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AndreaRigoni
383
src/Vtk/vtkVoxImage.cpp
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383
src/Vtk/vtkVoxImage.cpp
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/*//////////////////////////////////////////////////////////////////////////////
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// CMT Cosmic Muon Tomography project //////////////////////////////////////////
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////////////////////////////////////////////////////////////////////////////////
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Copyright (c) 2014, Universita' degli Studi di Padova, INFN sez. di Padova
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All rights reserved
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Authors: Andrea Rigoni Garola < andrea.rigoni@pd.infn.it >
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------------------------------------------------------------------
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This library is free software; you can redistribute it and/or
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modify it under the terms of the GNU Lesser General Public
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License as published by the Free Software Foundation; either
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version 3.0 of the License, or (at your option) any later version.
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This library is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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Lesser General Public License for more details.
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You should have received a copy of the GNU Lesser General Public
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License along with this library.
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//////////////////////////////////////////////////////////////////////////////*/
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#ifdef HAVE_CONFIG_H
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#include "config.h"
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#endif
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#include <vtkSmartPointer.h>
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#include <vtkVolume.h>
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#include <vtkImageData.h>
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#include <vtkImageImport.h>
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#include <vtkImageExport.h>
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#include <vtkFloatArray.h>
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#include <vtkPointData.h>
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#include <vtkXMLImageDataReader.h>
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#include <vtkXMLImageDataWriter.h>
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#include <vtkGenericDataObjectReader.h>
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#include <vtkImageShiftScale.h>
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#include <vtkSmartVolumeMapper.h>
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#include <vtkColorTransferFunction.h>
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#include <vtkPiecewiseFunction.h>
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#include <vtkVolumeProperty.h>
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#include <vtkActor.h>
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#include <vtkProperty.h>
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#include <vtkCubeSource.h>
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#include <vtkPolyDataMapper.h>
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#include <Math/VoxImage.h>
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#include "vtkVoxImage.h"
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namespace uLib {
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namespace Vtk {
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////////////////////////////////////////////////////////////////////////////////
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////////////////////////////////////////////////////////////////////////////////
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////////////////////////////////////////////////////////////////////////////////
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// PIMPL
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class vtkVoxImagePimpl {
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public:
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vtkVoxImagePimpl(vtkVoxImage::Content &content) :
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m_Content(content),
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m_Actor(vtkVolume::New()),
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m_Image(vtkImageData::New()),
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m_Outline(vtkCubeSource::New()),
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m_Reader(NULL),
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m_Writer(NULL)
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{}
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~vtkVoxImagePimpl()
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{
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m_Image->Delete();
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m_Actor->Delete();
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m_Outline->Delete();
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}
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void GetContent();
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void SetContent();
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// members //
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vtkVolume *m_Actor;
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vtkImageData *m_Image;
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vtkCubeSource *m_Outline;
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// io //
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vtkXMLImageDataReader *m_Reader;
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vtkXMLImageDataWriter *m_Writer;
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// content //
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vtkVoxImage::Content &m_Content;
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// visual //
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float m_Window;
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float m_Level;
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};
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void vtkVoxImagePimpl::GetContent()
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{
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// ULIB -> VTK //
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const int *dims = static_cast<const int *>(m_Content.GetDims().data());
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m_Image->SetDimensions(dims);
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float *spacing = m_Content.GetSpacing().data();
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m_Image->SetSpacing(spacing[0],spacing[1],spacing[2]);
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// Warning .. TODO: Read complete Transform matrix //
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float *pos = m_Content.GetPosition().data();
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m_Image->SetOrigin(pos[0],pos[1],pos[2]);
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vtkFloatArray *array = vtkFloatArray::SafeDownCast
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(m_Image->GetPointData()->GetScalars());
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array->SetNumberOfTuples(m_Content.GetDims().prod());
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Vector3i index(0,0,0);
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int i=0;
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for (int zv = 0; zv < dims[2]; ++zv) {
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for (int yv = 0; yv < dims[1]; ++yv) {
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for (int xv = 0; xv < dims[0]; ++xv) {
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index << xv,yv,zv;
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array->SetValue(i++,m_Content.GetValue(index));
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}
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}
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}
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m_Image->GetPointData()->SetScalars(array);
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// m_Image->Update();
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}
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void vtkVoxImagePimpl::SetContent()
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{
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// VTK -> ULIB //
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int *ext = m_Image->GetExtent();
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int dims[3] = { ext[1]-ext[0] + 1, ext[3]-ext[2] + 1, ext[5]-ext[4] + 1 };
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m_Content.SetDims(Vector3i(dims[0],dims[1],dims[2]));
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double *spacing = m_Image->GetSpacing();
