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cxBinaryThinningImageFilter3DFilter.cpp
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32 
33 #include "cxBinaryThinningImageFilter3DFilter.h"
34 
35 #include <itkBinaryThinningImageFilter3D.h>
36 
37 #include "cxLogger.h"
38 #include "cxRegistrationTransform.h"
39 #include "cxMesh.h"
40 #include "cxImage.h"
41 #include "cxColorProperty.h"
42 #include "vesselReg/SeansVesselReg.hxx"
43 #include "cxSelectDataStringProperty.h"
44 #include "cxAlgorithmHelpers.h"
45 #include "cxPatientModelService.h"
46 #include "cxVolumeHelpers.h"
47 #include "cxVisServices.h"
48 
49 namespace cx
50 {
51 BinaryThinningImageFilter3DFilter::BinaryThinningImageFilter3DFilter(VisServicesPtr services) :
52  FilterImpl(services)
53 {
54 }
55 
56 QString BinaryThinningImageFilter3DFilter::getName() const
57 {
58  return "Centerline";
59 }
60 
61 QString BinaryThinningImageFilter3DFilter::getType() const
62 {
63  return "BinaryThinningImageFilter3DFilter";
64 }
65 
66 QString BinaryThinningImageFilter3DFilter::getHelp() const
67 {
68  return "<html>"
69  "<h3>itk::BinaryThinningImageFilter3D</h3>"
70  "<p>"
71  "This filter computes one-pixel-wide skeleton of a 3D input image."
72  "</p><p>"
73  "This class is parametrized over the type of the input image "
74  "and the type of the output image."
75  "</p><p>"
76  "The input is assumed to be a binary image. All non-zero valued voxels "
77  "are set to 1 internally to simplify the computation. The filter will "
78  "produce a skeleton of the object. The output background values are 0, "
79  "and the foreground values are 1."
80  "</p><p>"
81  "A 26-neighbourhood configuration is used for the foreground and a "
82  "6-neighbourhood configuration for the background. Thinning is performed "
83  "symmetrically in order to guarantee that the skeleton lies medial within "
84  "the object."
85  "</p><p>"
86  "This filter is a parallel thinning algorithm and is an implementation "
87  "of the algorithm described in:"
88  "</p><p>"
89  "T.C. Lee, R.L. Kashyap, and C.N. Chu.<br>"
90  "Building skeleton models via 3-D medial surface/axis thinning algorithms.<br>"
91  "Computer Vision, Graphics, and Image Processing, 56(6):462--478, 1994."
92  "</p></html>";
93 }
94 
95 ColorPropertyBasePtr BinaryThinningImageFilter3DFilter::getColorOption(QDomElement root)
96 {
97  return ColorProperty::initialize("Color", "",
98  "Color of output model.",
99  QColor("green"), root);
100 }
101 
102 void BinaryThinningImageFilter3DFilter::createOptions()
103 {
104  mOptionsAdapters.push_back(this->getColorOption(mOptions));
105 }
106 
107 void BinaryThinningImageFilter3DFilter::createInputTypes()
108 {
109  SelectDataStringPropertyBasePtr temp;
110 
111  temp = StringPropertySelectImage::New(mServices->patient());
112  temp->setValueName("Input");
113  temp->setHelp("Select binary volume input for thinning");
114  // connect(temp.get(), SIGNAL(dataChanged(QString)), this, SLOT(imageChangedSlot(QString)));
115  mInputTypes.push_back(temp);
116 }
117 
118 void BinaryThinningImageFilter3DFilter::createOutputTypes()
119 {
120  SelectDataStringPropertyBasePtr temp;
121 
122  temp = StringPropertySelectMesh::New((mServices->patient()));
123  temp->setValueName("Output");
124  temp->setHelp("Output centerline model");
125  mOutputTypes.push_back(temp);
126 }
127 
128 bool BinaryThinningImageFilter3DFilter::preProcess()
129 {
130  bool retval = FilterImpl::preProcess();
131  if (!retval)
132  return false;
133 
134  ImagePtr input = this->getCopiedInputImage();
135  if (!input)
136  return false;
137 
138  if (input->getMax() != 1 || input->getMin() != 0)
139  {
140  reportWarning(QString("Centerline: Input image %1 must be binary, aborting.").arg(input->getName()));
141  return false;
142  }
143 
144  return true;
145 }
146 
147 bool BinaryThinningImageFilter3DFilter::execute()
148 {
149  ImagePtr input = this->getCopiedInputImage();
150  if (!input)
151  return false;
152 
153  if (input->getMax() != 1 || input->getMin() != 0)
154  {
155  return false;
156  }
157 
158  // report(QString("Creating centerline from \"%1\"...").arg(input->getName()));
159 
160  itkImageType::ConstPointer itkImage = AlgorithmHelper::getITKfromSSCImage(input);
161 
162  //Centerline extraction
163  typedef itk::BinaryThinningImageFilter3D<itkImageType, itkImageType> centerlineFilterType;
164  centerlineFilterType::Pointer centerlineFilter = centerlineFilterType::New();
165  centerlineFilter->SetInput(itkImage);
166  centerlineFilter->Update();
167  itkImage = centerlineFilter->GetOutput();
168 
169  //Convert ITK to VTK
