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
  26 // VV include
  27 #include "vvMainWindow.h"
  28 #include "vvHelpDialog.h"
  29 #include "vvRegisterForm.h"
  30 #include "vvDocumentation.h"
  31 #include "vvProgressDialog.h"
  32 #include "vvQDicomSeriesSelector.h"
  33 #include "vvSlicerManager.h"
  34 #include "clitkImageCommon.h"
  35 #include "vvSlicer.h"
  36 #include "vvInteractorStyleNavigator.h"
  37 #include "vvImageWriter.h"
  38 #include "vvSegmentationDialog.h"
  39 #include "vvSurfaceViewerDialog.h"
  40 #include "vvDeformationDialog.h"
  41 #include "vvImageWarp.h"
  42 #include "vvUtils.h"
  43 #include "vvMidPosition.h"
  44 #include "vvMesh.h"
  45 #include "vvStructSelector.h"
  46 #include "vvMeshReader.h"
  47 #include "clitkConfiguration.h"
  48
  49 // ITK include
  50 #include <itkImage.h>
  51 #include <itkImageFileReader.h>
  52 #include <itkByteSwapper.h>
  53 #include <itkCommand.h>
  54 #include <itkNumericSeriesFileNames.h>
  55
  56 // VTK include
  57 #include <vtkImageData.h>
  58 #include <vtkImageActor.h>
  59 #include <vtkCornerAnnotation.h>
  60 #include <vtkRenderWindow.h>
  61 #include <vtkRenderWindowInteractor.h>
  62 #include <vtkRenderer.h>
  63 #include <vtkRendererCollection.h>
  64 #include <vtkWindowToImageFilter.h>
  65 #include <vtkBMPWriter.h>
  66 #include <vtkTIFFWriter.h>
  67 #include <vtkPNMWriter.h>
  68 #include <vtkPNGWriter.h>
  69 #include <vtkJPEGWriter.h>
  70 #include <vtkFFMPEGWriter.h>
  71 #ifdef VTK_USE_MPEG2_ENCODER
  72   #include <vtkMPEG2Writer.h>
  73 #endif
  74 #include <vtkMatrix4x4.h>
  75 #include <vtkTransform.h>
  76
  77 // Standard includes
  78 #include <iostream>
  79 #include <sstream>
  80 #include <iomanip>
  81
  82 #define COLUMN_TREE 0
  83 #define COLUMN_UL_VIEW 1
  84 #define COLUMN_UR_VIEW 2
  85 #define COLUMN_DL_VIEW 3
  86 #define COLUMN_DR_VIEW 4
  87 #define COLUMN_CLOSE_IMAGE 5
  88 #define COLUMN_RELOAD_IMAGE 6
  89 #define COLUMN_IMAGE_NAME 7
  90
  91 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN )"
  92
  93 /*Data Tree values
  94   0,Qt::UserRole full filename
  95   1,Qt::CheckStateRole checkbutton UL View
  96   1,Qt::UserRole overlay, fusion or vector
  97   2,Qt::CheckStateRole checkbutton UR View
  98   3,Qt::CheckStateRole checkbutton DL View
  99   4,Qt::CheckStateRole checkbutton DR View
 100   5,0  short filename
 101   5,Qt::UserRole mSlicerManager id*/
 102
 103 //------------------------------------------------------------------------------
 104 vvMainWindow::vvMainWindow():vvMainWindowBase()
 105 {
 106   setupUi(this); // this sets up the GUI
 107
 108   mInputPathName = "";
 109   mMenuTools = menuTools;
 110   //  mMenuSegmentation = menuSegmentation;
 111   mContextMenu = &contextMenu;
 112   mMenuExperimentalTools = menuExperimental;
 113   mMainWidget = this;
 114   mCurrentTime = -1;
 115   mCurrentSelectedImageId = "";
 116   mCurrentPickedImageId = "";
 117   mCurrentPickedImageIndex = 0;
 118
 119   //Init the contextMenu
 120   this->setContextMenuPolicy(Qt::CustomContextMenu);
 121   contextActions.resize(0);
 122   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 123                                   tr("O&pen new Image"));
 124   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 125   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 126   contextActions.push_back(actionOpen_new_image);
 127   contextMenu.addSeparator();
 128
 129   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 130                                tr("Close Current Image"));
 131   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 132   contextActions.push_back(actionClose_Image);
 133
 134   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 135                                 tr("Reload Current Image"));
 136   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 137   contextActions.push_back(actionReload_image);
 138
 139   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 140                               tr("Save Current Image"));
 141   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 142   contextActions.push_back(actionSave_image);
 143
 144   contextMenu.addSeparator();
 145
 146   contextMenu.addAction(actionAdd_VF_to_current_Image);
 147   contextActions.push_back(actionAdd_VF_to_current_Image);
 148
 149   QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 150       tr("Add overlay image to current image"));
 151   contextMenu.addAction(actionAdd_Overlay_to_current_Image);
 152   contextActions.push_back(actionAdd_Overlay_to_current_Image);
 153
 154   connect(actionAdd_Overlay_to_current_Image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 155
 156   contextMenu.addAction(actionAdd_fusion_image);
 157   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 158   contextActions.push_back(actionAdd_fusion_image);
 159
 160   // TRIAL DS
 161   /*
 162   QMenu * m = new QMenu(menubar);
 163   m->setTitle("TOTO");
 164   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 165   contextMenu.addMenu(m);
 166   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 167                      tr("BIDON"));
 168   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 169                      tr("BIDON2"));
 170   m->addAction(a);
 171   m->addAction(b);
 172   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 173   */
 174
 175   //init the DataTree
 176   mSlicerManagers.resize(0);
 177
 178   QStringList header;
 179   header.append("");
 180   header.append("TL");
 181   header.append("TR");
 182   header.append("BL");
 183   header.append("BR");
 184   header.append("");
 185   header.append("");
 186   header.append("Name");
 187
 188   DataTree->setHeaderLabels(header);
 189   DataTree->resizeColumnToContents(COLUMN_TREE);
 190   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 191   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 192   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 193   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 194   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 195   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 196   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 197
 198   viewMode = 1;
 199   documentation = new vvDocumentation();
 200   help_dialog = new vvHelpDialog();
 201   dicomSeriesSelector = new vvDicomSeriesSelector();
 202
 203   inverseButton->setEnabled(0);
 204   actionAdd_Overlay_to_current_Image->setEnabled(0);
 205   actionSave_As->setEnabled(0);
 206   actionAdd_VF_to_current_Image->setEnabled(0);
 207   actionAdd_fusion_image->setEnabled(0);
 208
 209   //init the sliders
 210   verticalSliders.push_back(NOVerticalSlider);
 211   verticalSliders.push_back(NEVerticalSlider);
 212   verticalSliders.push_back(SOVerticalSlider);
 213   verticalSliders.push_back(SEVerticalSlider);
 214
 215   for (int i =0; i < 4; i++)
 216     verticalSliders[i]->hide();
 217
 218   horizontalSliders.push_back(NOHorizontalSlider);
 219   horizontalSliders.push_back(NEHorizontalSlider);
 220   horizontalSliders.push_back(SOHorizontalSlider);
 221   horizontalSliders.push_back(SEHorizontalSlider);
 222
 223   for (int i =0; i < 4; i++)
 224     horizontalSliders[i]->hide();
 225
 226
 227   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 228   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 229   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 230   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 231
 232   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 233   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 234   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 235   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 236
 237   //connect everything
 238   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 239   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 240   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 241   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 242   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 243   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 244   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 245   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 246   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 247   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 248   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 249   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 250   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 251   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 252   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 253   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 254
 255   ///////////////////////////////////////////////
 256   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 257   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 258   ///////////////////////////////////////////////
 259
 260   actionNorth_East_Window->setEnabled(0);
 261   actionNorth_West_Window->setEnabled(0);
 262   actionSouth_East_Window->setEnabled(0);
 263   actionSouth_West_Window->setEnabled(0);
 264
 265   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 266   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 267   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 268   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 269
 270   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 271   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 272           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 273
 274   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 275   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 276   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 277   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 278   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 279   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 280   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 281
 282
 283   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 284
 285   connect(linkPanel,SIGNAL(addLink(QString,QString)),this,SLOT(AddLink(QString,QString)));
 286   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 287   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 288   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int)),this,SLOT(SetOverlayProperty(int)));
