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cxBinaryThresholdImageFilter.cpp
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32 
33 #include "cxBinaryThresholdImageFilter.h"
34 
35 #include "cxAlgorithmHelpers.h"
36 #include <itkBinaryThresholdImageFilter.h>
37 #include <vtkImageCast.h>
38 #include "cxUtilHelpers.h"
39 #include "cxRegistrationTransform.h"
40 #include "cxStringProperty.h"
41 #include "cxColorProperty.h"
42 #include "cxBoolProperty.h"
43 #include "cxTypeConversions.h"
44 #include "cxDoublePairProperty.h"
45 #include "cxContourFilter.h"
46 #include "cxMesh.h"
47 #include "cxImage.h"
48 #include "cxSelectDataStringProperty.h"
49 #include "cxPatientModelService.h"
50 #include "cxViewService.h"
51 #include "cxVolumeHelpers.h"
52 #include "cxVisServices.h"
53 
54 namespace cx
55 {
56 
57 BinaryThresholdImageFilter::BinaryThresholdImageFilter(VisServicesPtr services) :
58  FilterImpl(services)
59 {
60 }
61 
62 QString BinaryThresholdImageFilter::getName() const
63 {
64  return "Segmentation";
65 }
66 
67 QString BinaryThresholdImageFilter::getType() const
68 {
69  return "BinaryThresholdImageFilter";
70 }
71 
72 QString BinaryThresholdImageFilter::getHelp() const
73 {
74  return "<html>"
75  "<h3>Binary Threshold Image Filter.</h3>"
76  "<p><i>Segment out areas from the selected image using a threshold.</i></p>"
77  "<p>This filter produces an output image whose pixels are either one of two values"
78  "( OutsideValue or InsideValue ), depending on whether the corresponding input"
79  "image pixels lie between the two thresholds ( LowerThreshold and UpperThreshold )."
80  "Values equal to either threshold is considered to be between the thresholds.<p>"
81  "</html>";
82 }
83 
84 DoublePairPropertyPtr BinaryThresholdImageFilter::getThresholdOption(QDomElement root)
85 {
86  DoublePairPropertyPtr retval = DoublePairProperty::initialize("Thresholds", "",
87  "Select lower and upper threshold for the segmentation", DoubleRange(0, 100, 1), 0,
88  root);
89  return retval;
90 }
91 
92 BoolPropertyPtr BinaryThresholdImageFilter::getGenerateSurfaceOption(QDomElement root)
93 {
94  BoolPropertyPtr retval = BoolProperty::initialize("Generate Surface", "",
95  "Generate a surface of the output volume", true,
96  root);
97  return retval;
98 }
99 
100 ColorPropertyPtr BinaryThresholdImageFilter::getColorOption(QDomElement root)
101 {
102  return ColorProperty::initialize("Color", "",
103  "Color of output model.",
104  QColor("green"), root);
105 }
106 
107 void BinaryThresholdImageFilter::createOptions()
108 {
109  mThresholdOption = this->getThresholdOption(mOptions);
110  connect(mThresholdOption.get(), SIGNAL(changed()), this, SLOT(thresholdSlot()));
111  mOptionsAdapters.push_back(mThresholdOption);
112  mOptionsAdapters.push_back(this->getGenerateSurfaceOption(mOptions));
113  mOptionsAdapters.push_back(this->getColorOption(mOptions));
114 }
115 
116 void BinaryThresholdImageFilter::createInputTypes()
117 {
118  SelectDataStringPropertyBasePtr temp;
119 
120  temp = StringPropertySelectImage::New(mServices->getPatientService());
121  temp->setValueName("Input");
122  temp->setHelp("Select image input for thresholding");
123  connect(temp.get(), SIGNAL(dataChanged(QString)), this, SLOT(imageChangedSlot(QString)));
124  mInputTypes.push_back(temp);
125 }
126 
127 void BinaryThresholdImageFilter::createOutputTypes()
128 {
129  SelectDataStringPropertyBasePtr temp;
130 
131  temp = StringPropertySelectData::New(mServices->getPatientService());
132  temp->setValueName("Output");
133  temp->setHelp("Output thresholded binary image");
134  mOutputTypes.push_back(temp);
135 
136  temp = StringPropertySelectData::New(mServices->getPatientService());
137  temp->setValueName("Contour");
138  temp->setHelp("Output contour generated from thresholded binary image.");
139  mOutputTypes.push_back(temp);
140 }
141 
142 void BinaryThresholdImageFilter::setActive(bool on)
143 {
144  FilterImpl::setActive(on);
145 
146  if (!mActive)
147  mServices->visualizationService->removePreview();
148 }
149 
150 void BinaryThresholdImageFilter::imageChangedSlot(QString uid)
151 {
152  this->updateThresholdPairFromImageChange(uid, mThresholdOption);
153  mServices->visualizationService->removePreview();
154 }
155 
