unstructured vol

Author: Xuan Huang

src/Core/Algorithms/Visualization/OsprayDataAlgorithm.cc

@@ -327,11 +327,11 @@ OsprayGeometryObjectHandle OsprayDataAlgorithm::addQuadSurface(FieldHandle field
     return obj;
 }
 
-OsprayGeometryObjectHandle OsprayDataAlgorithm::addVol(FieldHandle field, ColorMapHandle colorMap) const
+OsprayGeometryObjectHandle OsprayDataAlgorithm::addStructVol(FieldHandle field, ColorMapHandle colorMap) const
 {
   auto obj = makeObject(field);
   obj->isVolume = true;
-  obj->GeomType="Volume";
+  obj->GeomType="structVol";
 
   auto& fieldData = obj->data;
 
@@ -340,21 +340,25 @@ OsprayGeometryObjectHandle OsprayDataAlgorithm::addVol(FieldHandle field, ColorM
 
   auto facade(field->mesh()->getFacade());
   auto vfield = field->vfield();
+  auto vmesh = field->vmesh();
+  
+  const BBox bbox = vmesh->get_bounding_box();
+  Vector size = bbox.diagonal();
+  Point center = bbox.center();
+  VMesh::dimension_type dim;
+  vmesh->get_dimensions(dim);
+  Vector dimensions_ = Vector(1.0,1.0,1.0);
+  for (size_t p=0;p<dim.size();p++) dimensions_[p] = static_cast<double>(dim[p]);
 
-  // //cast mesh to latvol and fill dim, space, origin
-  //auto latVolM = (boost::shared_ptr<LatVolMesh<Core::Basis::HexTrilinearLgn<Core::Geometry::Point> > >) field->mesh();
-  //std::vector<int> dim; latVolM->get_dim(dim);
-  // std::vector<float> min; latVolM.get_min(min);
-  /*fieldData.origin_x = latVolM->get_min_i();
-  fieldData.origin_y = latVolM->get_min_j();
-  fieldData.origin_z = latVolM->get_min_k();
-  fieldData.dim_x = latVolM->get_ni();
-  fieldData.dim_y = latVolM->get_nj();
-  fieldData.dim_z = latVolM->get_nk();*/
-  //get_ni
-  fieldData.dim_x = 100; fieldData.dim_y = 100; fieldData.dim_z = 100;
-  fieldData.origin_x = -1; fieldData.origin_y = -1; fieldData.origin_z = -1;
-  fieldData.spacing_x = 0.02; fieldData.spacing_y = 0.02; fieldData.spacing_z = 0.02;
+  fieldData.dim_x = dimensions_[0];
+  fieldData.dim_y = dimensions_[1];
+  fieldData.dim_z = dimensions_[2];
+  fieldData.origin_x = center.x() - size.x()/2.0;
+  fieldData.origin_y = center.y() - size.y()/2.0;
+  fieldData.origin_z = center.z() - size.z()/2.0;
+  fieldData.spacing_x = size.x()/dimensions_[0];
+  fieldData.spacing_y = size.y()/dimensions_[1];
+  fieldData.spacing_z = size.z()/dimensions_[2];
 
   double value;
   //std::cout << "mname:" << field->mesh()->type_name << std::endl;
@@ -372,15 +376,91 @@ OsprayGeometryObjectHandle OsprayDataAlgorithm::addVol(FieldHandle field, ColorM
     vertex_new.push_back(static_cast<float>(point.z()));
 
   }
+  //auto alpha = static_cast<float>(get(Parameters::DefaultColorA).toDouble());
+  if (colorMap)
+  {
+    ColorMap_OSP_helper cmp(colorMap->getColorMapName());
+    obj->tfn.colors = cmp.colorList;
+    
+    // set default opacity for now
+    // obj->tfn.opacities = cmp.opacityList;
+    auto alpha = static_cast<float>(get(Parameters::DefaultColorA).toDouble());
+    obj->tfn.opacities.push_back(alpha);
+    obj->tfn.opacities.push_back(alpha);
+  }
+  fieldData.color = voxels;
+  fieldData.vertex = vertex_new;
+  return obj;
+}
+
+OsprayGeometryObjectHandle OsprayDataAlgorithm::addUnstructVol(FieldHandle field, ColorMapHandle colorMap) const
+{
+  auto obj = makeObject(field);
+  obj->isVolume = true;
+  obj->GeomType="unstructVol";
+  
+  auto& fieldData = obj->data;
+  
+  std::vector<float> voxels;
+  std::vector<float> vertex_new;
+  std::vector<int32_t> index_new;
+  
+  auto facade(field->mesh()->getFacade());
+  auto vfield = field->vfield();
+  auto vmesh = field->vmesh();
+  
 