 289   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,double,double)),
 290           this,SLOT(SetFusionProperty(int,int,double,double)));
 291   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 292
 293   playMode = 0;//pause
 294   mFrameRate = 10;
 295   playButton->setEnabled(0);
 296   frameRateLabel->setEnabled(0);
 297   frameRateSpinBox->setEnabled(0);
 298   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 299   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 300
 301   goToCursorPushButton->setEnabled(0);
 302   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 303
 304   NOViewWidget->hide();
 305   NEViewWidget->hide();
 306   SOViewWidget->hide();
 307   SEViewWidget->hide();
 308
 309   //Recently opened files
 310   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 311   recentlyOpenedFilesMenu=NULL;
 312   if ( !recent_files.empty() ) {
 313     createRecentlyOpenedFilesMenu();
 314     updateRecentlyOpenedFilesMenu(recent_files);
 315   }
 316
 317   // Adding all new tools (insertion in the menu)
 318   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 319
 320   if (!CLITK_EXPERIMENTAL)
 321     menuExperimental->menuAction()->setVisible(false);
 322
 323
 324   QTimer * timerMemory = new QTimer(this);
 325   //timerMemory->setInterval(5);
 326   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 327   timerMemory->start(2000);
 328
 329
 330   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://localhost/vvregister/write.php"));
 331   registerForm->show();
 332
 333 }
 334 //------------------------------------------------------------------------------
 335
 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 void vvMainWindow::ShowHelpDialog()
1219 {
1220   help_dialog->show();
1221 }
1222 //------------------------------------------------------------------------------
1223
1224 //------------------------------------------------------------------------------
1225 void vvMainWindow::ChangeViewMode()
1226 {
1227   QListIterator<int> it0(splitter_3->sizes());
1228   QListIterator<int> it1(splitter_3->sizes());
1229   int max0 = 0;
1230   int max1 = 1;
1231   while (it0.hasNext()) {
1232     max0 += it0.next();
1233   }
1234   while (it1.hasNext()) {
1235     max1 += it1.next();
1236   }
1237   QList<int> size0;
1238   QList<int> size1;
1239   if (viewMode == 1) {
1240     viewMode = 0;
1241     size0.push_back(max0);
1242     size0.push_back(0);
1243     size1.push_back(max1);
1244     size1.push_back(0);
1245     splitter_3->setSizes(size0);
1246     OSplitter->setSizes(size1);
1247     DataTree->setColumnHidden(2,1);
1248     DataTree->setColumnHidden(3,1);
1249     DataTree->setColumnHidden(4,1);
1250   } else {
1251     viewMode = 1;
1252     size0.push_back(int(max0/2));
1253     size0.push_back(int(max0/2));
1254     size1.push_back(int(max1/2));
1255     size1.push_back(int(max1/2));
1256     splitter_3->setSizes(size0);
1257     OSplitter->setSizes(size1);
1258     DataTree->setColumnHidden(2,0);
1259     DataTree->setColumnHidden(3,0);
1260     DataTree->setColumnHidden(4,0);
1261   }
1262 }
1263 //------------------------------------------------------------------------------
1264
1265 //------------------------------------------------------------------------------
1266 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1267 {
1268   QString result = "";// QString::number(size);
1269   //result += " bytes (";
1270   if (size > 1000000000) {
1271     size /= 1000000000;
1272     result += QString::number(size);
1273     result += "Gb";//)";
1274   } else if (size > 1000000) {
1275     size /= 1000000;
1276     result += QString::number(size);
1277     result += "Mb";//)";
1278   } else if (size > 1000) {
1279     size /= 1000;
1280     result += QString::number(size);
1281     result += "kb";//)";
1282   }
1283   return result;
1284 }
1285 //------------------------------------------------------------------------------
1286
1287 //------------------------------------------------------------------------------
1288 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix)
1289 {
1290   std::ostringstream strmatrix;
1291
1292   for (unsigned int i = 0; i < 4; i++) {
1293     for (unsigned int j = 0; j < 4; j++) {
1294       strmatrix.flags(ios::showpos);
1295       strmatrix.width(10);
1296       strmatrix.precision(3);
1297       strmatrix.setf(ios::fixed,ios::floatfield);
1298       strmatrix.fill(' ');
1299       strmatrix << std::left << matrix->GetElement(i, j);
1300       //strmatrix.width(10);
1301       strmatrix << " ";
1302     }
1303     strmatrix << std::endl;
1304   }
1305   QString result = strmatrix.str().c_str();
1306   return result;
1307 }
1308 //------------------------------------------------------------------------------
1309
1310 //------------------------------------------------------------------------------
1311 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1312 {
1313   QString result;
1314   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1315     if (i != 0)
1316       result += " ";
1317     result += QString::number(vectorDouble[i]);
1318   }
1319   return result;
1320 }
1321 //------------------------------------------------------------------------------
1322
1323 //------------------------------------------------------------------------------
1324 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1325 {
1326   QString result;
1327   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1328     if (i != 0)
1329       result += " ";
1330     result += QString::number(vectorInt[i]);
1331   }
1332   return result;
1333 }
1334 //------------------------------------------------------------------------------
1335
1336 //------------------------------------------------------------------------------
1337 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1338 {
1339   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1340   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1341     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1342       return i;
1343   }
1344   return -1;
1345 }
1346 //------------------------------------------------------------------------------
1347
1348 //------------------------------------------------------------------------------
1349 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1350 {
1351   QString id = sm->GetId().c_str();
1352   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1353     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1354       return DataTree->topLevelItem(i);
1355   }
1356   return NULL;
1357 }
1358 //------------------------------------------------------------------------------
1359
1360 //------------------------------------------------------------------------------
1361 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clicked_item, int column)
1362 {
1363   int index = GetSlicerIndexFromItem(clicked_item);
1364   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1365     return;
1366   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1367     //Trick to avoid redoing twice the job for a key (sr)
1368     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()-> GetInteractor()->SetKeySym("Crap");
1369
1370     QTreeWidgetItem* current_row=DataTree->topLevelItem(i);
1371     if (DataTree->topLevelItem(index) == current_row) {
1372       vvSlicer* clicked_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1373       if (current_row == clicked_item) {
1374         //If we just activated a slicer
1375         if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1376           mSlicerManagers[i]->UpdateSlicer(column-1,clicked_item->data(column,Qt::CheckStateRole).toInt());
1377           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1378           DisplaySliders(i,column-1);
1379           std::map<std::string,int> overlay_counts;
1380           for (int child = 0; child < current_row->childCount(); child++) {
1381             std::string overlay_type =
1382               current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1383             overlay_counts[overlay_type]++;
1384             current_row->child(child)->setData(column,Qt::CheckStateRole,
1385                                                current_row->data(column,Qt::CheckStateRole));
1386             clicked_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,true);
1387           }
1388         } else { //We don't allow simply desactivating a slicer
1389           clicked_item->setData(column,Qt::CheckStateRole,2);
1390           return;
1391         }
1392       }
1393       //if we clicked on the vector(or overlay) and not the image
1394       else {
1395         if (clicked_item->data(column,Qt::CheckStateRole).toInt()) {
1396           current_row->setData(column,Qt::CheckStateRole,2);
1397           mSlicerManagers[i]->UpdateSlicer(column-1,2);
1398           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1399           DisplaySliders(i,column-1);
1400         }
1401         int vis = clicked_item->data(column,Qt::CheckStateRole).toInt();
1402         std::string overlay_type = clicked_item->data(1,Qt::UserRole).toString().toStdString();
1403         int overlay_index=0;
1404         for (int child = 0; child < current_row->childCount(); child++) {
1405           if (current_row->child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1406             overlay_index++;
1407           if (current_row->child(child) == clicked_item) break;
1408         }
1409         clicked_slicer->SetActorVisibility(
1410           clicked_item->data(1,Qt::UserRole).toString().toStdString(), overlay_index-1,vis);
1411       }
1412     } else if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1413       current_row->setData(column,Qt::CheckStateRole,0);
1414       mSlicerManagers[i]->UpdateSlicer(column-1,0);
1415       std::map<std::string,int> overlay_counts;
1416       for (int child = 0; child < current_row->childCount(); child++) {
1417         std::string overlay_type =
1418           current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1419         overlay_counts[overlay_type]++;
1420         current_row->child(child)->setData(column,Qt::CheckStateRole,0);