156 void BinaryThresholdImageFilter::thresholdSlot()
157 {
158  if (mActive)
159  {
160  ImagePtr image = boost::dynamic_pointer_cast<Image>(mInputTypes[0]->getData());
161  std::vector<double> threshold;
162  threshold.push_back(mThresholdOption->getValue()[0]);
163  threshold.push_back(mThresholdOption->getValue()[1]);
164  mServices->visualizationService->setPreview(image, threshold);
165  }
166 }
167 
168 bool BinaryThresholdImageFilter::preProcess()
169 {
170  mServices->visualizationService->removePreview();
171  return FilterImpl::preProcess();
172 
173 }
174 
175 bool BinaryThresholdImageFilter::execute()
176 {
177  ImagePtr input = this->getCopiedInputImage();
178  if (!input)
179  return false;
180 
181  DoublePairPropertyPtr thresholds = this->getThresholdOption(mCopiedOptions);
182  BoolPropertyPtr generateSurface = this->getGenerateSurfaceOption(mCopiedOptions);
183 
184  itkImageType::ConstPointer itkImage = AlgorithmHelper::getITKfromSSCImage(input);
185 
186  //Binary Thresholding
187  typedef itk::BinaryThresholdImageFilter<itkImageType, itkImageType> thresholdFilterType;
188  thresholdFilterType::Pointer thresholdFilter = thresholdFilterType::New();
189  thresholdFilter->SetInput(itkImage);
190  thresholdFilter->SetOutsideValue(0);
191  thresholdFilter->SetInsideValue(1);
192  thresholdFilter->SetLowerThreshold(thresholds->getValue()[0]);
193  thresholdFilter->SetUpperThreshold(thresholds->getValue()[1]);
194  thresholdFilter->Update();
195  itkImage = thresholdFilter->GetOutput();
196 
197  //Convert ITK to VTK
198  itkToVtkFilterType::Pointer itkToVtkFilter = itkToVtkFilterType::New();
199  itkToVtkFilter->SetInput(itkImage);
200  itkToVtkFilter->Update();
201 
202  vtkImageDataPtr rawResult = vtkImageDataPtr::New();
203  rawResult->DeepCopy(itkToVtkFilter->GetOutput());
204 
205  vtkImageCastPtr imageCast = vtkImageCastPtr::New();
206  imageCast->SetInputData(rawResult);
207  imageCast->SetOutputScalarTypeToUnsignedChar();
208  imageCast->Update();
209  rawResult = imageCast->GetOutput();
210 
211  // TODO: possible memory problem here - check debug mem system of itk/vtk
212 
213  mRawResult = rawResult;
214 
215  if (generateSurface->getValue())
216  {
217  double threshold = 1;
218  mRawContour = ContourFilter::execute(mRawResult, threshold);
219  }
220 
221  return true;
222 }
223 
224 bool BinaryThresholdImageFilter::postProcess()
225 {
226  if (!mRawResult)
227  return false;
228 
229  ImagePtr input = this->getCopiedInputImage();
230 
231  if (!input)
232  return false;
233 
234  QString uid = input->getUid() + "_seg%1";
235  QString name = input->getName()+" seg%1";
236  ImagePtr output = createDerivedImage(mServices->getPatientService(),
237  uid, name,
238  mRawResult, input);
239 
240  mRawResult = NULL;
241 
242  output->resetTransferFunctions();
243  mServices->getPatientService()->insertData(output);
244 
245  // set output
246  mOutputTypes.front()->setValue(output->getUid());
247 
248  // set contour output
249  if (mRawContour!=NULL)
250  {
251  ColorPropertyPtr colorOption = this->getColorOption(mOptions);
252  MeshPtr contour = ContourFilter::postProcess(mServices->getPatientService(), mRawContour, output, colorOption->getValue());
253  mOutputTypes[1]->setValue(contour->getUid());
254  mRawContour = vtkPolyDataPtr();
255  }
256 
257  return true;
258 }
259 
260 
261 }//namespace cx
cx::BoolProperty::initialize
static BoolPropertyPtr initialize(const QString &uid, QString name, QString help, bool value, QDomNode root=QDomNode())
Definition: cxBoolProperty.cpp:51
cx::FilterImpl::mInputTypes
std::vector< SelectDataStringPropertyBasePtr > mInputTypes
Definition: cxFilterImpl.h:94
cx::FilterImpl::mCopiedOptions
QDomElement mCopiedOptions
Definition: cxFilterImpl.h:101
cx::ColorPropertyPtr
boost::shared_ptr< class ColorProperty > ColorPropertyPtr
Definition: cxForwardDeclarations.h:158
cx::VisServicesPtr
boost::shared_ptr< class VisServices > VisServicesPtr
Definition: cxMainWindow.h:61
cx::FilterImpl::preProcess
virtual bool preProcess()
Definition: cxFilterImpl.cpp:106
cx::FilterImpl::updateThresholdPairFromImageChange
void updateThresholdPairFromImageChange(QString uid, DoublePairPropertyPtr threshold)
Definition: cxFilterImpl.cpp:150
cx::DoubleRange
Utility class for describing a bounded numeric range.
