QmitkTensorReconstructionView.cpp
Go to the documentation of this file.
00001 /*========================================================================= 00002 00003 Program: Medical Imaging & Interaction Toolkit 00004 Module: $RCSfile$ 00005 Language: C++ 00006 Date: $Date: 2009-05-28 17:19:30 +0200 (Do, 28 Mai 2009) $ 00007 Version: $Revision: 17495 $ 00008 00009 Copyright (c) German Cancer Research Center, Division of Medical and 00010 Biological Informatics. All rights reserved. 00011 See MITKCopyright.txt or https://www.mitk.org/copyright.html for details. 00012 00013 This software is distributed WITHOUT ANY WARRANTY; without even 00014 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 00015 PURPOSE. See the above copyright notices for more information. 00016 00017 =========================================================================*/ 00018 00019 #include "QmitkTensorReconstructionView.h" 00020 #include "mitkDiffusionImagingConfigure.h" 00021 00022 // qt includes 00023 #include <QMessageBox> 00024 00025 // itk includes 00026 #include "itkTimeProbe.h" 00027 00028 // mitk includes 00029 #include "mitkProgressBar.h" 00030 #include "mitkStatusBar.h" 00031 00032 #include "mitkNodePredicateDataType.h" 00033 #include "QmitkDataStorageComboBox.h" 00034 #include "QmitkStdMultiWidget.h" 00035 00036 #include "mitkTeemDiffusionTensor3DReconstructionImageFilter.h" 00037 #include "itkDiffusionTensor3DReconstructionImageFilter.h" 00038 #include "itkTensorImageToDiffusionImageFilter.h" 00039 #include "itkPointShell.h" 00040 #include "itkVector.h" 00041 00042 #include "mitkTensorImage.h" 00043 #include "mitkProperties.h" 00044 #include "mitkDataNodeObject.h" 00045 #include "mitkOdfNormalizationMethodProperty.h" 00046 #include "mitkOdfScaleByProperty.h" 00047 #include "mitkDiffusionImageMapper.h" 00048 00049 #include "berryIStructuredSelection.h" 00050 #include "berryIWorkbenchWindow.h" 00051 #include "berryISelectionService.h" 00052 00053 const std::string QmitkTensorReconstructionView::VIEW_ID = 00054 "org.mitk.views.tensorreconstruction"; 00055 00056 #define DI_INFO MITK_INFO("DiffusionImaging") 00057 00058 typedef float TTensorPixelType; 00059 00060 using namespace berry; 00061 00062 struct TrSelListener : ISelectionListener 00063 { 00064 00065 berryObjectMacro(TrSelListener); 00066 00067 TrSelListener(QmitkTensorReconstructionView* view) 00068 { 00069 m_View = view; 00070 } 00071 00072 void DoSelectionChanged(ISelection::ConstPointer selection) 00073 { 00074 // if(!m_View->IsVisible()) 00075 // return; 00076 // save current selection in member variable 00077 m_View->m_CurrentSelection = selection.Cast<const IStructuredSelection>(); 00078 00079 // do something with the selected items 00080 if(m_View->m_CurrentSelection) 00081 { 00082 bool foundDwiVolume = false; 00083 bool foundTensorVolume = false; 00084 00085 // iterate selection 00086 for (IStructuredSelection::iterator i = m_View->m_CurrentSelection->Begin(); 00087 i != m_View->m_CurrentSelection->End(); ++i) 00088 { 00089 00090 // extract datatree node 00091 if (mitk::DataNodeObject::Pointer nodeObj = i->Cast<mitk::DataNodeObject>()) 00092 { 00093 mitk::DataNode::Pointer node = nodeObj->GetDataNode(); 00094 00095 // only look at interesting types 00096 