vv/vvMainWindow.cxx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://www.centreleonberard.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17 ===========================================================================**/
  18
  19 #include <algorithm>
  20 #include <QMessageBox>
  21 #include <QInputDialog>
  22 #include <QTimer>
  23 #include "QTreePushButton.h"
  24 #include <QUrl>
  25 #include <QSettings>
  26
  27 // VV include
  28 #include "vvMainWindow.h"
  29 #include "vvHelpDialog.h"
  30 #include "vvRegisterForm.h"
  31 #include "vvDocumentation.h"
  32 #include "vvProgressDialog.h"
  33 #include "vvQDicomSeriesSelector.h"
  34 #include "vvSlicerManager.h"
  35 #include "clitkImageCommon.h"
  36 #include "vvSlicer.h"
  37 #include "vvInteractorStyleNavigator.h"
  38 #include "vvImageWriter.h"
  39 #include "vvSegmentationDialog.h"
  40 #include "vvSurfaceViewerDialog.h"
  41 #include "vvDeformationDialog.h"
  42 #include "vvImageWarp.h"
  43 #include "vvUtils.h"
  44 #include "vvMidPosition.h"
  45 #include "vvMesh.h"
  46 #include "vvStructSelector.h"
  47 #include "vvMeshReader.h"
  48 #include "clitkConfiguration.h"
  49
  50 // ITK include
  51 #include <itkImage.h>
  52 #include <itkImageFileReader.h>
  53 #include <itkByteSwapper.h>
  54 #include <itkCommand.h>
  55 #include <itkNumericSeriesFileNames.h>
  56
  57 // VTK include
  58 #include <vtkImageData.h>
  59 #include <vtkImageActor.h>
  60 #include <vtkCornerAnnotation.h>
  61 #include <vtkRenderWindow.h>
  62 #include <vtkRenderWindowInteractor.h>
  63 #include <vtkRenderer.h>
  64 #include <vtkRendererCollection.h>
  65 #include <vtkWindowToImageFilter.h>
  66 #include <vtkBMPWriter.h>
  67 #include <vtkTIFFWriter.h>
  68 #include <vtkPNMWriter.h>
  69 #include <vtkPNGWriter.h>
  70 #include <vtkJPEGWriter.h>
  71 #include <vtkFFMPEGWriter.h>
  72 #ifdef VTK_USE_MPEG2_ENCODER
  73   #include <vtkMPEG2Writer.h>
  74 #endif
  75 #include <vtkMatrix4x4.h>
  76 #include <vtkTransform.h>
  77
  78 // Standard includes
  79 #include <iostream>
  80 #include <sstream>
  81 #include <iomanip>
  82
  83 #define COLUMN_TREE 0
  84 #define COLUMN_UL_VIEW 1
  85 #define COLUMN_UR_VIEW 2
  86 #define COLUMN_DL_VIEW 3
  87 #define COLUMN_DR_VIEW 4
  88 #define COLUMN_CLOSE_IMAGE 5
  89 #define COLUMN_RELOAD_IMAGE 6
  90 #define COLUMN_IMAGE_NAME 7
  91
  92 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN )"
  93
  94 /*Data Tree values
  95   0,Qt::UserRole full filename
  96   1,Qt::CheckStateRole checkbutton UL View
  97   1,Qt::UserRole overlay, fusion or vector
  98   2,Qt::CheckStateRole checkbutton UR View
  99   3,Qt::CheckStateRole checkbutton DL View
 100   4,Qt::CheckStateRole checkbutton DR View
 101   5,0  short filename
 102   5,Qt::UserRole mSlicerManager id*/
 103
 104 //------------------------------------------------------------------------------
 105 vvMainWindow::vvMainWindow():vvMainWindowBase()
 106 {
 107   setupUi(this); // this sets up the GUI
 108
 109   mInputPathName = "";
 110   mMenuTools = menuTools;
 111   //  mMenuSegmentation = menuSegmentation;
 112   mContextMenu = &contextMenu;
 113   mMenuExperimentalTools = menuExperimental;
 114   mMainWidget = this;
 115   mCurrentTime = -1;
 116   mCurrentSelectedImageId = "";
 117   mCurrentPickedImageId = "";
 118   mCurrentPickedImageIndex = 0;
 119
 120   //Init the contextMenu
 121   this->setContextMenuPolicy(Qt::CustomContextMenu);
 122   contextActions.resize(0);
 123   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 124                                   tr("O&pen new Image"));
 125   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 126   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 127   contextActions.push_back(actionOpen_new_image);
 128   contextMenu.addSeparator();
 129
 130   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 131                                tr("Close Current Image"));
 132   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 133   contextActions.push_back(actionClose_Image);
 134
 135   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 136                                 tr("Reload Current Image"));
 137   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 138   contextActions.push_back(actionReload_image);
 139
 140   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 141                               tr("Save Current Image"));
 142   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 143   contextActions.push_back(actionSave_image);
 144
 145   contextMenu.addSeparator();
 146
 147   contextMenu.addAction(actionAdd_VF_to_current_Image);
 148   contextActions.push_back(actionAdd_VF_to_current_Image);
 149
 150   QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 151       tr("Add overlay image to current image"));
 152   contextMenu.addAction(actionAdd_Overlay_to_current_Image);
 153   contextActions.push_back(actionAdd_Overlay_to_current_Image);
 154
 155   connect(actionAdd_Overlay_to_current_Image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 156
 157   contextMenu.addAction(actionAdd_fusion_image);
 158   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 159   contextActions.push_back(actionAdd_fusion_image);
 160
 161   // TRIAL DS
 162   /*
 163   QMenu * m = new QMenu(menubar);
 164   m->setTitle("TOTO");
 165   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 166   contextMenu.addMenu(m);
 167   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 168                      tr("BIDON"));
 169   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 170                      tr("BIDON2"));
 171   m->addAction(a);
 172   m->addAction(b);
 173   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 174   */
 175
 176   //init the DataTree
 177   mSlicerManagers.resize(0);
 178
 179   QStringList header;
 180   header.append("");
 181   header.append("TL");
 182   header.append("TR");
 183   header.append("BL");
 184   header.append("BR");
 185   header.append("");
 186   header.append("");
 187   header.append("Name");
 188
 189   DataTree->setHeaderLabels(header);
 190   DataTree->resizeColumnToContents(COLUMN_TREE);
 191   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 192   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 193   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 194   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 195   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 196   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 197   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 198
 199   viewMode = 1;
 200   documentation = new vvDocumentation();
 201   help_dialog = new vvHelpDialog();
 202   dicomSeriesSelector = new vvDicomSeriesSelector();
 203
 204   inverseButton->setEnabled(0);
 205   actionAdd_Overlay_to_current_Image->setEnabled(0);
 206   actionSave_As->setEnabled(0);
 207   actionAdd_VF_to_current_Image->setEnabled(0);
 208   actionAdd_fusion_image->setEnabled(0);
 209
 210   //init the sliders
 211   verticalSliders.push_back(NOVerticalSlider);
 212   verticalSliders.push_back(NEVerticalSlider);
 213   verticalSliders.push_back(SOVerticalSlider);
 214   verticalSliders.push_back(SEVerticalSlider);
 215
 216   for (int i =0; i < 4; i++)
 217     verticalSliders[i]->hide();
 218
 219   horizontalSliders.push_back(NOHorizontalSlider);
 220   horizontalSliders.push_back(NEHorizontalSlider);
 221   horizontalSliders.push_back(SOHorizontalSlider);
 222   horizontalSliders.push_back(SEHorizontalSlider);
 223
 224   for (int i =0; i < 4; i++)
 225     horizontalSliders[i]->hide();
 226
 227
 228   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 229   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 230   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 231   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 232
 233   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 234   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 235   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 236   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 237
 238   //connect everything
 239   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 240   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 241   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 242   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 243   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 244   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 245   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 246   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 247   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 248   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 249   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 250   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 251   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 252   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 253   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 254   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 255   connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
 256
 257   ///////////////////////////////////////////////
 258   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 259   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 260   ///////////////////////////////////////////////
 261
 262   actionNorth_East_Window->setEnabled(0);
 263   actionNorth_West_Window->setEnabled(0);
 264   actionSouth_East_Window->setEnabled(0);
 265   actionSouth_West_Window->setEnabled(0);
 266
 267   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 268   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 269   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 270   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 271
 272   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 273   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 274           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 275
 276   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 277   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 278   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 279   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 280   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 281   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 282   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 283
 284
 285   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 286
 287   connect(linkPanel,SIGNAL(addLink(QString,QString)),this,SLOT(AddLink(QString,QString)));
 288   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 289   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 290   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int)),this,SLOT(SetOverlayProperty(int)));
 291   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,double,double)),
 292           this,SLOT(SetFusionProperty(int,int,double,double)));
 293   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 294
 295   playMode = 0;//pause
 296   mFrameRate = 10;
 297   playButton->setEnabled(0);
 298   frameRateLabel->setEnabled(0);
 299   frameRateSpinBox->setEnabled(0);
 300   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 301   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 302
 303   goToCursorPushButton->setEnabled(0);
 304   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 305
 306   NOViewWidget->hide();
 307   NEViewWidget->hide();
 308   SOViewWidget->hide();
 309   SEViewWidget->hide();
 310
 311   //Recently opened files
 312   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 313   recentlyOpenedFilesMenu=NULL;
 314   if ( !recent_files.empty() ) {
 315     createRecentlyOpenedFilesMenu();
 316     updateRecentlyOpenedFilesMenu(recent_files);
 317   }
 318
 319   // Adding all new tools (insertion in the menu)
 320   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 321
 322   if (!CLITK_EXPERIMENTAL)
 323     menuExperimental->menuAction()->setVisible(false);
 324
 325
 326   QTimer * timerMemory = new QTimer(this);
 327   //timerMemory->setInterval(5);
 328   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 329   timerMemory->start(2000);
 330 }
 331 //------------------------------------------------------------------------------
 332
 333 void vvMainWindow::show(){
 334   vvMainWindowBase::show();
 335   PopupRegisterForm(true);
 336 }
 337 //------------------------------------------------------------------------------
 338 void vvMainWindow::UpdateMemoryUsage()
 339 {
 340   //  clitk::PrintMemory(true);
 341   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 342   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 343 }
 344 //------------------------------------------------------------------------------
 345
 346
 347 //------------------------------------------------------------------------------
 348 void vvMainWindow::createRecentlyOpenedFilesMenu()
 349 {
 350     recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
 351     recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 352     menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
 353     menuFile->insertSeparator(actionOpen_Image_With_Time);
 354 }
 355 //------------------------------------------------------------------------------
 356
 357
 358 //------------------------------------------------------------------------------
 359
 360 void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
 361 {
 362   if(recentlyOpenedFilesMenu==NULL){
 363     createRecentlyOpenedFilesMenu();
 364   }else{
 365     recentlyOpenedFilesMenu->clear();
 366   }
 367   for (std::list<std::string>::const_iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 368     QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")), i->c_str(),this);
 369     recentlyOpenedFilesMenu->addAction(current);
 370     connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 371   }
 372 }
 373 //------------------------------------------------------------------------------
 374
 375
 376 //------------------------------------------------------------------------------
 377 void vvMainWindow::ComputeMidPosition()
 378 {
 379   bool ok;
 380   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 381   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 382                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 383   if (ok) {
 384     vvMidPosition midp;
 385     midp.slicer_manager = mSlicerManagers[index];
 386     midp.reference_image_index = ref;
 387     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 388     midp.Update();
 389     if (midp.error)
 390       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 391     else {
 392       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 393       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 394     }
 395     QApplication::restoreOverrideCursor();
 396   }
 397 }
 398 //------------------------------------------------------------------------------
 399
 400
 401 //------------------------------------------------------------------------------
