diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportView.cpp index 769e407db9..ea108c33c7 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportView.cpp @@ -1,542 +1,556 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "QmitkDiffusionDicomImportView.h" // qt includes #include // itk includes #include "itkTimeProbesCollectorBase.h" #include "itkGDCMSeriesFileNames.h" #include "itksys/SystemTools.hxx" // mitk includes #include "mitkProgressBar.h" #include "mitkStatusBar.h" #include "mitkProperties.h" #include "mitkRenderingManager.h" #include "mitkMemoryUtilities.h" #include "mitkIOUtil.h" // diffusion module includes #include "mitkDicomDiffusionImageHeaderReader.h" #include "mitkDicomDiffusionImageReader.h" #include "mitkDiffusionImage.h" #include "mitkDiffusionDICOMFileReader.h" #include "mitkDICOMTagBasedSorter.h" #include "mitkDICOMSortByTag.h" +#include "mitkSortByImagePositionPatient.h" #include "gdcmDirectory.h" #include "gdcmScanner.h" #include "gdcmSorter.h" #include "gdcmIPPSorter.h" #include "gdcmAttribute.h" #include "gdcmVersion.h" #include #include #include const std::string QmitkDiffusionDicomImport::VIEW_ID = "org.mitk.views.diffusiondicomimport"; QmitkDiffusionDicomImport::QmitkDiffusionDicomImport(QObject* /*parent*/, const char* /*name*/) : QmitkFunctionality(), m_Controls(NULL), m_MultiWidget(NULL), m_OutputFolderName(""), m_OutputFolderNameSet(false) { } QmitkDiffusionDicomImport::QmitkDiffusionDicomImport(const QmitkDiffusionDicomImport& other) { Q_UNUSED(other) throw std::runtime_error("Copy constructor not implemented"); } QmitkDiffusionDicomImport::~QmitkDiffusionDicomImport() {} void QmitkDiffusionDicomImport::CreateQtPartControl(QWidget *parent) { m_Parent = parent; if (m_Controls == NULL) { m_Controls = new Ui::QmitkDiffusionDicomImportControls; m_Controls->setupUi(parent); this->CreateConnections(); m_Controls->m_DicomLoadRecursiveCheckbox->setChecked(false); m_Controls->m_DicomLoadAverageDuplicatesCheckbox->setChecked(false); m_Controls->m_DicomLoadRecursiveCheckbox->setVisible(true); m_Controls->m_OverrideOptionCheckbox->setVisible(false); m_Controls->m_SubdirPrefixLineEdit->setVisible(false); m_Controls->m_SetPrefixButton->setVisible(false); m_Controls->m_ResetPrefixButton->setVisible(false); AverageClicked(); } } void QmitkDiffusionDicomImport::CreateConnections() { if ( m_Controls ) { connect( m_Controls->m_AddFoldersButton, SIGNAL(clicked()), this, SLOT(DicomLoadAddFolderNames()) ); connect( m_Controls->m_DeleteFoldersButton, SIGNAL(clicked()), this, SLOT(DicomLoadDeleteFolderNames()) ); //connect( m_Controls->m_DicomLoadStartLoadButton, SIGNAL(clicked()), this, SLOT(DicomLoadStartLoad()) ); connect( m_Controls->m_DicomLoadStartLoadButton, SIGNAL(clicked()), this, SLOT(NewDicomLoadStartLoad()) ); connect( m_Controls->m_DicomLoadAverageDuplicatesCheckbox, SIGNAL(clicked()), this, SLOT(AverageClicked()) ); connect( m_Controls->m_OutputSetButton, SIGNAL(clicked()), this, SLOT(OutputSet()) ); connect( m_Controls->m_OutputClearButton, SIGNAL(clicked()), this, SLOT(OutputClear()) ); connect( m_Controls->m_Remove, SIGNAL(clicked()), this, SLOT(Remove()) ); connect( m_Controls->m_SetPrefixButton, SIGNAL(clicked()), this, SLOT(SetPrefixButtonPushed())); connect( m_Controls->m_ResetPrefixButton, SIGNAL(clicked()), this, SLOT(ResetPrefixButtonPushed())); connect( m_Controls->m_DicomLoadRecursiveCheckbox, SIGNAL(clicked()), this, SLOT(RecursiveSettingsChanged()) ); } } void QmitkDiffusionDicomImport::RecursiveSettingsChanged() { m_Controls->m_SubdirPrefixLineEdit->setVisible( m_Controls->m_DicomLoadRecursiveCheckbox->isChecked() ); m_Controls->m_SetPrefixButton->setVisible( m_Controls->m_DicomLoadRecursiveCheckbox->isChecked() ); m_Controls->m_SubdirPrefixLineEdit->clear(); this->m_Controls->m_SubdirPrefixLineEdit->setEnabled(true); } void