CustusX  16.5
An IGT application
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Groups Pages
cxBinaryThresholdImageFilter.cpp
Go to the documentation of this file.
1 /*=========================================================================
2 This file is part of CustusX, an Image Guided Therapy Application.
3 
4 Copyright (c) 2008-2014, SINTEF Department of Medical Technology
5 All rights reserved.
6 
7 Redistribution and use in source and binary forms, with or without
8 modification, are permitted provided that the following conditions are met:
9 
10 1. Redistributions of source code must retain the above copyright notice,
11  this list of conditions and the following disclaimer.
12 
13 2. Redistributions in binary form must reproduce the above copyright notice,
14  this list of conditions and the following disclaimer in the documentation
15  and/or other materials provided with the distribution.
16 
17 3. Neither the name of the copyright holder nor the names of its contributors
18  may be used to endorse or promote products derived from this software
19  without specific prior written permission.
20 
21 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
22 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
23 IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
24 DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
25 FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
26 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
27 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
28 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
29 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
30 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
31 =========================================================================*/
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 the lower and upper thresholds 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  "The color of the output model.",
104  QColor("green"), root);
105 }
106 
107 void BinaryThresholdImageFilter::createOptions()
108 {
109  mThresholdOption = this->getThresholdOption(mOptions);
110  connect(mThresholdOption.get(), &Property::changed, this, &BinaryThresholdImageFilter::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->patient());
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->patient());
132  temp->setValueName("Output");
133  temp->setHelp("Output thresholded binary image");
134  mOutputTypes.push_back(temp);
135 
136  temp = StringPropertySelectData::New(mServices->patient());
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  if (mActive)
166  {
167  mPreviewImage = boost::dynamic_pointer_cast<Image>(mInputTypes[0]->getData());
168  if(!mPreviewImage)
169  return;
170  Eigen::Vector2d threshold = Eigen::Vector2d(mThresholdOption->getValue()[0], mThresholdOption->getValue()[1]);
171  mPreviewImage->startThresholdPreview(threshold);
172  }
173 }
174 
175 bool BinaryThresholdImageFilter::preProcess()
176 {
177  this->stopPreview();
178  return FilterImpl::preProcess();
179 
180 }
181 
182 bool BinaryThresholdImageFilter::execute()
183 {
184  ImagePtr input = this->getCopiedInputImage();
185  if (!input)
186  return false;
187 
188  DoublePairPropertyPtr thresholds = this->getThresholdOption(mCopiedOptions);
189  BoolPropertyPtr generateSurface = this->getGenerateSurfaceOption(mCopiedOptions);
190 
191  itkImageType::ConstPointer itkImage = AlgorithmHelper::getITKfromSSCImage(input);
192 
193  //Binary Thresholding
194  typedef itk::BinaryThresholdImageFilter<itkImageType, itkImageType> thresholdFilterType;
195  thresholdFilterType::Pointer thresholdFilter = thresholdFilterType::New();
196  thresholdFilter->SetInput(itkImage);
197  thresholdFilter->SetOutsideValue(0);
198  thresholdFilter->SetInsideValue(1);
199  thresholdFilter->SetLowerThreshold(thresholds->getValue()[0]);
200  thresholdFilter->SetUpperThreshold(thresholds->getValue()[1]);
201  thresholdFilter->Update();
202  itkImage = thresholdFilter->GetOutput();
203 
204  //Convert ITK to VTK
205  itkToVtkFilterType::Pointer itkToVtkFilter = itkToVtkFilterType::New();
206  itkToVtkFilter->SetInput(itkImage);
207  itkToVtkFilter->Update();
208 
209  vtkImageDataPtr rawResult = vtkImageDataPtr::New();
210  rawResult->DeepCopy(itkToVtkFilter->GetOutput());
211 
212  vtkImageCastPtr imageCast = vtkImageCastPtr::New();
213  imageCast->SetInputData(rawResult);
214  imageCast->SetOutputScalarTypeToUnsignedChar();
215  imageCast->Update();
216  rawResult = imageCast->GetOutput();
217 
218  // TODO: possible memory problem here - check debug mem system of itk/vtk
219 
220  mRawResult = rawResult;
221 
222  if (generateSurface->getValue())
223  {
224  double threshold = 1;
225  mRawContour = ContourFilter::execute(mRawResult, threshold);
226  }
227 
228  return true;
229 }
230 
231 bool BinaryThresholdImageFilter::postProcess()
232 {
233  if (!mRawResult)
234  return false;
235 
236  ImagePtr input = this->getCopiedInputImage();
237 
238  if (!input)
239  return false;
240 
241  QString uid = input->getUid() + "_seg%1";
242  QString name = input->getName()+" seg%1";
243  ImagePtr output = createDerivedImage(mServices->patient(),
244  uid, name,
245  mRawResult, input);
246 
247  mRawResult = NULL;
248 
249  output->setInitialWindowLevel(-1, -1);
250  output->resetTransferFunctions();
251  mServices->patient()->insertData(output);
252 
253  // set output
254  mOutputTypes.front()->setValue(output->getUid());
255 
256  // set contour output
257  if (mRawContour!=NULL)
258  {
259  ColorPropertyPtr colorOption = this->getColorOption(mOptions);
260  MeshPtr contour = ContourFilter::postProcess(mServices->patient(), mRawContour, output, colorOption->getValue());
261  mOutputTypes[1]->setValue(contour->getUid());
262  mRawContour = vtkPolyDataPtr();
263  }
264 
265  return true;
266 }
267 
268 
269 }//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:159
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::StringPropertySelectData::New
static StringPropertySelectDataPtr New(PatientModelServicePtr patientModelService, QString typeRegexp=".*")
Definition: cxSelectDataStringProperty.h:122
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
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::ContourFilter::execute
virtual bool execute()
Definition: cxContourFilter.cpp:215
cx::Image
A volumetric data set.
Definition: cxImage.h:66
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:88
cx::Property::changed
void changed()
emit when the underlying data value is changed: The user interface will be updated.
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:160
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:97
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: cxNetworkDataTransfer.h:42
cx::MeshPtr
boost::shared_ptr< class Mesh > MeshPtr
Definition: cxForwardDeclarations.h:68
vtkImageDataPtr
vtkSmartPointer< class vtkImageData > vtkImageDataPtr
Definition: cxVideoConnectionWidget.h:51