vv/vvMainWindow.cxx

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