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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  this->stopPreview();
148 }
149 
150 void BinaryThresholdImageFilter::imageChangedSlot(QString uid)
151 {
152  this->stopPreview();
153  this->updateThresholdPairFromImageChange(uid, mThresholdOption);
154 }
155 
156 void BinaryThresholdImageFilter::stopPreview()
157 {
158  if(mPreviewImage)
159  mPreviewImage->stopThresholdPreview();
160  mPreviewImage.reset();
161 }
162 
163 void BinaryThresholdImageFilter::thresholdSlot()
164 {
165 // this->stopPreview();
166  if (mActive)
167  {
168  mPreviewImage = boost::dynamic_pointer_cast<Image>(mInputTypes[0]->getData());
169  Eigen::Vector2d threshold = Eigen::Vector2d(mThresholdOption->getValue()[0], mThresholdOption->getValue()[1]);
170  mPreviewImage->startThresholdPreview(threshold);
171  }
172 }
173 
174 bool BinaryThresholdImageFilter::preProcess()
175 {
176  this->stopPreview();
177  return FilterImpl::preProcess();
178 
179 }
180 
181 bool BinaryThresholdImageFilter::execute()
182 {
183  ImagePtr input = this->getCopiedInputImage();
184  if (!input)
185  return false;
186 
187  DoublePairPropertyPtr thresholds = this->getThresholdOption(mCopiedOptions);
188  BoolPropertyPtr generateSurface = this->getGenerateSurfaceOption(mCopiedOptions);
189 
190  itkImageType::ConstPointer itkImage = AlgorithmHelper::getITKfromSSCImage(input);
191 
192  //Binary Thresholding
193  typedef itk::BinaryThresholdImageFilter<itkImageType, itkImageType> thresholdFilterType;
194  thresholdFilterType::Pointer thresholdFilter = thresholdFilterType::New();
195  thresholdFilter->SetInput(itkImage);
196  thresholdFilter->SetOutsideValue(0);
197  thresholdFilter->SetInsideValue(1);
198  thresholdFilter->SetLowerThreshold(thresholds->getValue()[0]);
199  thresholdFilter->SetUpperThreshold(thresholds->getValue()[1]);
200  thresholdFilter->Update();
201  itkImage = thresholdFilter->GetOutput();
202 
203  //Convert ITK to VTK
204  itkToVtkFilterType::Pointer itkToVtkFilter = itkToVtkFilterType::New();
205  itkToVtkFilter->SetInput(itkImage);
206  itkToVtkFilter->Update();
207 
208  vtkImageDataPtr rawResult = vtkImageDataPtr::New();
209  rawResult->DeepCopy(itkToVtkFilter->GetOutput());
210 
211  vtkImageCastPtr imageCast = vtkImageCastPtr::New();
212  imageCast->SetInputData(rawResult);
213  imageCast->SetOutputScalarTypeToUnsignedChar();
214  imageCast->Update();
215  rawResult = imageCast->GetOutput();
216 
217  // TODO: possible memory problem here - check debug mem system of itk/vtk
218 
219  mRawResult = rawResult;
220 
221  if (generateSurface->getValue())
222  {
223  double threshold = 1;
224  mRawContour = ContourFilter::execute(mRawResult, threshold);
225  }
226 
227  return true;
228 }
229 
230 bool BinaryThresholdImageFilter::postProcess()
231 {
232  if (!mRawResult)
233  return false;
234 
235  ImagePtr input = this->getCopiedInputImage();
236 
237  if (!input)
238  return false;
239 
240  QString uid = input->getUid() + "_seg%1";
241  QString name = input->getName()+" seg%1";
242  ImagePtr output = createDerivedImage(mServices->getPatientService(),
243  uid, name,
244  mRawResult, input);
245 
246  mRawResult = NULL;
247 
248  output->resetTransferFunctions();
249  mServices->getPatientService()->insertData(output);
250 
251  // set output
252  mOutputTypes.front()->setValue(output->getUid());
253 
254  // set contour output
255  if (mRawContour!=NULL)
256  {
257  ColorPropertyPtr colorOption = this->getColorOption(mOptions);
258  MeshPtr contour = ContourFilter::postProcess(mServices->getPatientService(), mRawContour, output, colorOption->getValue());
259  mOutputTypes[1]->setValue(contour->getUid());
260  mRawContour = vtkPolyDataPtr();
261  }
262 
263  return true;
264 }
265 
266 
267 }//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:62
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: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: cxSelectDataStringPropertyBase.h:43
cx::ContourFilter::execute
virtual bool execute()
Definition: cxContourFilter.cpp:215
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:316
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()