+  double value;
+  //std::cout << "mname:" << field->mesh()->type_name << std::endl;
+  for (const auto& node : facade->nodes())
+  {
+    auto point = node.point();
+    if (vfield->num_values() > 0)
+    {
+      vfield->get_value(value, node.index());
+      voxels.push_back(value);
+    }
+    vertex_new.push_back(static_cast<float>(point.x()));
+    vertex_new.push_back(static_cast<float>(point.y()));
+    vertex_new.push_back(static_cast<float>(point.z()));
+  }
+  
+  VMesh::Cell::iterator meshCellIter;
+  VMesh::Cell::iterator meshCellEnd;
+  vmesh->end(meshCellEnd);
+  
+  int numVPerCell = -1;
+  FieldInformation info(field);
+  
+  if(info.is_tetvol()) numVPerCell =4;
+  else numVPerCell =8;
+  //else THROW_ALGORITHM_INPUT_ERROR("hex or tet only for unstructured volume!");
+  
+  for (vmesh->begin(meshCellIter); meshCellIter != meshCellEnd; ++meshCellIter)
+  {
+    VMesh::Cell::index_type elemID = *meshCellIter;
+    VMesh::Node::array_type nodesFromCell(8);
+    vmesh->get_nodes(nodesFromCell, elemID);
+    for(int i=numVPerCell;i<8;i++)
+      nodesFromCell[i] = -4/(8-numVPerCell);
+    for(int i=numVPerCell;i<16-numVPerCell;i++){
+      index_new.push_back(nodesFromCell[i%8]);
+    }
+  }
   if (colorMap)
   {
     ColorMap_OSP_helper cmp(colorMap->getColorMapName());
     obj->tfn.colors = cmp.colorList;
-    obj->tfn.opacities = cmp.opacityList;
+    
+    // set default opacity for now
+    // obj->tfn.opacities = cmp.opacityList;
+    auto alpha = static_cast<float>(get(Parameters::DefaultColorA).toDouble());
+    obj->tfn.opacities.push_back(alpha);
+    obj->tfn.opacities.push_back(alpha);
   }
   fieldData.color = voxels;
   fieldData.vertex = vertex_new;
+  fieldData.index = index_new;
   return obj;
 }
 
@@ -546,7 +626,6 @@ AlgorithmOutput OsprayDataAlgorithm::run(const AlgorithmInput& input) const
   OsprayGeometryObjectHandle renderable;
 
   FieldInformation info(field);
-
   if (info.is_trisurfmesh())
   {
     // currently only supports one output, so no point in doing both
@@ -565,13 +644,16 @@ AlgorithmOutput OsprayDataAlgorithm::run(const AlgorithmInput& input) const
   }
   else if (info.is_volume())
   {
-    if(info.is_latvol()){
-      renderable = addVol(field, colorMap);
-    }else if(info.is_tetvol()){
-      THROW_ALGORITHM_INPUT_ERROR("Tet vol not supported. LatVol only at this point");
-    }else if(info.is_hexvol()){
+    if(info.is_hexvol()){
+      //renderable = addUnstructVol(field, colorMap);
       THROW_ALGORITHM_INPUT_ERROR("Hex vol not supported. LatVol only at this point");
-    }else{
+    }else if(info.is_latvol()){
+      renderable = addStructVol(field, colorMap);
+      //renderable = addStructVol(field, colorMap);
+    }else if(info.is_tetvol()){
+      renderable = addUnstructVol(field, colorMap);
+      //THROW_ALGORITHM_INPUT_ERROR("Tet vol not supported. LatVol only at this point");
+    }else {
       THROW_ALGORITHM_INPUT_ERROR("Unknown vol type. LatVol only at this point");
     }
   }

src/Core/Algorithms/Visualization/OsprayDataAlgorithm.h

@@ -68,7 +68,8 @@ namespace SCIRun
           Core::Datatypes::OsprayGeometryObjectHandle addSphere(FieldHandle field, Core::Datatypes::ColorMapHandle colorMap) const;
           Core::Datatypes::OsprayGeometryObjectHandle addTriSurface(FieldHandle field, Core::Datatypes::ColorMapHandle colorMap) const;
           Core::Datatypes::OsprayGeometryObjectHandle addQuadSurface(FieldHandle field, Core::Datatypes::ColorMapHandle colorMap) const;
-          Core::Datatypes::OsprayGeometryObjectHandle addVol(FieldHandle field, Core::Datatypes::ColorMapHandle colorMap) const;
+          Core::Datatypes::OsprayGeometryObjectHandle addStructVol(FieldHandle field, Core::Datatypes::ColorMapHandle colorMap) const;
+          Core::Datatypes::OsprayGeometryObjectHandle addUnstructVol(FieldHandle field, Core::Datatypes::ColorMapHandle colorMap) const;
           Core::Datatypes::OsprayGeometryObjectHandle addCylinder(FieldHandle field, Core::Datatypes::ColorMapHandle colorMap) const;
           void connected_component_edges(EdgeVector all_edges, std::vector<EdgeVector>& subsets, std::vector<int>& size_regions)const;
           void ReorderNodes(std::vector<int32_t> index, std::vector<int32_t> cc_index, std::vector<float> vertex, std::vector<float> color, std::vector<int32_t>& index_new, std::vector<float>& vertex_new,std::vector<float>& color_new) const;