QmitkDiffusionDicomImport::SetPrefixButtonPushed() { m_Prefix = this->m_Controls->m_SubdirPrefixLineEdit->text().toStdString(); if( !this->m_Controls->m_ResetPrefixButton->isVisible() ) this->m_Controls->m_ResetPrefixButton->setVisible(true); this->m_Controls->m_SubdirPrefixLineEdit->setEnabled(false); this->m_Controls->m_ResetPrefixButton->setEnabled(true); this->m_Controls->m_SetPrefixButton->setEnabled(false); } void QmitkDiffusionDicomImport::ResetPrefixButtonPushed() { m_Controls->m_SubdirPrefixLineEdit->clear(); this->m_Controls->m_SubdirPrefixLineEdit->setEnabled(true); this->m_Controls->m_ResetPrefixButton->setEnabled(false); this->m_Controls->m_SetPrefixButton->setEnabled(true); } void QmitkDiffusionDicomImport::Remove() { int i = m_Controls->listWidget->currentRow(); m_Controls->listWidget->takeItem(i); } void QmitkDiffusionDicomImport::OutputSet() { // SELECT FOLDER DIALOG QFileDialog* w = new QFileDialog( m_Parent, QString("Select folders containing DWI data") ); w->setFileMode( QFileDialog::Directory ); // RETRIEVE SELECTION if ( w->exec() != QDialog::Accepted ) return; m_OutputFolderName = w->selectedFiles()[0]; m_OutputFolderNameSet = true; m_Controls->m_OutputLabel->setText(m_OutputFolderName); // show file override option checkbox m_Controls->m_OverrideOptionCheckbox->setVisible(true); } void QmitkDiffusionDicomImport::OutputClear() { m_OutputFolderName = ""; m_OutputFolderNameSet = false; m_Controls->m_OutputLabel->setText("... optional out-folder ..."); // hide file override option checkbox - no output specified m_Controls->m_OverrideOptionCheckbox->setVisible(false); } void QmitkDiffusionDicomImport::AverageClicked() { m_Controls->m_Blur->setEnabled(m_Controls->m_DicomLoadAverageDuplicatesCheckbox->isChecked()); } void QmitkDiffusionDicomImport::Activated() { QmitkFunctionality::Activated(); } void QmitkDiffusionDicomImport::DicomLoadDeleteFolderNames() { m_Controls->listWidget->clear(); } void QmitkDiffusionDicomImport::DicomLoadAddFolderNames() { // SELECT FOLDER DIALOG QFileDialog* w = new QFileDialog( m_Parent, QString("Select folders containing DWI data") ); w->setFileMode( QFileDialog::Directory ); // RETRIEVE SELECTION if ( w->exec() != QDialog::Accepted ) return; m_Controls->listWidget->addItems(w->selectedFiles()); } bool SortBySeriesUID(gdcm::DataSet const & ds1, gdcm::DataSet const & ds2 ) { gdcm::Attribute<0x0020,0x000e> at1; at1.Set( ds1 ); gdcm::Attribute<0x0020,0x000e> at2; at2.Set( ds2 ); return at1 < at2; } bool SortByAcquisitionNumber(gdcm::DataSet const & ds1, gdcm::DataSet const & ds2 ) { gdcm::Attribute<0x0020,0x0012> at1; at1.Set( ds1 ); gdcm::Attribute<0x0020,0x0012> at2; at2.Set( ds2 ); return at1 < at2; } bool SortBySeqName(gdcm::DataSet const & ds1, gdcm::DataSet const & ds2 ) { gdcm::Attribute<0x0018, 0x0024> at1; at1.Set( ds1 ); gdcm::Attribute<0x0018, 0x0024> at2; at2.Set( ds2 ); std::string str1 = at1.GetValue().Trim(); std::string str2 = at2.GetValue().Trim(); return std::lexicographical_compare(str1.begin(), str1.end(), str2.begin(), str2.end() ); } void QmitkDiffusionDicomImport::Status(QString status) { mitk::StatusBar::GetInstance()->DisplayText(status.toAscii()); MITK_INFO << status.toStdString().c_str(); } void QmitkDiffusionDicomImport::Status(std::string status) { mitk::StatusBar::GetInstance()->DisplayText(status.c_str()); MITK_INFO << status.c_str(); } void QmitkDiffusionDicomImport::Status(const char* status) { mitk::StatusBar::GetInstance()->DisplayText(status); MITK_INFO << status; } void QmitkDiffusionDicomImport::Error(QString status) { mitk::StatusBar::GetInstance()->DisplayErrorText(status.toAscii()); MITK_ERROR << status.toStdString().c_str(); } void QmitkDiffusionDicomImport::Error(std::string status) { mitk::StatusBar::GetInstance()->DisplayErrorText(status.c_str()); MITK_ERROR << status.c_str(); } void QmitkDiffusionDicomImport::Error(const char* status) { mitk::StatusBar::GetInstance()->DisplayErrorText(status); MITK_ERROR << status; } void QmitkDiffusionDicomImport::PrintMemoryUsage() { size_t processSize = mitk::MemoryUtilities::GetProcessMemoryUsage(); size_t totalSize = mitk::MemoryUtilities::GetTotalSizeOfPhysicalRam(); float percentage = ( (float) processSize / (float) totalSize ) * 100.0; MITK_INFO << "Current memory usage: " << GetMemoryDescription( processSize, percentage ); } std::string QmitkDiffusionDicomImport::FormatMemorySize( size_t size ) { double val = size; std::string descriptor("B"); if ( val >= 1000.0 ) { val /= 1024.0; descriptor = "KB"; } if ( val >= 1000.0 ) { val /= 1024.0; descriptor = "MB"; } if ( val >= 1000.0 ) { val /= 1024.0; descriptor = "GB"; } std::ostringstream str; str << std::fixed << std::setprecision(2) << val << " " << descriptor; return str.str(); } std::string QmitkDiffusionDicomImport::FormatPercentage( double val ) { std::ostringstream str; str << std::fixed << std::setprecision(2) << val << " " << "%"; return str.str(); } std::string QmitkDiffusionDicomImport::GetMemoryDescription( size_t processSize, float percentage ) { std::ostringstream str; str << FormatMemorySize(processSize) << " (" << FormatPercentage( percentage ) <<")" ; return str.str(); } void QmitkDiffusionDicomImport::NewDicomLoadStartLoad() { itk::TimeProbesCollectorBase clock; bool imageSuccessfullySaved = true; bool has_prefix = true; try { const std::string& locale = "C"; const std::string& currLocale = setlocale( LC_ALL, NULL ); if ( locale.compare(currLocale)!=0 ) { try { MITK_INFO << " ** Changing locale from " << setlocale(LC_ALL, NULL) << " to '" << locale << "'"; setlocale(LC_ALL, locale.c_str()); } catch(...) { MITK_INFO << "Could not set locale " << locale; } } int nrFolders = m_Controls->listWidget->count(); if(!nrFolders) { Error(QString("No input folders were selected. ABORTING.")); return; } Status(QString("GDCM %1 used for DICOM parsing and sorting!").arg(gdcm::Version::GetVersion())); PrintMemoryUsage(); QString status; mitk::DataNode::Pointer node; mitk::ProgressBar::GetInstance()->AddStepsToDo(2*nrFolders); gdcm::Directory::FilenamesType complete_list; while(m_Controls->listWidget->count()) { // RETREIVE FOLDERNAME QListWidgetItem * item = m_Controls->listWidget->takeItem(0); QString folderName = item->text(); if( this->m_Controls->m_DicomLoadRecursiveCheckbox->isChecked() ) { std::string subdir_prefix = ""; if( has_prefix ) { subdir_prefix = this->m_Prefix; } itksys::Directory rootdir; rootdir.Load( folderName.toStdString().c_str() ); for( unsigned int idx=0; idxm_Controls->m_DicomLoadRecursiveCheckbox->isChecked() ); // recursive ! const gdcm::Directory::FilenamesType &l1 = d.GetFilenames(); const unsigned int ntotalfiles = l1.size(); Status(QString(" ... found %1 different files").arg(ntotalfiles)); for( unsigned int i=0; i< ntotalfiles; i++) { complete_list.push_back( l1.at(i) ); } } } { mitk::DiffusionDICOMFileReader::Pointer gdcmReader = mitk::DiffusionDICOMFileReader::New(); mitk::DICOMTagBasedSorter::Pointer tagSorter = mitk::DICOMTagBasedSorter::New(); // Use tags as in Qmitk // all the things that split by tag in DicomSeriesReader tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0028, 0x0010) ); // Number of Rows tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0028, 0x0011) ); // Number of Columns tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0028, 0x0030) ); // Pixel Spacing tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0018, 0x1164) ); // Imager Pixel Spacing tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0020, 0x0037) ); // Image Orientation (Patient) // TODO add tolerance parameter (l. 1572 of