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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 #include "cxUtilHelpers.h"
55 // Test
56 #include "FAST/Algorithms/AirwaySegmentation/AirwaySegmentation.hpp"
57 #include "FAST/Algorithms/CenterlineExtraction/CenterlineExtraction.hpp"
58 #include "FAST/Importers/ImageFileImporter.hpp"
59 #include "FAST/Exporters/VTKImageExporter.hpp"
60 #include "FAST/Exporters/VTKLineSetExporter.hpp"
61 #include "FAST/Data/Segmentation.hpp"
62 #include "FAST/SceneGraph.hpp"
63 
64 namespace cx {
65 
66 AirwaysFilter::AirwaysFilter(VisServicesPtr services) :
67  FilterImpl(services)
68 {
69 
70 }
71 
72 QString AirwaysFilter::getName() const
73 {
74  return "Airway Segmentation Filter";
75 }
76 
77 QString AirwaysFilter::getType() const
78 {
79  return "AirwaysFilter";
80 }
81 
82 QString AirwaysFilter::getHelp() const
83 {
84  return "<html>"
85  "<h3>Airway Segmentation.</h3>"
86  "<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>"
87  "</html>";
88 }
89 
90 bool AirwaysFilter::execute()
91 {
92  CX_LOG_INFO() << "EXECUTING AIRWAYS FILTER";
93  ImagePtr input = this->getCopiedInputImage();
94  if (!input)
95  return false;
96  mInputImage = input;
97  std::string filename = (patientService()->getActivePatientFolder()+"/"+mInputImage->getFilename()).toStdString();
98 
99  try {
100  // Import image data from disk
101  fast::ImageFileImporter::pointer importer = fast::ImageFileImporter::New();
102  importer->setFilename(filename);
103 
104  // Need to know the data type
105  importer->update();
106  fast::Image::pointer image = importer->getOutputData<fast::Image>();
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  CX_LOG_SUCCESS() << "FINISHED AIRWAY SEGMENTATION";
118 
119  //HACK: there is some kind of race condition where data is not ready to be accessed, thus we need to wait a bit
120  //This only happens on mac release build (disapears if cout's are added for example.)
121  sleep_ms(500);
122 
123  // Get output segmentation data
124  fast::Segmentation::pointer segmentationData = segmentation->getOutputData<fast::Segmentation>(0);
125 
126  // Get the transformation of the segmentation
127  Eigen::Affine3f T = fast::SceneGraph::getEigenAffineTransformationFromData(segmentationData);
128  mTransformation.matrix() = T.matrix().cast<double>(); // cast to double
129 
130  // Extract centerline
131  fast::CenterlineExtraction::pointer centerline = fast::CenterlineExtraction::New();
132  centerline->setInputConnection(segmentation->getOutputPort());
133 
134  // Get centerline
135  vtkSmartPointer<fast::VTKLineSetExporter> vtkCenterlineExporter = fast::VTKLineSetExporter::New();
136  vtkCenterlineExporter->setInputConnection(centerline->getOutputPort());
137  mCenterlineOutput = vtkCenterlineExporter->GetOutput();
138  vtkCenterlineExporter->Update();
139 
140  } catch(fast::Exception& e) {
141  std::string error = e.what();
142  reportError("fast::Exception: "+qstring_cast(error));
143 
144  return false;
145  } catch(cl::Error& e) {
146  reportError("cl::Error:"+qstring_cast(e.what()));
147 
148  return false;
149  } catch (std::exception& e){
150  reportError("std::exception:"+qstring_cast(e.what()));
151 
152  return false;
153  } catch (...){
154  reportError("Airway segmentation algorithm threw a unknown exception.");
155 
156  return false;
157  }
158  return true;
159 }
160 
161 bool AirwaysFilter::postProcess()
162 {
163  if(!mSegmentationOutput)
164  return false;
165 
166  std::cout << "POST PROCESS" << std::endl;
167 
168  // Make contour of segmented volume
169  double threshold = 1;
170  vtkPolyDataPtr rawContour = ContourFilter::execute(
171  mSegmentationOutput,
172  threshold,
173  false, // reduce resolution
174  true, // smoothing