src/Interface/Modules/Render/Ospray/VolumeViewer.cpp

@@ -766,32 +766,10 @@ void VolumeViewer::loadVolume(OSPVolume vol, const vec2f& voxelRange, const box3
   //  modelStates_.push_back(ModelState(ospNewModel()));
 
   assert(vol);
-  /*std::vector<float> colors;
-  std::vector<float> opacities;
-  colors.push_back(1);
-  colors.push_back(0);
-  colors.push_back(0);
-  colors.push_back(0);
-  colors.push_back(0);
-  colors.push_back(1);
-  opacities.push_back(0.5);
-  opacities.push_back(0.5);
-  OSPData cData = ospNewData(colors.size(), OSP_FLOAT3, colors.data());
-  OSPData oData = ospNewData(opacities.size(), OSP_FLOAT, opacities.data());
 
-  ospSetData(transferFunction, "colors", cData);
-  ospSetData(transferFunction, "opacities", oData);
-  
-  // the transfer function will apply over this volume value range
-  ospSet2f(transferFunction, "valueRange", 0, 1);
-  ospCommit(transferFunction);
-  // For now we set the same transfer function on all volumes.
-  ospSetObject(vol, "transferFunction", transferFunction);*/
   ospCommit(vol);
-
   // Add the loaded volume(s) to the model.
   ospAddVolume(modelStates_.back().model, vol);
-  //std::cout<<"load volume "<<(int)vol<<std::endl;
   assert(!bounds.empty());
   // Add to volumes vector for the current model.
   modelStates_.back().volumes.push_back(std::make_shared<ModelState::Volume>(vol, bounds, voxelRange));

src/Interface/Modules/Render/OsprayViewerDialog.cc

@@ -225,47 +225,84 @@ namespace
     const auto& radius = obj->radius;
     const auto& geom_type = obj->GeomType;
 
-    SCIRun::LOG_DEBUG("adding Volume");
-    OSPVolume vol = ospNewVolume("shared_structured_volume");
-    
-    //bounds = ospcommon::box3f(ospcommon::vec3f(0.f), 1);
-    
-    int numVoxels = obj->data.color.size();
-    OSPData voxelData = ospNewData(numVoxels, OSP_FLOAT, obj->data.color.data());
-    ospSetObject(vol, "voxelData", voxelData);
-    //ospRelease(voxelData);
-    SCIRun::LOG_DEBUG(std::to_string(numVoxels));
-    
-    ospSetString(vol, "voxelType", "float");
-    ospSet3i(vol, "dimensions", obj->data.dim_x, obj->data.dim_y, obj->data.dim_z);
-    ospSet3f(vol, "gridSpacing", fieldData.spacing_x, fieldData.spacing_y, fieldData.spacing_z);
-    ospSet3f(vol, "gridOrigin", fieldData.origin_x, fieldData.origin_y, fieldData.origin_z);
-    
-    std::for_each(obj->data.color.begin(), obj->data.color.end(), [&](float &v) {
-      if (!std::isnan(v))
-        voxelRange.extend(v);
-      //SCIRun::LOG_DEBUG(std::to_string(v));
-    });
-    for(int i=0;i<vertex.size();i+=3){
-      ospcommon::vec3f v = ospcommon::vec3f(vertex[i], vertex[i+1], vertex[i+2]);
-      bounds.extend(v);
-    }
     const auto& func = obj->tfn;
     OSPTransferFunction transferFunction = ospNewTransferFunction("piecewise_linear");
-    
-    
     OSPData cData = ospNewData(func.colors.size()/3, OSP_FLOAT3, func.colors.data());
     OSPData oData = ospNewData(func.opacities.size(), OSP_FLOAT, func.opacities.data());
 
