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cxAirwaysFilterService.cpp
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1 /*=========================================================================
2 This file is part of CustusX, an Image Guided Therapy Application.
3 
4 Copyright (c) 2008-2014, SINTEF Department of Medical Technology
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32 
33 #include "cxAirwaysFilterService.h"
34 
35 #include <QTimer>
36 
37 #include <vtkImageImport.h>
38 #include <vtkImageData.h>
39 #include <vtkImageShiftScale.h>
40 #include <ctkPluginContext.h>
41 
42 #include "cxTime.h"
43 #include "cxTypeConversions.h"
44 #include "cxLogger.h"
45 #include "cxDataReaderWriter.h"
46 #include "cxRegistrationTransform.h"
47 #include "cxDoubleProperty.h"
48 #include "cxContourFilter.h"
49 #include "cxDataLocations.h"
50 #include "cxSelectDataStringProperty.h"
51 #include "vtkForwardDeclarations.h"
52 #include "cxPatientModelServiceProxy.h"
53 #include "cxVisServices.h"
54 // Test
55 #include "FAST/Algorithms/AirwaySegmentation/AirwaySegmentation.hpp"
56 #include "FAST/Algorithms/CenterlineExtraction/CenterlineExtraction.hpp"
57 #include "FAST/Importers/ImageFileImporter.hpp"
58 #include "FAST/Exporters/VTKImageExporter.hpp"
59 #include "FAST/Exporters/VTKLineSetExporter.hpp"
60 #include "FAST/Data/Segmentation.hpp"
61 #include "FAST/SceneGraph.hpp"
62 
63 namespace cx {
64 
65 AirwaysFilter::AirwaysFilter(VisServicesPtr services) :
66  FilterImpl(services)
67 {
68 
69 }
70 
71 QString AirwaysFilter::getName() const
72 {
73  return "Airway Segmentation Filter";
74 }
75 
76 QString AirwaysFilter::getType() const
77 {
78  return "AirwaysFilter";
79 }
80 
81 QString AirwaysFilter::getHelp() const
82 {
83  return "<html>"
84  "<h3>Airway Segmentation.</h3>"
85  "<p><i>Extracts segmentation and centerline from a CT volume. If method fails, try to crop volume. </br>Algorithm written by Erik Smistad.</i></p>"
86  "</html>";
87 }
88 
89 bool AirwaysFilter::execute()
90 {
91  std::cout << "EXECUTING AIRWAYS FILTER" << std::endl;
92  ImagePtr input = this->getCopiedInputImage();
93  if (!input)
94  return false;
95  mInputImage = input;
96  std::string filename = (patientService()->getActivePatientFolder()+"/"+mInputImage->getFilename()).toStdString();
97 
98  try {
99  // Import image data from disk
100  fast::ImageFileImporter::pointer importer = fast::ImageFileImporter::New();
101  importer->setFilename(filename);
102 
103  // Need to know the data type
104  importer->update();
105  fast::Image::pointer image = importer->getOutputData<fast::Image>();
106  std::cout << "IMAGE LOADED" << std::endl;
107 
108  // Do segmentation
109  fast::AirwaySegmentation::pointer segmentation = fast::AirwaySegmentation::New();
110  segmentation->setInputConnection(importer->getOutputPort());
111 
112  // Convert fast segmentation data to VTK data which CX can use
113  vtkSmartPointer<fast::VTKImageExporter> vtkExporter = fast::VTKImageExporter::New();
114  vtkExporter->setInputConnection(segmentation->getOutputPort());
115  vtkExporter->Update();
116  mSegmentationOutput = vtkExporter->GetOutput();
117  std::cout << "FINISHED AIRWAY SEGMENTATION" << std::endl;
118 
119  // Get output segmentation data
120  fast::Segmentation::pointer segmentationData = segmentation->getOutputData<fast::Segmentation>(0);
121 
122  // Get the transformation of the segmentation
123  Eigen::Affine3f T = fast::SceneGraph::getEigenAffineTransformationFromData(segmentationData);
124  mTransformation.matrix() = T.matrix().cast<double>(); // cast to double
125 
126  // Extract centerline
127  fast::CenterlineExtraction::pointer centerline = fast::CenterlineExtraction::New();
128  centerline->setInputConnection(segmentation->getOutputPort());
129 
130  // Get centerline
131  vtkSmartPointer<fast::VTKLineSetExporter> vtkCenterlineExporter = fast::VTKLineSetExporter::New();
132  vtkCenterlineExporter->setInputConnection(centerline->getOutputPort());