 402 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 403 {
 404   QTreeWidgetItem *item = new QTreeWidgetItem();
 405   item->setData(0,Qt::UserRole,"filename.vtk");
 406   item->setData(1,Qt::UserRole,tr("contour"));
 407   QBrush brush;
 408   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 409   brush.setStyle(Qt::SolidPattern);
 410   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 411   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 412
 413   for (int j = 1; j <= 4; j++)
 414     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 415
 416   QTreePushButton* cButton = new QTreePushButton;
 417   cButton->setItem(item);
 418   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 419   cButton->setToolTip(tr("close image"));
 420   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 421   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 422           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 423
 424   QTreePushButton* rButton = new QTreePushButton;
 425   rButton->setItem(item);
 426   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 427   rButton->setToolTip(tr("reload image"));
 428   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 429   rButton->setEnabled(false);
 430   //Not implemented
 431   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 432   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 433
 434   DataTree->topLevelItem(image_index)->setExpanded(1);
 435   DataTree->topLevelItem(image_index)->addChild(item);
 436   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 437   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 438   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 439   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 440
 441   UpdateTree();
 442   mSlicerManagers[image_index]->AddContour(contour,propagation);
 443   mSlicerManagers[image_index]->Render();
 444 }
 445 //------------------------------------------------------------------------------
 446
 447
 448 //------------------------------------------------------------------------------
 449 void vvMainWindow::OpenVTKContour()
 450 {
 451   if (mSlicerManagers.size() > 0) {
 452     QString Extensions = "Images ( *.vtk *.obj)";
 453     Extensions += ";;All Files (*)";
 454     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 455     if (file.isNull())
 456       return;
 457     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 458     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 459     vvMeshReader reader;
 460     reader.SetImage(mSlicerManagers[index]->GetImage());
 461     reader.SetModeToVTK();
 462     reader.SetFilename(file.toStdString());
 463     reader.Update();
 464     AddContour(index,reader.GetOutput()[0],false);
 465     QApplication::restoreOverrideCursor();
 466   }
 467 }
 468 //------------------------------------------------------------------------------
 469
 470
 471 //------------------------------------------------------------------------------
 472 void vvMainWindow::OpenDCStructContour()
 473 {
 474   if (mSlicerManagers.size() > 0) {
 475     QString Extensions = "Dicom Files ( *.dcm RS*)";
 476     Extensions += ";;All Files (*)";
 477     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 478     if (file.isNull())
 479       return;
 480     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 481     vvMeshReader reader;
 482     reader.SetFilename(file.toStdString());
 483     vvStructSelector selector;
 484     selector.SetStructures(reader.GetROINames());
 485     if (!mSlicerManagers[index]->GetVF().IsNull())
 486       selector.EnablePropagationCheckBox();
 487     if (selector.exec()) {
 488       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 489       reader.SetSelectedItems(selector.getSelectedItems());
 490       reader.SetImage(mSlicerManagers[index]->GetImage());
 491       if (selector.PropagationEnabled())
 492         reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 493       reader.Update();
 494       std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 495       for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 496            i!=contours.end(); i++)
 497         AddContour(index,*i,selector.PropagationEnabled());
 498       QApplication::restoreOverrideCursor();
 499     }
 500   }
 501 }
 502 //------------------------------------------------------------------------------
 503
 504
 505 //------------------------------------------------------------------------------
 506 void vvMainWindow::ComputeDeformableRegistration()
 507 {
 508   if (mSlicerManagers.size() > 0) {
 509     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 510     vvDeformationDialog dialog(index,mSlicerManagers);
 511     if (dialog.exec()) {
 512       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 513       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 514       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 515     } else
 516       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 517   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 518 }
 519 //------------------------------------------------------------------------------
 520
 521
 522 //------------------------------------------------------------------------------
 523 void vvMainWindow::WarpImage()
 524 {
 525   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 526   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 527     bool ok;
 528     int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 529                                        mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 530     if (ok) {
 531       WarpImage(mSlicerManagers[index],ref);
 532     }
 533   } else
 534     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 535 }
 536 //------------------------------------------------------------------------------
 537
 538
 539 //------------------------------------------------------------------------------
 540 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 541 {
 542   if (!selected_slicer->GetVF().IsNull()) {
 543     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 544     QFileInfo info(selected_slicer->GetFileName().c_str());
 545     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 546                      reference_phase,this);
 547     if (warp.ComputeWarpedImage()) {
 548       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 549       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 550       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 551       QApplication::restoreOverrideCursor();
 552     } else {
 553       QApplication::restoreOverrideCursor();
 554       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 555     }
 556   } else
 557     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 558 }
 559 //------------------------------------------------------------------------------
 560
 561
 562 //------------------------------------------------------------------------------
 563 vvMainWindow::~vvMainWindow()
 564 {
 565   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 566     if (mSlicerManagers[i] != NULL)
 567       delete mSlicerManagers[i];
 568   }
 569 }
 570 //------------------------------------------------------------------------------
 571
 572 //------------------------------------------------------------------------------
 573 QTabWidget * vvMainWindow::GetTab()
 574 {
 575   return tabWidget;
 576 }
 577 //------------------------------------------------------------------------------
 578
 579
 580 //------------------------------------------------------------------------------
 581 void vvMainWindow::MergeImages()
 582 {
 583   QString Extensions = EXTENSIONS;
 584   Extensions += ";;All Files (*)";
 585   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 586   if (files.isEmpty())
 587     return;
 588   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 589   std::vector<std::string> vector;
 590
 591   unsigned int currentDim = 0;
 592   std::vector<double> currentSpacing;
 593   std::vector<int> currentSize;
 594   std::vector<double> currentOrigin;
 595
 596   for (int i = 0; i < files.size(); i++) {
 597     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 598                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 599     reader->SetFileName(files[i].toStdString().c_str());
 600     reader->ReadImageInformation();
 601     if (reader)        {
 602       //NOViewWidget->hide();
 603       //NEViewWidget->hide();
 604       //SOViewWidget->hide();
 605       //SEViewWidget->hide();
 606       if (i == 0)
 607         currentDim = reader->GetNumberOfDimensions();
 608       bool IsOk = true;
 609       for (unsigned int j = 0; j < currentDim; j++) {
 610         if (i == 0) {
 611           if (j == 0) {
 612             currentSpacing.resize(currentDim);
 613             currentSize.resize(currentDim);
 614             currentOrigin.resize(currentDim);
 615           }
 616           currentOrigin[j] = reader->GetOrigin(j);
 617           currentSpacing[j] = reader->GetSpacing(j);
 618           currentSize[j] = reader->GetDimensions(j);
 619         } else if (currentDim != reader->GetNumberOfDimensions()
 620                    || currentSpacing[j] != reader->GetSpacing(j)
 621                    || currentSize[j] != (int)reader->GetDimensions(j)
 622                    || currentOrigin[j] != reader->GetOrigin(j)) {
 623           QString error = "Cannot read file (too different from others ";
 624           error += files[i].toStdString().c_str();
 625           QMessageBox::information(this,tr("Reading problem"),error);
 626           IsOk = false;
 627           break;
 628         }
 629       }
 630       if (IsOk)
 631         vector.push_back(files[i].toStdString());
 632     }
 633   }
 634   if (vector.size() > 0)
 635     LoadImages(vector, vvImageReader::MERGED);
 636 }
 637 //------------------------------------------------------------------------------
 638
 639 //------------------------------------------------------------------------------
 640 void vvMainWindow::SliceImages()
 641 {
 642   QString Extensions = EXTENSIONS;
 643   Extensions += ";;All Files (*)";
 644
 645   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 646   if (files.isEmpty())
 647     return;
 648   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 649   std::vector<std::string> vector;
 650   for (int i = 0; i < files.size(); i++)
 651     vector.push_back(files[i].toStdString());
 652   LoadImages(vector, vvImageReader::SLICED);
 653 }
 654 //------------------------------------------------------------------------------
 655
 656 //------------------------------------------------------------------------------
 657 void vvMainWindow::MergeImagesWithTime()
 658 {
 659   QString Extensions = EXTENSIONS;
 660   Extensions += ";;All Files (*)";
 661   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 662   if (files.isEmpty())
 663     return;
 664   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 665   std::vector<std::string> vector;
 666
 667   unsigned int currentDim = 0;
 668   std::vector<double> currentSpacing;
 669   std::vector<int> currentSize;
 670   std::vector<double> currentOrigin;
 671
 672   for (int i = 0; i < files.size(); i++) {
 673     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 674                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 675     if (reader) {
 676       reader->SetFileName(files[i].toStdString().c_str());
 677       reader->ReadImageInformation();
 678       if (i == 0)
 679         currentDim = reader->GetNumberOfDimensions();
 680       bool IsOk = true;
 681       for (unsigned int j = 0; j < currentDim; j++) {
 682         if (i == 0) {
 683           if (j == 0) {
 684             currentSpacing.resize(currentDim);
 685             currentSize.resize(currentDim);
 686             currentOrigin.resize(currentDim);
 687           }
 688           currentOrigin[j] = reader->GetOrigin(j);
 689           currentSpacing[j] = reader->GetSpacing(j);
 690           currentSize[j] = reader->GetDimensions(j);
 691         } else if (currentDim != reader->GetNumberOfDimensions()
 692                    || currentSpacing[j] != reader->GetSpacing(j)
 693                    || currentSize[j] != (int)reader->GetDimensions(j)
 694                    || currentOrigin[j] != reader->GetOrigin(j)) {
 695           QString error = "Cannot read file (too different from others ";
 696           error += files[i].toStdString().c_str();
 697           QMessageBox::information(this,tr("Reading problem"),error);
 698           IsOk = false;
 699           break;
 700         }
 701       }
 702       if (IsOk)
 703         vector.push_back(files[i].toStdString());
 704     } else {
 705       QString error = "Cannot read file info for ";
 706       error += files[i].toStdString().c_str();
 707       error += "\n";
 708       error += "Maybe you're trying to open an image in an unsupported format?\n";
 709       QMessageBox::information(this,tr("Reading problem"),error);
 710     }
 711   }
 712   sort(vector.begin(),vector.end());
 713   if (vector.size() > 1)
 714     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 715   else
 716     QMessageBox::warning(this,tr("Reading problem"),"You need to select at least two images to merge images with time.\nIf you only want to open one image, please use the \"Open Image\" function.");
 717 }
 718 //------------------------------------------------------------------------------
 719
 720
 721 //------------------------------------------------------------------------------
 722 void vvMainWindow::OpenDicom()
 723 {
 724   std::vector<std::string> files;
 725
 726   std::cout << "dicomSeriesSelector " << std::endl;
 727   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 728     files = *(dicomSeriesSelector->GetFilenames());
 729     LoadImages(files, vvImageReader::DICOM);
 730   }
 731 }
 732 //------------------------------------------------------------------------------
 733
 734 //------------------------------------------------------------------------------
 735 void vvMainWindow::OpenImages()
 736 {
 737   QString Extensions = EXTENSIONS;
 738   Extensions += ";;All Files (*)";
 739
 740   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 741   if (files.isEmpty())
 742     return;
 743   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 744   std::vector<std::string> vector;
 745   for (int i = 0; i < files.size(); i++)
 746     vector.push_back(files[i].toStdString());
 747   LoadImages(vector, vvImageReader::IMAGE);
 748 }
 749 //------------------------------------------------------------------------------
 750 void vvMainWindow::OpenRecentImage()
 751 {
 752   QAction * caller = qobject_cast<QAction*>(sender());
 753   std::vector<std::string> images;
 754   images.push_back(caller->text().toStdString());
 755   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 756   LoadImages(images, vvImageReader::IMAGE);
 757 }
 758 //------------------------------------------------------------------------------
 759
 760
 761 //------------------------------------------------------------------------------