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m_Content.SetSpacing(Vector3f(spacing[0],spacing[1],spacing[2]));
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// Warning .. TODO: Read complete Transform matrix //
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double *pos = m_Image->GetOrigin();
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m_Content.SetPosition(Vector3f(pos[0],pos[1],pos[2]));
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vtkFloatArray *array = vtkFloatArray::SafeDownCast
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(m_Image->GetPointData()->GetScalars());
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if(array) {
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Vector3i index(0,0,0);
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int i=0;
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for (int zv = 0; zv < dims[2]; ++zv) {
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for (int yv = 0; yv < dims[1]; ++yv) {
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for (int xv = 0; xv < dims[0]; ++xv) {
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index << xv,yv,zv;
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m_Content.SetValue(index,array->GetValue(i++));
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}
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}
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}
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}
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else {
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std::cerr << "Error reading array Value Data\n";
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}
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}
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////////////////////////////////////////////////////////////////////////////////
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////////////////////////////////////////////////////////////////////////////////
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////////////////////////////////////////////////////////////////////////////////
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// VTK VOXIMAGE
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vtkVoxImage::vtkVoxImage(Content &content) :
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d(new vtkVoxImagePimpl(content))
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{
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init_properties();
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d->GetContent();
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InstallPipe();
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}
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vtkVoxImage::~vtkVoxImage()
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{
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delete d;
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}
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vtkImageData *vtkVoxImage::GetImageData()
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{
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d->GetContent();
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return d->m_Image;
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}
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void vtkVoxImage::SaveToXMLFile(const char *fname)
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{
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vtkSmartPointer<vtkXMLImageDataWriter> writer =
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vtkSmartPointer<vtkXMLImageDataWriter>::New();
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writer->SetFileName(fname);
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d->GetContent();
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vtkSmartPointer<vtkImageShiftScale> vtkscale =
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vtkSmartPointer<vtkImageShiftScale>::New();
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# if VTK_MAJOR_VERSION <= 5
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vtkscale->SetInputConnection(d->m_Image->GetProducerPort());
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# else
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vtkscale->SetInputData(d->m_Image);
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# endif
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vtkscale->SetScale(p().writer_factor);
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vtkscale->Update();
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writer->SetInputConnection(vtkscale->GetOutputPort());
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writer->Update();
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writer->Write();
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}
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void vtkVoxImage::ReadFromVKTFile(const char *fname)
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{
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vtkSmartPointer<vtkGenericDataObjectReader> reader =
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vtkSmartPointer<vtkGenericDataObjectReader>::New();
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reader->SetFileName(fname);
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reader->Update();
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if(reader->IsFileStructuredPoints())
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{
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vtkSmartPointer<vtkImageShiftScale> vtkscale =
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vtkSmartPointer<vtkImageShiftScale>::New();
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vtkscale->SetInputConnection(reader->GetOutputPort());
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vtkscale->SetScale(1/p().writer_factor);
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vtkscale->Update();
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d->m_Image->DeepCopy(vtkscale->GetOutput()); // FIX! (pipe connection)
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d->SetContent();
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}
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else {
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std::cerr << "Error: file does not contain structured points\n";
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}
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d->m_Actor->Update();
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}
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void vtkVoxImage::ReadFromXMLFile(const char *fname)
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{
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vtkSmartPointer<vtkXMLImageDataReader> reader =
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vtkSmartPointer<vtkXMLImageDataReader>::New();
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reader->SetFileName(fname);
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reader->Update();
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vtkSmartPointer<vtkImageShiftScale> vtkscale =
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vtkSmartPointer<vtkImageShiftScale>::New();
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vtkscale->SetInputConnection(reader->GetOutputPort());
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vtkscale->SetScale(1/p().writer_factor);
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vtkscale->Update();
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d->m_Image->DeepCopy(vtkscale->GetOutput());
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d->SetContent();
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}
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void vtkVoxImage::setShadingPreset(int blendType)
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{
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vtkSmartVolumeMapper *mapper =
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(vtkSmartVolumeMapper *)d->m_Actor->GetMapper();
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vtkVolumeProperty *property = d->m_Actor->GetProperty();
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static vtkColorTransferFunction *colorFun = vtkColorTransferFunction::New();
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static vtkPiecewiseFunction *opacityFun = vtkPiecewiseFunction::New();
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float window = 40 / $$.writer_factor;
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float level = 20 / $$.writer_factor;
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property->SetColor(colorFun);
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property->SetScalarOpacity(opacityFun);
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property->SetInterpolationTypeToLinear();
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if(blendType != 6) {
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colorFun->RemoveAllPoints();
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opacityFun->RemoveAllPoints();
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}
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switch (blendType) {
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// MIP
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// Create an opacity ramp from the window and level values.