1421         vvSlicer * current_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1422         current_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,false);
1423       }
1424     }
1425     //mSlicerManagers[i]->SetColorMap(-1);
1426     mSlicerManagers[i]->SetColorMap();
1427   }
1428   mSlicerManagers[index]->GetSlicer(column-1)->Render();
1429 }
1430 //------------------------------------------------------------------------------
1431
1432 void vvMainWindow::InitSlicers()
1433 {
1434   if (mSlicerManagers.size()) {
1435     mSlicerManagers.back()->GenerateDefaultLookupTable();
1436
1437     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1438     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1439     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1440     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1441   }
1442 }
1443
1444 //------------------------------------------------------------------------------
1445 void vvMainWindow::InitDisplay()
1446 {
1447   if (mSlicerManagers.size()) {
1448     //BE CAREFUL : this is absolutely necessary to set the interactor style
1449     //in order to have the same style instanciation for all SlicerManagers in
1450     // a same window
1451     for (int j = 0; j < 4; j++) {
1452       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1453       style->SetAutoAdjustCameraClippingRange(1);
1454       bool AlreadySelected = false;
1455       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1456         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1457
1458         //select the image only if previous are not selected
1459         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1460           mSlicerManagers[i]->UpdateSlicer(j,1);
1461           AlreadySelected = true;
1462         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1463           if (DataTree->selectedItems().size() == 0)
1464             DataTree->topLevelItem(i)->setSelected(1);
1465           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1466           mSlicerManagers[i]->UpdateSlicer(j,1);
1467           DisplaySliders(i,j);
1468         } else {
1469           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1470           mSlicerManagers[i]->UpdateSlicer(j,0);
1471         }
1472       }
1473       style->Delete();
1474     }
1475   }
1476 }
1477 //------------------------------------------------------------------------------
1478
1479 //------------------------------------------------------------------------------
1480 void vvMainWindow::DisplaySliders(int slicer, int window)
1481 {
1482   int range[2];
1483   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1484   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1485
1486   int tRange[2];
1487   tRange[0] = 0;
1488   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1489   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1490   bool showHorizontal = false;
1491   bool showVertical = false;
1492   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1493       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1494           && mSlicerManagers[slicer]->GetType() != vvImageReader::IMAGEWITHTIME
1495           && mSlicerManagers[slicer]->GetType() != vvImageReader::MERGEDWITHTIME))
1496     showVertical = true;
1497   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1498       || mSlicerManagers[slicer]->GetType() == vvImageReader::IMAGEWITHTIME
1499       || mSlicerManagers[slicer]->GetType() == vvImageReader::MERGEDWITHTIME)
1500     showHorizontal = true;
1501
1502   if (showVertical)
1503     verticalSliders[window]->show();
1504   else
1505     verticalSliders[window]->hide();
1506   verticalSliders[window]->setRange(range[0],range[1]);
1507   verticalSliders[window]->setValue(position);
1508
1509   if (showHorizontal)
1510     horizontalSliders[window]->show();
1511   else
1512     horizontalSliders[window]->hide();
1513   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1514   horizontalSliders[window]->setValue(tPosition);
1515 }
1516 //------------------------------------------------------------------------------
1517
1518 //------------------------------------------------------------------------------
1519 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1520 {
1521   int index = GetSlicerIndexFromItem(item);
1522
1523   if (DataTree->topLevelItem(index) != item) {
1524     QString warning = "Do you really want to close the overlay : ";
1525     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1526     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1527                        warning, 0, this);
1528     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1529     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1530     if (msgBox.exec() == QMessageBox::AcceptRole) {
1531       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1532       int overlay_index=0;
1533       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1534         if (DataTree->topLevelItem(index)->\
1535             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1536           overlay_index++;
1537         if (DataTree->topLevelItem(index)->child(child) == item) break;
1538       }
1539       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1540       mSlicerManagers[index]->SetColorMap(0);
1541       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1542       mSlicerManagers[index]->Render();
1543     }
1544   } else if (DataTree->topLevelItemCount() <= 1) {
1545     QString warning = "Do you really want to close the image : ";
1546     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1547     warning += "\nThis is the last image, you're about to close vv !!!";
1548     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1549                        warning, 0, this);
1550     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1551     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1552     if (msgBox.exec() == QMessageBox::AcceptRole) {
1553       this->close();
1554     }
1555   } else {
1556     QString warning = "Do you really want to close the image : ";
1557     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1558     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1559                        warning, 0, this);
1560     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1561     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1562     if (msgBox.exec() == QMessageBox::AcceptRole) {
1563
1564       // Tell tools that we close an image
1565       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1566
1567       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1568       DataTree->takeTopLevelItem(index);
1569       for (int i = 0; i < index; i++) {
1570         Manageriter++;
1571       }
1572       linkPanel->removeImage(index);
1573       mSlicerManagers[index]->RemoveActors();
1574       delete mSlicerManagers[index];
1575       mSlicerManagers.erase(Manageriter);
1576
1577       //
1578       InitDisplay();
1579     }
1580   }
1581   ImageInfoChanged();
1582 }
1583 //------------------------------------------------------------------------------
1584
1585 //------------------------------------------------------------------------------
1586 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1587 {
1588   // int index = GetSlicerIndexFromItem(item);
1589   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1590   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1591   //     mSlicerManagers[index]->ReloadVF();
1592   //   else
1593   //     mSlicerManagers[index]->Reload();
1594
1595   //   QApplication::restoreOverrideCursor();
1596   int index = GetSlicerIndexFromItem(item);
1597   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1598   QString role=item->data(1,Qt::UserRole).toString();
1599   if ( role == "vector")
1600     mSlicerManagers[index]->ReloadVF();
1601   else if (role == "overlay")
1602     mSlicerManagers[index]->ReloadOverlay();
1603   else if (role == "fusion")
1604     mSlicerManagers[index]->ReloadFusion();
1605   else
1606     mSlicerManagers[index]->Reload();
1607
1608   // Update view and info
1609   ImageInfoChanged();
1610   mSlicerManagers[index]->Render();
1611   QApplication::restoreOverrideCursor();
1612 }
1613 //------------------------------------------------------------------------------
1614
1615 //------------------------------------------------------------------------------
1616 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1617 {
1618   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1619 }
1620 //------------------------------------------------------------------------------
1621
1622 //------------------------------------------------------------------------------
1623 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1624 {
1625   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1626 }
1627 //------------------------------------------------------------------------------
1628
1629 //------------------------------------------------------------------------------
1630 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1631 {
1632   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1633 }
1634 //------------------------------------------------------------------------------
1635
1636 //------------------------------------------------------------------------------
1637 void vvMainWindow::FusionChanged(int visibility, double value)
1638 {
1639   overlayPanel->getCurrentFusionInfo(visibility,value);
1640 }
1641 //------------------------------------------------------------------------------
1642
1643 //------------------------------------------------------------------------------
1644 void vvMainWindow::WindowsChanged(int window, int view, int slice)
1645 {
1646   infoPanel->setViews(window, view, slice);
1647 }
1648 //------------------------------------------------------------------------------
1649
1650 //------------------------------------------------------------------------------
1651 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap)
1652 {
1653   windowSpinBox->setValue(window);
1654   levelSpinBox->setValue(level);
1655   colorMapComboBox->setCurrentIndex(colormap);
1656   presetComboBox->setCurrentIndex(preset);
1657 }