 762 void vvMainWindow::OpenImageWithTime()
 763 {
 764   QString Extensions = EXTENSIONS;
 765   Extensions += ";;All Files (*)";
 766
 767   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 768   if (files.isEmpty())
 769     return;
 770   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 771   std::vector<std::string> vector;
 772   for (int i = 0; i < files.size(); i++) {
 773     vector.push_back(files[i].toStdString());
 774   }
 775   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 776 }
 777 //------------------------------------------------------------------------------
 778
 779
 780 //------------------------------------------------------------------------------
 781 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 782 {
 783   //Separate the way to open images and dicoms
 784   int fileSize;
 785   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 786     fileSize = files.size();
 787   else
 788     fileSize = 1;
 789
 790   // For SLICED, we need the number of slices (ndim and #slices)
 791   std::vector<unsigned int> nSlices;
 792   nSlices.resize(files.size());
 793   std::fill(nSlices.begin(), nSlices.end(), 1);
 794   if (filetype == vvImageReader::SLICED) {
 795     for (int i = 0; i < fileSize; i++) {
 796       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 797       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 798       if (!header) {
 799         nSlices[i] = 0;
 800         QString error = "Cannot open file \n";
 801         error += files[i].c_str();
 802         QMessageBox::information(this,tr("Reading problem"),error);
 803         return;
 804       }
 805       if (header->GetNumberOfDimensions() < 3) {
 806         nSlices[i] = 0;
 807         QString error = "Dimension problem. Cannot slice \n";
 808         error += files[i].c_str();
 809         QMessageBox::information(this,tr("Reading problem"),error);
 810         return;
 811       }
 812       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 813     }
 814   }
 815
 816   //Only add to the list of recently opened files when a single file is opened,
 817   //to avoid polluting the list of recently opened files
 818   if (files.size() == 1) {
 819     QFileInfo finfo=tr(files[0].c_str());
 820     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 821     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 822   }
 823   //init the progress events
 824   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 825   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 826   qApp->processEvents();
 827
 828   int numberofsuccesulreads=0;
 829   //open images as 1 or multiples
 830   for (int i = 0; i < fileSize; i++) {
 831
 832     progress.SetText("Opening " + files[i]);
 833     progress.SetProgress(i,fileSize);
 834     qApp->processEvents();
 835
 836     for (unsigned int j = 0; j < nSlices[i]; j++) {
 837       //read the image and put it in mSlicerManagers
 838       vvSlicerManager* imageManager = new vvSlicerManager(4);
 839       qApp->processEvents();
 840
 841       bool SetImageSucceed=false;
 842
 843       // Change filename if an image with the same already exist
 844       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 845
 846       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED)
 847         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 848       else {
 849         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 850       }
 851       if (!SetImageSucceed) {
 852         QApplication::restoreOverrideCursor();
 853         QString error = "Cannot open file \n";
 854         error += imageManager->GetLastError().c_str();
 855         QMessageBox::information(this,tr("Reading problem"),error);
 856         delete imageManager;
 857       } else {
 858         mSlicerManagers.push_back(imageManager);
 859
 860         //create an item in the tree with good settings
 861         QTreeWidgetItem *item = new QTreeWidgetItem();
 862         item->setData(0,Qt::UserRole,files[i].c_str());
 863         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 864         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 865         item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
 866         qApp->processEvents();
 867
 868         //Create the buttons for reload and close
 869         qApp->processEvents();
 870         QTreePushButton* cButton = new QTreePushButton;
 871         cButton->setItem(item);
 872         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 873         cButton->setToolTip(tr("close image"));
 874         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 875         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 876                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 877
 878         QTreePushButton* rButton = new QTreePushButton;
 879         rButton->setItem(item);
 880         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 881         rButton->setToolTip(tr("reload image"));
 882         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 883         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 884                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 885
 886         DataTree->addTopLevelItem(item);
 887         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 888         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 889
 890         //set the id of the image
 891         QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 892         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 893         mSlicerManagers.back()->SetId(id.toStdString());
 894
 895         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 896
 897         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 898                 this,SLOT(CurrentImageChanged(std::string)));
 899         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 900                 this, SLOT(CurrentPickedImageChanged(std::string)));
 901         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 902                 this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 903         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 904                 this, SLOT(VectorChanged(int,double,double,double, double)));
 905         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 906                 this, SLOT(OverlayChanged(int,double,double)));
 907         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 908                 this, SLOT(FusionChanged(int,double)));
 909         connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
 910                 this,SLOT(WindowsChanged(int, int, int)));
 911         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
 912                 this,SLOT(WindowLevelChanged(double, double, int, int)));
 913         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 914                 this,SLOT(UpdateSlice(int,int)));
 915         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 916                 this,SLOT(UpdateTSlice(int, int)));
 917         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 918                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 919         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 920                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 921         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 922                 this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 923         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 924                 this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 925         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 926         InitSlicers();
 927         numberofsuccesulreads++;
 928       }
 929     }
 930   }
 931   if (numberofsuccesulreads) {
 932     NOViewWidget->show();
 933     NEViewWidget->show();
 934     SOViewWidget->show();
 935     SEViewWidget->show();
 936     UpdateTree();
 937     InitDisplay();
 938     ShowLastImage();
 939
 940     // Try to guess default WindowLevel
 941     double range[2];
 942     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 943     if ((range[0] == 0) && (range[1] == 1)) {
 944       presetComboBox->setCurrentIndex(5);// binary
 945     } else {
 946       // TODO
 947     }
 948   }
 949   QApplication::restoreOverrideCursor();
 950 }
 951 //------------------------------------------------------------------------------
 952
 953 //------------------------------------------------------------------------------
 954 void vvMainWindow::UpdateTree()
 955 {
 956   DataTree->resizeColumnToContents(COLUMN_TREE);
 957   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 958   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 959   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 960   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 961   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 962   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 963   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 964 }
 965 //------------------------------------------------------------------------------
 966
 967 //------------------------------------------------------------------------------
 968 void vvMainWindow::CurrentImageChanged(std::string id)
 969 {
 970   if (id == mCurrentSelectedImageId) return; // Do nothing
 971   int selected = 0;
 972   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 973     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 974       selected = i;
 975     } else {
 976       DataTree->topLevelItem(i)->setSelected(0);
 977     }
 978     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 979       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 980
 981   }
 982   DataTree->topLevelItem(selected)->setSelected(1);
 983   mCurrentSelectedImageId = id;
 984   emit SelectedImageHasChanged(mSlicerManagers[selected]);
 985 }
 986 //------------------------------------------------------------------------------
 987
 988 //------------------------------------------------------------------------------
 989 void vvMainWindow::CurrentPickedImageChanged(std::string id)
 990 {
 991   if (id == mCurrentPickedImageId) return; // Do nothing
 992   int selected = 0;
 993   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 994     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 995       selected = i;
 996     } else {
 997       DataTree->topLevelItem(i)->setSelected(0);
 998     }
 999     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1000       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1001
1002   }
1003   DataTree->topLevelItem(selected)->setSelected(1);
1004   mCurrentPickedImageId = id;
1005   mCurrentPickedImageIndex = selected;
1006 }
1007 //------------------------------------------------------------------------------
1008
1009 //------------------------------------------------------------------------------
1010 void vvMainWindow::ImageInfoChanged()
1011 {
1012   contextActions[6]->setEnabled(1);
1013   contextActions[5]->setEnabled(1);
1014   actionSave_As->setEnabled(1);
1015   actionAdd_VF_to_current_Image->setEnabled(1);
1016   actionAdd_fusion_image->setEnabled(1);
1017   actionNorth_East_Window->setEnabled(1);
1018   actionNorth_West_Window->setEnabled(1);
1019   actionSouth_East_Window->setEnabled(1);
1020   actionSouth_West_Window->setEnabled(1);
1021   inverseButton->setEnabled(1);
1022
1023   goToCursorPushButton->setEnabled(1);
1024
1025   if (DataTree->selectedItems().size()) {
1026     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1027
1028     colorMapComboBox->setEnabled(1);
1029     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1030       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1031           DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion") {
1032         colorMapComboBox->setEnabled(0);
1033         break;
1034       }
1035     }
1036
1037     std::vector<double> origin;
1038     std::vector<double> inputSpacing;
1039     std::vector<int> inputSize;
1040     std::vector<double> sizeMM;
1041     vtkSmartPointer<vtkMatrix4x4> transformation;
1042     int dimension=0;
1043     QString pixelType;
1044     QString inputSizeInBytes;
1045     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1046
1047     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1) {
1048       playButton->setEnabled(1);
1049       frameRateLabel->setEnabled(1);
1050       frameRateSpinBox->setEnabled(1);
1051     } else {
1052       playButton->setEnabled(0);
1053       frameRateLabel->setEnabled(0);
1054       frameRateSpinBox->setEnabled(0);
1055     }
1056
1057     //read image header
1058     int NPixel = 1;
1059
1060     vvImage::Pointer imageSelected;
1061     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1062       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1063       dimension = imageSelected->GetNumberOfDimensions();
1064       origin.resize(dimension);
1065       inputSpacing.resize(dimension);
1066       inputSize.resize(dimension);
1067       sizeMM.resize(dimension);
1068       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1069       for (int i = 0; i < dimension; i++) {
1070         origin[i] = imageSelected->GetOrigin()[i];
1071         inputSpacing[i] = imageSelected->GetSpacing()[i];
1072         inputSize[i] = imageSelected->GetSize()[i];
1073         sizeMM[i] = inputSize[i]*inputSpacing[i];
1074         NPixel *= inputSize[i];
1075       }
1076       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1077     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1078       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1079       dimension = imageSelected->GetNumberOfDimensions();
1080       origin.resize(dimension);
1081       inputSpacing.resize(dimension);
1082       inputSize.resize(dimension);
1083       sizeMM.resize(dimension);
1084       pixelType = mSlicerManagers[index]->GetVF()->GetScalarTypeAsITKString().c_str();
1085       for (int i = 0; i < dimension; i++) {
1086         origin[i] = imageSelected->GetOrigin()[i];
1087         inputSpacing[i] = imageSelected->GetSpacing()[i];
1088         inputSize[i] = imageSelected->GetSize()[i];
1089         sizeMM[i] = inputSize[i]*inputSpacing[i];
1090         NPixel *= inputSize[i];
1091       }
1092       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1093     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1094       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1095       dimension = imageSelected->GetNumberOfDimensions();
1096       origin.resize(dimension);
1097       inputSpacing.resize(dimension);
1098       inputSize.resize(dimension);
1099       sizeMM.resize(dimension);
1100       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1101       for (int i = 0; i < dimension; i++) {
1102         origin[i] = imageSelected->GetOrigin()[i];
1103         inputSpacing[i] = imageSelected->GetSpacing()[i];
1104         inputSize[i] = imageSelected->GetSize()[i];
1105         sizeMM[i] = inputSize[i]*inputSpacing[i];
1106         NPixel *= inputSize[i];