if(QString("DiffusionImage").compare(node->GetData()->GetNameOfClass())==0) 00097 { 00098 foundDwiVolume = true; 00099 } 00100 00101 // only look at interesting types 00102 if(QString("TensorImage").compare(node->GetData()->GetNameOfClass())==0) 00103 { 00104 foundTensorVolume = true; 00105 } 00106 } 00107 } 00108 00109 m_View->m_Controls->m_ItkReconstruction->setEnabled(foundDwiVolume); 00110 m_View->m_Controls->m_TeemReconstruction->setEnabled(foundDwiVolume); 00111 00112 m_View->m_Controls->m_TensorsToDWIButton->setEnabled(foundTensorVolume); 00113 00114 } 00115 } 00116 00117 void SelectionChanged(IWorkbenchPart::Pointer part, ISelection::ConstPointer selection) 00118 { 00119 // check, if selection comes from datamanager 00120 if (part) 00121 { 00122 QString partname(part->GetPartName().c_str()); 00123 if(partname.compare("Datamanager")==0) 00124 { 00125 00126 // apply selection 00127 DoSelectionChanged(selection); 00128 00129 } 00130 } 00131 } 00132 00133 QmitkTensorReconstructionView* m_View; 00134 }; 00135 00136 QmitkTensorReconstructionView::QmitkTensorReconstructionView() 00137 : QmitkFunctionality(), 00138 m_Controls(NULL), 00139 m_MultiWidget(NULL) 00140 { 00141 } 00142 00143 QmitkTensorReconstructionView::~QmitkTensorReconstructionView() 00144 { 00145 this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->RemovePostSelectionListener(/*"org.mitk.views.datamanager",*/ m_SelListener); 00146 } 00147 00148 void QmitkTensorReconstructionView::CreateQtPartControl(QWidget *parent) 00149 { 00150 if (!m_Controls) 00151 { 00152 // create GUI widgets 00153 m_Controls = new Ui::QmitkTensorReconstructionViewControls; 00154 m_Controls->setupUi(parent); 00155 this->CreateConnections(); 00156 00157 m_Controls->m_TensorReconstructionNumberThreadsSpinbox->setValue(8); 00158 00159 QStringList items; 00160 items << "LLS (Linear Least Squares)" 00161 << "MLE (Maximum Likelihood)" 00162 << "NLS (Nonlinear Least Squares)" 00163 << "WLS (Weighted Least Squares)"; 00164 m_Controls->m_TensorEstimationTeemEstimationMethodCombo->addItems(items); 00165 m_Controls->m_TensorEstimationTeemEstimationMethodCombo->setCurrentIndex(0); 00166 00167 m_Controls->m_TensorEstimationManualThreashold->setChecked(false); 00168 m_Controls->m_TensorEstimationTeemSigmaEdit->setText("NaN"); 00169 m_Controls->m_TensorEstimationTeemNumItsSpin->setValue(1); 00170 m_Controls->m_TensorEstimationTeemFuzzyEdit->setText("0.0"); 00171 m_Controls->m_TensorEstimationTeemMinValEdit->setText("1.0"); 00172 00173 m_Controls->m_TensorEstimationTeemNumItsLabel_2->setEnabled(true); 00174 m_Controls->m_TensorEstimationTeemNumItsSpin->setEnabled(true); 00175 00176 m_Controls->m_TensorsToDWIBValueEdit->setText("1000"); 00177 00178 Advanced1CheckboxClicked(); 00179 Advanced2CheckboxClicked(); 00180 TeemCheckboxClicked(); 00181 00182 #ifndef DIFFUSION_IMAGING_EXTENDED 00183 m_Controls->m_TeemToggle->setVisible(false); 00184 #endif 00185 00186 // define data type for combobox 00187 //m_Controls->m_ImageSelector->SetDataStorage( this->GetDefaultDataStorage() ); 00188 //m_Controls->m_ImageSelector->SetPredicate( mitk::NodePredicateDataType::New("DiffusionImage") ); 00189 } 00190 00191 m_SelListener = berry::ISelectionListener::Pointer(new TrSelListener(this)); 00192 this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->AddPostSelectionListener(/*"org.mitk.views.datamanager",*/ m_SelListener); 00193 berry::ISelection::ConstPointer sel( 00194 this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); 00195 m_CurrentSelection = sel.Cast<const IStructuredSelection>(); 00196 m_SelListener.Cast<TrSelListener>()->DoSelectionChanged(sel); 00197 } 00198 00199 void QmitkTensorReconstructionView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) 00200 { 00201 berry::ISelection::ConstPointer sel( 00202 this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); 00203 m_CurrentSelection = sel.Cast<const IStructuredSelection>(); 00204 m_SelListener.Cast<TrSelListener>()->DoSelectionChanged(sel); 00205 m_MultiWidget = &stdMultiWidget; 00206 } 00207 00208 void QmitkTensorReconstructionView::StdMultiWidgetNotAvailable() 00209 { 00210 m_MultiWidget = NULL; 00211 } 00212 00213 void QmitkTensorReconstructionView::CreateConnections() 00214 { 00215 if ( m_Controls ) 00216 { 00217 connect( (QObject*)(m_Controls->m_TeemToggle), SIGNAL(clicked()), this, SLOT(TeemCheckboxClicked()) ); 00218 connect( (QObject*)(m_Controls->m_ItkReconstruction), SIGNAL(clicked()), this, SLOT(ItkReconstruction()) ); 00219 connect( (QObject*)(m_Controls->m_TeemReconstruction), SIGNAL(clicked()), this, SLOT(TeemReconstruction()) ); 00220 connect( (QObject*)(m_Controls->m_TensorEstimationTeemEstimationMethodCombo), SIGNAL(currentIndexChanged(int)), this, SLOT(MethodChoosen(int)) ); 00221 connect( (QObject*)(m_Controls->m_Advanced1), SIGNAL(clicked()), this, SLOT(Advanced1CheckboxClicked()) ); 00222 connect( (QObject*)(m_Controls->m_Advanced2), SIGNAL(clicked()), this, SLOT(Advanced2CheckboxClicked()) ); 00223 connect( (QObject*)(m_Controls->m_TensorEstimationManualThreashold), SIGNAL(clicked()), this, SLOT(ManualThresholdClicked()) ); 00224 connect( (QObject*)(m_Controls->m_TensorsToDWIButton), SIGNAL(clicked()), this, SLOT(TensorsToDWI()) ); 00225 } 00226 } 00227 00228 void QmitkTensorReconstructionView::TeemCheckboxClicked() 00229 { 00230 m_Controls->groupBox_3->setVisible(m_Controls-> 00231 m_TeemToggle->isChecked()); 00232 } 00233 00234 void QmitkTensorReconstructionView::Advanced1CheckboxClicked() 00235 { 00236 bool check = m_Controls-> 00237 m_Advanced1->isChecked(); 00238 00239 m_Controls->frame->setVisible(check); 00240 } 00241 00242 void QmitkTensorReconstructionView::Advanced2CheckboxClicked() 00243 { 00244 bool check = m_Controls-> 00245 m_Advanced2->isChecked(); 00246 00247 m_Controls->frame_2->setVisible(check); 00248 } 00249 00250 void QmitkTensorReconstructionView::ManualThresholdClicked() 00251 { 00252 m_Controls->m_TensorReconstructionThreasholdEdit_2->setEnabled( 00253 m_Controls->m_TensorEstimationManualThreashold->isChecked()); 00254 } 00255 00256 void QmitkTensorReconstructionView::Activated() 00257 { 00258 QmitkFunctionality::Activated(); 00259 } 00260 00261 void QmitkTensorReconstructionView::Deactivated() 00262 { 00263 QmitkFunctionality::Deactivated(); 00264 } 00265 00266 void QmitkTensorReconstructionView::MethodChoosen(int method) 00267 { 00268 m_Controls->m_TensorEstimationTeemNumItsLabel_2->setEnabled(method==3); 00269 m_Controls->m_TensorEstimationTeemNumItsSpin->setEnabled(method==3); 00270 } 00271 00272 void QmitkTensorReconstructionView::ItkReconstruction() 00273 { 00274 