1658 //------------------------------------------------------------------------------
1659
1660 //------------------------------------------------------------------------------
1661 void vvMainWindow::WindowLevelEdited()
1662 {
1663   presetComboBox->setCurrentIndex(6);
1664   UpdateWindowLevel();
1665 }
1666 //------------------------------------------------------------------------------
1667
1668 //------------------------------------------------------------------------------
1669 void vvMainWindow::UpdateWindowLevel()
1670 {
1671   if (DataTree->selectedItems().size()) {
1672     if (presetComboBox->currentIndex() == 7) //For ventilation
1673       colorMapComboBox->setCurrentIndex(5);
1674     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1675     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1676     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1677     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1678     mSlicerManagers[index]->Render();
1679     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1680     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1681   }
1682 }
1683 //------------------------------------------------------------------------------
1684
1685 //------------------------------------------------------------------------------
1686 void vvMainWindow::UpdateColorMap()
1687 {
1688   if (DataTree->selectedItems().size()) {
1689     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1690     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1691     mSlicerManagers[index]->Render();
1692   }
1693 }
1694 //------------------------------------------------------------------------------
1695 void vvMainWindow::SwitchWindowLevel()
1696 {
1697   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1698   int window = mSlicerManagers[index]->GetColorWindow();
1699   presetComboBox->setCurrentIndex(6);
1700   windowSpinBox->setValue(-window);
1701   UpdateWindowLevel();
1702 }
1703 //------------------------------------------------------------------------------
1704
1705 //------------------------------------------------------------------------------
1706 void vvMainWindow::ApplyWindowLevelToAllImages()
1707 {
1708   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1709     if (mSlicerManagers[i] == NULL)
1710       continue;
1711     mSlicerManagers[i]->SetColorWindow(windowSpinBox->value());
1712     mSlicerManagers[i]->SetColorLevel(levelSpinBox->value());
1713     mSlicerManagers[i]->SetPreset(6);
1714     mSlicerManagers[i]->Render();
1715   }
1716 }
1717 //------------------------------------------------------------------------------
1718
1719 //------------------------------------------------------------------------------
1720 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1721 {
1722   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1723     if (mSlicerManagers[i]->GetId() == id) {
1724       //mSlicerManagers[i]->SetTSlice(temps);
1725       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1726       mSlicerManagers[i]->UpdateViews(0,slicer);
1727       break;
1728     }
1729   }
1730 }
1731 //------------------------------------------------------------------------------
1732
1733 //------------------------------------------------------------------------------
1734 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1735 {
1736   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1737     if (id == mSlicerManagers[i]->GetId()) {
1738       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1739     }
1740   }
1741 }
1742 //------------------------------------------------------------------------------
1743
1744 //------------------------------------------------------------------------------
1745 void vvMainWindow::ShowContextMenu(QPoint point)
1746 {
1747   if (!DataTree->selectedItems().size()) {
1748     contextActions[1]->setEnabled(0);
1749     contextActions[2]->setEnabled(0);
1750     contextActions[3]->setEnabled(0);
1751     contextActions[4]->setEnabled(0);
1752     contextActions[5]->setEnabled(0);
1753     contextActions[6]->setEnabled(0);
1754   } else {
1755     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1756     contextActions[1]->setEnabled(1);
1757     contextActions[2]->setEnabled(
1758       DataTree->itemWidget(DataTree->selectedItems()[0],
1759                            COLUMN_RELOAD_IMAGE)->isEnabled());
1760     contextActions[3]->setEnabled(1);
1761     contextActions[5]->setEnabled(1);
1762     contextActions[6]->setEnabled(1);
1763
1764     if (mSlicerManagers[index]->GetDimension() < 3)
1765       contextActions[4]->setEnabled(0);
1766     else
1767       contextActions[4]->setEnabled(1);
1768   }
1769   contextMenu.exec(QCursor::pos());
1770 }
1771 //------------------------------------------------------------------------------
1772
1773 //------------------------------------------------------------------------------
1774 void vvMainWindow::CloseImage()
1775 {
1776   CloseImage(DataTree->selectedItems()[0],0);
1777 }
1778 //------------------------------------------------------------------------------
1779
1780 //------------------------------------------------------------------------------
1781 void vvMainWindow::ReloadImage()
1782 {
1783   ReloadImage(DataTree->selectedItems()[0],0);
1784 }
1785 //------------------------------------------------------------------------------
1786
1787 //------------------------------------------------------------------------------
1788 void vvMainWindow::SelectOverlayImage()
1789 {
1790   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1791
1792   //check if one overlay image is added
1793   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1794     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1795       QString error = "Cannot add more than one compared image\n";
1796       error += "Please remove first ";
1797       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1798       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1799       return;
1800     }
1801
1802   QString Extensions = EXTENSIONS;
1803   Extensions += ";;All Files (*)";
1804   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1805   if (!file.isEmpty())
1806     AddOverlayImage(index,file);
1807 }
1808 //------------------------------------------------------------------------------
1809
1810 //------------------------------------------------------------------------------
1811 void vvMainWindow::AddOverlayImage(int index, QString file)
1812 {
1813
1814   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1815   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1816                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1817   reader->SetFileName(file.toStdString().c_str());
1818   reader->ReadImageInformation();
1819   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1820   int dimension = reader->GetNumberOfDimensions();
1821   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1822   vvProgressDialog progress("Opening " + file.toStdString());
1823   qApp->processEvents();
1824
1825   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1826   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component)) {
1827     //create an item in the tree with good settings
1828     QTreeWidgetItem *item = new QTreeWidgetItem();
1829     item->setData(0,Qt::UserRole,file.toStdString().c_str());
1830     item->setData(1,Qt::UserRole,tr("overlay"));
1831     QFileInfo fileinfo(file); //Do not show the path
1832     item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1833     item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1834     qApp->processEvents();
1835
1836     for (int j = 1; j <= 4; j++) {
1837       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1838       mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("overlay",0,
1839           DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1840     }
1841
1842     //Create the buttons for reload and close
1843     qApp->processEvents();
1844     QTreePushButton* cButton = new QTreePushButton;
1845     cButton->setItem(item);
1846     cButton->setColumn(COLUMN_CLOSE_IMAGE);
1847     cButton->setToolTip(tr("close image"));
1848     cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1849     connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1850             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1851
1852     QTreePushButton* rButton = new QTreePushButton;
1853     rButton->setItem(item);
1854     rButton->setColumn(COLUMN_RELOAD_IMAGE);
1855     rButton->setToolTip(tr("reload image"));
1856     rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1857     connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1858             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1859
1860     DataTree->topLevelItem(index)->setExpanded(1);
1861     DataTree->topLevelItem(index)->addChild(item);
1862     DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1863     DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1864
1865     //set the id of the image
1866     QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1867     item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1868     UpdateTree();
1869     qApp->processEvents();
1870     ImageInfoChanged();
1871     QApplication::restoreOverrideCursor();
1872   } else {
1873     QApplication::restoreOverrideCursor();
1874     QString error = "Cannot import the new image.\n";
1875     error += mSlicerManagers[index]->GetLastError().c_str();
1876     QMessageBox::information(this,tr("Problem reading image !"),error);
1877   }
1878 }
1879 //------------------------------------------------------------------------------
1880
1881
1882 //------------------------------------------------------------------------------
1883 void vvMainWindow::AddROI(int index, QString file)
1884 {
1885   /*
1886   // Get slice manager
1887
1888   // Load image
1889
1890   vvImageReader * mReader = new vvImageReader;
1891   mReader->SetInputFilename(filename.toStdString());
1892   mReader->Update(IMAGE);
1893   if (mReader->GetLastError().size() != 0) {
1894     std::cerr << "Error while reading " << filename.toStdString() << std::endl;
1895     QString error = "Cannot open file \n";
1896     error += mReader->GetLastError().c_str();
1897     QMessageBox::information(this,tr("Reading problem"),error);