1107       }
1108       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1109     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1110       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1111       dimension = imageSelected->GetNumberOfDimensions();
1112       origin.resize(dimension);
1113       inputSpacing.resize(dimension);
1114       inputSize.resize(dimension);
1115       sizeMM.resize(dimension);
1116       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1117       for (int i = 0; i < dimension; i++) {
1118         origin[i] = imageSelected->GetOrigin()[i];
1119         inputSpacing[i] = imageSelected->GetSpacing()[i];
1120         inputSize[i] = imageSelected->GetSize()[i];
1121         sizeMM[i] = inputSize[i]*inputSpacing[i];
1122         NPixel *= inputSize[i];
1123       }
1124       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1125     }
1126
1127     QString dim = QString::number(dimension) + " (";
1128     dim += pixelType + ")";
1129
1130     infoPanel->setFileName(image);
1131     infoPanel->setDimension(dim);
1132     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1133     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1134     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1135     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1136     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1137     transformation = imageSelected->GetTransform()->GetMatrix();
1138     infoPanel->setTransformation(Get4x4MatrixDoubleAsString(transformation));
1139
1140     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1141                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1142     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1143     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1144
1145     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1146     for (int i = 0; i < 4; i++) {
1147       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1148         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1149         break;
1150       }
1151     }
1152     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1153     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1154     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1155     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1156
1157     infoPanel->setFileName(image);
1158     infoPanel->setDimension(dim);
1159     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1160     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1161     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1162     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1163     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1164
1165     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1166                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1167     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1168     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1169
1170     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1171     for (int i = 0; i < 4; i++) {
1172       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1173         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1174         break;
1175       }
1176     }
1177     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1178     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1179     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1180     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1181
1182     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1183       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1184       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1185                                   mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1186                                   mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1187     } else {
1188       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1189       overlayPanel->getVFProperty(-1,-1,-1);
1190     }
1191     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1192       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1193       overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1194     } else {
1195       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1196       overlayPanel->getOverlayProperty(-1);
1197     }
1198     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1199       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1200       overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1201                                       mSlicerManagers[index]->GetFusionColorMap(),
1202                                       mSlicerManagers[index]->GetFusionWindow(),
1203                                       mSlicerManagers[index]->GetFusionLevel());
1204     } else {
1205       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1206       overlayPanel->getFusionProperty(-1, -1,-1,-1);
1207     }
1208   }
1209 }
1210 //------------------------------------------------------------------------------
1211
1212 //------------------------------------------------------------------------------
1213 void vvMainWindow::ShowDocumentation()
1214 {
1215   documentation->show();
1216 }
1217 //------------------------------------------------------------------------------
1218
1219 //------------------------------------------------------------------------------
1220 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1221 {
1222   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1223   if(!checkCanPush){
1224     registerForm->show();
1225   }else{
1226     if(registerForm->canPush()){
1227       registerForm->show();
1228       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1229     }
1230   }
1231 }
1232 //------------------------------------------------------------------------------
1233
1234 //------------------------------------------------------------------------------
1235 void vvMainWindow::ShowHelpDialog()
1236 {
1237   help_dialog->show();
1238 }
1239 //------------------------------------------------------------------------------
1240
1241 //------------------------------------------------------------------------------
1242 void vvMainWindow::ChangeViewMode()
1243 {
1244   QListIterator<int> it(splitter_3->sizes());
1245   int max_size = 0;
1246   while (it.hasNext()) {
1247     max_size += it.next();
1248   }
1249   QList<int> size0;
1250   QList<int> size1;
1251   if (viewMode == 1) {
1252     viewMode = 0;
1253     size0.push_back(max_size);
1254     size0.push_back(0);
1255     size1.push_back(max_size + 1);
1256     size1.push_back(0);
1257     splitter_3->setSizes(size0);
1258     OSplitter->setSizes(size1);
1259     DataTree->setColumnHidden(2,1);
1260     DataTree->setColumnHidden(3,1);
1261     DataTree->setColumnHidden(4,1);
1262   } else {
1263     viewMode = 1;
1264     size0.push_back(max_size / 2);
1265     size0.push_back(max_size / 2);
1266     size1.push_back((max_size + 1) / 2);
1267     size1.push_back((max_size + 1) / 2);
1268     splitter_3->setSizes(size0);
1269     OSplitter->setSizes(size1);
1270     DataTree->setColumnHidden(2,0);
1271     DataTree->setColumnHidden(3,0);
1272     DataTree->setColumnHidden(4,0);
1273   }
1274 }
1275 //------------------------------------------------------------------------------
1276
1277 //------------------------------------------------------------------------------
1278 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1279 {
1280   QString result = "";// QString::number(size);
1281   //result += " bytes (";
1282   if (size > 1000000000) {
1283     size /= 1000000000;
1284     result += QString::number(size);
1285     result += "Gb";//)";
1286   } else if (size > 1000000) {
1287     size /= 1000000;
1288     result += QString::number(size);
1289     result += "Mb";//)";
1290   } else if (size > 1000) {
1291     size /= 1000;
1292     result += QString::number(size);
1293     result += "kb";//)";
1294   }
1295   return result;
1296 }
1297 //------------------------------------------------------------------------------
1298
1299 //------------------------------------------------------------------------------
1300 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix)
1301 {
1302   std::ostringstream strmatrix;
1303
1304   for (unsigned int i = 0; i < 4; i++) {
1305     for (unsigned int j = 0; j < 4; j++) {
1306       strmatrix.flags(ios::showpos);
1307       strmatrix.width(10);
1308       strmatrix.precision(3);
1309       strmatrix.setf(ios::fixed,ios::floatfield);
1310       strmatrix.fill(' ');
1311       strmatrix << std::left << matrix->GetElement(i, j);
1312       //strmatrix.width(10);
1313       strmatrix << " ";
1314     }
1315     strmatrix << std::endl;
1316   }
1317   QString result = strmatrix.str().c_str();
1318   return result;
1319 }
1320 //------------------------------------------------------------------------------
1321
1322 //------------------------------------------------------------------------------
1323 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1324 {
1325   QString result;
1326   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1327     if (i != 0)
1328       result += " ";
1329     result += QString::number(vectorDouble[i]);
1330   }
1331   return result;
1332 }
1333 //------------------------------------------------------------------------------
1334
1335 //------------------------------------------------------------------------------
1336 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1337 {
1338   QString result;
1339   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1340     if (i != 0)
1341       result += " ";
1342     result += QString::number(vectorInt[i]);
1343   }
1344   return result;
1345 }
1346 //------------------------------------------------------------------------------
1347
1348 //------------------------------------------------------------------------------
1349 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1350 {
1351   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1352   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1353     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1354       return i;
1355   }
1356   return -1;
1357 }
1358 //------------------------------------------------------------------------------
1359
1360 //------------------------------------------------------------------------------
1361 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1362 {
1363   QString id = sm->GetId().c_str();
1364   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1365     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1366       return DataTree->topLevelItem(i);
1367   }
1368   return NULL;
1369 }
1370 //------------------------------------------------------------------------------
1371
1372 //------------------------------------------------------------------------------
1373 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clicked_item, int column)
1374 {
1375   int index = GetSlicerIndexFromItem(clicked_item);
1376   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1377     return;
1378   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1379     //Trick to avoid redoing twice the job for a key (sr)
1380     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()-> GetInteractor()->SetKeySym("Crap");
1381
1382     QTreeWidgetItem* current_row=DataTree->topLevelItem(i);
1383     if (DataTree->topLevelItem(index) == current_row) {
1384       vvSlicer* clicked_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1385       if (current_row == clicked_item) {
1386         //If we just activated a slicer
1387         if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1388           mSlicerManagers[i]->UpdateSlicer(column-1,clicked_item->data(column,Qt::CheckStateRole).toInt());
1389           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1390           DisplaySliders(i,column-1);
1391           std::map<std::string,int> overlay_counts;
1392           for (int child = 0; child < current_row->childCount(); child++) {
1393             std::string overlay_type =
1394               current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1395             overlay_counts[overlay_type]++;
1396             current_row->child(child)->setData(column,Qt::CheckStateRole,
1397                                                current_row->data(column,Qt::CheckStateRole));
1398             clicked_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,true);
1399           }
1400         } else { //We don't allow simply desactivating a slicer
1401           clicked_item->setData(column,Qt::CheckStateRole,2);
1402           return;
1403         }
1404       }
1405       //if we clicked on the vector(or overlay) and not the image
1406       else {
1407         if (clicked_item->data(column,Qt::CheckStateRole).toInt()) {
1408           current_row->setData(column,Qt::CheckStateRole,2);
1409           mSlicerManagers[i]->UpdateSlicer(column-1,2);
1410           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1411           DisplaySliders(i,column-1);
1412         }
1413         int vis = clicked_item->data(column,Qt::CheckStateRole).toInt();
1414         std::string overlay_type = clicked_item->data(1,Qt::UserRole).toString().toStdString();
1415         int overlay_index=0;
1416         for (int child = 0; child < current_row->childCount(); child++) {
1417           if (current_row->child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1418             overlay_index++;
1419           if (current_row->child(child) == clicked_item) break;
1420         }
1421         clicked_slicer->SetActorVisibility(
1422           clicked_item->data(1,Qt::UserRole).toString().toStdString(), overlay_index-1,vis);
1423       }
1424     } else if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1425       current_row->setData(column,Qt::CheckStateRole,0);
1426       mSlicerManagers[i]->UpdateSlicer(column-1,0);
1427       std::map<std::string,int> overlay_counts;
1428       for (int child = 0; child < current_row->childCount(); child++) {
1429         std::string overlay_type =
1430           current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1431         overlay_counts[overlay_type]++;
1432         current_row->child(child)->setData(column,Qt::CheckStateRole,0);
1433         vvSlicer * current_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1434         current_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,false);
1435       }
1436     }
1437     //mSlicerManagers[i]->SetColorMap(-1);
1438     mSlicerManagers[i]->SetColorMap();
1439   }
1440   mSlicerManagers[index]->GetSlicer(column-1)->Render();
1441 }
1442 //------------------------------------------------------------------------------
1443
1444 void vvMainWindow::InitSlicers()
1445 {
1446   if (mSlicerManagers.size()) {
1447     mSlicerManagers.back()->GenerateDefaultLookupTable();
1448
1449     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1450     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1451     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1452     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1453   }