Reconstruct(0); 00275 } 00276 00277 void QmitkTensorReconstructionView::TeemReconstruction() 00278 { 00279 Reconstruct(1); 00280 } 00281 00282 void QmitkTensorReconstructionView::Reconstruct(int method) 00283 { 00284 if (m_CurrentSelection) 00285 { 00286 mitk::DataStorage::SetOfObjects::Pointer set = 00287 mitk::DataStorage::SetOfObjects::New(); 00288 00289 int at = 0; 00290 for (IStructuredSelection::iterator i = m_CurrentSelection->Begin(); 00291 i != m_CurrentSelection->End(); 00292 ++i) 00293 { 00294 00295 if (mitk::DataNodeObject::Pointer nodeObj = i->Cast<mitk::DataNodeObject>()) 00296 { 00297 mitk::DataNode::Pointer node = nodeObj->GetDataNode(); 00298 if(QString("DiffusionImage").compare(node->GetData()->GetNameOfClass())==0) 00299 { 00300 set->InsertElement(at++, node); 00301 } 00302 } 00303 } 00304 00305 if(method == 0) 00306 { 00307 ItkTensorReconstruction(set); 00308 } 00309 00310 if(method == 1) 00311 { 00312 TeemTensorReconstruction(set); 00313 } 00314 00315 } 00316 } 00317 00318 void QmitkTensorReconstructionView::ItkTensorReconstruction 00319 (mitk::DataStorage::SetOfObjects::Pointer inImages) 00320 { 00321 try 00322 { 00323 itk::TimeProbe clock; 00324 00325 int nrFiles = inImages->size(); 00326 if (!nrFiles) return; 00327 00328 QString status; 00329 mitk::ProgressBar::GetInstance()->AddStepsToDo(nrFiles); 00330 00331 mitk::DataStorage::SetOfObjects::const_iterator itemiter( inImages->begin() ); 00332 mitk::DataStorage::SetOfObjects::const_iterator itemiterend( inImages->end() ); 00333 00334 std::vector<mitk::DataNode::Pointer> nodes; 00335 while ( itemiter != itemiterend ) // for all items 00336 { 00337 00338 mitk::DiffusionImage<DiffusionPixelType>* vols = 00339 static_cast<mitk::DiffusionImage<DiffusionPixelType>*>( 00340 (*itemiter)->GetData()); 00341 00342 std::string nodename; 00343 (*itemiter)->GetStringProperty("name", nodename); 00344 ++itemiter; 00345 00346 // TENSOR RECONSTRUCTION 00347 clock.Start(); 00348 MBI_INFO << "Tensor reconstruction "; 00349 mitk::StatusBar::GetInstance()->DisplayText(status.sprintf( 00350 "Tensor reconstruction for %s", nodename.c_str()).toAscii()); 00351 typedef itk::DiffusionTensor3DReconstructionImageFilter< 00352 DiffusionPixelType, DiffusionPixelType, TTensorPixelType > TensorReconstructionImageFilterType; 00353 TensorReconstructionImageFilterType::Pointer tensorReconstructionFilter = 00354 TensorReconstructionImageFilterType::New(); 00355 tensorReconstructionFilter->SetGradientImage( vols->GetDirections(), vols->GetVectorImage() ); 00356 tensorReconstructionFilter->SetNumberOfThreads( m_Controls->m_TensorReconstructionNumberThreadsSpinbox->value() ); 00357 tensorReconstructionFilter->SetBValue(vols->GetB_Value()); 00358 tensorReconstructionFilter->SetThreshold( m_Controls->m_TensorReconstructionThreasholdEdit->text().toFloat() ); 00359 tensorReconstructionFilter->Update(); 00360 clock.Stop(); 00361 MBI_DEBUG << "took " << clock.GetMeanTime() << "s."; 00362 00363 // TENSORS TO DATATREE 00364 mitk::TensorImage::Pointer image = mitk::TensorImage::New(); 00365 image->InitializeByItk( tensorReconstructionFilter->GetOutput() ); 00366 image->SetVolume( tensorReconstructionFilter->GetOutput()->GetBufferPointer() ); 00367 mitk::DataNode::Pointer node=mitk::DataNode::New(); 00368 node->SetData( image ); 00369 00370 QString newname; 00371 newname = newname.append(nodename.c_str()); 00372 newname = newname.append("_dti"); 00373 00374 SetDefaultNodeProperties(node, newname.toStdString()); 00375 nodes.push_back(node); 00376 00377 mitk::ProgressBar::GetInstance()->Progress(); 00378 00379 } 00380 00381 std::vector<mitk::DataNode::Pointer>::iterator nodeIt; 00382 for(nodeIt = nodes.begin(); nodeIt != nodes.end(); ++nodeIt) 00383 GetDefaultDataStorage()->Add(*nodeIt); 00384 00385 mitk::StatusBar::GetInstance()->DisplayText(status.sprintf("Finished Processing %d Files", nrFiles).toAscii()); 00386 m_MultiWidget->RequestUpdate(); 00387 00388 } 00389 catch (itk::ExceptionObject &ex) 00390 { 00391 MBI_INFO << ex ; 00392 return ; 00393 } 00394 } 00395 00396 00397 00398 void QmitkTensorReconstructionView::TeemTensorReconstruction 00399 (mitk::DataStorage::SetOfObjects::Pointer inImages) 00400 { 00401 try 00402 { 00403 itk::TimeProbe clock; 00404 00405 int nrFiles = inImages->size(); 00406 if (!nrFiles) return; 00407 00408 QString status; 00409 mitk::ProgressBar::GetInstance()->AddStepsToDo(nrFiles); 00410 00411 mitk::DataStorage::SetOfObjects::const_iterator itemiter( inImages->begin() ); 00412 mitk::DataStorage::SetOfObjects::const_iterator itemiterend( inImages->end() ); 00413 00414 std::vector<mitk::DataNode::Pointer> nodes; 00415 while ( itemiter != itemiterend ) // for all items 00416 { 00417 00418 mitk::DiffusionImage<DiffusionPixelType>* vols = 00419 static_cast<mitk::DiffusionImage<DiffusionPixelType>*>( 00420 (*itemiter)->GetData()); 00421 00422 std::string nodename; 00423 (*itemiter)->GetStringProperty("name", nodename); 00424 ++itemiter; 00425 00426 // TENSOR RECONSTRUCTION 00427 clock.Start(); 00428 MBI_INFO << "Teem Tensor reconstruction "; 00429 mitk::StatusBar::GetInstance()->DisplayText(status.sprintf( 00430 "Teem Tensor reconstruction for %s", nodename.c_str()).toAscii()); 00431 typedef mitk::TeemDiffusionTensor3DReconstructionImageFilter< 00432 DiffusionPixelType, TTensorPixelType > TensorReconstructionImageFilterType; 00433 TensorReconstructionImageFilterType::Pointer tensorReconstructionFilter = 00434 TensorReconstructionImageFilterType::New(); 00435 tensorReconstructionFilter->SetInput( vols ); 00436 if(!m_Controls->m_TensorEstimationTeemSigmaEdit->text().contains(QString("NaN"))) 00437 tensorReconstructionFilter->SetSigma( m_Controls->m_TensorEstimationTeemSigmaEdit->text().toFloat() ); 00438 switch(m_Controls->m_TensorEstimationTeemEstimationMethodCombo->currentIndex()) 00439 { 00440 // items << "LLS (Linear Least Squares)" 00441 //<< "MLE (Maximum Likelihood)" 00442 //<< "NLS (Nonlinear Least Squares)" 00443 //<< "WLS (Weighted Least Squares)"; 00444 case 0: 00445 tensorReconstructionFilter->SetEstimationMethod(mitk::TeemTensorEstimationMethodsLLS); 00446 break; 00447 case 1: 00448 tensorReconstructionFilter->SetEstimationMethod(mitk::TeemTensorEstimationMethodsMLE); 00449 break; 00450 case 2: 00451 tensorReconstructionFilter->SetEstimationMethod(mitk::TeemTensorEstimationMethodsNLS); 00452 break; 00453 case 3: 00454 tensorReconstructionFilter->SetEstimationMethod(mitk::TeemTensorEstimationMethodsWLS); 00455 break; 00456 default: 00457 tensorReconstructionFilter->SetEstimationMethod(mitk::TeemTensorEstimationMethodsLLS); 00458 } 00459 tensorReconstructionFilter->SetNumIterations( m_Controls->m_TensorEstimationTeemNumItsSpin->value() ); 00460 if(m_Controls->m_TensorEstimationManualThreashold->isChecked()) 00461 tensorReconstructionFilter->SetConfidenceThreshold( m_Controls->m_TensorReconstructionThreasholdEdit_2->text().toDouble() ); 00462 tensorReconstructionFilter->SetConfidenceFuzzyness( m_Controls->m_TensorEstimationTeemFuzzyEdit->text().toFloat() ); 00463 tensorReconstructionFilter->SetMinPlausibleValue( m_Controls->m_TensorEstimationTeemMinValEdit->text().toDouble() ); 00464 tensorReconstructionFilter->Update(); 00465 clock.Stop(); 00466 MBI_DEBUG << "took " << clock.GetMeanTime() << "s." ; 00467 00468 // TENSORS TO DATATREE 00469 mitk::DataNode::Pointer node2=mitk::DataNode::New(); 00470 node2->SetData( tensorReconstructionFilter->GetOutputItk() ); 00471 00472 QString newname; 00473 newname = newname.append(nodename.c_str()); 00474 newname = newname.append("_dtix"); 00475 00476 SetDefaultNodeProperties(node2, newname.toStdString()); 00477 nodes.push_back(node2); 00478 00479 mitk::ProgressBar::GetInstance()->Progress(); 00480 00481 } 00482 00483 std::vector<mitk::DataNode::Pointer>::iterator nodeIt; 00484 for(nodeIt = nodes.begin(); nodeIt != nodes.end(); ++nodeIt) 00485 GetDefaultDataStorage()->Add(*nodeIt); 00486 00487 mitk::StatusBar::GetInstance()->DisplayText(status.sprintf("Finished Processing %d Files", nrFiles).toAscii()); 00488 m_MultiWidget->RequestUpdate(); 00489 00490 } 00491 catch (itk::ExceptionObject &ex) 00492 { 00493 MBI_INFO << ex ; 00494 return ; 00495 } 00496 } 00497 00498 void QmitkTensorReconstructionView::SetDefaultNodeProperties(mitk::DataNode::Pointer node, std::string name) 00499 { 00500 node->SetProperty( "ShowMaxNumber", mitk::IntProperty::New( 500 ) ); 00501 node->SetProperty( "Scaling", mitk::FloatProperty::New( 1.0 ) ); 00502 node->SetProperty( "Normalization", mitk::OdfNormalizationMethodProperty::New()); 00503 node->SetProperty( "ScaleBy", mitk::OdfScaleByProperty::New()); 00504 node->SetProperty( "IndexParam1", mitk::FloatProperty::New(2)); 00505 node->SetProperty( "IndexParam2", mitk::FloatProperty::New(1)); 00506 node->SetProperty( "visible", mitk::BoolProperty::New( true ) ); 00507 node->SetProperty( "VisibleOdfs", mitk::BoolProperty::New( false ) ); 00508 node->SetProperty ("layer", mitk::IntProperty::New(100)); 00509 node->SetProperty( "DoRefresh", mitk::BoolProperty::New( true ) ); 00510 //node->SetProperty( "opacity", mitk::FloatProperty::New(1.0f) ); 00511 00512 node->SetProperty( "name", mitk::StringProperty::New(name) ); 00513 } 00514 00515 00516 //node->SetProperty( "volumerendering", mitk::BoolProperty::New( false ) ); 00517 //node->SetProperty( "use color", mitk::BoolProperty::New( true ) ); 00518 //node->SetProperty( "texture interpolation", mitk::BoolProperty::New( true ) ); 00519 //node->SetProperty( "reslice interpolation", mitk::VtkResliceInterpolationProperty::New() ); 00520 //node->SetProperty( "layer", mitk::IntProperty::New(0)); 00521 //node->SetProperty( "in plane resample extent by geometry", mitk::BoolProperty::New( false ) ); 00522 //node->SetOpacity(1.0f); 00523 //node->SetColor(1.0,1.0,1.0); 00524 //node->SetVisibility(true); 00525 //node->SetProperty( "IsTensorVolume", mitk::BoolProperty::New( true ) ); 00526 00527 //mitk::LevelWindowProperty::Pointer levWinProp = mitk::LevelWindowProperty::New(); 00528 //mitk::LevelWindow levelwindow; 00530 //levWinProp->SetLevelWindow( levelwindow ); 00531 //node->GetPropertyList()->SetProperty( "levelwindow", levWinProp ); 00532 00534 //if(!node->GetProperty("LookupTable")) 00535 //{ 00536 // mitk::LookupTable::Pointer mitkLut = mitk::LookupTable::New(); 00537 // vtkLookupTable* vtkLut = mitkLut->GetVtkLookupTable(); 00538 // vtkLut->SetHueRange(0.6667, 0.0); 00539 // vtkLut->SetTableRange(0.0, 20.0); 00540 // vtkLut->Build(); 00541 // mitk::LookupTableProperty::Pointer mitkLutProp = mitk::LookupTableProperty::New(); 00542 // mitkLutProp->SetLookupTable(mitkLut); 00543 // node->SetProperty( "LookupTable", mitkLutProp ); 00544 //} 00545 //if(!node->GetProperty("binary")) 00546 // node->SetProperty( "binary", mitk::BoolProperty::New( false ) ); 00547 00549 //mitk::TransferFunction::Pointer tf = mitk::TransferFunction::New(); 00550 //node->SetProperty ( "TransferFunction", mitk::TransferFunctionProperty::New ( tf.GetPointer() ) ); 00551 00553 //mitk::StringProperty::Pointer nameProp = mitk::StringProperty::New( name ); 00554 //node->SetProperty( "name", nameProp ); 00555 00556 void QmitkTensorReconstructionView::TensorsToDWI() 00557 { 00558 if (m_CurrentSelection) 00559 { 00560 mitk::DataStorage::SetOfObjects::Pointer set = 00561 mitk::DataStorage::SetOfObjects::New(); 00562 00563 int at = 0; 00564 for (IStructuredSelection::iterator i = m_CurrentSelection->Begin(); 00565 i != m_CurrentSelection->End(); 00566 ++i) 00567 { 00568 00569 if (mitk::DataNodeObject::Pointer nodeObj = i->Cast<mitk::DataNodeObject>()) 00570 { 00571 mitk::DataNode::Pointer node = nodeObj->GetDataNode(); 00572 if(QString("TensorImage").compare(node->GetData()->GetNameOfClass())==0) 00573 { 00574 set->InsertElement(at++, node); 00575 } 00576 } 00577 } 00578 00579 DoTensorsToDWI(set); 00580 } 00581 } 00582 00583 template<int ndirs> 00584 std::vector<itk::Vector<double,3> > QmitkTensorReconstructionView::MakeGradientList() 00585 { 00586 std::vector<itk::Vector<double,3> > retval; 00587 vnl_matrix_fixed<double, 3, ndirs>* U = 00588 itk::PointShell<ndirs, vnl_matrix_fixed<double, 3, ndirs> >::DistributePointShell(); 00589 00590 for(int i=0; i<ndirs;i++) 00591 { 00592 itk::Vector<double,3> v; 00593 v[0] = U->get(0,i); v[1] = U->get(1,i); v[2] = U->get(2,i); 00594 retval.push_back(v); 00595 } 00596 return retval; 00597 } 00598 00599 void QmitkTensorReconstructionView::DoTensorsToDWI 00600 (mitk::DataStorage::SetOfObjects::Pointer inImages) 00601 { 00602 try 00603 { 00604 itk::TimeProbe clock; 00605 00606 int nrFiles = inImages->size(); 00607 if (!nrFiles) return; 00608 00609 QString status; 00610 mitk::ProgressBar::GetInstance()->AddStepsToDo(nrFiles); 00611 00612 mitk::DataStorage::SetOfObjects::const_iterator itemiter( inImages->begin() ); 00613 mitk::DataStorage::SetOfObjects::const_iterator itemiterend( inImages->end() ); 00614 00615 std::vector<mitk::DataNode::Pointer> nodes; 00616 while ( itemiter != itemiterend ) // for all items 00617 { 00618 00619 std::string nodename; 00620 (*itemiter)->GetStringProperty("name", nodename); 00621 00622 mitk::TensorImage* vol = 00623 static_cast<mitk::TensorImage*>((*itemiter)->GetData()); 00624 