1898     delete mReader;
1899     return;
1900   }
1901   vvImage::Pointer roi = mReader->GetOutput();
1902
1903   // Create roi in new tool
1904   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
1905   */
1906 }
1907 //------------------------------------------------------------------------------
1908
1909 //------------------------------------------------------------------------------
1910 void vvMainWindow::SelectFusionImage()
1911 {
1912   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1913
1914   //check if one fusion image is added
1915   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1916     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
1917       QString error = "Cannot add more than one fusion image\n";
1918       error += "Please remove first ";
1919       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1920       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1921       return;
1922     }
1923
1924   QString Extensions = EXTENSIONS;
1925   Extensions += ";;All Files (*)";
1926   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1927   if (!file.isEmpty())
1928     AddFusionImage(index,file);
1929 }
1930 //------------------------------------------------------------------------------
1931
1932 //------------------------------------------------------------------------------
1933 void vvMainWindow::AddFusionImage(int index, QString file)
1934 {
1935   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1936   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1937                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1938   reader->SetFileName(file.toStdString().c_str());
1939   reader->ReadImageInformation();
1940   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1941   if (reader) {
1942     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1943     vvProgressDialog progress("Opening fusion");
1944     qApp->processEvents();
1945
1946     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1947     if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1948                                           reader->GetNumberOfDimensions(), component)) {
1949       //create an item in the tree with good settings
1950       QTreeWidgetItem *item = new QTreeWidgetItem();
1951       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1952       item->setData(1,Qt::UserRole,tr("fusion"));
1953       QFileInfo fileinfo(filename.c_str()); //Do not show the path
1954       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1955       item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1956       qApp->processEvents();
1957
1958       for (int j = 1; j <= 4; j++) {
1959         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1960         mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("fusion",0,
1961             DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1962       }
1963
1964       //Create the buttons for reload and close
1965       qApp->processEvents();
1966       QTreePushButton* cButton = new QTreePushButton;
1967       cButton->setItem(item);
1968       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1969       cButton->setToolTip(tr("close image"));
1970       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1971       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1972               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1973
1974       QTreePushButton* rButton = new QTreePushButton;
1975       rButton->setItem(item);
1976       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1977       rButton->setToolTip(tr("reload image"));
1978       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1979       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1980               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1981
1982       DataTree->topLevelItem(index)->setExpanded(1);
1983       DataTree->topLevelItem(index)->addChild(item);
1984       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1985       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1986
1987       //set the id of the image
1988       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1989       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1990       UpdateTree();
1991       qApp->processEvents();
1992       ImageInfoChanged();
1993       QApplication::restoreOverrideCursor();
1994     } else {
1995       QApplication::restoreOverrideCursor();
1996       QString error = "Cannot import the new image.\n";
1997       error += mSlicerManagers[index]->GetLastError().c_str();
1998       QMessageBox::information(this,tr("Problem reading image !"),error);
1999     }
2000   } else {
2001     QString error = "Cannot import the new image.\n";
2002     QMessageBox::information(this,tr("Problem reading image !"),error);
2003   }
2004 }
2005 //------------------------------------------------------------------------------
2006
2007
2008 //------------------------------------------------------------------------------
2009 void vvMainWindow::OpenField()
2010 {
2011   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2012   //check if a vector field has already been added
2013   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2014     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
2015       QString error = "Cannot add more than one vector field\n";
2016       error += "Please remove first ";
2017       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2018       QMessageBox::information(this,tr("Problem adding vector field!"),error);
2019       return;
2020     }
2021
2022   QString Extensions = "Images ( *.mhd)";
2023   Extensions += ";;Images ( *.vf)";
2024   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2025   if (!file.isEmpty())
2026     AddField(file,index);
2027 }
2028 //------------------------------------------------------------------------------
2029
2030
2031 //------------------------------------------------------------------------------
2032 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2033 {
2034   //create an item in the tree with good settings
2035   QTreeWidgetItem *item = new QTreeWidgetItem();
2036   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2037   item->setData(1,Qt::UserRole,tr("vector"));
2038   QFileInfo fileinfo(filename); //Do not show the path
2039   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2040   item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
2041   qApp->processEvents();
2042
2043   for (int j = 1; j <= 4; j++) {
2044     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2045     mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("vector",0,
2046         DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
2047   }
2048
2049   //Create the buttons for reload and close
2050   qApp->processEvents();
2051   QTreePushButton* cButton = new QTreePushButton;
2052   cButton->setItem(item);
2053   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2054   cButton->setToolTip(tr("close vector field"));
2055   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2056   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2057           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2058
2059   QTreePushButton* rButton = new QTreePushButton;
2060   rButton->setItem(item);
2061   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2062   rButton->setToolTip(tr("reload vector field"));
2063   rButton->setEnabled(from_disk);
2064   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2065   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2066           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2067
2068   DataTree->topLevelItem(index)->setExpanded(1);
2069   DataTree->topLevelItem(index)->addChild(item);
2070   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2071   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2072
2073   //set the id of the image
2074   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2075   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2076   UpdateTree();
2077   qApp->processEvents();
2078   ImageInfoChanged();
2079   QApplication::restoreOverrideCursor();
2080 }
2081 //------------------------------------------------------------------------------
2082
2083
2084 //------------------------------------------------------------------------------
2085 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2086 {
2087   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2088   vvSlicerManager* imageManager = mSlicerManagers[index];
2089   if (imageManager->SetVF(vf,file.toStdString())) {
2090     AddFieldEntry(file,index,false);
2091   } else {
2092     QString error = "Cannot import the vector field for this image.\n";
2093     error += imageManager->GetLastError().c_str();
2094     QMessageBox::information(this,tr("Problem reading VF !"),error);
2095   }
2096   QApplication::restoreOverrideCursor();
2097 }
2098 //------------------------------------------------------------------------------
2099
2100
2101 //------------------------------------------------------------------------------
2102 void vvMainWindow::AddField(QString file,int index)
2103 {
2104   if (QFile::exists(file)) {
2105     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2106
2107     //init the progress events
2108     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2109     vvProgressDialog progress("Opening " + file.toStdString());
2110     qApp->processEvents();
2111
2112     //read the vector and put it in the current mSlicerManager
2113     vvSlicerManager* imageManager = mSlicerManagers[index];
2114     qApp->processEvents();
2115
2116     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2117     if (imageManager->SetVF(file.toStdString())) {
2118       imageManager->Render();
2119       AddFieldEntry(file,index,true);
2120     } else {
2121       QApplication::restoreOverrideCursor();
2122       QString error = "Cannot import the vector field for this image.\n";
2123       error += imageManager->GetLastError().c_str();
2124       QMessageBox::information(this,tr("Problem reading VF !"),error);
2125     }
2126   } else
2127     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2128
2129 }
2130 //------------------------------------------------------------------------------