1454 }
1455
1456 //------------------------------------------------------------------------------
1457 void vvMainWindow::InitDisplay()
1458 {
1459   if (mSlicerManagers.size()) {
1460     //BE CAREFUL : this is absolutely necessary to set the interactor style
1461     //in order to have the same style instanciation for all SlicerManagers in
1462     // a same window
1463     for (int j = 0; j < 4; j++) {
1464       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1465       style->SetAutoAdjustCameraClippingRange(1);
1466       bool AlreadySelected = false;
1467       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1468         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1469
1470         //select the image only if previous are not selected
1471         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1472           mSlicerManagers[i]->UpdateSlicer(j,1);
1473           AlreadySelected = true;
1474         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1475           if (DataTree->selectedItems().size() == 0)
1476             DataTree->topLevelItem(i)->setSelected(1);
1477           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1478           mSlicerManagers[i]->UpdateSlicer(j,1);
1479           DisplaySliders(i,j);
1480         } else {
1481           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1482           mSlicerManagers[i]->UpdateSlicer(j,0);
1483         }
1484       }
1485       style->Delete();
1486     }
1487   }
1488 }
1489 //------------------------------------------------------------------------------
1490
1491 //------------------------------------------------------------------------------
1492 void vvMainWindow::DisplaySliders(int slicer, int window)
1493 {
1494   int range[2];
1495   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1496   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1497
1498   int tRange[2];
1499   tRange[0] = 0;
1500   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1501   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1502   bool showHorizontal = false;
1503   bool showVertical = false;
1504   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1505       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1506           && mSlicerManagers[slicer]->GetType() != vvImageReader::IMAGEWITHTIME
1507           && mSlicerManagers[slicer]->GetType() != vvImageReader::MERGEDWITHTIME))
1508     showVertical = true;
1509   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1510       || mSlicerManagers[slicer]->GetType() == vvImageReader::IMAGEWITHTIME
1511       || mSlicerManagers[slicer]->GetType() == vvImageReader::MERGEDWITHTIME)
1512     showHorizontal = true;
1513
1514   if (showVertical)
1515     verticalSliders[window]->show();
1516   else
1517     verticalSliders[window]->hide();
1518   verticalSliders[window]->setRange(range[0],range[1]);
1519   verticalSliders[window]->setValue(position);
1520
1521   if (showHorizontal)
1522     horizontalSliders[window]->show();
1523   else
1524     horizontalSliders[window]->hide();
1525   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1526   horizontalSliders[window]->setValue(tPosition);
1527 }
1528 //------------------------------------------------------------------------------
1529
1530 //------------------------------------------------------------------------------
1531 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1532 {
1533   int index = GetSlicerIndexFromItem(item);
1534
1535   if (DataTree->topLevelItem(index) != item) {
1536     QString warning = "Do you really want to close the overlay : ";
1537     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1538     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1539                        warning, 0, this);
1540     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1541     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1542     if (msgBox.exec() == QMessageBox::AcceptRole) {
1543       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1544       int overlay_index=0;
1545       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1546         if (DataTree->topLevelItem(index)->\
1547             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1548           overlay_index++;
1549         if (DataTree->topLevelItem(index)->child(child) == item) break;
1550       }
1551       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1552       mSlicerManagers[index]->SetColorMap(0);
1553       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1554       mSlicerManagers[index]->Render();
1555     }
1556   } else if (DataTree->topLevelItemCount() <= 1) {
1557     QString warning = "Do you really want to close the image : ";
1558     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1559     warning += "\nThis is the last image, you're about to close vv !!!";
1560     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1561                        warning, 0, this);
1562     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1563     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1564     if (msgBox.exec() == QMessageBox::AcceptRole) {
1565       this->close();
1566     }
1567   } else {
1568     QString warning = "Do you really want to close the image : ";
1569     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1570     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1571                        warning, 0, this);
1572     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1573     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1574     if (msgBox.exec() == QMessageBox::AcceptRole) {
1575
1576       // Tell tools that we close an image
1577       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1578
1579       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1580       DataTree->takeTopLevelItem(index);
1581       for (int i = 0; i < index; i++) {
1582         Manageriter++;
1583       }
1584       linkPanel->removeImage(index);
1585       mSlicerManagers[index]->RemoveActors();
1586       delete mSlicerManagers[index];
1587       mSlicerManagers.erase(Manageriter);
1588
1589       //
1590       InitDisplay();
1591     }
1592   }
1593   ImageInfoChanged();
1594 }
1595 //------------------------------------------------------------------------------
1596
1597 //------------------------------------------------------------------------------
1598 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1599 {
1600   // int index = GetSlicerIndexFromItem(item);
1601   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1602   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1603   //     mSlicerManagers[index]->ReloadVF();
1604   //   else
1605   //     mSlicerManagers[index]->Reload();
1606
1607   //   QApplication::restoreOverrideCursor();
1608   int index = GetSlicerIndexFromItem(item);
1609   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1610   QString role=item->data(1,Qt::UserRole).toString();
1611   if ( role == "vector")
1612     mSlicerManagers[index]->ReloadVF();
1613   else if (role == "overlay")
1614     mSlicerManagers[index]->ReloadOverlay();
1615   else if (role == "fusion")
1616     mSlicerManagers[index]->ReloadFusion();
1617   else
1618     mSlicerManagers[index]->Reload();
1619
1620   // Update view and info
1621   ImageInfoChanged();
1622   mSlicerManagers[index]->Render();
1623   QApplication::restoreOverrideCursor();
1624 }
1625 //------------------------------------------------------------------------------
1626
1627 //------------------------------------------------------------------------------
1628 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1629 {
1630   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1631 }
1632 //------------------------------------------------------------------------------
1633
1634 //------------------------------------------------------------------------------
1635 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1636 {
1637   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1638 }
1639 //------------------------------------------------------------------------------
1640
1641 //------------------------------------------------------------------------------
1642 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1643 {
1644   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1645 }
1646 //------------------------------------------------------------------------------
1647
1648 //------------------------------------------------------------------------------
1649 void vvMainWindow::FusionChanged(int visibility, double value)
1650 {
1651   overlayPanel->getCurrentFusionInfo(visibility,value);
1652 }
1653 //------------------------------------------------------------------------------
1654
1655 //------------------------------------------------------------------------------
1656 void vvMainWindow::WindowsChanged(int window, int view, int slice)
1657 {
1658   infoPanel->setViews(window, view, slice);
1659 }
1660 //------------------------------------------------------------------------------
1661
1662 //------------------------------------------------------------------------------
1663 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap)
1664 {
1665   windowSpinBox->setValue(window);
1666   levelSpinBox->setValue(level);
1667   colorMapComboBox->setCurrentIndex(colormap);
1668   presetComboBox->setCurrentIndex(preset);
1669 }
1670 //------------------------------------------------------------------------------
1671
1672 //------------------------------------------------------------------------------
1673 void vvMainWindow::WindowLevelEdited()
1674 {
1675   presetComboBox->setCurrentIndex(6);
1676   UpdateWindowLevel();
1677 }
1678 //------------------------------------------------------------------------------
1679
1680 //------------------------------------------------------------------------------
1681 void vvMainWindow::UpdateWindowLevel()
1682 {
1683   if (DataTree->selectedItems().size()) {
1684     if (presetComboBox->currentIndex() == 7) //For ventilation
1685       colorMapComboBox->setCurrentIndex(5);
1686     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1687     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1688     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1689     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1690     mSlicerManagers[index]->Render();
1691     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1692     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1693   }
1694 }
1695 //------------------------------------------------------------------------------
1696
1697 //------------------------------------------------------------------------------
1698 void vvMainWindow::UpdateColorMap()
1699 {
1700   if (DataTree->selectedItems().size()) {
1701     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1702     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1703     mSlicerManagers[index]->Render();
1704   }
1705 }
1706 //------------------------------------------------------------------------------
1707 void vvMainWindow::SwitchWindowLevel()
1708 {
1709   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1710   int window = mSlicerManagers[index]->GetColorWindow();
1711   presetComboBox->setCurrentIndex(6);
1712   windowSpinBox->setValue(-window);
1713   UpdateWindowLevel();
1714 }
1715 //------------------------------------------------------------------------------
1716
1717 //------------------------------------------------------------------------------
1718 void vvMainWindow::ApplyWindowLevelToAllImages()
1719 {
1720   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1721     if (mSlicerManagers[i] == NULL)
1722       continue;
1723     mSlicerManagers[i]->SetColorWindow(windowSpinBox->value());
1724     mSlicerManagers[i]->SetColorLevel(levelSpinBox->value());
1725     mSlicerManagers[i]->SetPreset(6);
1726     mSlicerManagers[i]->Render();
1727   }
1728 }
1729 //------------------------------------------------------------------------------
1730
1731 //------------------------------------------------------------------------------
1732 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1733 {
1734   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1735     if (mSlicerManagers[i]->GetId() == id) {
1736       //mSlicerManagers[i]->SetTSlice(temps);
1737       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1738       mSlicerManagers[i]->UpdateViews(0,slicer);
1739       break;
1740     }
1741   }
1742 }
1743 //------------------------------------------------------------------------------
1744
1745 //------------------------------------------------------------------------------
1746 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1747 {
1748   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1749     if (id == mSlicerManagers[i]->GetId()) {
1750       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1751     }
1752   }
1753 }
1754 //------------------------------------------------------------------------------
1755
1756 //------------------------------------------------------------------------------
1757 void vvMainWindow::ShowContextMenu(QPoint point)
1758 {
1759   if (!DataTree->selectedItems().size()) {
1760     contextActions[1]->setEnabled(0);
1761     contextActions[2]->setEnabled(0);
1762     contextActions[3]->setEnabled(0);
1763     contextActions[4]->setEnabled(0);
1764     contextActions[5]->setEnabled(0);
1765     contextActions[6]->setEnabled(0);
1766   } else {
1767     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1768     contextActions[1]->setEnabled(1);
1769     contextActions[2]->setEnabled(
1770       DataTree->itemWidget(DataTree->selectedItems()[0],
1771                            COLUMN_RELOAD_IMAGE)->isEnabled());
1772     contextActions[3]->setEnabled(1);
1773     contextActions[5]->setEnabled(1);
1774     contextActions[6]->setEnabled(1);
1775
1776     if (mSlicerManagers[index]->GetDimension() < 3)
1777       contextActions[4]->setEnabled(0);
1778     else
1779       contextActions[4]->setEnabled(1);
1780   }
1781   contextMenu.exec(QCursor::pos());
1782 }
1783 //------------------------------------------------------------------------------
1784
1785 //------------------------------------------------------------------------------
1786 void vvMainWindow::CloseImage()
1787 {
1788   CloseImage(DataTree->selectedItems()[0],0);
1789 }
1790 //------------------------------------------------------------------------------
1791
1792 //------------------------------------------------------------------------------
1793 void vvMainWindow::ReloadImage()
1794 {
1795   ReloadImage(DataTree->selectedItems()[0],0);
1796 }
1797 //------------------------------------------------------------------------------
1798
1799 //------------------------------------------------------------------------------
1800 void vvMainWindow::SelectOverlayImage()
1801 {
1802   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1803
1804   //check if one overlay image is added