original code) // TODO handle as real vectors! cluster with configurable errors! - //tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0020, 0x000e) ); // Series Instance UID + tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0020, 0x000e) ); // Series Instance UID tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0018, 0x0050) ); // Slice Thickness tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0028, 0x0008) ); // Number of Frames - tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0020, 0x0052) ); // Frame of Reference UID + //tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0020, 0x0052) ); // Frame of Reference UID // gdcmReader->AddSortingElement( tagSorter ); //mitk::DICOMFileReaderTestHelper::TestOutputsContainInputs( gdcmReader ); mitk::DICOMSortCriterion::ConstPointer sorting = - mitk::DICOMSortByTag::New( mitk::DICOMTag(0x0020, 0x0013), // instance number + mitk::SortByImagePositionPatient::New( // Image Position (Patient) + //mitk::DICOMSortByTag::New( mitk::DICOMTag(0x0020, 0x0013), // instance number mitk::DICOMSortByTag::New( mitk::DICOMTag(0x0020, 0x0012), // aqcuisition number mitk::DICOMSortByTag::New( mitk::DICOMTag(0x0008, 0x0032), // aqcuisition time mitk::DICOMSortByTag::New( mitk::DICOMTag(0x0018, 0x1060), // trigger time mitk::DICOMSortByTag::New( mitk::DICOMTag(0x0008, 0x0018) // SOP instance UID (last resort, not really meaningful but decides clearly) ).GetPointer() ).GetPointer() ).GetPointer() ).GetPointer() - ).GetPointer(); + // ).GetPointer() + ).GetPointer(); tagSorter->SetSortCriterion( sorting ); gdcmReader->AddSortingElement( tagSorter ); gdcmReader->SetInputFiles( complete_list ); - gdcmReader->AnalyzeInputFiles(); + try + { + gdcmReader->AnalyzeInputFiles(); + } + catch( const itk::ExceptionObject &e) + { + MITK_ERROR << "Failed to analyze data. " << e.what(); + } + catch( const std::exception &se) + { + MITK_ERROR << "Std Exception " << se.what(); + } gdcmReader->LoadImages(); for( int o = 0; o < gdcmReader->GetNumberOfOutputs(); o++ ) { mitk::Image::Pointer loaded_image = gdcmReader->GetOutput(o).GetMitkImage(); mitk::DiffusionImage::Pointer d_img = static_cast*>( loaded_image.GetPointer() ); std::stringstream ss; ss << "ImportedData_" << o; node = mitk::DataNode::New(); node->SetData( d_img ); std::string outname; d_img->GetPropertyList()->GetStringProperty("diffusion.dicom.importname", outname ); node->SetName( outname.c_str() ); GetDefaultDataStorage()->Add(node); //SetDwiNodeProperties(node, ss.str() ); //Status(QString("Image %1 added to datastorage").arg(descr)); } } Status("Timing information"); clock.Report(); if(!m_OutputFolderNameSet && node.IsNotNull()) { mitk::BaseData::Pointer basedata = node->GetData(); if (basedata.IsNotNull()) { mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); try { MITK_INFO << " ** Changing locale back from " << setlocale(LC_ALL, NULL) << " to '" << currLocale << "'"; setlocale(LC_ALL, currLocale.c_str()); } catch(...) { MITK_INFO << "Could not reset locale " << currLocale; } } catch (itk::ExceptionObject &ex) { Error(QString("%1\n%2\n%3\n%4\n%5\n%6").arg(ex.GetNameOfClass()).arg(ex.GetFile()).arg(ex.GetLine()).arg(ex.GetLocation()).arg(ex.what()).arg(ex.GetDescription())); return ; } if (!imageSuccessfullySaved) QMessageBox::warning(NULL,"WARNING","One or more files could not be saved! The according files where moved to the datastorage."); Status(QString("Finished import with memory:")); PrintMemoryUsage(); } void QmitkDiffusionDicomImport::SetDwiNodeProperties(mitk::DataNode::Pointer node, std::string name) { node->SetProperty( "IsDWIRawVolume", mitk::BoolProperty::New( true ) ); // set foldername as string property mitk::StringProperty::Pointer nameProp = mitk::StringProperty::New( name ); node->SetProperty( "name", nameProp ); }