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
1169     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1170       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1171       overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1172                                       mSlicerManagers[index]->GetFusionThresholdOpacity(),
1173                                       mSlicerManagers[index]->GetFusionColorMap(),
1174                                       mSlicerManagers[index]->GetFusionWindow(),
1175                                       mSlicerManagers[index]->GetFusionLevel());
1176     } else {
1177       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1178       overlayPanel->getFusionProperty(-1, -1, -1, -1, -1);
1179     }
1180   }
1181 }
1182 //------------------------------------------------------------------------------
1183
1184 //------------------------------------------------------------------------------
1185 void vvMainWindow::ShowDocumentation()
1186 {
1187   documentation->show();
1188 }
1189 //------------------------------------------------------------------------------
1190
1191 //------------------------------------------------------------------------------
1192 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1193 {
1194   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1195   if(!checkCanPush) {
1196     registerForm->show();
1197   } else {
1198     if(registerForm->canPush()) {
1199       registerForm->show();
1200       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1201     }
1202   }
1203 }
1204 //------------------------------------------------------------------------------
1205
1206 //------------------------------------------------------------------------------
1207 void vvMainWindow::ShowHelpDialog()
1208 {
1209   help_dialog->show();
1210 }
1211 //------------------------------------------------------------------------------
1212
1213 //------------------------------------------------------------------------------
1214 void vvMainWindow::ChangeViewMode()
1215 {
1216   QList<int> size;
1217   if (viewMode == 1) {
1218     viewMode = 0;
1219     size.push_back(1);
1220     size.push_back(0);
1221     splitter_3->setSizes(size);
1222     OSplitter->setSizes(size);
1223     DataTree->setColumnHidden(2,1);
1224     DataTree->setColumnHidden(3,1);
1225     DataTree->setColumnHidden(4,1);
1226   } else {
1227     viewMode = 1;
1228     size.push_back(1);
1229     size.push_back(1);
1230     splitter_3->setSizes(size);
1231     OSplitter->setSizes(size);
1232     DataTree->setColumnHidden(2,0);
1233     DataTree->setColumnHidden(3,0);
1234     DataTree->setColumnHidden(4,0);
1235   }
1236   UpdateRenderWindows();
1237   /*
1238   ** I don't know why but for both resized QVTKWidget we also need to render
1239   ** the associated Slicer to redraw crosses.
1240   */
1241   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1242     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1243       mSlicerManagers[i]->GetSlicer(0)->Render();
1244     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1245       mSlicerManagers[i]->GetSlicer(2)->Render();
1246   }
1247 }
1248 //------------------------------------------------------------------------------
1249
1250 //------------------------------------------------------------------------------
1251 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1252 {
1253   QString result = "";// QString::number(size);
1254   //result += " bytes (";
1255   if (size > 1000000000) {
1256     size /= 1000000000;
1257     result += QString::number(size);
1258     result += "Gb";//)";
1259   } else if (size > 1000000) {
1260     size /= 1000000;
1261     result += QString::number(size);
1262     result += "Mb";//)";
1263   } else if (size > 1000) {
1264     size /= 1000;
1265     result += QString::number(size);
1266     result += "kb";//)";
1267   }
1268   return result;
1269 }
1270 //------------------------------------------------------------------------------
1271
1272 //------------------------------------------------------------------------------
1273 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix)
1274 {
1275   std::ostringstream strmatrix;
1276
1277   for (unsigned int i = 0; i < 4; i++) {
1278     for (unsigned int j = 0; j < 4; j++) {
1279       strmatrix.flags(ios::showpos);
1280       strmatrix.width(10);
1281       strmatrix.precision(3);
1282       strmatrix.setf(ios::fixed,ios::floatfield);
1283       strmatrix.fill(' ');
1284       strmatrix << std::left << matrix->GetElement(i, j);
1285       //strmatrix.width(10);
1286       strmatrix << " ";
1287     }
1288     strmatrix << std::endl;
1289   }
1290   QString result = strmatrix.str().c_str();
1291   return result;
1292 }
1293 //------------------------------------------------------------------------------
1294
1295 //------------------------------------------------------------------------------
1296 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1297 {
1298   QString result;
1299   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1300     if (i != 0)
1301       result += " ";
1302     result += QString::number(vectorDouble[i]);
1303   }
1304   return result;
1305 }
1306 //------------------------------------------------------------------------------
1307
1308 //------------------------------------------------------------------------------
1309 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1310 {
1311   QString result;
1312   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1313     if (i != 0)
1314       result += " ";
1315     result += QString::number(vectorInt[i]);
1316   }
1317   return result;
1318 }
1319 //------------------------------------------------------------------------------
1320
1321 //------------------------------------------------------------------------------
1322 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1323 {
1324   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1325   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1326     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1327       return i;
1328   }
1329   return -1;
1330 }
1331 //------------------------------------------------------------------------------
1332
1333 //------------------------------------------------------------------------------
1334 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1335 {
1336   QString id = sm->GetId().c_str();
1337   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1338     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1339       return DataTree->topLevelItem(i);
1340   }
1341   return NULL;
1342 }
1343 //------------------------------------------------------------------------------
1344
1345 //------------------------------------------------------------------------------
1346 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clickedItem, int column)
1347 {