1805   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1806     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1807       QString error = "Cannot add more than one compared image\n";
1808       error += "Please remove first ";
1809       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1810       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1811       return;
1812     }
1813
1814   QString Extensions = EXTENSIONS;
1815   Extensions += ";;All Files (*)";
1816   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1817   if (!file.isEmpty())
1818     AddOverlayImage(index,file);
1819 }
1820 //------------------------------------------------------------------------------
1821
1822 //------------------------------------------------------------------------------
1823 void vvMainWindow::AddOverlayImage(int index, QString file)
1824 {
1825
1826   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1827   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1828                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1829   reader->SetFileName(file.toStdString().c_str());
1830   reader->ReadImageInformation();
1831   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1832   int dimension = reader->GetNumberOfDimensions();
1833   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1834   vvProgressDialog progress("Opening " + file.toStdString());
1835   qApp->processEvents();
1836
1837   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1838   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component)) {
1839     //create an item in the tree with good settings
1840     QTreeWidgetItem *item = new QTreeWidgetItem();
1841     item->setData(0,Qt::UserRole,file.toStdString().c_str());
1842     item->setData(1,Qt::UserRole,tr("overlay"));
1843     QFileInfo fileinfo(file); //Do not show the path
1844     item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1845     item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1846     qApp->processEvents();
1847
1848     for (int j = 1; j <= 4; j++) {
1849       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1850       mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("overlay",0,
1851           DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1852     }
1853
1854     //Create the buttons for reload and close
1855     qApp->processEvents();
1856     QTreePushButton* cButton = new QTreePushButton;
1857     cButton->setItem(item);
1858     cButton->setColumn(COLUMN_CLOSE_IMAGE);
1859     cButton->setToolTip(tr("close image"));
1860     cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1861     connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1862             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1863
1864     QTreePushButton* rButton = new QTreePushButton;
1865     rButton->setItem(item);
1866     rButton->setColumn(COLUMN_RELOAD_IMAGE);
1867     rButton->setToolTip(tr("reload image"));
1868     rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1869     connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1870             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1871
1872     DataTree->topLevelItem(index)->setExpanded(1);
1873     DataTree->topLevelItem(index)->addChild(item);
1874     DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1875     DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1876
1877     //set the id of the image
1878     QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1879     item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1880     UpdateTree();
1881     qApp->processEvents();
1882     ImageInfoChanged();
1883     QApplication::restoreOverrideCursor();
1884   } else {
1885     QApplication::restoreOverrideCursor();
1886     QString error = "Cannot import the new image.\n";
1887     error += mSlicerManagers[index]->GetLastError().c_str();
1888     QMessageBox::information(this,tr("Problem reading image !"),error);
1889   }
1890 }
1891 //------------------------------------------------------------------------------
1892
1893
1894 //------------------------------------------------------------------------------
1895 void vvMainWindow::AddROI(int index, QString file)
1896 {
1897   /*
1898   // Get slice manager
1899
1900   // Load image
1901
1902   vvImageReader * mReader = new vvImageReader;
1903   mReader->SetInputFilename(filename.toStdString());
1904   mReader->Update(IMAGE);
1905   if (mReader->GetLastError().size() != 0) {
1906     std::cerr << "Error while reading " << filename.toStdString() << std::endl;
1907     QString error = "Cannot open file \n";
1908     error += mReader->GetLastError().c_str();
1909     QMessageBox::information(this,tr("Reading problem"),error);
1910     delete mReader;
1911     return;
1912   }
1913   vvImage::Pointer roi = mReader->GetOutput();
1914
1915   // Create roi in new tool
1916   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
1917   */
1918 }
1919 //------------------------------------------------------------------------------
1920
1921 //------------------------------------------------------------------------------
1922 void vvMainWindow::SelectFusionImage()
1923 {
1924   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1925
1926   //check if one fusion image is added
1927   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1928     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
1929       QString error = "Cannot add more than one fusion image\n";
1930       error += "Please remove first ";
1931       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1932       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1933       return;
1934     }
1935
1936   QString Extensions = EXTENSIONS;
1937   Extensions += ";;All Files (*)";
1938   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1939   if (!file.isEmpty())
1940     AddFusionImage(index,file);
1941 }
1942 //------------------------------------------------------------------------------
1943
1944 //------------------------------------------------------------------------------
1945 void vvMainWindow::AddFusionImage(int index, QString file)
1946 {
1947   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1948   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1949                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1950   reader->SetFileName(file.toStdString().c_str());
1951   reader->ReadImageInformation();
1952   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1953   if (reader) {
1954     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1955     vvProgressDialog progress("Opening fusion");
1956     qApp->processEvents();
1957
1958     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1959     if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1960                                           reader->GetNumberOfDimensions(), component)) {
1961       //create an item in the tree with good settings
1962       QTreeWidgetItem *item = new QTreeWidgetItem();
1963       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1964       item->setData(1,Qt::UserRole,tr("fusion"));
1965       QFileInfo fileinfo(filename.c_str()); //Do not show the path
1966       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1967       item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1968       qApp->processEvents();
1969
1970       for (int j = 1; j <= 4; j++) {
1971         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1972         mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("fusion",0,
1973             DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1974       }
1975
1976       //Create the buttons for reload and close
1977       qApp->processEvents();
1978       QTreePushButton* cButton = new QTreePushButton;
1979       cButton->setItem(item);
1980       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1981       cButton->setToolTip(tr("close image"));
1982       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1983       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1984               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1985
1986       QTreePushButton* rButton = new QTreePushButton;
1987       rButton->setItem(item);
1988       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1989       rButton->setToolTip(tr("reload image"));
1990       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1991       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1992               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1993
1994       DataTree->topLevelItem(index)->setExpanded(1);
1995       DataTree->topLevelItem(index)->addChild(item);
1996       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1997       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1998
1999       //set the id of the image
2000       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2001       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2002       UpdateTree();
2003       qApp->processEvents();
2004       ImageInfoChanged();
2005       QApplication::restoreOverrideCursor();
2006     } else {
2007       QApplication::restoreOverrideCursor();
2008       QString error = "Cannot import the new image.\n";
2009       error += mSlicerManagers[index]->GetLastError().c_str();
2010       QMessageBox::information(this,tr("Problem reading image !"),error);
2011     }
2012   } else {
2013     QString error = "Cannot import the new image.\n";
2014     QMessageBox::information(this,tr("Problem reading image !"),error);
2015   }
2016 }
2017 //------------------------------------------------------------------------------
2018
2019
2020 //------------------------------------------------------------------------------
2021 void vvMainWindow::OpenField()
2022 {
2023   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2024   //check if a vector field has already been added
2025   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2026     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
2027       QString error = "Cannot add more than one vector field\n";
2028       error += "Please remove first ";
2029       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2030       QMessageBox::information(this,tr("Problem adding vector field!"),error);
2031       return;
2032     }
2033
2034   QString Extensions = "Images ( *.mhd)";
2035   Extensions += ";;Images ( *.vf)";
2036   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2037   if (!file.isEmpty())
2038     AddField(file,index);
2039 }
2040 //------------------------------------------------------------------------------
2041
2042
2043 //------------------------------------------------------------------------------
2044 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2045 {
2046   //create an item in the tree with good settings
2047   QTreeWidgetItem *item = new QTreeWidgetItem();
2048   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2049   item->setData(1,Qt::UserRole,tr("vector"));
2050   QFileInfo fileinfo(filename); //Do not show the path
2051   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2052   item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
2053   qApp->processEvents();
2054
2055   for (int j = 1; j <= 4; j++) {
2056     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2057     mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("vector",0,
2058         DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
2059   }
2060
2061   //Create the buttons for reload and close
2062   qApp->processEvents();
2063   QTreePushButton* cButton = new QTreePushButton;
2064   cButton->setItem(item);
2065   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2066   cButton->setToolTip(tr("close vector field"));
2067   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2068   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2069           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2070
2071   QTreePushButton* rButton = new QTreePushButton;
2072   rButton->setItem(item);
2073   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2074   rButton->setToolTip(tr("reload vector field"));
2075   rButton->setEnabled(from_disk);
2076   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2077   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2078           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2079
2080   DataTree->topLevelItem(index)->setExpanded(1);
2081   DataTree->topLevelItem(index)->addChild(item);
2082   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2083   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2084
2085   //set the id of the image
2086   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2087   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2088   UpdateTree();
2089   qApp->processEvents();
2090   ImageInfoChanged();
2091   QApplication::restoreOverrideCursor();
2092 }
2093 //------------------------------------------------------------------------------
2094
2095
2096 //------------------------------------------------------------------------------
2097 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2098 {
2099   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2100   vvSlicerManager* imageManager = mSlicerManagers[index];
2101   if (imageManager->SetVF(vf,file.toStdString())) {
2102     AddFieldEntry(file,index,false);
2103   } else {
2104     QString error = "Cannot import the vector field for this image.\n";
2105     error += imageManager->GetLastError().c_str();
2106     QMessageBox::information(this,tr("Problem reading VF !"),error);
2107   }
2108   QApplication::restoreOverrideCursor();
2109 }
2110 //------------------------------------------------------------------------------
2111
2112
2113 //------------------------------------------------------------------------------
2114 void vvMainWindow::AddField(QString file,int index)
2115 {
2116   if (QFile::exists(file)) {
2117     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2118
2119     //init the progress events
2120     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2121     vvProgressDialog progress("Opening " + file.toStdString());
2122     qApp->processEvents();
2123
2124     //read the vector and put it in the current mSlicerManager
2125     vvSlicerManager* imageManager = mSlicerManagers[index];
2126     qApp->processEvents();
2127
2128     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2129     if (imageManager->SetVF(file.toStdString())) {
2130       imageManager->Render();
2131       AddFieldEntry(file,index,true);
2132     } else {
2133       QApplication::restoreOverrideCursor();
2134       QString error = "Cannot import the vector field for this image.\n";
2135       error += imageManager->GetLastError().c_str();
2136       QMessageBox::information(this,tr("Problem reading VF !"),error);
2137     }
2138   } else
2139     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2140
2141 }
2142 //------------------------------------------------------------------------------
2143
2144
2145 //------------------------------------------------------------------------------
2146 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2147 {