133  mCenterlineOutput = vtkCenterlineExporter->GetOutput();
134  vtkCenterlineExporter->Update();
135 
136  } catch(fast::Exception& e) {
137  std::string error = e.what();
138  reportError("fast::Exception: "+qstring_cast(error));
139 
140  return false;
141  } catch(cl::Error& e) {
142  reportError("cl::Error:"+qstring_cast(e.what()));
143 
144  return false;
145  } catch (std::exception& e){
146  reportError("std::exception:"+qstring_cast(e.what()));
147 
148  return false;
149  } catch (...){
150  reportError("Airway segmentation algorithm threw a unknown exception.");
151 
152  return false;
153  }
154  return true;
155 }
156 
157 bool AirwaysFilter::postProcess()
158 {
159  if(!mSegmentationOutput)
160  return false;
161 
162  std::cout << "POST PROCESS" << std::endl;
163 
164  // Make contour of segmented volume
165  double threshold = 1;
166  vtkPolyDataPtr rawContour = ContourFilter::execute(
167  mSegmentationOutput,
168  threshold,
169  false, // reduce resolution
170  true, // smoothing
171  true, // keep topology
172  0 // target decimation
173  );
174  //outputSegmentation->get_rMd_History()->setRegistration(rMd_i);
175  //patientService()->insertData(outputSegmentation);
176 
177  // Add contour internally to cx
178  MeshPtr contour = ContourFilter::postProcess(
179  patientService(),
180  rawContour,
181  mInputImage,
182  QColor("green")
183  );
184  contour->get_rMd_History()->setRegistration(mTransformation);
185 
186  // Set output
187  mOutputTypes[1]->setValue(contour->getUid());
188 
189  // TODO get centerline somehow
190  QString uid = mInputImage->getUid() + "_centerline%1";
191  QString name = mInputImage->getName() + " centerline%1";
192  MeshPtr centerline = patientService()->createSpecificData<Mesh>(uid, name);
193  centerline->setVtkPolyData(mCenterlineOutput);
194  centerline->get_rMd_History()->setParentSpace(mInputImage->getUid());
195  centerline->get_rMd_History()->setRegistration(mTransformation);
196  patientService()->insertData(centerline);
197  mOutputTypes[0]->setValue(centerline->getUid());
198 
199  return true;
200 }
201 
202 void AirwaysFilter::createOptions()
203 {
204  //mOptionsAdapters.push_back(getNoiseLevelOption(mOptions));
205 }
206 
207 void AirwaysFilter::createInputTypes()
208 {
209  SelectDataStringPropertyBasePtr temp;
210 
211  temp = StringPropertySelectImage::New(patientService());
212  temp->setValueName("Input");
213  temp->setHelp("Select input to run airway segmentation on.");
214  mInputTypes.push_back(temp);
215 }
216 
217 void AirwaysFilter::createOutputTypes()
218 {
219  StringPropertySelectMeshPtr tempMeshStringAdapter;
220 
221  //0
222  tempMeshStringAdapter = StringPropertySelectMesh::New(patientService());
223  tempMeshStringAdapter->setValueName("Centerline");
224  tempMeshStringAdapter->setHelp("Generated centerline mesh (vtk-format).");
225  mOutputTypes.push_back(tempMeshStringAdapter);
226 
227  //1
228  tempMeshStringAdapter = StringPropertySelectMesh::New(patientService());
229  tempMeshStringAdapter->setValueName("Segmentation");
230  tempMeshStringAdapter->setHelp("Generated surface of the segmented volume.");
231  mOutputTypes.push_back(tempMeshStringAdapter);
232 
233 }
234 
235 /*
236 DoublePropertyPtr AirwaysFilter::getNoiseLevelOption(QDomElement root)
237 {
238  DoublePropertyPtr retval = DoubleProperty::initialize("Noise level",
239  "", "Select the amount of noise present in the image", 0.5,
240  DoubleRange(0.0, 2, 0.5), 1, root);
241  retval->setGuiRepresentation(DoubleProperty::grSLIDER);
242  return retval;
243 }
244 */
245 
246 AirwaysFilter::~AirwaysFilter() {
247 }
248 
249 } /* namespace cx */
250 
qstring_cast
QString qstring_cast(const T &val)
Definition: cxTypeConversions.h:67
cx::FilterImpl::mInputTypes
std::vector< SelectDataStringPropertyBasePtr > mInputTypes
Definition: cxFilterImpl.h:94
cx::reportError
void reportError(QString msg)
Definition: cxLogger.cpp:92
cx::Mesh
A mesh data set.
