Merge pull request #252 from mleotta/dev/volume-improvements

Volume improvements

doc/manuals/telesculptor.rst

@@ -102,7 +102,7 @@ Tool Bar
   Toggles visibility of the depth map (if avaialble) rendered as a 3D point
   cloud or mesh; see `3D Depth Map Options`_.
 
-:icon:`blank` Surface from Volume
+:icon:`volume` Surface from Volume
   Toggles the visibility of the surface mesh extracted from volumetric data.
   This option is disabled if no volume data is loaded; see
   `Volume Surface Options`_.
@@ -167,7 +167,7 @@ view as well.  See `Depth Map View`_.
 Volume Surface Options
 ----------------------
 
-The :action:`- Volume from Surface` pop-up provides additional controls on the
+The :action:`volume Volume from Surface` pop-up provides additional controls on the
 extraction and coloring of a surface from volumetric data.  The "Surface
 threshold" parameter controls the value of the iso-surface at which the surface
 is extracted from the volume.  The "Colorize surface" option, if checked,

gui/CMakeLists.txt

@@ -75,9 +75,7 @@ set(gui_moc_headers
   tools/BundleAdjustTool.h
   tools/CanonicalTransformTool.h
   tools/InitCamerasLandmarksTool.h
-  tools/MeshColoration.h
   tools/NeckerReversalTool.h
-  tools/ReconstructionData.h
   tools/TrackFilterTool.h
   tools/TrackFeaturesTool.h
 )

gui/Project.cxx

@@ -129,6 +129,10 @@ bool Project::read(QString const& path)
     {
       this->volumePath = getPath(config, base, "volume_file");
       this->imageListPath = getPath(config, base, "image_list_file");
+      if (this->imageListPath.isEmpty())
+      {
+        this->imageListPath = getPath(config, base, "video_source");
+      }
     }
 
     return true;

gui/WorldView.ui

@@ -273,6 +273,10 @@
    <property name="checkable">
     <bool>true</bool>
    </property>
+   <property name="icon">
+    <iconset resource="icons/icons.qrc">
+     <normaloff>:/icons/22x22/volume</normaloff>:/icons/22x22/volume</iconset>
+   </property>
    <property name="enabled">
     <bool>false</bool>
    </property>

gui/icons/icons.qrc

@@ -18,6 +18,7 @@
     <file alias="residual">16x16/residual.png</file>
     <file alias="save">16x16/save.png</file>
     <file alias="view-reset">16x16/view-reset.png</file>
+    <file alias="volume">16x16/volume.png</file>
   </qresource>
   <qresource prefix="icons/22x22">
     <file alias="camera">22x22/camera.png</file>
@@ -37,6 +38,7 @@
     <file alias="residual">22x22/residual.png</file>
     <file alias="save">22x22/save.png</file>
     <file alias="view-reset">22x22/view-reset.png</file>
+    <file alias="volume">22x22/volume.png</file>
   </qresource>
   <qresource prefix="icons/32x32">
     <file alias="telesculptor">32x32/telesculptor.png</file>

gui/tools/MeshColoration.cxx

@@ -143,8 +143,7 @@ static std::vector<std::string> ExtractAllKRTDFilePath(const char* globalPath, c
 
 
 //----------------------------------------------------------------------------
-// Description
-// Compute median of a vector
+/// Compute median of a vector
 template <typename T>
 static void ComputeMedian(std::vector<T> vector, double& median)
 {
@@ -178,35 +177,41 @@ MeshColoration::MeshColoration(vtkPolyData* mesh, std::string frameList, std::st
   this->frameList = ExtractAllFilePath(frameList.c_str());
   this->krtdFolder = ExtractAllKRTDFilePath(krtdFolder.c_str(), frameList.c_str());
   if (this->krtdFolder.size() < frameList.size())
-    {
+  {
     std::cerr << "Error, not enough krtd file for each vti file" << std::endl;
     return;
-    }
+  }
 