2148   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2149   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2150     for (int i = 0; i < 4; i++) {
2151       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2152       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2153       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2154       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2155       if (log > 0)
2156         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2157       else
2158         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2159     }
2160   }
2161 }
2162 //------------------------------------------------------------------------------
2163
2164
2165 //------------------------------------------------------------------------------
2166 void vvMainWindow::SetOverlayProperty(int color)
2167 {
2168   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2169   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2170     mSlicerManagers[index]->SetOverlayColor(color);
2171     mSlicerManagers[index]->SetColorMap(0);
2172     mSlicerManagers[index]->Render();
2173   }
2174 }
2175 //------------------------------------------------------------------------------
2176
2177 //------------------------------------------------------------------------------
2178 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level)
2179 {
2180   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2181   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2182     mSlicerManagers[index]->SetFusionOpacity(opacity);
2183     mSlicerManagers[index]->SetFusionColorMap(colormap);
2184     mSlicerManagers[index]->SetFusionWindow(window);
2185     mSlicerManagers[index]->SetFusionLevel(level);
2186     mSlicerManagers[index]->SetColorMap(0);
2187     mSlicerManagers[index]->Render();
2188   }
2189 }
2190 //------------------------------------------------------------------------------
2191
2192 //------------------------------------------------------------------------------
2193 void vvMainWindow::SaveAs()
2194 {
2195   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2196     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2197     return;
2198   }
2199
2200   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2201   int dimension = mSlicerManagers[index]->GetDimension();
2202   QStringList OutputListeFormat;
2203   OutputListeFormat.clear();
2204   if (dimension == 1) {
2205     OutputListeFormat.push_back(".mhd");
2206   }
2207   if (dimension == 2) {
2208     OutputListeFormat.push_back(".bmp");
2209     OutputListeFormat.push_back(".png");
2210     OutputListeFormat.push_back(".jpeg");
2211     OutputListeFormat.push_back(".tif");
2212     OutputListeFormat.push_back(".mhd");
2213     OutputListeFormat.push_back(".hdr");
2214     OutputListeFormat.push_back(".vox");
2215   } else if (dimension == 3) {
2216     OutputListeFormat.push_back(".mhd");
2217     OutputListeFormat.push_back(".hdr");
2218     OutputListeFormat.push_back(".vox");
2219   } else if (dimension == 4) {
2220     OutputListeFormat.push_back(".mhd");
2221   }
2222   QString Extensions = "AllFiles(*.*)";
2223   for (int i = 0; i < OutputListeFormat.count(); i++) {
2224     Extensions += ";;Images ( *";
2225     Extensions += OutputListeFormat[i];
2226     Extensions += ")";
2227   }
2228   QString fileName = QFileDialog::getSaveFileName(this,
2229                      tr("Save As"),
2230                      mSlicerManagers[index]->GetFileName().c_str(),
2231                      Extensions);
2232   if (!fileName.isEmpty()) {
2233     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2234     if (OutputListeFormat.contains(
2235           fileformat.c_str())) {
2236       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2237       std::string action = "Saving";
2238       vvProgressDialog progress("Saving "+fileName.toStdString());
2239       qApp->processEvents();
2240       vvImageWriter::Pointer writer = vvImageWriter::New();
2241       writer->SetOutputFileName(fileName.toStdString());
2242       writer->SetInput(mSlicerManagers[index]->GetImage());
2243       writer->Update();
2244       QApplication::restoreOverrideCursor();
2245       if (writer->GetLastError().size()) {
2246         QString error = "Saving did not succeed\n";
2247         error += writer->GetLastError().c_str();
2248         QMessageBox::information(this,tr("Saving Problem"),error);
2249         SaveAs();
2250       }
2251     } else {
2252       QString error = fileformat.c_str();
2253       if (error.isEmpty())
2254         error += "no file format specified !";
2255       else
2256         error += " format unknown !!!\n";
2257       QMessageBox::information(this,tr("Saving Problem"),error);
2258       SaveAs();
2259     }
2260   }
2261 }
2262 //------------------------------------------------------------------------------
2263
2264
2265 //------------------------------------------------------------------------------
2266 void vvMainWindow::AddLink(QString image1,QString image2)
2267 {
2268   unsigned int sm1 = 0;
2269   unsigned int sm2 = 0;
2270
2271   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2272     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2273       mSlicerManagers[i]->AddLink(image2.toStdString());
2274       sm1 = i;
2275     }
2276     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2277       mSlicerManagers[i]->AddLink(image1.toStdString());
2278       sm2 = i;
2279     }
2280   }
2281
2282   if (linkPanel->isLinkAll())   {
2283     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2284     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2285   }
2286   else {
2287     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2288   }
2289 }
2290
2291 //------------------------------------------------------------------------------
2292
2293
2294 //------------------------------------------------------------------------------
2295 void vvMainWindow::RemoveLink(QString image1,QString image2)
2296 {
2297   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2298     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2299       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2300     }
2301     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2302       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2303     }
2304   }
2305 }
2306 //------------------------------------------------------------------------------
2307
2308 //------------------------------------------------------------------------------
2309 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2310 {
2311   int index = 0;
2312   while(sm != mSlicerManagers[index])
2313     index++;
2314   index = (index+offset) % mSlicerManagers.size();
2315
2316   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2317   //CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2318   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2319   DisplayChanged(item,slicer+1);
2320 }
2321 //------------------------------------------------------------------------------
2322
2323 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2324 {
2325   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2326     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2327       for (int j = 0; j < 4; j++) {
2328         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2329         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2330         //UpdateTSlice(j,value);
2331       }
2332       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2333       break;
2334     }
2335   }
2336 }
2337 //------------------------------------------------------------------------------
2338
2339
2340 //------------------------------------------------------------------------------
2341 void vvMainWindow::NOHorizontalSliderMoved()
2342 {
2343   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2344   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2345 //  mCurrentTime = NOHorizontalSlider->value();
2346 }
2347 //------------------------------------------------------------------------------
2348
2349
2350 //------------------------------------------------------------------------------
2351 void vvMainWindow::NEHorizontalSliderMoved()
2352 {
2353   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2354   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2355 //  mCurrentTime = NEHorizontalSlider->value();
2356 }
2357 //------------------------------------------------------------------------------
2358
2359
2360 //------------------------------------------------------------------------------
2361 void vvMainWindow::SOHorizontalSliderMoved()
2362 {
2363   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2364   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2365   // mCurrentTime = SOHorizontalSlider->value();
2366 }
2367 //------------------------------------------------------------------------------
2368
2369
2370 //------------------------------------------------------------------------------
2371 void vvMainWindow::SEHorizontalSliderMoved()
2372 {
2373   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2374   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2375   // mCurrentTime = SEHorizontalSlider->value();
2376 }
2377 //------------------------------------------------------------------------------
2378
2379 //------------------------------------------------------------------------------
2380 void vvMainWindow::NOVerticalSliderChanged()
2381 {
2382   static int value=-1;
2383   if (value == NOVerticalSlider->value()) return;
2384   else value = NOVerticalSlider->value();
2385   //  int value = NOVerticalSlider->value();
2386   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2387     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2388       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2389         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2390         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2391
2392         // If nor Update/Render -> slider not work
2393         // only render = ok navigation, but for contour Update needed but slower ?
2394
2395         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2396         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2397       }
2398       break;
2399     }
2400   }
2401 }
2402 //------------------------------------------------------------------------------
2403
2404
2405 //------------------------------------------------------------------------------
2406 void vvMainWindow::NEVerticalSliderChanged()
2407 {
2408   static int value=-1;
2409   if (value == NEVerticalSlider->value()) return;
2410   else value = NEVerticalSlider->value();
2411   //  int value = NEVerticalSlider->value();
2412   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2413     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2414       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2415         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2416         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2417         mSlicerManagers[i]->UpdateSlice(1);
2418         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2419       }
2420       break;
2421     }
2422   }
2423 }
2424 //------------------------------------------------------------------------------
2425
2426
2427 //------------------------------------------------------------------------------
2428 void vvMainWindow::SOVerticalSliderChanged()
2429 {
2430   static int value=-1;
2431   if (value == SOVerticalSlider->value()) return;
2432   else value = SOVerticalSlider->value();
2433   //int value = SOVerticalSlider->value();
2434   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2435     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2436       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2437         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2438         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2439         mSlicerManagers[i]->UpdateSlice(2);
2440         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2441       }
2442       // else { DD("avoid SOVerticalSlider slicer update"); }
2443       break;
2444     }
2445   }
2446 }
2447 //------------------------------------------------------------------------------
2448
2449
2450 //------------------------------------------------------------------------------
2451 void vvMainWindow::SEVerticalSliderChanged()
2452 {
2453   static int value=-1;
2454   if (value == SEVerticalSlider->value()) return;
2455   else value = SEVerticalSlider->value();
2456   // int value = SEVerticalSlider->value();
2457   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2458     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2459       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2460         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2461         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2462         mSlicerManagers[i]->UpdateSlice(3);
2463         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2464       }
2465       break;
2466     }
2467   }
2468 }
2469 //------------------------------------------------------------------------------
2470
2471
2472 //------------------------------------------------------------------------------
2473 void vvMainWindow::UpdateSlice(int slicer, int slice)
2474 {
2475   // DD("vvMainWindow::UpdateSlice");
2476 //   DD(slicer);
2477 //   DD(slice);
2478   if (slicer == 0) {
2479     //    if (slice != NOVerticalSlider->value())
2480     NOVerticalSlider->setValue(slice);
2481   } else {
2482     if (slicer == 1)
2483       NEVerticalSlider->setValue(slice);
2484     else {
2485       if (slicer == 2)
2486         SOVerticalSlider->setValue(slice);
2487       else {
2488         if (slicer == 3)
2489           SEVerticalSlider->setValue(slice);
2490       }
2491     }
2492   }
2493   // DD("vvMainWindow:UpdateSlice END");
2494 }
2495 //------------------------------------------------------------------------------
2496
2497
2498 //------------------------------------------------------------------------------
2499 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2500 {
2501   switch (slicer) {
2502   case 0:
2503     NOHorizontalSlider->setValue(slice);
2504     break;
2505   case 1:
2506     NEHorizontalSlider->setValue(slice);
2507     break;
2508   case 2:
2509     SOHorizontalSlider->setValue(slice);
2510     break;
2511   case 3:
2512     SEHorizontalSlider->setValue(slice);
2513     break;
2514   }
2515 }
2516 //------------------------------------------------------------------------------
2517
2518
2519 //------------------------------------------------------------------------------
2520 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2521 {
2522   int position = int((min+max)/2);
2523   int tPosition = int((tmin+tmax)/2);
2524   if (slicer == 0) {
2525     NOVerticalSlider->setValue(position);
2526     NOVerticalSlider->setRange(min,max);
2527     NOHorizontalSlider->setRange(tmin,tmax);
2528     NOHorizontalSlider->setValue(tPosition);
2529   } else if (slicer == 1) {
2530     NEVerticalSlider->setValue(position);
2531     NEVerticalSlider->setRange(min,max);