2131
2132
2133 //------------------------------------------------------------------------------
2134 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2135 {
2136   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2137   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2138     for (int i = 0; i < 4; i++) {
2139       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2140       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2141       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2142       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2143       if (log > 0)
2144         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2145       else
2146         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2147     }
2148   }
2149 }
2150 //------------------------------------------------------------------------------
2151
2152
2153 //------------------------------------------------------------------------------
2154 void vvMainWindow::SetOverlayProperty(int color)
2155 {
2156   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2157   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2158     mSlicerManagers[index]->SetOverlayColor(color);
2159     mSlicerManagers[index]->SetColorMap(0);
2160     mSlicerManagers[index]->Render();
2161   }
2162 }
2163 //------------------------------------------------------------------------------
2164
2165 //------------------------------------------------------------------------------
2166 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level)
2167 {
2168   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2169   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2170     mSlicerManagers[index]->SetFusionOpacity(opacity);
2171     mSlicerManagers[index]->SetFusionColorMap(colormap);
2172     mSlicerManagers[index]->SetFusionWindow(window);
2173     mSlicerManagers[index]->SetFusionLevel(level);
2174     mSlicerManagers[index]->SetColorMap(0);
2175     mSlicerManagers[index]->Render();
2176   }
2177 }
2178 //------------------------------------------------------------------------------
2179
2180 //------------------------------------------------------------------------------
2181 void vvMainWindow::SaveAs()
2182 {
2183   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2184     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2185     return;
2186   }
2187
2188   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2189   int dimension = mSlicerManagers[index]->GetDimension();
2190   QStringList OutputListeFormat;
2191   OutputListeFormat.clear();
2192   if (dimension == 1) {
2193     OutputListeFormat.push_back(".mhd");
2194   }
2195   if (dimension == 2) {
2196     OutputListeFormat.push_back(".bmp");
2197     OutputListeFormat.push_back(".png");
2198     OutputListeFormat.push_back(".jpeg");
2199     OutputListeFormat.push_back(".tif");
2200     OutputListeFormat.push_back(".mhd");
2201     OutputListeFormat.push_back(".hdr");
2202     OutputListeFormat.push_back(".vox");
2203   } else if (dimension == 3) {
2204     OutputListeFormat.push_back(".mhd");
2205     OutputListeFormat.push_back(".hdr");
2206     OutputListeFormat.push_back(".vox");
2207   } else if (dimension == 4) {
2208     OutputListeFormat.push_back(".mhd");
2209   }
2210   QString Extensions = "AllFiles(*.*)";
2211   for (int i = 0; i < OutputListeFormat.count(); i++) {
2212     Extensions += ";;Images ( *";
2213     Extensions += OutputListeFormat[i];
2214     Extensions += ")";
2215   }
2216   QString fileName = QFileDialog::getSaveFileName(this,
2217                      tr("Save As"),
2218                      mSlicerManagers[index]->GetFileName().c_str(),
2219                      Extensions);
2220   if (!fileName.isEmpty()) {
2221     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2222     if (OutputListeFormat.contains(
2223           fileformat.c_str())) {
2224       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2225       std::string action = "Saving";
2226       vvProgressDialog progress("Saving "+fileName.toStdString());
2227       qApp->processEvents();
2228       vvImageWriter::Pointer writer = vvImageWriter::New();
2229       writer->SetOutputFileName(fileName.toStdString());
2230       writer->SetInput(mSlicerManagers[index]->GetImage());
2231       writer->Update();
2232       QApplication::restoreOverrideCursor();
2233       if (writer->GetLastError().size()) {
2234         QString error = "Saving did not succeed\n";
2235         error += writer->GetLastError().c_str();
2236         QMessageBox::information(this,tr("Saving Problem"),error);
2237         SaveAs();
2238       }
2239     } else {
2240       QString error = fileformat.c_str();
2241       if (error.isEmpty())
2242         error += "no file format specified !";
2243       else
2244         error += " format unknown !!!\n";
2245       QMessageBox::information(this,tr("Saving Problem"),error);
2246       SaveAs();
2247     }
2248   }
2249 }
2250 //------------------------------------------------------------------------------
2251
2252
2253 //------------------------------------------------------------------------------
2254 void vvMainWindow::AddLink(QString image1,QString image2)
2255 {
2256   unsigned int sm1 = 0;
2257   unsigned int sm2 = 0;
2258
2259   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2260     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2261       mSlicerManagers[i]->AddLink(image2.toStdString());
2262       sm1 = i;
2263     }
2264     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2265       mSlicerManagers[i]->AddLink(image1.toStdString());
2266       sm2 = i;
2267     }
2268   }
2269
2270   if (linkPanel->isLinkAll())   {
2271     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2272     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2273   }
2274   else {
2275     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2276   }
2277 }
2278
2279 //------------------------------------------------------------------------------
2280
2281
2282 //------------------------------------------------------------------------------
2283 void vvMainWindow::RemoveLink(QString image1,QString image2)
2284 {
2285   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2286     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2287       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2288     }
2289     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2290       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2291     }
2292   }
2293 }
2294 //------------------------------------------------------------------------------
2295
2296 //------------------------------------------------------------------------------
2297 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2298 {
2299   int index = 0;
2300   while(sm != mSlicerManagers[index])
2301     index++;
2302   index = (index+offset) % mSlicerManagers.size();
2303
2304   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2305   //CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2306   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2307   DisplayChanged(item,slicer+1);
2308 }
2309 //------------------------------------------------------------------------------
2310
2311 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2312 {
2313   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2314     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2315       for (int j = 0; j < 4; j++) {
2316         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2317         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2318         //UpdateTSlice(j,value);
2319       }
2320       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2321       break;
2322     }
2323   }
2324 }
2325 //------------------------------------------------------------------------------
2326
2327
2328 //------------------------------------------------------------------------------
2329 void vvMainWindow::NOHorizontalSliderMoved()
2330 {
2331   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2332   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2333 //  mCurrentTime = NOHorizontalSlider->value();
2334 }
2335 //------------------------------------------------------------------------------
2336
2337
2338 //------------------------------------------------------------------------------
2339 void vvMainWindow::NEHorizontalSliderMoved()
2340 {
2341   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2342   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2343 //  mCurrentTime = NEHorizontalSlider->value();
2344 }
2345 //------------------------------------------------------------------------------
2346
2347
2348 //------------------------------------------------------------------------------
2349 void vvMainWindow::SOHorizontalSliderMoved()
2350 {
2351   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2352   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2353   // mCurrentTime = SOHorizontalSlider->value();
2354 }
2355 //------------------------------------------------------------------------------
2356
2357
2358 //------------------------------------------------------------------------------
2359 void vvMainWindow::SEHorizontalSliderMoved()
2360 {
2361   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2362   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2363   // mCurrentTime = SEHorizontalSlider->value();
2364 }
2365 //------------------------------------------------------------------------------
2366
2367 //------------------------------------------------------------------------------
2368 void vvMainWindow::NOVerticalSliderChanged()
2369 {
2370   static int value=-1;
2371   if (value == NOVerticalSlider->value()) return;
2372   else value = NOVerticalSlider->value();
2373   //  int value = NOVerticalSlider->value();
2374   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2375     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2376       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2377         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2378         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2379
2380         // If nor Update/Render -> slider not work
2381         // only render = ok navigation, but for contour Update needed but slower ?