170  itkToVtkFilterType::Pointer itkToVtkFilter = itkToVtkFilterType::New();
171  itkToVtkFilter->SetInput(itkImage);
172  itkToVtkFilter->Update();
173 
174  vtkImageDataPtr rawResult = vtkImageDataPtr::New();
175  rawResult->DeepCopy(itkToVtkFilter->GetOutput());
176 
177  mRawResult = rawResult;
178  return true;
179 }
180 
181 bool BinaryThinningImageFilter3DFilter::postProcess()
182 {
183  bool success = false;
184  if(!mRawResult)
185  return success;
186 
187  ColorPropertyBasePtr outputColor = this->getColorOption(mCopiedOptions);
188 
189  ImagePtr input = this->getCopiedInputImage();
190 
191  ImagePtr outImage = createDerivedImage(mServices->patient(),
192  input->getUid() + "_cl_temp%1", input->getName()+" cl_temp%1",
193  mRawResult, input);
194 
195  mRawResult = NULL;
196  outImage->resetTransferFunctions();
197 
198  //automatically generate a mesh from the centerline
199  vtkPolyDataPtr centerlinePolyData = SeansVesselReg::extractPolyData(outImage, 1, 0);
200 
201  QString uid = input->getUid() + "_cl%1";
202  QString name = input->getName()+" cl%1";
203  MeshPtr mesh = mServices->patient()->createSpecificData<Mesh>(uid, name);
204  mesh->setVtkPolyData(centerlinePolyData);
205  mesh->setColor(outputColor->getValue());
206  mesh->get_rMd_History()->setParentSpace(input->getUid());
207  mServices->patient()->insertData(mesh);
208 
209  // set output
210  mOutputTypes.front()->setValue(mesh->getUid());
211  success = true;
212 
213  return success;
214 }
215 
216 
217 
218 } // namespace cx
219 
cx::FilterImpl::mInputTypes
std::vector< SelectDataStringPropertyBasePtr > mInputTypes
Definition: cxFilterImpl.h:94
cx::FilterImpl::mCopiedOptions
QDomElement mCopiedOptions
Definition: cxFilterImpl.h:101
cx::Mesh
A mesh data set.
Definition: cxMesh.h:61
cx::VisServicesPtr
boost::shared_ptr< class VisServices > VisServicesPtr
Definition: cxMainWindow.h:62
cx::FilterImpl::preProcess
virtual bool preProcess()
Definition: cxFilterImpl.cpp:106
cx::ImagePtr
boost::shared_ptr< class Image > ImagePtr
Definition: cxDicomWidget.h:48
cx::FilterImpl::mOptionsAdapters
std::vector< PropertyPtr > mOptionsAdapters
Definition: cxFilterImpl.h:96
vtkPolyDataPtr
vtkSmartPointer< class vtkPolyData > vtkPolyDataPtr
Definition: cxAirwaysFilterService.h:52
cx::FilterImpl::mServices
VisServicesPtr mServices
Definition: cxFilterImpl.h:103
cx::createDerivedImage
ImagePtr createDerivedImage(PatientModelServicePtr dataManager, QString uid, QString name, vtkImageDataPtr raw, ImagePtr parent)
Definition: cxVolumeHelpers.cpp:170
cx::SelectDataStringPropertyBasePtr
boost::shared_ptr< class SelectDataStringPropertyBase > SelectDataStringPropertyBasePtr
Definition: cxMeshInfoWidget.h:48
cx::reportWarning
void reportWarning(QString msg)
Definition: cxLogger.cpp:91
cx::Mesh::setVtkPolyData
void setVtkPolyData(const vtkPolyDataPtr &polyData)
Definition: cxMesh.cpp:100
cx::BinaryThinningImageFilter3DFilter::getColorOption
ColorPropertyBasePtr getColorOption(QDomElement root)
Definition: cxBinaryThinningImageFilter3DFilter.cpp:95
SeansVesselReg.hxx
cx::FilterImpl::getCopiedInputImage
ImagePtr getCopiedInputImage(int index=0)
Definition: cxFilterImpl.cpp:125
cx::FilterImpl::mOptions
QDomElement mOptions
Definition: cxFilterImpl.h:97
cx::SeansVesselReg::extractPolyData
static vtkPolyDataPtr extractPolyData(ImagePtr image, int p_neighborhoodFilterThreshold, double p_BoundingBox[6])
Definition: SeansVesselReg.cxx:813
cx::FilterImpl::mOutputTypes
std::vector< SelectDataStringPropertyBasePtr > mOutputTypes
Definition: cxFilterImpl.h:95
cx::ColorPropertyBasePtr
boost::shared_ptr< class ColorPropertyBase > ColorPropertyBasePtr
Definition: cxForwardDeclarations.h:154
cx::StringPropertySelectMesh::New
static StringPropertySelectMeshPtr New(PatientModelServicePtr patientModelService)
Definition: cxSelectDataStringProperty.h:152
cx::AlgorithmHelper::getITKfromSSCImage
static itkImageType::ConstPointer getITKfromSSCImage(ImagePtr image)
Definition: cxAlgorithmHelpers.cpp:56
cx::StringPropertySelectImage::New
static StringPropertySelectImagePtr New(PatientModelServicePtr patientModelService)
Definition: cxSelectDataStringProperty.h:97
cx::ColorProperty::initialize
static ColorPropertyPtr initialize(const QString &uid, QString name, QString help, QColor value, QDomNode root=QDomNode())
Definition: cxColorProperty.cpp:45
cx::MeshPtr
boost::shared_ptr< class Mesh > MeshPtr
Definition: cxForwardDeclarations.h:68
vtkImageDataPtr
vtkSmartPointer< class vtkImageData > vtkImageDataPtr
Definition: cxVideoConnectionWidget.h:51
itk::BinaryThinningImageFilter3D
This filter computes one-pixel-wide skeleton of a 3D input image.
Definition: itkBinaryThinningImageFilter3D.h:78