00625 ++itemiter; 00626 00627 typedef float TTensorPixelType; 00628 typedef itk::DiffusionTensor3D< TTensorPixelType > TensorPixelType; 00629 typedef itk::Image< TensorPixelType, 3 > TensorImageType; 00630 00631 00632 TensorImageType::Pointer itkvol = TensorImageType::New(); 00633 mitk::CastToItkImage<TensorImageType>(vol, itkvol); 00634 00635 typedef itk::TensorImageToDiffusionImageFilter< 00636 TTensorPixelType, DiffusionPixelType > FilterType; 00637 00638 FilterType::GradientListType gradientList; 00639 00640 switch(m_Controls->m_TensorsToDWINumDirsSelect->currentIndex()) 00641 { 00642 case 0: 00643 gradientList = MakeGradientList<12>(); 00644 break; 00645 case 1: 00646 gradientList = MakeGradientList<42>(); 00647 break; 00648 case 2: 00649 gradientList = MakeGradientList<92>(); 00650 break; 00651 case 3: 00652 gradientList = MakeGradientList<162>(); 00653 break; 00654 case 4: 00655 gradientList = MakeGradientList<252>(); 00656 break; 00657 case 5: 00658 gradientList = MakeGradientList<362>(); 00659 break; 00660 case 6: 00661 gradientList = MakeGradientList<492>(); 00662 break; 00663 case 7: 00664 gradientList = MakeGradientList<642>(); 00665 break; 00666 case 8: 00667 gradientList = MakeGradientList<812>(); 00668 break; 00669 case 9: 00670 gradientList = MakeGradientList<1002>(); 00671 break; 00672 default: 00673 gradientList = MakeGradientList<92>(); 00674 00675 } 00676 00677 double bVal = m_Controls->m_TensorsToDWIBValueEdit->text().toDouble(); 00678 00679 // DWI ESTIMATION 00680 clock.Start(); 00681 MBI_INFO << "DWI Estimation "; 00682 mitk::StatusBar::GetInstance()->DisplayText(status.sprintf( 00683 "DWI Estimation for %s", nodename.c_str()).toAscii()); 00684 FilterType::Pointer filter = FilterType::New(); 00685 filter->SetInput( itkvol ); 00686 filter->SetBValue(bVal); 00687 filter->SetGradientList(gradientList); 00688 filter->SetNumberOfThreads(1); 00689 filter->Update(); 00690 clock.Stop(); 00691 MBI_DEBUG << "took " << clock.GetMeanTime() << "s."; 00692 00693 itk::Vector<double,3> v; 00694 v[0] = 0; v[1] = 0; v[2] = 0; 00695 gradientList.push_back(v); 00696 00697 // TENSORS TO DATATREE 00698 mitk::DiffusionImage<DiffusionPixelType>::Pointer image = mitk::DiffusionImage<DiffusionPixelType>::New(); 00699 image->SetVectorImage( filter->GetOutput() ); 00700 image->SetB_Value(bVal); 00701 image->SetDirections(gradientList); 00702 image->InitializeFromVectorImage(); 00703 mitk::DataNode::Pointer node=mitk::DataNode::New(); 00704 node->SetData( image ); 00705 00706 mitk::DiffusionImageMapper<short>::SetDefaultProperties(node); 00707 00708 QString newname; 00709 newname = newname.append(nodename.c_str()); 00710 newname = newname.append("_dwi"); 00711 node->SetName(newname.toAscii()); 00712 00713 nodes.push_back(node); 00714 00715 mitk::ProgressBar::GetInstance()->Progress(); 00716 00717 } 00718 00719 std::vector<mitk::DataNode::Pointer>::iterator nodeIt; 00720 for(nodeIt = nodes.begin(); nodeIt != nodes.end(); ++nodeIt) 00721 GetDefaultDataStorage()->Add(*nodeIt); 00722 00723 mitk::StatusBar::GetInstance()->DisplayText(status.sprintf("Finished Processing %d Files", nrFiles).toAscii()); 00724 m_MultiWidget->RequestUpdate(); 00725 00726 } 00727 catch (itk::ExceptionObject &ex) 00728 { 00729 MBI_INFO << ex ; 00730 return ; 00731 } 00732 }