2382
2383         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2384         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2385       }
2386       break;
2387     }
2388   }
2389 }
2390 //------------------------------------------------------------------------------
2391
2392
2393 //------------------------------------------------------------------------------
2394 void vvMainWindow::NEVerticalSliderChanged()
2395 {
2396   static int value=-1;
2397   if (value == NEVerticalSlider->value()) return;
2398   else value = NEVerticalSlider->value();
2399   //  int value = NEVerticalSlider->value();
2400   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2401     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2402       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2403         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2404         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2405         mSlicerManagers[i]->UpdateSlice(1);
2406         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2407       }
2408       break;
2409     }
2410   }
2411 }
2412 //------------------------------------------------------------------------------
2413
2414
2415 //------------------------------------------------------------------------------
2416 void vvMainWindow::SOVerticalSliderChanged()
2417 {
2418   static int value=-1;
2419   if (value == SOVerticalSlider->value()) return;
2420   else value = SOVerticalSlider->value();
2421   //int value = SOVerticalSlider->value();
2422   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2423     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2424       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2425         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2426         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2427         mSlicerManagers[i]->UpdateSlice(2);
2428         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2429       }
2430       // else { DD("avoid SOVerticalSlider slicer update"); }
2431       break;
2432     }
2433   }
2434 }
2435 //------------------------------------------------------------------------------
2436
2437
2438 //------------------------------------------------------------------------------
2439 void vvMainWindow::SEVerticalSliderChanged()
2440 {
2441   static int value=-1;
2442   if (value == SEVerticalSlider->value()) return;
2443   else value = SEVerticalSlider->value();
2444   // int value = SEVerticalSlider->value();
2445   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2446     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2447       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2448         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2449         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2450         mSlicerManagers[i]->UpdateSlice(3);
2451         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2452       }
2453       break;
2454     }
2455   }
2456 }
2457 //------------------------------------------------------------------------------
2458
2459
2460 //------------------------------------------------------------------------------
2461 void vvMainWindow::UpdateSlice(int slicer, int slice)
2462 {
2463   // DD("vvMainWindow::UpdateSlice");
2464 //   DD(slicer);
2465 //   DD(slice);
2466   if (slicer == 0) {
2467     //    if (slice != NOVerticalSlider->value())
2468     NOVerticalSlider->setValue(slice);
2469   } else {
2470     if (slicer == 1)
2471       NEVerticalSlider->setValue(slice);
2472     else {
2473       if (slicer == 2)
2474         SOVerticalSlider->setValue(slice);
2475       else {
2476         if (slicer == 3)
2477           SEVerticalSlider->setValue(slice);
2478       }
2479     }
2480   }
2481   // DD("vvMainWindow:UpdateSlice END");
2482 }
2483 //------------------------------------------------------------------------------
2484
2485
2486 //------------------------------------------------------------------------------
2487 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2488 {
2489   switch (slicer) {
2490   case 0:
2491     NOHorizontalSlider->setValue(slice);
2492     break;
2493   case 1:
2494     NEHorizontalSlider->setValue(slice);
2495     break;
2496   case 2:
2497     SOHorizontalSlider->setValue(slice);
2498     break;
2499   case 3:
2500     SEHorizontalSlider->setValue(slice);
2501     break;
2502   }
2503 }
2504 //------------------------------------------------------------------------------
2505
2506
2507 //------------------------------------------------------------------------------
2508 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2509 {
2510   int position = int((min+max)/2);
2511   int tPosition = int((tmin+tmax)/2);
2512   if (slicer == 0) {
2513     NOVerticalSlider->setValue(position);
2514     NOVerticalSlider->setRange(min,max);
2515     NOHorizontalSlider->setRange(tmin,tmax);
2516     NOHorizontalSlider->setValue(tPosition);
2517   } else if (slicer == 1) {
2518     NEVerticalSlider->setValue(position);
2519     NEVerticalSlider->setRange(min,max);
2520     NEHorizontalSlider->setRange(tmin,tmax);
2521     NEHorizontalSlider->setValue(tPosition);
2522   } else if (slicer == 2) {
2523     SOVerticalSlider->setValue(position);
2524     SOVerticalSlider->setRange(min,max);
2525     SOHorizontalSlider->setRange(tmin,tmax);
2526     SOHorizontalSlider->setValue(tPosition);
2527   } else if (slicer == 3) {
2528     SEVerticalSlider->setValue(position);
2529     SEVerticalSlider->setRange(min,max);
2530     SEHorizontalSlider->setRange(tmin,tmax);
2531     SEHorizontalSlider->setValue(tPosition);
2532   }
2533 }
2534 //------------------------------------------------------------------------------
2535
2536
2537 //------------------------------------------------------------------------------
2538 void vvMainWindow::SaveNOScreenshot()
2539 {
2540   SaveScreenshot(NOViewWidget);
2541 }
2542 //------------------------------------------------------------------------------
2543
2544
2545 //------------------------------------------------------------------------------
2546 void vvMainWindow::SaveNEScreenshot()
2547 {
2548   SaveScreenshot(NEViewWidget);
2549 }
2550 //------------------------------------------------------------------------------
2551
2552
2553 //------------------------------------------------------------------------------
2554 void vvMainWindow::SaveSOScreenshot()
2555 {
2556   SaveScreenshot(SOViewWidget);
2557 }
2558 //------------------------------------------------------------------------------
2559
2560
2561 //------------------------------------------------------------------------------
2562 void vvMainWindow::SaveSEScreenshot()
2563 {
2564   SaveScreenshot(SEViewWidget);
2565 }
2566 //------------------------------------------------------------------------------
2567
2568
2569 //------------------------------------------------------------------------------
2570 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
2571 {
2572   QString Extensions = "Images( *.png);;";
2573   Extensions += "Images( *.jpg);;";
2574   Extensions += "Images( *.bmp);;";
2575   Extensions += "Images( *.tif);;";
2576   Extensions += "Images( *.ppm)";
2577 #ifdef VTK_USE_FFMPEG_ENCODER
2578   Extensions += "Images( *.avi)";
2579 #endif
2580 #ifdef VTK_USE_MPEG2_ENCODER
2581   Extensions += "Images( *.mpg)";
2582 #endif
2583
2584   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2585   QString fileName = QFileDialog::getSaveFileName(this,
2586                      tr("Save As"),
2587                      itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
2588                      Extensions);
2589
2590   if (!fileName.isEmpty()) {
2591     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2592     w2i->SetInput(widget->GetRenderWindow());
2593     w2i->Update();
2594     vtkImageData *image = w2i->GetOutput();
2595
2596     const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2597     if (!strcmp(ext, ".bmp")) {
2598       vtkBMPWriter *bmp = vtkBMPWriter::New();
2599       bmp->SetInput(image);
2600       bmp->SetFileName(fileName.toStdString().c_str());
2601       bmp->Write();
2602       bmp->Delete();
2603     } else if (!strcmp(ext, ".tif")) {
2604       vtkTIFFWriter *tif = vtkTIFFWriter::New();
2605       tif->SetInput(image);
2606       tif->SetFileName(fileName.toStdString().c_str());
2607       tif->Write();
2608       tif->Delete();
2609     } else if (!strcmp(ext, ".ppm")) {
2610       vtkPNMWriter *pnm = vtkPNMWriter::New();
2611       pnm->SetInput(image);
2612       pnm->SetFileName(fileName.toStdString().c_str());
2613       pnm->Write();
2614       pnm->Delete();
2615     } else if (!strcmp(ext, ".png")) {
2616       vtkPNGWriter *png = vtkPNGWriter::New();
2617       png->SetInput(image);
2618       png->SetFileName(fileName.toStdString().c_str());
2619       png->Write();
2620       png->Delete();
2621     } else if (!strcmp(ext, ".jpg")) {
2622       vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2623       jpg->SetInput(image);
2624       jpg->SetFileName(fileName.toStdString().c_str());
2625       jpg->Write();
2626       jpg->Delete();
2627 #ifdef VTK_USE_FFMPEG_ENCODER
2628     } else if (!strcmp(ext, ".avi")) {
2629       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
2630       mpg->SetInput(image);
2631       mpg->SetFileName(fileName.toStdString().c_str());
2632       mpg->SetQuality(2);
2633       mpg->SetRate(5);
2634       mpg->Start();
2635
2636       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2637       int nSlice = vvImg->GetVTKImages().size();
2638       for(int i=0; i<nSlice; i++)
2639       {
2640         mSlicerManagers[smIndex]->SetNextTSlice(0);
2641         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2642         w2i->SetInput(widget->GetRenderWindow());
2643         w2i->Update();
2644         mpg->SetInput(w2i->GetOutput());
2645         mpg->Write();
2646       }
2647       mpg->End();
2648       mpg->Delete();
2649 #endif
2650 #ifdef VTK_USE_MPEG2_ENCODER
2651     } else if (!strcmp(ext, ".mpg")) {
2652       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
