with 'WallID' array value 0. 
  //
+ /* dp
  thresholder->SetInputData(surfaceWithSize);
  thresholder->SetInputArrayToProcess(0,0,0,1,"WallID");
- //dp thresholder->ThresholdBetween(0,0);
+ dp thresholder->ThresholdBetween(0,0);
  thresholder->Update();
-
  surfacer->SetInputData(thresholder->GetOutput());
  surfacer->Update();
-
  surfaceMeshCaps->DeepCopy(surfacer->GetOutput());
+ */
+ auto threshold_caps = VtkUtils_ThresholdSurface(0.0, 0.0, "WallID", surfaceWithSize);
+ surfaceMeshCaps->DeepCopy(threshold_caps);
 
  // Set the values of the 'ModelFaceID' array for the caps to 9999(?). 
  //

Code/Source/sv/Model/OCCTSolidModel/sv_OCCTSolidModel.cxx

@@ -1707,33 +1707,36 @@ int cvOCCTSolidModel::GetOnlyPD(vtkPolyData *pd,double &max_dist) const
  cleaner->SetInputData(pd);
  cleaner->PointMergingOn();
  cleaner->Update();
+
+ auto threshold_surface = VtkUtils_ThresholdSurface(7.0, 7.0, "MESH_TYPES", cleaner->GetOutput());
+
+ #ifdef dp_old 
  vtkSmartPointer<vtkThreshold> thresholder =
  vtkSmartPointer<vtkThreshold>::New();
  thresholder->SetInputData(cleaner->GetOutput());
+
  //Set Input Array to 0 port,0 connection,1 for Cell Data, and MESh_TYPES is the type name
- thresholder->SetInputArrayToProcess(0,0,0,1,"MESH_TYPES");
  //Source polydata is on MESH_TYPE 7
- //dp thresholder->ThresholdBetween(7,7);
+ thresholder->SetInputArrayToProcess(0,0,0,1,"MESH_TYPES");
+ thresholder->ThresholdBetween(7,7);
  thresholder->Update();
  //Extract surface
  vtkSmartPointer<vtkDataSetSurfaceFilter> surfacer =
  vtkSmartPointer<vtkDataSetSurfaceFilter>::New();
  surfacer->SetInputData(thresholder->GetOutput());
  surfacer->Update();
- //For polydata of just edges, MESH_TYPE is not 7
- //Only want if not edges
- //fprintf(stderr,"Num Points bef! %d\n",surfacer->GetOutput()->GetNumberOfPoints());
- // vtkSmartPointer<vtkQuadricDecimation> decimator =
- // vtkSmartPointer<vtkQuadricDecimation>::New();
- // decimator->SetInputData(surfacer->GetOutput());
- // decimator->SetTargetReduction(0.2);
- // decimator->GetOutput();
- // pd->DeepCopy(decimator->GetOutput());
+ #endif
+
+ if (threshold_surface->GetNumberOfPoints() != 0)
+ {
+ pd->DeepCopy(threshold_surface);
+ }
+ /* dp
  if (surfacer->GetOutput()->GetNumberOfPoints() != 0)
  {
  pd->DeepCopy(surfacer->GetOutput());
  }
- //fprintf(stderr,"Num Points now! %d\n",pd->GetNumberOfPoints());
+ */
  }
 
  return SV_OK;

Code/Source/sv/Utils/sv_vtk_utils.cxx

@@ -38,13 +38,16 @@
 #include "sv_misc_utils.h"
 #include "sv_cgeom.h"
 
+#include <vtkDataSetSurfaceFilter.h>
+#include <vtkSmartPointer.h>
+#include <vtkThreshold.h>
+#include <vtkUnstructuredGrid.h>
 
 #define START -1
 #define INTERMED 0
 #define DEADEND 1
 #define CLOSED 2
 
-
 typedef struct {
  double x, y, z;
  int postId;
@@ -78,6 +81,47 @@ static int GetStartPt( int *state, int stateSz );
 static int UpdateCells( int *cells, int numCells,
  vtkIdType **newCells, int *numNewCells );
 
+//-------------------------
+// VtkUtils_ThresholdUgrid
+//-------------------------
+// Create a vtkUnstructuredGrid object from a threshold of a cellular 
+// data array contained in a vtkDataObject object.
+//
+vtkSmartPointer<vtkUnstructuredGrid>
+VtkUtils_ThresholdUgrid(const double lower, const double upper, const std::string& data_name, 
+ vtkDataObject* vtk_data)
+{
+ int idx = 0;
+ int port = 0;
+ int connection = 0;
+ auto fieldAssociation = vtkDataObject::FieldAssociations::FIELD_ASSOCIATION_CELLS;
+
+ auto threshold = vtkSmartPointer<vtkThreshold>::New();
+ threshold->SetLowerThreshold(lower);
+ threshold->SetUpperThreshold(upper);
+ threshold->SetInputData(vtk_data);
+ threshold->SetInputArrayToProcess(idx, port, connection, fieldAssociation, data_name.c_str());
+ threshold->Update();
+ return threshold->GetOutput();
+}
+
+//---------------------------
+// VtkUtils_ThresholdSurface
+//---------------------------
+// Create a vtkPolyData object from a threshold of a cellular 
+// data array contained in a vtkDataObject object.
+//
+vtkSmartPointer<vtkPolyData>
+VtkUtils_ThresholdSurface(const double lower, const double upper, const std::string& data_name, 
+ vtkDataObject* vtk_data)
+{
+ auto threshold_ugrid = VtkUtils_ThresholdUgrid(lower, upper, data_name, vtk_data);
+
+ auto surfacer = vtkSmartPointer<vtkDataSetSurfaceFilter>::New();
+ surfacer->SetInputData(vtk_data);
+ surfacer->Update();
+ return surfacer->GetOutput();
+}
 
