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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
5 All rights reserved.
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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  QString kernelDir = cx::DataLocations::findConfigFolder("/FAST", FAST_SOURCE_DIR);
101  fast::DeviceManager::getInstance().setKernelRootPath(kernelDir.toStdString());
102  // Import image data from disk
103  fast::ImageFileImporter::pointer importer = fast::ImageFileImporter::New();
104  importer->setFilename(filename);
105 
106  // Need to know the data type
107  importer->update();
108  fast::Image::pointer image = importer->getOutputData<fast::Image>();
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  CX_LOG_SUCCESS() << "FINISHED AIRWAY SEGMENTATION";
120 
121  // Get output segmentation data
122  fast::Segmentation::pointer segmentationData = segmentation->getOutputData<fast::Segmentation>(0);
123 
124  //HACK: there is some kind of race condition where data is not ready to be accessed, thus we need to wait a bit
125  //This only happens on mac release build (disapears if cout's are added for example.)
126  sleep_ms(500);
127  std::cout << segmentationData << std::endl;
128  std::cout << segmentationData->getTimestamp() << std::endl;
129 
130  // Get the transformation of the segmentation
131  Eigen::Affine3f T = fast::SceneGraph::getEigenAffineTransformationFromData(segmentationData);
132  mTransformation.matrix() = T.matrix().cast<double>(); // cast to double
133 
134  // Extract centerline
135  fast::CenterlineExtraction::pointer centerline = fast::CenterlineExtraction::New();
136  centerline->setInputConnection(segmentation->getOutputPort());
137 
138  // Get centerline
139  vtkSmartPointer<fast::VTKLineSetExporter> vtkCenterlineExporter = fast::VTKLineSetExporter::New();
140  vtkCenterlineExporter->setInputConnection(centerline->getOutputPort());
141  mCenterlineOutput = vtkCenterlineExporter->GetOutput();
142  vtkCenterlineExporter->Update();
143 
144  } catch(fast::Exception& e) {
145  std::string error = e.what();
146  reportError("fast::Exception: "+qstring_cast(error));
147 
148  return false;
149  } catch(cl::Error& e) {
150  reportError("cl::Error:"+qstring_cast(e.what()));
151 
152  return false;
153  } catch (std::exception& e){
154  reportError("std::exception:"+qstring_cast(e.what()));
155 
156  return false;
157  } catch (...){
158  reportError("Airway segmentation algorithm threw a unknown exception.");
159 
160  return false;
161  }
162  return true;
163 }
164 
165 bool AirwaysFilter::postProcess()
166 {
167  if(!mSegmentationOutput)
168  return false;
169 
170  std::cout << "POST PROCESS" << std::endl;
171 
172  // Make contour of segmented volume
173  double threshold = 1;
174  vtkPolyDataPtr rawContour = ContourFilter::execute(
175  mSegmentationOutput,
176  threshold,
177  false, // reduce resolution
178  true, // smoothing
179  true, // keep topology
180  0 // target decimation
181  );
182  //outputSegmentation->get_rMd_History()->setRegistration(rMd_i);
183  //patientService()->insertData(outputSegmentation);
184 
185  // Add contour internally to cx
186  MeshPtr contour = ContourFilter::postProcess(
187  patientService(),
188  rawContour,
189  mInputImage,
190  QColor("green")
191  );
192  contour->get_rMd_History()->setRegistration(mTransformation);
193 
194  // Set output
195  mOutputTypes[1]->setValue(contour->getUid());
196 
197  // TODO get centerline somehow
198  QString uid = mInputImage->getUid() + "_centerline%1";
199  QString name = mInputImage->getName() + " centerline%1";
200  MeshPtr centerline = patientService()->createSpecificData<Mesh>(uid, name);
201  centerline->setVtkPolyData(mCenterlineOutput);
202  centerline->get_rMd_History()->setParentSpace(mInputImage->getUid());
203  centerline->get_rMd_History()->setRegistration(mTransformation);
204  patientService()->insertData(centerline);
205  mOutputTypes[0]->setValue(centerline->getUid());
206 
207  return true;
208 }
209 
210 void AirwaysFilter::createOptions()
211 {
212  //mOptionsAdapters.push_back(getNoiseLevelOption(mOptions));
213 }
214 
215 void AirwaysFilter::createInputTypes()
216 {
217  SelectDataStringPropertyBasePtr temp;
218 
219  temp = StringPropertySelectImage::New(patientService());
220  temp->setValueName("Input");
221  temp->setHelp("Select input to run airway segmentation on.");
222  mInputTypes.push_back(temp);
223 }
224 
225 void AirwaysFilter::createOutputTypes()
226 {
227  StringPropertySelectMeshPtr tempMeshStringAdapter;
228 
229  //0
230  tempMeshStringAdapter = StringPropertySelectMesh::New(patientService());
231  tempMeshStringAdapter->setValueName("Centerline");
232  tempMeshStringAdapter->setHelp("Generated centerline mesh (vtk-format).");
233  mOutputTypes.push_back(tempMeshStringAdapter);
234 
235  //1
236  tempMeshStringAdapter = StringPropertySelectMesh::New(patientService());
237  tempMeshStringAdapter->setValueName("Segmentation");
238  tempMeshStringAdapter->setHelp("Generated surface of the segmented volume.");
239  mOutputTypes.push_back(tempMeshStringAdapter);
240 
241 }
242 
243 /*
244 DoublePropertyPtr AirwaysFilter::getNoiseLevelOption(QDomElement root)
245 {
246  DoublePropertyPtr retval = DoubleProperty::initialize("Noise level",
247  "", "Select the amount of noise present in the image", 0.5,
248  DoubleRange(0.0, 2, 0.5), 1, root);
249  retval->setGuiRepresentation(DoubleProperty::grSLIDER);
250  return retval;
251 }
252 */
253 
254 AirwaysFilter::~AirwaysFilter() {
255 }
256 
257 } /* namespace cx */
258 
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:225
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::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