Definition: cxMesh.h:61
cx::VisServicesPtr
boost::shared_ptr< class VisServices > VisServicesPtr
Definition: cxMainWindow.h:62
cx::ImagePtr
boost::shared_ptr< class Image > ImagePtr
Definition: cxDicomWidget.h:48
cx::AirwaysFilter::createOutputTypes
virtual void createOutputTypes()
Definition: cxAirwaysFilterService.cpp:217
cx::AirwaysFilter::AirwaysFilter
AirwaysFilter(VisServicesPtr services)
Definition: cxAirwaysFilterService.cpp:65
vtkPolyDataPtr
vtkSmartPointer< class vtkPolyData > vtkPolyDataPtr
Definition: cxAirwaysFilterService.h:52
cx::SelectDataStringPropertyBasePtr
boost::shared_ptr< class SelectDataStringPropertyBase > SelectDataStringPropertyBasePtr
Definition: cxMeshInfoWidget.h:48
cx::FilterImpl::patientService
PatientModelServicePtr patientService()
Definition: cxFilterImpl.cpp:51
cx::ContourFilter::execute
virtual bool execute()
Definition: cxContourFilter.cpp:215
cx::Mesh::setVtkPolyData
void setVtkPolyData(const vtkPolyDataPtr &polyData)
Definition: cxMesh.cpp:100
cx::FilterImpl::getCopiedInputImage
ImagePtr getCopiedInputImage(int index=0)
Definition: cxFilterImpl.cpp:125
cx::AirwaysFilter::getType
virtual QString getType() const
Definition: cxAirwaysFilterService.cpp:76
cx::FilterImpl::mOutputTypes
std::vector< SelectDataStringPropertyBasePtr > mOutputTypes
Definition: cxFilterImpl.h:95
cx::StringPropertySelectMesh::New
static StringPropertySelectMeshPtr New(PatientModelServicePtr patientModelService)
Definition: cxSelectDataStringProperty.h:152
cx::ContourFilter::postProcess
virtual bool postProcess()
Definition: cxContourFilter.cpp:316
cx::StringPropertySelectImage::New
static StringPropertySelectImagePtr New(PatientModelServicePtr patientModelService)
Definition: cxSelectDataStringProperty.h:97
cx::MeshPtr
boost::shared_ptr< class Mesh > MeshPtr
Definition: cxForwardDeclarations.h:68
cx::StringPropertySelectMeshPtr
boost::shared_ptr< class StringPropertySelectMesh > StringPropertySelectMeshPtr
Definition: cxRecordSessionSelector.h:47
cx::AirwaysFilter::getName
virtual QString getName() const
Definition: cxAirwaysFilterService.cpp:71
cx::AirwaysFilter::getHelp
virtual QString getHelp() const
Definition: cxAirwaysFilterService.cpp:81