175  true, // keep topology
176  0 // target decimation
177  );
178  //outputSegmentation->get_rMd_History()->setRegistration(rMd_i);
179  //patientService()->insertData(outputSegmentation);
180 
181  // Add contour internally to cx
182  MeshPtr contour = ContourFilter::postProcess(
183  patientService(),
184  rawContour,
185  mInputImage,
186  QColor("green")
187  );
188  contour->get_rMd_History()->setRegistration(mTransformation);
189 
190  // Set output
191  mOutputTypes[1]->setValue(contour->getUid());
192 
193  // TODO get centerline somehow
194  QString uid = mInputImage->getUid() + "_centerline%1";
195  QString name = mInputImage->getName() + " centerline%1";
196  MeshPtr centerline = patientService()->createSpecificData<Mesh>(uid, name);
197  centerline->setVtkPolyData(mCenterlineOutput);
198  centerline->get_rMd_History()->setParentSpace(mInputImage->getUid());
199  centerline->get_rMd_History()->setRegistration(mTransformation);
200  patientService()->insertData(centerline);
201  mOutputTypes[0]->setValue(centerline->getUid());
202 
203  return true;
204 }
205 
206 void AirwaysFilter::createOptions()
207 {
208  //mOptionsAdapters.push_back(getNoiseLevelOption(mOptions));
209 }
210 
211 void AirwaysFilter::createInputTypes()
212 {
213  SelectDataStringPropertyBasePtr temp;
214 
215  temp = StringPropertySelectImage::New(patientService());
216  temp->setValueName("Input");
217  temp->setHelp("Select input to run airway segmentation on.");
218  mInputTypes.push_back(temp);
219 }
220 
221 void AirwaysFilter::createOutputTypes()
222 {
223  StringPropertySelectMeshPtr tempMeshStringAdapter;
224 
225  //0
226  tempMeshStringAdapter = StringPropertySelectMesh::New(patientService());
227  tempMeshStringAdapter->setValueName("Centerline");
228  tempMeshStringAdapter->setHelp("Generated centerline mesh (vtk-format).");
229  mOutputTypes.push_back(tempMeshStringAdapter);
230 
231  //1
232  tempMeshStringAdapter = StringPropertySelectMesh::New(patientService());
233  tempMeshStringAdapter->setValueName("Segmentation");
234  tempMeshStringAdapter->setHelp("Generated surface of the segmented volume.");
235  mOutputTypes.push_back(tempMeshStringAdapter);
236 
237 }
238 
239 /*
240 DoublePropertyPtr AirwaysFilter::getNoiseLevelOption(QDomElement root)
241 {
242  DoublePropertyPtr retval = DoubleProperty::initialize("Noise level",
243  "", "Select the amount of noise present in the image", 0.5,
244  DoubleRange(0.0, 2, 0.5), 1, root);
245  retval->setGuiRepresentation(DoubleProperty::grSLIDER);
246  return retval;
247 }
248 */
249 
250 AirwaysFilter::~AirwaysFilter() {
251 }
252 
253 } /* namespace cx */
254 
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_LOG_INFO
#define CX_LOG_INFO
Definition: cxLogger.h:111
cx::ImagePtr
boost::shared_ptr< class Image > ImagePtr
Definition: cxDicomWidget.h:48
cx::AirwaysFilter::createOutputTypes
virtual void createOutputTypes()
Definition: cxAirwaysFilterService.cpp:221
cx::AirwaysFilter::AirwaysFilter
AirwaysFilter(VisServicesPtr services)
Definition: cxAirwaysFilterService.cpp:66
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_LOG_SUCCESS
#define CX_LOG_SUCCESS
Definition: cxLogger.h:112
cx::AirwaysFilter::getType
virtual QString getType() const
Definition: cxAirwaysFilterService.cpp:77
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::sleep_ms
void sleep_ms(int ms)
Definition: cxUtilHelpers.cpp:82
cx::StringPropertySelectMeshPtr
boost::shared_ptr< class StringPropertySelectMesh > StringPropertySelectMeshPtr
Definition: cxRecordSessionSelector.h:47
cx::AirwaysFilter::getName
virtual QString getName() const
Definition: cxAirwaysFilterService.cpp:72
cx::AirwaysFilter::getHelp
virtual QString getHelp() const
Definition: cxAirwaysFilterService.cpp:82