     ospSetData(transferFunction, "colors", cData);
     ospSetData(transferFunction, "opacities", oData);
-    ospSet2f(transferFunction, "valueRange", voxelRange.lower, voxelRange.upper);
-    ospCommit(transferFunction);
-    ospSetObject(vol, "transferFunction", transferFunction);
-    return vol;
+    
+    if (boost::iequals(geom_type, "structVol"))
+    {
+      
+      SCIRun::LOG_DEBUG("adding Volume");
+      OSPVolume vol = ospNewVolume("shared_structured_volume");
+      
+      int numVoxels = obj->data.color.size();
+      OSPData voxelData = ospNewData(numVoxels, OSP_FLOAT, obj->data.color.data());
+      ospSetObject(vol, "voxelData", voxelData);
+      ospRelease(voxelData);
+      SCIRun::LOG_DEBUG(std::to_string(numVoxels));
+      
+      ospSetString(vol, "voxelType", "float");
+      ospSet3i(vol, "dimensions", obj->data.dim_x, obj->data.dim_y, obj->data.dim_z);
+      ospSet3f(vol, "gridSpacing", fieldData.spacing_x, fieldData.spacing_y, fieldData.spacing_z);
+      ospSet3f(vol, "gridOrigin", fieldData.origin_x, fieldData.origin_y, fieldData.origin_z);
+      
+      std::for_each(obj->data.color.begin(), obj->data.color.end(), [&](float &v) {
+        if (!std::isnan(v))
+          voxelRange.extend(v);
+        //SCIRun::LOG_DEBUG(std::to_string(v));
+      });
+      for(int i=0;i<vertex.size();i+=3){
+        ospcommon::vec3f v = ospcommon::vec3f(vertex[i], vertex[i+1], vertex[i+2]);
+        bounds.extend(v);
+      }
+      
+      ospSet2f(transferFunction, "valueRange", voxelRange.lower, voxelRange.upper);
+      ospCommit(transferFunction);
+      ospSetObject(vol, "transferFunction", transferFunction);
+      ospRelease(transferFunction);
+      return vol;
+    }else if (boost::iequals(geom_type, "unstructVol")){
+      SCIRun::LOG_DEBUG("adding unstructured Volume");
+      OSPVolume vol = ospNewVolume("unstructured_volume");
+      
+      //int numVoxels = obj->data.color.size();
+      OSPData vertexData = ospNewData(vertex.size()/3, OSP_FLOAT3, vertex.data());
+      OSPData fieldsData = ospNewData(color.size(), OSP_FLOAT, color.data());
+      OSPData indicesData = ospNewData(index.size()/4, OSP_INT4, index.data());
+      
+      
+      ospSetObject(vol, "vertices", vertexData);
+      ospSetData(vol, "field", fieldsData);
+      ospSetData(vol, "indices", indicesData);
+      
+      
+      ospRelease(vertexData);
+      ospRelease(fieldsData);
+      ospRelease(indicesData);
+      
+      std::for_each(obj->data.color.begin(), obj->data.color.end(), [&](float &v) {
+        if (!std::isnan(v))
+          voxelRange.extend(v);
+      });
+      for(int i=0;i<vertex.size();i+=3){
+        ospcommon::vec3f v = ospcommon::vec3f(vertex[i], vertex[i+1], vertex[i+2]);
+        bounds.extend(v);
+      }
+      
+      ospSet2f(transferFunction, "valueRange", voxelRange.lower, voxelRange.upper);
+      ospCommit(transferFunction);
+      ospSetObject(vol, "transferFunction", transferFunction);
+      ospRelease(transferFunction);
+      return vol;
+      
+    }
 
   }
-
+  
   ospcommon::box3f toOsprayBox(const BBox& box)
   {
     auto min = box.get_min();
@@ -431,7 +468,7 @@ void OsprayViewerDialog::createViewer(const CompositeOsprayGeometryObject& geom)
     std::vector<ospcommon::box3f> bounds_list;
 
     for (const auto& obj : geom.objects()){
-      if(boost::iequals(obj->GeomType, "Volume")){
+      if((boost::iequals(obj->GeomType, "structVol"))||(boost::iequals(obj->GeomType, "unstructVol")) )   {
         ospcommon::range1f r;
         ospcommon::box3f b;
         vol_list.push_back(duplicatedCodeFromAlgorithm_vol(obj, r, b));
@@ -441,8 +478,11 @@ void OsprayViewerDialog::createViewer(const CompositeOsprayGeometryObject& geom)
         impl_->geoms_.push_back(duplicatedCodeFromAlgorithm(obj));
     }
     viewer_ = new VolumeViewer(params, guiParams, { impl_->geoms_, toOsprayBox(geom.box) }, this);
-
+    
+    
     setupViewer(viewer_);
+    
+    SCIRun::LOG_DEBUG("num of vol: "+std::to_string(vol_list.size()));
     // load volume here
     for(int i=0;i<vol_list.size();i++){
       viewer_->loadVolume(vol_list[i], voxelRange_list[i].toVec2f(), bounds_list[i]);