2532     NEHorizontalSlider->setRange(tmin,tmax);
2533     NEHorizontalSlider->setValue(tPosition);
2534   } else if (slicer == 2) {
2535     SOVerticalSlider->setValue(position);
2536     SOVerticalSlider->setRange(min,max);
2537     SOHorizontalSlider->setRange(tmin,tmax);
2538     SOHorizontalSlider->setValue(tPosition);
2539   } else if (slicer == 3) {
2540     SEVerticalSlider->setValue(position);
2541     SEVerticalSlider->setRange(min,max);
2542     SEHorizontalSlider->setRange(tmin,tmax);
2543     SEHorizontalSlider->setValue(tPosition);
2544   }
2545 }
2546 //------------------------------------------------------------------------------
2547
2548
2549 //------------------------------------------------------------------------------
2550 void vvMainWindow::SaveNOScreenshot()
2551 {
2552   SaveScreenshot(NOViewWidget);
2553 }
2554 //------------------------------------------------------------------------------
2555
2556
2557 //------------------------------------------------------------------------------
2558 void vvMainWindow::SaveNEScreenshot()
2559 {
2560   SaveScreenshot(NEViewWidget);
2561 }
2562 //------------------------------------------------------------------------------
2563
2564
2565 //------------------------------------------------------------------------------
2566 void vvMainWindow::SaveSOScreenshot()
2567 {
2568   SaveScreenshot(SOViewWidget);
2569 }
2570 //------------------------------------------------------------------------------
2571
2572
2573 //------------------------------------------------------------------------------
2574 void vvMainWindow::SaveSEScreenshot()
2575 {
2576   SaveScreenshot(SEViewWidget);
2577 }
2578 //------------------------------------------------------------------------------
2579
2580
2581 //------------------------------------------------------------------------------
2582 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
2583 {
2584   QString Extensions = "Images( *.png);;";
2585   Extensions += "Images( *.jpg);;";
2586   Extensions += "Images( *.bmp);;";
2587   Extensions += "Images( *.tif);;";
2588   Extensions += "Images( *.ppm)";
2589 #ifdef VTK_USE_FFMPEG_ENCODER
2590   Extensions += "Images( *.avi)";
2591 #endif
2592 #ifdef VTK_USE_MPEG2_ENCODER
2593   Extensions += "Images( *.mpg)";
2594 #endif
2595
2596   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2597   QString fileName = QFileDialog::getSaveFileName(this,
2598                      tr("Save As"),
2599                      itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
2600                      Extensions);
2601
2602   if (!fileName.isEmpty()) {
2603     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2604     w2i->SetInput(widget->GetRenderWindow());
2605     w2i->Update();
2606     vtkImageData *image = w2i->GetOutput();
2607
2608     const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2609     if (!strcmp(ext, ".bmp")) {
2610       vtkBMPWriter *bmp = vtkBMPWriter::New();
2611       bmp->SetInput(image);
2612       bmp->SetFileName(fileName.toStdString().c_str());
2613       bmp->Write();
2614       bmp->Delete();
2615     } else if (!strcmp(ext, ".tif")) {
2616       vtkTIFFWriter *tif = vtkTIFFWriter::New();
2617       tif->SetInput(image);
2618       tif->SetFileName(fileName.toStdString().c_str());
2619       tif->Write();
2620       tif->Delete();
2621     } else if (!strcmp(ext, ".ppm")) {
2622       vtkPNMWriter *pnm = vtkPNMWriter::New();
2623       pnm->SetInput(image);
2624       pnm->SetFileName(fileName.toStdString().c_str());
2625       pnm->Write();
2626       pnm->Delete();
2627     } else if (!strcmp(ext, ".png")) {
2628       vtkPNGWriter *png = vtkPNGWriter::New();
2629       png->SetInput(image);
2630       png->SetFileName(fileName.toStdString().c_str());
2631       png->Write();
2632       png->Delete();
2633     } else if (!strcmp(ext, ".jpg")) {
2634       vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2635       jpg->SetInput(image);
2636       jpg->SetFileName(fileName.toStdString().c_str());
2637       jpg->Write();
2638       jpg->Delete();
2639 #ifdef VTK_USE_FFMPEG_ENCODER
2640     } else if (!strcmp(ext, ".avi")) {
2641       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
2642       mpg->SetInput(image);
2643       mpg->SetFileName(fileName.toStdString().c_str());
2644       mpg->SetQuality(2);
2645       mpg->SetRate(5);
2646       mpg->Start();
2647
2648       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2649       int nSlice = vvImg->GetVTKImages().size();
2650       for(int i=0; i<nSlice; i++)
2651       {
2652         mSlicerManagers[smIndex]->SetNextTSlice(0);
2653         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2654         w2i->SetInput(widget->GetRenderWindow());
2655         w2i->Update();
2656         mpg->SetInput(w2i->GetOutput());
2657         mpg->Write();
2658       }
2659       mpg->End();
2660       mpg->Delete();
2661 #endif
2662 #ifdef VTK_USE_MPEG2_ENCODER
2663     } else if (!strcmp(ext, ".mpg")) {
2664       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
2665       mpg->SetInput(image);
2666       mpg->SetFileName(fileName.toStdString().c_str());
2667       mpg->Start();
2668
2669       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2670       int nSlice = vvImg->GetVTKImages().size();
2671       for(int i=0; i<nSlice; i++)
2672       {
2673         mSlicerManagers[smIndex]->SetNextTSlice(0);
2674         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2675         w2i->SetInput(widget->GetRenderWindow());
2676         w2i->Update();
2677         mpg->SetInput(w2i->GetOutput());
2678         mpg->Write();
2679       }
2680       mpg->End();
2681       mpg->Delete();
2682 #endif
2683     } else {
2684       QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2685     }
2686   }
2687 }
2688 //------------------------------------------------------------------------------
2689
2690
2691 //------------------------------------------------------------------------------
2692 void vvMainWindow::GoToCursor()
2693 {
2694   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2695   for (int column = 1; column < 5; column++) {
2696     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
2697       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2698       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2699         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2700       mSlicerManagers[index]->UpdateViews(1,column-1);
2701       mSlicerManagers[index]->UpdateLinked(column-1);
2702       break;
2703     }
2704   }
2705 }
2706 //------------------------------------------------------------------------------
2707
2708 //------------------------------------------------------------------------------
2709 void vvMainWindow::PlayPause()
2710 {
2711   if (playMode) {
2712     playMode = 0;
2713     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2714     ImageInfoChanged();
2715     return;
2716   } else {
2717     int image_number=DataTree->topLevelItemCount();
2718     bool has_temporal;
2719     for (int i=0; i<image_number; i++)
2720       if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1) {
2721         has_temporal=true;
2722         break;
2723       }
2724     if (has_temporal) {
2725       playMode = 1;
2726       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2727       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2728     }
2729   }
2730 }
2731 //------------------------------------------------------------------------------
2732
2733 //------------------------------------------------------------------------------
2734 void vvMainWindow::PlayNext()
2735 {
2736   if (playMode && !this->isHidden()) {
2737     int image_number=DataTree->topLevelItemCount();
2738     ///Only play one slicer per SM, and only if the SM is being displayed
2739     for (int i=0; i<image_number; i++)
2740       for (int j=0; j<4; j++)
2741         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2742             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
2743           mSlicerManagers[i]->SetNextTSlice(j);
2744           break;
2745         }
2746     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2747   }
2748 }
2749 //------------------------------------------------------------------------------
2750
2751 void vvMainWindow::ShowLastImage()
2752 {
2753   if (mSlicerManagers.size() > 1) {
2754     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2755     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2756     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2757     DisplayChanged(item,1);
2758   }
2759 }
2760
2761 //------------------------------------------------------------------------------
2762 void vvMainWindow::UpdateRenderWindows()
2763 {
2764   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2765   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2766   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2767   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2768 }
2769 //------------------------------------------------------------------------------
2770
2771 //------------------------------------------------------------------------------
2772 void vvMainWindow::SegmentationOnCurrentImage()
2773 {
2774   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2775
2776   vvSegmentationDialog segmentation;
2777   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2778   segmentation.exec();
2779 }
2780 //------------------------------------------------------------------------------
2781
2782 void vvMainWindow::SurfaceViewerLaunch()
2783 {
2784   vvSurfaceViewerDialog surfaceViewer;
2785   surfaceViewer.exec();
2786 }
2787 //------------------------------------------------------------------------------
2788
2789
2790 //------------------------------------------------------------------------------
2791 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
2792 {
2793   int number=0;
2794   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
2795     vvSlicerManager * v = mSlicerManagers[l];
2796     if (v->GetBaseFileName() ==
2797         vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
2798       number = std::max(number, v->GetBaseFileNameNumber()+1);
2799     }
2800   }
2801   return number;
2802 }
2803 //------------------------------------------------------------------------------
2804
2805
2806 //------------------------------------------------------------------------------
2807 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2808 {
2809   // Change filename if another image exist with the same name
2810   int number = GetImageDuplicateFilenameNumber(filename);
2811
2812   // Create new SliceManager
2813   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
2814   slicer_manager->SetImage(image);//, IMAGE, number);
2815   //  filename = filename+"_"+clitk::toString(number);
2816   slicer_manager->SetFilename(filename, number);
2817   mSlicerManagers.push_back(slicer_manager);
2818
2819   //create an item in the tree with good settings
2820   QTreeWidgetItem *item = new QTreeWidgetItem();
2821   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2822   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
2823   qApp->processEvents();
2824
2825   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2826
2827   //Create the buttons for reload and close
2828   qApp->processEvents();
2829   QTreePushButton* cButton = new QTreePushButton;
2830   cButton->setItem(item);
2831   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2832   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2833   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2834           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2835
2836   QTreePushButton* rButton = new QTreePushButton;
2837   rButton->setItem(item);
2838   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2839   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2840   rButton->setEnabled(0);
2841   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2842           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2843
2844   DataTree->addTopLevelItem(item);
2845   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2846   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2847
2848   //set the id of the image
2849   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2850   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2851   mSlicerManagers.back()->SetId(id.toStdString());
2852
2853   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
2854                       , id.toStdString());
2855
2856   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
2857           this, SLOT(CurrentImageChanged(std::string)));
2858   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
2859           this, SLOT(CurrentPickedImageChanged(std::string)));
2860   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
2861           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2862   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
2863           this, SLOT(VectorChanged(int,double,double,double, double)));
2864   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
2865           this, SLOT(OverlayChanged(int,double,double)));
2866   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
2867           this, SLOT(FusionChanged(int,double)));
2868   connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
2869           this,SLOT(WindowsChanged(int, int, int)));
2870   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
2871           this,SLOT(WindowLevelChanged(double, double, int, int)));
2872   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
2873           this,SLOT(UpdateSlice(int,int)));
2874   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
2875           this,SLOT(UpdateTSlice(int, int)));
2876   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2877           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2878   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2879           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2880   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
2881           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
2882   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
2883           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
2884   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2885   UpdateTree();
2886   qApp->processEvents();
2887   InitSlicers();
2888   ShowLastImage();
2889   InitDisplay();
2890   qApp->processEvents();
2891
2892   // End
2893   ImageInfoChanged();
2894   return slicer_manager;
2895 }
2896 //------------------------------------------------------------------------------
2897
2898
2899 //------------------------------------------------------------------------------
2900 void vvMainWindow::UpdateCurrentSlicer()
2901 {
2902   int index = -1;
2903   if (DataTree->selectedItems().size() > 0) {
2904     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2905   }
2906   mSlicerManagerCurrentIndex = index;
2907 }
2908 //------------------------------------------------------------------------------
2909