2653       mpg->SetInput(image);
2654       mpg->SetFileName(fileName.toStdString().c_str());
2655       mpg->Start();
2656
2657       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2658       int nSlice = vvImg->GetVTKImages().size();
2659       for(int i=0; i<nSlice; i++)
2660       {
2661         mSlicerManagers[smIndex]->SetNextTSlice(0);
2662         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2663         w2i->SetInput(widget->GetRenderWindow());
2664         w2i->Update();
2665         mpg->SetInput(w2i->GetOutput());
2666         mpg->Write();
2667       }
2668       mpg->End();
2669       mpg->Delete();
2670 #endif
2671     } else {
2672       QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2673     }
2674   }
2675 }
2676 //------------------------------------------------------------------------------
2677
2678
2679 //------------------------------------------------------------------------------
2680 void vvMainWindow::GoToCursor()
2681 {
2682   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2683   for (int column = 1; column < 5; column++) {
2684     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
2685       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2686       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2687         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2688       mSlicerManagers[index]->UpdateViews(1,column-1);
2689       mSlicerManagers[index]->UpdateLinked(column-1);
2690       break;
2691     }
2692   }
2693 }
2694 //------------------------------------------------------------------------------
2695
2696 //------------------------------------------------------------------------------
2697 void vvMainWindow::PlayPause()
2698 {
2699   if (playMode) {
2700     playMode = 0;
2701     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2702     ImageInfoChanged();
2703     return;
2704   } else {
2705     int image_number=DataTree->topLevelItemCount();
2706     bool has_temporal;
2707     for (int i=0; i<image_number; i++)
2708       if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1) {
2709         has_temporal=true;
2710         break;
2711       }
2712     if (has_temporal) {
2713       playMode = 1;
2714       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2715       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2716     }
2717   }
2718 }
2719 //------------------------------------------------------------------------------
2720
2721 //------------------------------------------------------------------------------
2722 void vvMainWindow::PlayNext()
2723 {
2724   if (playMode && !this->isHidden()) {
2725     int image_number=DataTree->topLevelItemCount();
2726     ///Only play one slicer per SM, and only if the SM is being displayed
2727     for (int i=0; i<image_number; i++)
2728       for (int j=0; j<4; j++)
2729         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2730             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
2731           mSlicerManagers[i]->SetNextTSlice(j);
2732           break;
2733         }
2734     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2735   }
2736 }
2737 //------------------------------------------------------------------------------
2738
2739 void vvMainWindow::ShowLastImage()
2740 {
2741   if (mSlicerManagers.size() > 1) {
2742     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2743     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2744     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2745     DisplayChanged(item,1);
2746   }
2747 }
2748
2749 //------------------------------------------------------------------------------
2750 void vvMainWindow::UpdateRenderWindows()
2751 {
2752   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2753   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2754   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2755   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2756 }
2757 //------------------------------------------------------------------------------
2758
2759 //------------------------------------------------------------------------------
2760 void vvMainWindow::SegmentationOnCurrentImage()
2761 {
2762   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2763
2764   vvSegmentationDialog segmentation;
2765   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2766   segmentation.exec();
2767 }
2768 //------------------------------------------------------------------------------
2769
2770 void vvMainWindow::SurfaceViewerLaunch()
2771 {
2772   vvSurfaceViewerDialog surfaceViewer;
2773   surfaceViewer.exec();
2774 }
2775 //------------------------------------------------------------------------------
2776
2777
2778 //------------------------------------------------------------------------------
2779 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
2780 {
2781   int number=0;
2782   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
2783     vvSlicerManager * v = mSlicerManagers[l];
2784     if (v->GetBaseFileName() ==
2785         vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
2786       number = std::max(number, v->GetBaseFileNameNumber()+1);
2787     }
2788   }
2789   return number;
2790 }
2791 //------------------------------------------------------------------------------
2792
2793
2794 //------------------------------------------------------------------------------
2795 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2796 {
2797   // Change filename if another image exist with the same name
2798   int number = GetImageDuplicateFilenameNumber(filename);
2799
2800   // Create new SliceManager
2801   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
2802   slicer_manager->SetImage(image);//, IMAGE, number);
2803   //  filename = filename+"_"+clitk::toString(number);
2804   slicer_manager->SetFilename(filename, number);
2805   mSlicerManagers.push_back(slicer_manager);
2806
2807   //create an item in the tree with good settings
2808   QTreeWidgetItem *item = new QTreeWidgetItem();
2809   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2810   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
2811   qApp->processEvents();
2812
2813   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2814
2815   //Create the buttons for reload and close
2816   qApp->processEvents();
2817   QTreePushButton* cButton = new QTreePushButton;
2818   cButton->setItem(item);
2819   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2820   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2821   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2822           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2823
2824   QTreePushButton* rButton = new QTreePushButton;
2825   rButton->setItem(item);
2826   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2827   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2828   rButton->setEnabled(0);
2829   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2830           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2831
2832   DataTree->addTopLevelItem(item);
2833   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2834   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2835
2836   //set the id of the image
2837   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2838   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2839   mSlicerManagers.back()->SetId(id.toStdString());
2840
2841   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
2842                       , id.toStdString());
2843
2844   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
2845           this, SLOT(CurrentImageChanged(std::string)));
2846   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
2847           this, SLOT(CurrentPickedImageChanged(std::string)));
2848   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
2849           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2850   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
2851           this, SLOT(VectorChanged(int,double,double,double, double)));
2852   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
2853           this, SLOT(OverlayChanged(int,double,double)));
2854   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
2855           this, SLOT(FusionChanged(int,double)));
2856   connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
2857           this,SLOT(WindowsChanged(int, int, int)));
2858   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
2859           this,SLOT(WindowLevelChanged(double, double, int, int)));
2860   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
2861           this,SLOT(UpdateSlice(int,int)));
2862   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
2863           this,SLOT(UpdateTSlice(int, int)));
2864   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2865           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2866   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2867           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2868   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
2869           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
2870   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
2871           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
2872   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2873   UpdateTree();
2874   qApp->processEvents();
2875   InitSlicers();
2876   ShowLastImage();
2877   InitDisplay();
2878   qApp->processEvents();
2879
2880   // End
2881   ImageInfoChanged();
2882   return slicer_manager;
2883 }
2884 //------------------------------------------------------------------------------
2885
2886
2887 //------------------------------------------------------------------------------
2888 void vvMainWindow::UpdateCurrentSlicer()
2889 {
2890   int index = -1;
2891   if (DataTree->selectedItems().size() > 0) {
2892     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2893   }
2894   mSlicerManagerCurrentIndex = index;
2895 }
2896 //------------------------------------------------------------------------------
2897