Definition: cxDoubleRange.h:53
cx::ImagePtr
boost::shared_ptr< class Image > ImagePtr
Definition: cxDicomWidget.h:48
cx::BinaryThresholdImageFilter::getGenerateSurfaceOption
BoolPropertyPtr getGenerateSurfaceOption(QDomElement root)
Definition: cxBinaryThresholdImageFilter.cpp:92
vtkPolyDataPtr
vtkSmartPointer< class vtkPolyData > vtkPolyDataPtr
Definition: cxProbeSector.h:47
cx::FilterImpl::mOptionsAdapters
std::vector< PropertyPtr > mOptionsAdapters
Definition: cxFilterImpl.h:96
cx::FilterImpl::mServices
VisServicesPtr mServices
Definition: cxFilterImpl.h:104
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: cxSelectDataStringPropertyBase.h:43
cx::ContourFilter::execute
virtual bool execute()
Definition: cxContourFilter.cpp:208
cx::BinaryThresholdImageFilter::getThresholdOption
DoublePairPropertyPtr getThresholdOption(QDomElement root)
Definition: cxBinaryThresholdImageFilter.cpp:84
cx::FilterImpl::getCopiedInputImage
ImagePtr getCopiedInputImage(int index=0)
Definition: cxFilterImpl.cpp:125
cx::FilterImpl::setActive
virtual void setActive(bool on)
Definition: cxFilterImpl.cpp:100
cx::FilterImpl::mOptions
QDomElement mOptions
Definition: cxFilterImpl.h:97
vtkImageCastPtr
vtkSmartPointer< class vtkImageCast > vtkImageCastPtr
Definition: vtkForwardDeclarations.h:86
cx::StringPropertySelectData::New
static StringPropertySelectDataPtr New(PatientModelServicePtr patientModelService)
Definition: cxSelectDataStringProperty.h:93
cx::BinaryThresholdImageFilter::getColorOption
ColorPropertyPtr getColorOption(QDomElement root)
Definition: cxBinaryThresholdImageFilter.cpp:100
cx::FilterImpl::mOutputTypes
std::vector< SelectDataStringPropertyBasePtr > mOutputTypes
Definition: cxFilterImpl.h:95
cx::DoublePairPropertyPtr
boost::shared_ptr< class DoublePairProperty > DoublePairPropertyPtr
Definition: cxForwardDeclarations.h:159
cx::DoublePairProperty::initialize
static DoublePairPropertyPtr initialize(const QString &uid, QString name, QString help, DoubleRange range, int decimals, QDomNode root=QDomNode())
Definition: cxDoublePairProperty.cpp:43
cx::ContourFilter::postProcess
virtual bool postProcess()
Definition: cxContourFilter.cpp:309
cx::AlgorithmHelper::getITKfromSSCImage
static itkImageType::ConstPointer getITKfromSSCImage(ImagePtr image)
Definition: cxAlgorithmHelpers.cpp:56
cx::StringPropertySelectImage::New
static StringPropertySelectImagePtr New(PatientModelServicePtr patientModelService)
Definition: cxSelectDataStringProperty.h:68
cx::BinaryThresholdImageFilter::BinaryThresholdImageFilter
BinaryThresholdImageFilter(VisServicesPtr services)
Definition: cxBinaryThresholdImageFilter.cpp:57
cx::ColorProperty::initialize
static ColorPropertyPtr initialize(const QString &uid, QString name, QString help, QColor value, QDomNode root=QDomNode())
Definition: cxColorProperty.cpp:45
cx::BoolPropertyPtr
boost::shared_ptr< class BoolProperty > BoolPropertyPtr
Definition: cxForwardDeclarations.h:157
cx::MeshPtr
boost::shared_ptr< class Mesh > MeshPtr
Definition: cxForwardDeclarations.h:67
vtkImageDataPtr
vtkSmartPointer< class vtkImageData > vtkImageDataPtr
Definition: cxVideoConnectionWidget.h:51
cx::Filter::changed
void changed()