 // -----------------------
 // VtkUtils_NewVtkPolyData

Code/Source/sv/Utils/sv_vtk_utils.h

@@ -59,6 +59,14 @@ int SV_EXPORT_UTILS VtkUtils_NewVtkPolyDataLines( vtkPolyData **pd, int numPts,
 // same (potentially redundant) point set, and just change the id's
 // that get used by Lines and Polys.
 
+vtkSmartPointer<vtkUnstructuredGrid>
+VtkUtils_ThresholdUgrid(const double lower, const double upper, const std::string& data_name, 
+ vtkDataObject* vtk_data);
+
+vtkSmartPointer<vtkPolyData>
+VtkUtils_ThresholdSurface(const double lower, const double upper, const std::string& data_name, 
+ vtkDataObject* vtk_data);
+
 int SV_EXPORT_UTILS VtkUtils_FixTopology( vtkPolyData *pd, double tol );
 
 int SV_EXPORT_UTILS VtkUtils_GetPoints( vtkPolyData *pd, double **pts, int *numPts );

Code/Source/sv2/ImageProcessing/sv2_img_threshold.cxx

@@ -33,6 +33,8 @@
 #include "sv_VTK.h"
 #include "vtkThresholdPoints.h"
 
+// [TODO:DaveP] This does not seem to be used anywhere.
+//
 int img_threshold (vtkStructuredPoints *image, vtkFloatingPointType thrMin, vtkFloatingPointType thrMax,
  int max_num_pts, cvPolyData **result) {
 

Code/Source/sv3/Path/sv3_PathUtils.cxx

@@ -31,6 +31,7 @@
 
 #include "SimVascular.h"
 #include "sv3_PathUtils.h"
+#include "sv_vtk_utils.h"
 
 #include <vtkCellData.h>
 #include <vtkDataSetSurfaceFilter.h>
@@ -72,33 +73,40 @@ PathUtils::ExtractCenterlinesSections(vtkSmartPointer<vtkPolyData>& centerlines)
  // Extract sections based on cells with group IDs for each centerline ID.
  //
  for (int cid = minId; cid <= maxId; cid++) {
+ auto centerlinesCidThreshold = VtkUtils_ThresholdSurface(cid, cid, CenterlineIdsArrayName, centerlines);
+ /*dp
  auto threshold = vtkSmartPointer<vtkThreshold>::New();
  threshold->SetInputData(centerlines);
  threshold->SetInputArrayToProcess(0, 0, 0, "vtkDataObject::FIELD_ASSOCIATION_CELLS", CenterlineIdsArrayName.c_str());
- //dp threshold->ThresholdBetween(cid, cid);
+ threshold->ThresholdBetween(cid, cid);
  threshold->Update();
-
+ auto threshold_mesh = VtkUtils_ThresholdPolyData(CenterlineIdsArrayName, centerlines); 
  auto surfacer = vtkSmartPointer<vtkDataSetSurfaceFilter>::New();
- surfacer->SetInputData(threshold->GetOutput());
+ surfacer->SetInputData(threshold_mesh);
  surfacer->Update();
  auto centerlinesCidThreshold = surfacer->GetOutput();
+ */
 
  auto groupData = centerlinesCidThreshold->GetCellData()->GetArray(GroupIdsArrayName.c_str());
  double lowerValue = groupData->GetRange()[0];
  double upperValue = groupData->GetRange()[1];
 
+ auto group_threshold = VtkUtils_ThresholdSurface(lowerValue, upperValue, GroupIdsArrayName, centerlinesCidThreshold);
+ /* dp
  auto groupThreshold = vtkSmartPointer<vtkThreshold>::New();
  groupThreshold->SetInputData(centerlinesCidThreshold);
  groupThreshold->SetInputArrayToProcess(0, 0, 0, "vtkDataObject::FIELD_ASSOCIATION_CELLS", GroupIdsArrayName.c_str());
- //dp groupThreshold->ThresholdBetween(lowerValue, upperValue);
+ groupThreshold->ThresholdBetween(lowerValue, upperValue);
  groupThreshold->Update();
 
  auto groupSurfacer = vtkSmartPointer<vtkDataSetSurfaceFilter>::New();
  groupSurfacer->SetInputData(groupThreshold->GetOutput());
  groupSurfacer->Update();
+ */
 
  auto groupCenterlines = vtkSmartPointer<vtkPolyData>::New();
- groupCenterlines->DeepCopy(groupSurfacer->GetOutput());
+ groupCenterlines->DeepCopy(group_threshold);
+ //dp groupCenterlines->DeepCopy(groupSurfacer->GetOutput());
  pathsGeometry.push_back(groupCenterlines);
  }
 