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// Color is white. Blending is MIP.
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case 0:
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colorFun->AddRGBSegment(0.0, 1.0, 1.0, 1.0, 255.0, 1.0, 1.0, 1.0);
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opacityFun->AddSegment(level - 0.5 * window, 0.0,
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level + 0.5 * window, 1.0);
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mapper->SetBlendModeToMaximumIntensity();
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break;
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// CompositeRamp
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// Create a ramp from the window and level values. Use compositing
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// without shading. Color is a ramp from black to white.
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case 1:
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colorFun->AddRGBSegment(level - 0.5 * window, 0.0, 0.0, 0.0,
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level + 0.5 * window, 1.0, 1.0, 1.0);
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opacityFun->AddSegment(level - 0.5 * window, 0.0,
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level + 0.5 * window, 1.0);
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mapper->SetBlendModeToComposite();
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property->ShadeOff();
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break;
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// CompositeShadeRamp
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// Create a ramp from the window and level values. Use compositing
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// with shading. Color is white.
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case 2:
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colorFun->AddRGBSegment(0.0, 1.0, 1.0, 1.0, 255.0, 1.0, 1.0, 1.0);
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opacityFun->AddSegment(level - 0.5 * window, 0.0,
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level + 0.5 * window, 1.0);
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mapper->SetBlendModeToComposite();
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property->ShadeOn();
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break;
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// CT_Skin
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// Use compositing and functions set to highlight skin in CT data
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// Not for use on RGB data
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case 3:
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colorFun->AddRGBPoint(-3024, 0, 0, 0, 0.5, 0.0);
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colorFun->AddRGBPoint(-1000, .62, .36, .18, 0.5, 0.0);
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colorFun->AddRGBPoint(-500, .88, .60, .29, 0.33, 0.45);
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colorFun->AddRGBPoint(3071, .83, .66, 1, 0.5, 0.0);
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opacityFun->AddPoint(-3024, 0, 0.5, 0.0);
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opacityFun->AddPoint(-1000, 0, 0.5, 0.0);
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opacityFun->AddPoint(-500, 1.0, 0.33, 0.45);
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opacityFun->AddPoint(3071, 1.0, 0.5, 0.0);
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mapper->SetBlendModeToComposite();
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property->ShadeOn();
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property->SetAmbient(0.1);
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property->SetDiffuse(0.9);
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property->SetSpecular(0.2);
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property->SetSpecularPower(10.0);
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property->SetScalarOpacityUnitDistance(0.8919);
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break;
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default:
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vtkGenericWarningMacro("Unknown blend type.");
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break;
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}
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}
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void vtkVoxImage::Update() {
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d->m_Actor->Update();
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d->m_Outline->SetBounds(d->m_Image->GetBounds());
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d->m_Outline->Update();
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}
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void vtkVoxImage::InstallPipe()
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{
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vtkSmartPointer<vtkSmartVolumeMapper> mapper =
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vtkSmartPointer<vtkSmartVolumeMapper>::New();
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# if VTK_MAJOR_VERSION <= 5
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mapper->SetInputConnection(d->m_Image->GetProducerPort());
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# else
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mapper->SetInputData(d->m_Image);
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# endif
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mapper->Update();
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d->m_Actor->SetMapper(mapper);
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this->setShadingPreset(0);
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mapper->Update();
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d->m_Outline->SetBounds(d->m_Image->GetBounds());
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vtkSmartPointer<vtkPolyDataMapper> mmapper = vtkSmartPointer<vtkPolyDataMapper>::New();
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mmapper->SetInputConnection(d->m_Outline->GetOutputPort());
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vtkSmartPointer<vtkActor> actor = vtkSmartPointer<vtkActor>::New();
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actor->SetMapper(mmapper);
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actor->GetProperty()->SetRepresentationToWireframe();
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actor->GetProperty()->SetAmbient(0.7);
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// this->SetProp(actor);
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this->SetProp(d->m_Actor);
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}
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} // vtk
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} // uLib
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