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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 
98  QString q_filename = "";
99  QString activePatienFolder = patientService()->getActivePatientFolder();
100  QString inputImageFileName = mInputImage->getFilename();
101  if(!activePatienFolder.isEmpty())
102  q_filename = activePatienFolder+"/"+inputImageFileName;
103  else
104  q_filename = inputImageFileName;
105 
106  std::string filename = q_filename.toStdString();
107 
108  try {
109  QString kernelDir = cx::DataLocations::findConfigFolder("/FAST", FAST_SOURCE_DIR);
110  fast::DeviceManager::getInstance().setKernelRootPath(kernelDir.toStdString());
111  // Import image data from disk
112  fast::ImageFileImporter::pointer importer = fast::ImageFileImporter::New();
113  importer->setFilename(filename);
114 
115  // Need to know the data type
116  importer->update();
117  fast::Image::pointer image = importer->getOutputData<fast::Image>();
118 
119  // Do segmentation
120  fast::AirwaySegmentation::pointer segmentation = fast::AirwaySegmentation::New();
121  segmentation->setInputConnection(importer->getOutputPort());
122 
123  // Convert fast segmentation data to VTK data which CX can use
124  vtkSmartPointer<fast::VTKImageExporter> vtkExporter = fast::VTKImageExporter::New();
125  vtkExporter->setInputConnection(segmentation->getOutputPort());
126  vtkExporter->Update();
127  mSegmentationOutput = vtkExporter->GetOutput();
128  CX_LOG_SUCCESS() << "FINISHED AIRWAY SEGMENTATION";
129 
130  // Get output segmentation data
131  fast::Segmentation::pointer segmentationData = segmentation->getOutputData<fast::Segmentation>(0);
132 
133  // Get the transformation of the segmentation
134  Eigen::Affine3f T = fast::SceneGraph::getEigenAffineTransformationFromData(segmentationData);
135  mTransformation.matrix() = T.matrix().cast<double>(); // cast to double
136 
137  // Extract centerline
138  fast::CenterlineExtraction::pointer centerline = fast::CenterlineExtraction::New();
139  centerline->setInputConnection(segmentation->getOutputPort());
140 
141  // Get centerline
142  vtkSmartPointer<fast::VTKLineSetExporter> vtkCenterlineExporter = fast::VTKLineSetExporter::New();
143  vtkCenterlineExporter->setInputConnection(centerline->getOutputPort());
144  mCenterlineOutput = vtkCenterlineExporter->GetOutput();
145  vtkCenterlineExporter->Update();
146 
147  } catch(fast::Exception& e) {
148  std::string error = e.what();
149  reportError("fast::Exception: "+qstring_cast(error));
150 
151  return false;
152  } catch(cl::Error& e) {
153  reportError("cl::Error:"+qstring_cast(e.what()));
154 
155  return false;
156  } catch (std::exception& e){
157  reportError("std::exception:"+qstring_cast(e.what()));
158 
159  return false;
160  } catch (...){
161  reportError("Airway segmentation algorithm threw a unknown exception.");
162 
163  return false;
164  }
165  return true;
166 }
167 
168 bool AirwaysFilter::postProcess()
169 {
170  if(!mSegmentationOutput)
171  return false;
172 
173  std::cout << "POST PROCESS" << std::endl;
174 
175  // Make contour of segmented volume
176  double threshold = 1;
177  vtkPolyDataPtr rawContour = ContourFilter::execute(
178  mSegmentationOutput,
179  threshold,
180  false, // reduce resolution
181  true, // smoothing
182  true, // keep topology
183  0 // target decimation
184  );
185  //outputSegmentation->get_rMd_History()->setRegistration(rMd_i);
186  //patientService()->insertData(outputSegmentation);
187 
188  // Add contour internally to cx
189  MeshPtr contour = ContourFilter::postProcess(
190  patientService(),
191  rawContour,
192  mInputImage,
193  QColor("green")
194  );
195  contour->get_rMd_History()->setRegistration(mTransformation);
196 
197  // Set output
198  mOutputTypes[1]->setValue(contour->getUid());
199 
200  // TODO get centerline somehow
201  QString uid = mInputImage->getUid() + "_centerline%1";
202  QString name = mInputImage->getName() + " centerline%1";
203  MeshPtr centerline = patientService()->createSpecificData<Mesh>(uid, name);
204  centerline->setVtkPolyData(mCenterlineOutput);
205  centerline->get_rMd_History()->setParentSpace(mInputImage->getUid());
206  centerline->get_rMd_History()->setRegistration(mTransformation);
207  patientService()->insertData(centerline);
208  mOutputTypes[0]->setValue(centerline->getUid());
209 
210  return true;
211 }
212 
213 void AirwaysFilter::createOptions()
214 {
215  //mOptionsAdapters.push_back(getNoiseLevelOption(mOptions));
216 }
217 
218 void AirwaysFilter::createInputTypes()
219 {
220  SelectDataStringPropertyBasePtr temp;
221 
222  temp = StringPropertySelectImage::New(patientService());
223  temp->setValueName("Input");
224  temp->setHelp("Select input to run airway segmentation on.");
225  mInputTypes.push_back(temp);
226 }
227 
228 void AirwaysFilter::createOutputTypes()
229 {
230  StringPropertySelectMeshPtr tempMeshStringAdapter;
231 
232  //0
233  tempMeshStringAdapter = StringPropertySelectMesh::New(patientService());
234  tempMeshStringAdapter->setValueName("Centerline");
235  tempMeshStringAdapter->setHelp("Generated centerline mesh (vtk-format).");
236  mOutputTypes.push_back(tempMeshStringAdapter);
237 
238  //1
239  tempMeshStringAdapter = StringPropertySelectMesh::New(patientService());
240  tempMeshStringAdapter->setValueName("Segmentation");
241  tempMeshStringAdapter->setHelp("Generated surface of the segmented volume.");
242  mOutputTypes.push_back(tempMeshStringAdapter);
243 
244 }
245 
246 /*
247 DoublePropertyPtr AirwaysFilter::getNoiseLevelOption(QDomElement root)
248 {
249  DoublePropertyPtr retval = DoubleProperty::initialize("Noise level",
250  "", "Select the amount of noise present in the image", 0.5,
251  DoubleRange(0.0, 2, 0.5), 1, root);
252  retval->setGuiRepresentation(DoubleProperty::grSLIDER);
253  return retval;
254 }
255 */
256 
257 AirwaysFilter::~AirwaysFilter() {
258 }
259 
260 } /* namespace cx */
261 
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:228
cx::AirwaysFilter::AirwaysFilter
AirwaysFilter(VisServicesPtr services)
Definition: cxAirwaysFilterService.cpp:66
cx::DataLocations::findConfigFolder
static QString findConfigFolder(QString pathRelativeToConfigRoot, QString alternativeAbsolutePath="")
Definition: cxDataLocations.cpp:264
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::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