 }
 
 MeshColoration::~MeshColoration()
 {
   if (this->OutputMesh != 0)
+  {
     this->OutputMesh->Delete();
-  for (int i = 0; i < this->DataList.size(); i++)
-    {
+  }
+  for (size_t i = 0; i < this->DataList.size(); i++)
+  {
     delete this->DataList[i];
-    }
+  }
   this->DataList.clear();
 }
 
 void MeshColoration::SetInput(vtkPolyData* mesh)
 {
   if (this->OutputMesh != 0)
+  {
     this->OutputMesh->Delete();
+  }
   this->OutputMesh = mesh;
 }
 
 void MeshColoration::SetFrameSampling(int sample)
 {
   if (sample < 1)
+  {
     return;
+  }
   this->Sampling = sample;
 }
 
@@ -222,10 +227,10 @@ bool MeshColoration::ProcessColoration(std::string currentVtiPath)
   int nbDepthMap = (int)this->DataList.size();
 
   if (this->OutputMesh == 0 || nbDepthMap == 0 /*|| this->Sampling >= nbDepthMap*/)
-    {
+  {
     std::cerr << "Error when input has been set or during reading vti/krtd file path" << std::endl;
     return false;
-    }
+  }
 
   vtkPoints* meshPointList = this->OutputMesh->GetPoints();
   if (meshPointList == 0)
@@ -280,24 +285,26 @@ bool MeshColoration::ProcessColoration(std::string currentVtiPath)
 
 
     for (int idData = 0; idData < nbDepthMap; idData++)
-      {
+    {
       ReconstructionData* data = this->DataList[idData];
       vtkVector3d cameraCenter = data->GetCameraCenter();
       // Check if the 3D point is in front of the camera
       vtkVector3d cameraPointVec = vtkVector3d( position[0] - cameraCenter(0),
                                                 position[1] - cameraCenter(1),
                                                 position[2] - cameraCenter(2) );
       if (cameraPointVec.Dot(pointNormal)>0.0)
+      {
         continue;
+      }
       // project 3D point to pixel coordinates
       int pixelPosition[2];
       data->TransformWorldToDepthMapPosition(position, pixelPosition);
       // Test if pixel is inside depth map
       if (pixelPosition[0] < 0 || pixelPosition[0] >= depthMapDimensions[0] ||
           pixelPosition[1] < 0 || pixelPosition[1] >= depthMapDimensions[1])
-        {
+      {
         continue;
-        }
+      }
 
       double color[3];
       data->GetColorValue(pixelPosition, color);
@@ -309,7 +316,7 @@ bool MeshColoration::ProcessColoration(std::string currentVtiPath)
 
     // If we get elements
     if (list0.size() != 0)
-      {
+    {
       double sum0 = std::accumulate(list0.begin(), list0.end(), 0);
       double sum1 = std::accumulate(list1.begin(), list1.end(), 0);
       double sum2 = std::accumulate(list2.begin(), list2.end(), 0);
@@ -321,7 +328,7 @@ bool MeshColoration::ProcessColoration(std::string currentVtiPath)
       ComputeMedian<double>(list2, median2);
       medianValues->SetTuple3(id, median0, median1, median2);
       projectedDMValue->SetTuple1(id, list0.size());
-      }
+    }
 
     list0.clear();
     list1.clear();
@@ -337,7 +344,7 @@ bool MeshColoration::ProcessColoration(std::string currentVtiPath)
 
 void MeshColoration::initializeDataList(std::string currentVtiPath)
 {
-    int nbDepthMap = (int)frameList.size();
+  int nbDepthMap = (int)frameList.size();
 
   //Take a subset of depthmap
   if (currentVtiPath == "")

gui/tools/ReconstructionData.cxx

@@ -36,6 +36,8 @@
 // VTK includes
 #include "vtkDoubleArray.h"
 #include "vtkImageData.h"
+#include "vtkImageReader2Factory.h"
+#include "vtkImageReader2.h"
 #include "vtkVector.h"
 #include "vtkMatrix3x3.h"
 #include "vtkMatrix4x4.h"
@@ -44,7 +46,6 @@
 #include "vtkSmartPointer.h"
 #include "vtkTransform.h"
 #include "vtkUnsignedCharArray.h"
-#include "vtkPNGReader.h"
 
