CustusX  16.5
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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(ctkPluginContext *pluginContext) :
66  FilterImpl(VisServices::create(pluginContext))
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 
90 bool AirwaysFilter::execute()
91 {
92  std::cout << "EXECUTING AIRWAYS FILTER" << std::endl;
93  ImagePtr input = this->getCopiedInputImage();
94  if (!input)
95  return false;
96  mInputImage = input;
97 
98  std::string filename = (patientService()->getActivePatientFolder()+"/"+input->getFilename()).toStdString();
99 
100  try {
101  // Import image data from disk
102  fast::ImageFileImporter::pointer importer = fast::ImageFileImporter::New();
103  importer->setFilename(filename);
104 
105  // Need to know the data type
106  importer->update();
107  fast::Image::pointer image = importer->getOutputData<fast::Image>();
108  std::cout << "IMAGE LOADED" << std::endl;
109 
110  // Do segmentation
111  fast::AirwaySegmentation::pointer segmentation = fast::AirwaySegmentation::New();
112  segmentation->setInputConnection(importer->getOutputPort());
113 
114  // Convert fast segmentation data to VTK data which CX can use
115  vtkSmartPointer<fast::VTKImageExporter> vtkExporter = fast::VTKImageExporter::New();
116  vtkExporter->setInputConnection(segmentation->getOutputPort());
117  vtkExporter->Update();
118  mSegmentationOutput = vtkExporter->GetOutput();
119  std::cout << "FINISHED AIRWAY SEGMENTATION" << std::endl;
120 
121  // Get output segmentation data
122  fast::Segmentation::pointer segmentationData = segmentation->getOutputData<fast::Segmentation>(0);
123 
124  // Get the transformation of the segmentation
125  Eigen::Affine3f T = fast::SceneGraph::getEigenAffineTransformationFromData(segmentationData);
126  mTransformation.matrix() = T.matrix().cast<double>(); // cast to double
127 
128  // Extract centerline
129  fast::CenterlineExtraction::pointer centerline = fast::CenterlineExtraction::New();
130  centerline->setInputConnection(segmentation->getOutputPort());
131 
132  // Get centerline
133  vtkSmartPointer<fast::VTKLineSetExporter> vtkCenterlineExporter = fast::VTKLineSetExporter::New();
134  vtkCenterlineExporter->setInputConnection(centerline->getOutputPort());
135  mCenterlineOutput = vtkCenterlineExporter->GetOutput();
136  vtkCenterlineExporter->Update();
137 
138  } catch(fast::Exception& e) {
139  std::string error = e.what();
140  reportError("fast::Exception: "+qstring_cast(error));
141 
142  return false;
143  } catch(cl::Error& e) {
144  reportError("cl::Error:"+qstring_cast(e.what()));
145 
146  return false;
147  } catch (std::exception& e){
148  reportError("std::exception:"+qstring_cast(e.what()));
149 
150  return false;
151  } catch (...){
152  reportError("Airway segmentation algorithm threw a unknown exception.");
153 
154  return false;
155  }
156  return true;
157 }
158 
159 bool AirwaysFilter::postProcess()
160 {
161  if(!mSegmentationOutput)
162  return false;
163 
164  std::cout << "POST PROCESS" << std::endl;
165 
166  // Make contour of segmented volume
167  double threshold = 1;
168  vtkPolyDataPtr rawContour = ContourFilter::execute(
169  mSegmentationOutput,
170  threshold,
171  false, // reduce resolution
172  true, // smoothing
173  true, // keep topology
174  0 // target decimation
175  );
176  //outputSegmentation->get_rMd_History()->setRegistration(rMd_i);
177  //patientService()->insertData(outputSegmentation);
178 
179  // Add contour internally to cx
180  MeshPtr contour = ContourFilter::postProcess(
181  patientService(),
182  rawContour,
183  mInputImage,
184  QColor("green")
185  );
186  contour->get_rMd_History()->setRegistration(mTransformation);
187 
188  // Set output
189  mOutputTypes[1]->setValue(contour->getUid());
190 
191  // TODO get centerline somehow
192  QString uid = mInputImage->getUid() + "_centerline%1";
193  QString name = mInputImage->getName() + " centerline%1";
194  MeshPtr centerline = patientService()->createSpecificData<Mesh>(uid, name);
195  centerline->setVtkPolyData(mCenterlineOutput);
196  centerline->get_rMd_History()->setParentSpace(mInputImage->getUid());
197  centerline->get_rMd_History()->setRegistration(mTransformation);
198  patientService()->insertData(centerline);
199  mOutputTypes[0]->setValue(centerline->getUid());
200 
201  return true;
202 }
203 
204 void AirwaysFilter::createOptions()
205 {
206  //mOptionsAdapters.push_back(getNoiseLevelOption(mOptions));
207 }
208 
209 void AirwaysFilter::createInputTypes()
210 {
211  SelectDataStringPropertyBasePtr temp;
212 
213  temp = StringPropertySelectImage::New(patientService());
214  temp->setValueName("Input");
215  temp->setHelp("Select input to run airway segmentation on.");
216  mInputTypes.push_back(temp);
217 }
218 
219 void AirwaysFilter::createOutputTypes()
220 {
221  StringPropertySelectMeshPtr tempMeshStringAdapter;
222 
223  //0
224  tempMeshStringAdapter = StringPropertySelectMesh::New(patientService());
225  tempMeshStringAdapter->setValueName("Centerline");
226  tempMeshStringAdapter->setHelp("Generated centerline mesh (vtk-format).");
227  mOutputTypes.push_back(tempMeshStringAdapter);
228 
229  //1
230  tempMeshStringAdapter = StringPropertySelectMesh::New(patientService());
231  tempMeshStringAdapter->setValueName("Segmentation");
232  tempMeshStringAdapter->setHelp("Generated surface of the segmented volume.");
233  mOutputTypes.push_back(tempMeshStringAdapter);
234 
235 }
236 
237 /*
238 DoublePropertyPtr AirwaysFilter::getNoiseLevelOption(QDomElement root)
239 {
240  DoublePropertyPtr retval = DoubleProperty::initialize("Noise level",
241  "", "Select the amount of noise present in the image", 0.5,
242  DoubleRange(0.0, 2, 0.5), 1, root);
243  retval->setGuiRepresentation(DoubleProperty::grSLIDER);
244  return retval;
245 }
246 */
247 
248 AirwaysFilter::~AirwaysFilter() {
249 }
250 
251 } /* namespace cx */
252 
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::ImagePtr
boost::shared_ptr< class Image > ImagePtr
Definition: cxDicomWidget.h:48
cx::AirwaysFilter::createOutputTypes
virtual void createOutputTypes()
Definition: cxAirwaysFilterService.cpp:219
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::AirwaysFilter::AirwaysFilter
AirwaysFilter(ctkPluginContext *pluginContext)
Definition: cxAirwaysFilterService.cpp:65
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