Code/Source/sv4gui/Modules/Mesh/Common/sv4gui_MeshLegacyIO.cxx

@@ -33,6 +33,7 @@
 #include "sv4gui_MitkMeshIO.h"
 
 #include "sv_polydatasolid_utils.h"
+#include "sv_vtk_utils.h"
 
 #include <QDir>
 
@@ -185,10 +186,15 @@ bool sv4guiMeshLegacyIO::WriteFiles(mitk::DataNode::Pointer meshNode, sv4guiMode
 
  // Extract surface mesh.
  //
+ auto threshold_surface = VtkUtils_ThresholdSurface(i, i, "ModelRegionID", surfaceMesh);
+ if (threshold_surface->GetNumberOfCells() == 0) { 
+ continue;
+ }
+ /* dp
  auto surfThresholder = vtkSmartPointer<vtkThreshold>::New();
  surfThresholder->SetInputData(surfaceMesh);
  surfThresholder->SetInputArrayToProcess(0,0,0,1,"ModelRegionID");
- //dp surfThresholder->ThresholdBetween(i,i);
+ surfThresholder->ThresholdBetween(i,i);
  surfThresholder->Update();
  if (surfThresholder->GetOutput()->GetNumberOfCells() == 0) {
  continue;
@@ -200,23 +206,30 @@ bool sv4guiMeshLegacyIO::WriteFiles(mitk::DataNode::Pointer meshNode, sv4guiMode
  if (surfacer->GetOutput()->GetNumberOfCells() == 0) {
  continue;
  }
+ */
 
  // Extract volume mesh.
+ auto threshold_volume = VtkUtils_ThresholdUgrid(i, i, "ModelRegionID", volumeMesh);
+ if (threshold_volume->GetNumberOfCells() == 0) {
+ continue;
+ }
+ /* dp
  auto volumeThresholder = vtkSmartPointer<vtkThreshold>::New();
  volumeThresholder->SetInputData(volumeMesh);
  volumeThresholder->SetInputArrayToProcess(0,0,0,1,"ModelRegionID");
- //dp volumeThresholder->ThresholdBetween(i,i);
+ volumeThresholder->ThresholdBetween(i,i);
  volumeThresholder->Update();
  if (volumeThresholder->GetOutput()->GetNumberOfCells() == 0) {
  continue;
  }
+ */
 
  // Write meshes.
  //
  fprintf(stdout, "[sv4guiMeshLegacyIO::WriteFiles] Writing domain %d\n", i);
  QString newDir = meshDir+"_domain-" + QString::number(i);
  QDir().mkpath(newDir);
- if (WriteFiles(surfacer->GetOutput(), volumeThresholder->GetOutput(), modelElement, newDir) == false) {
+ if (WriteFiles(threshold_surface, threshold_volume, modelElement, newDir) == false) {
  return false;
  }
  }
@@ -322,10 +335,14 @@ bool sv4guiMeshLegacyIO::WriteFiles(vtkSmartPointer<vtkPolyData> surfaceMesh, vt
  if (connectFilter->GetNumberOfExtractedRegions() > 1) {
 
  for (int j = 0; j < connectFilter->GetNumberOfExtractedRegions(); j++) {
+ auto region_surface = VtkUtils_ThresholdSurface(j, j, "RegionId", connectFilter->GetOutput());
+ region_surface->GetCellData()->RemoveArray("RegionId");
+ region_surface->GetPointData()->RemoveArray("RegionId");
+ /* dp
  auto thresholder = vtkSmartPointer<vtkThreshold>::New();
  thresholder->SetInputData(connectFilter->GetOutput());
  thresholder->SetInputArrayToProcess(0,0,0,1,"RegionId");
- //dp thresholder->ThresholdBetween(j, j);
+ thresholder->ThresholdBetween(j, j);
  thresholder->Update();
 
  auto surfacer = vtkSmartPointer<vtkDataSetSurfaceFilter>::New();
@@ -334,6 +351,7 @@ bool sv4guiMeshLegacyIO::WriteFiles(vtkSmartPointer<vtkPolyData> surfaceMesh, vt
  surfacer->GetOutput()->GetCellData()->RemoveArray("RegionId");
  surfacer->GetOutput()->GetPointData()->RemoveArray("RegionId");
  auto region_surface = surfacer->GetOutput(); 
+ */
 
  vtpFilePath = meshDir + "/walls_combined_connected_region_" + QString::number(j) + ".vtp";
  vtpFilePath = QDir::toNativeSeparators(vtpFilePath);