 
 namespace
@@ -161,25 +162,33 @@ ReconstructionData::ReconstructionData(std::string depthPath,
 ReconstructionData::~ReconstructionData()
 {
   if (this->DepthMap)
+  {
     this->DepthMap->Delete();
+  }
   if (this->MatrixK)
+  {
     this->MatrixK->Delete();
+  }
   if (this->MatrixRT)
+  {
     this->MatrixRT->Delete();
+  }
   if (this->Matrix4K)
+  {
     this->Matrix4K->Delete();
+  }
 }
 
 void ReconstructionData::GetColorValue(int* pixelPosition, double rgb[3])
 {
   vtkUnsignedCharArray* color =
-    vtkUnsignedCharArray::SafeDownCast(this->DepthMap->GetPointData()->GetArray("PNGImage"));
+    vtkUnsignedCharArray::SafeDownCast(this->DepthMap->GetPointData()->GetArray(0));
 
   if (color == 0)
-    {
+  {
     std::cerr << "Error, no 'Color' array exists" << std::endl;
     return;
-    }
+  }
 
   int* depthDims = this->DepthMap->GetDimensions();
 
@@ -241,24 +250,24 @@ void ReconstructionData::ApplyDepthThresholdFilter(double thresholdBestCost)
     vtkDoubleArray::SafeDownCast(this->DepthMap->GetPointData()->GetArray("Best Cost Values"));
 
   if (depths == 0)
-    {
+  {
     std::cerr << "Error during threshold, depths is empty" << std::endl;
     return;
-    }
+  }
 
   int nbTuples = depths->GetNumberOfTuples();
 
   if (bestCost->GetNumberOfTuples() != nbTuples)
     return;
 
   for (int i = 0; i < nbTuples; i++)
-    {
+  {
     double v_bestCost = bestCost->GetTuple1(i);
     if (v_bestCost > thresholdBestCost)
-      {
+    {
       depths->SetTuple1(i, -1);
-      }
     }
+  }
 }
 
 void ReconstructionData::TransformWorldToDepthMapPosition(const double* worldCoordinate,
@@ -279,46 +288,56 @@ void ReconstructionData::TransformWorldToDepthMapPosition(const double* worldCoo
 void ReconstructionData::SetDepthMap(vtkImageData* data)
 {
   if (this->DepthMap != 0)
+  {
     this->DepthMap->Delete();
+  }
   this->DepthMap = data;
   this->DepthMap->Register(0);
 }
 
 void ReconstructionData::SetMatrixK(vtkMatrix3x3* matrix)
 {
   if (this->MatrixK != 0)
+  {
     this->MatrixK->Delete();
+  }
   this->MatrixK = matrix;
   this->MatrixK->Register(0);
 
   if (this->Matrix4K != 0)
+  {
     this->Matrix4K->Delete();
+  }
   this->Matrix4K = vtkMatrix4x4::New();
   this->Matrix4K->Identity();
   for (int i = 0; i < 3; i++)
-    {
+  {
     for (int j = 0; j < 3; j++)
-      {
+    {
       this->Matrix4K->SetElement(i, j, this->MatrixK->GetElement(i, j));
-      }
     }
+  }
 
   this->TransformCameraToDepthMap->SetMatrix(this->Matrix4K);
 }
 
 void ReconstructionData::SetMatrixRT(vtkMatrix4x4* matrix)
 {
   if (this->MatrixRT != 0)
+  {
     this->MatrixRT->Delete();
+  }
   this->MatrixRT = matrix;
   this->MatrixRT->Register(0);
   this->TransformWorldToCamera->SetMatrix(this->MatrixRT);
 }
 
 void ReconstructionData::ReadDepthMap(std::string path, vtkImageData* out)
 {
-  vtkSmartPointer<vtkPNGReader> depthMapReader = vtkSmartPointer<vtkPNGReader>::New();
-  depthMapReader->SetFileName(path.c_str());
-  depthMapReader->Update();
-  out->ShallowCopy(depthMapReader->GetOutput());
+  vtkSmartPointer<vtkImageReader2Factory> readerFactory =
+      vtkSmartPointer<vtkImageReader2Factory>::New();
+  vtkSmartPointer<vtkImageReader2> imageReader = readerFactory->CreateImageReader2(path.c_str());
+  imageReader->SetFileName(path.c_str());
+  imageReader->Update();
+  out->ShallowCopy(imageReader->GetOutput());
 }