1348   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1349     return;
1350
1351   // Get parent information (might be the same item)
1352   int slicerManagerIndex = GetSlicerIndexFromItem(clickedItem);
1353   QTreeWidgetItem* clickedParentItem = DataTree->topLevelItem(slicerManagerIndex);
1354   vvSlicer* clickedSlicer = mSlicerManagers[slicerManagerIndex]->GetSlicer(column-1);
1355
1356   // Go over the complete item tree (only 2 levels, parents and children)
1357   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1358     // Trick to avoid redoing twice the job for a key (sr)
1359     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()->GetInteractor()->SetKeySym("Crap");
1360
1361     QTreeWidgetItem* currentParentItem = DataTree->topLevelItem(i);
1362     if(currentParentItem != clickedParentItem) {
1363       // Not the branch of the clicked item, uncheck all
1364
1365       // Parent
1366       currentParentItem->setData(column,Qt::CheckStateRole, 0);
1367       mSlicerManagers[i]->UpdateSlicer(column-1, false);
1368
1369       // Children
1370       for (int iChild = 0; iChild < currentParentItem->childCount(); iChild++) {
1371         currentParentItem->child(iChild)->setData(column,Qt::CheckStateRole, 0);
1372       }
1373     }
1374     else {
1375       // Branch of the clicked one: get check status from actor visibility in slicer
1376       // and toggle the clicked one
1377
1378       // Parent
1379       bool vis = clickedSlicer->GetActorVisibility("image", 0);
1380       bool draw = clickedSlicer->GetRenderer()->GetDraw();
1381
1382       // Update slicer (after getting visibility)
1383       mSlicerManagers[slicerManagerIndex]->UpdateSlicer(column-1, true);
1384       mSlicerManagers[slicerManagerIndex]->UpdateInfoOnCursorPosition(column-1);
1385       DisplaySliders(slicerManagerIndex, column-1);
1386       if(clickedParentItem == clickedItem) {
1387         // Toggle
1388         vis = !draw || !vis;
1389       }
1390       clickedSlicer->SetActorVisibility("image", 0, vis);
1391       clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
1392
1393       // Children
1394       std::map<std::string, int> actorTypeCounts;
1395       for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
1396         QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
1397         std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
1398         vis = clickedSlicer->GetActorVisibility(actorType, actorTypeCounts[actorType]);
1399         if(currentChildItem == clickedItem) {
1400           // Toggle or force visibility if it was not on this branch so far
1401           vis = !draw || !vis;
1402           clickedSlicer->SetActorVisibility(actorType, actorTypeCounts[actorType], vis);
1403         }
1404         currentChildItem->setData(column, Qt::CheckStateRole, vis?2:0);
1405         actorTypeCounts[actorType]++;
1406       }
1407     }
1408   }
1409
1410   clickedSlicer->Render();
1411 }
1412 //------------------------------------------------------------------------------
1413
1414 void vvMainWindow::InitSlicers()
1415 {
1416   if (mSlicerManagers.size()) {
1417     mSlicerManagers.back()->GenerateDefaultLookupTable();
1418
1419     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1420     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1421     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1422     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1423   }
1424 }
1425
1426 //------------------------------------------------------------------------------
1427 void vvMainWindow::InitDisplay()
1428 {
1429   if (mSlicerManagers.size()) {
1430     //BE CAREFUL : this is absolutely necessary to set the interactor style
1431     //in order to have the same style instanciation for all SlicerManagers in
1432     // a same window
1433     for (int j = 0; j < 4; j++) {
1434       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1435       style->SetAutoAdjustCameraClippingRange(1);
1436       bool AlreadySelected = false;
1437       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1438         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1439
1440         //select the image only if previous are not selected
1441         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1442           mSlicerManagers[i]->UpdateSlicer(j,1);
1443           AlreadySelected = true;
1444         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1445           if (DataTree->selectedItems().size() == 0)
1446             DataTree->topLevelItem(i)->setSelected(1);
1447           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1448           mSlicerManagers[i]->UpdateSlicer(j,1);
1449           DisplaySliders(i,j);
1450         } else {
1451           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1452           mSlicerManagers[i]->UpdateSlicer(j,0);
1453         }
1454       }
1455       style->Delete();
1456     }
1457   }
1458 }
1459 //------------------------------------------------------------------------------
1460
1461 //------------------------------------------------------------------------------
1462 void vvMainWindow::DisplaySliders(int slicer, int window)
1463 {
1464   int range[2];
1465   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1466   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1467
1468   int tRange[2];
1469   tRange[0] = 0;
1470   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1471   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1472   bool showHorizontal = false;
1473   bool showVertical = false;
1474   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1475       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1476           && mSlicerManagers[slicer]->GetType() != vvImageReader::IMAGEWITHTIME
1477           && mSlicerManagers[slicer]->GetType() != vvImageReader::MERGEDWITHTIME))
1478     showVertical = true;
1479   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1480       || mSlicerManagers[slicer]->GetType() == vvImageReader::IMAGEWITHTIME
1481       || mSlicerManagers[slicer]->GetType() == vvImageReader::MERGEDWITHTIME)
1482     showHorizontal = true;
1483
1484   if (showVertical)
1485     verticalSliders[window]->show();
1486   else
1487     verticalSliders[window]->hide();
1488   verticalSliders[window]->setRange(range[0],range[1]);
1489   verticalSliders[window]->setValue(position);
1490
1491   if (showHorizontal)
1492     horizontalSliders[window]->show();
1493   else
1494     horizontalSliders[window]->hide();
1495   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1496   horizontalSliders[window]->setValue(tPosition);
1497 }
1498 //------------------------------------------------------------------------------
1499
1500 //------------------------------------------------------------------------------
1501 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1502 {
1503   int index = GetSlicerIndexFromItem(item);
1504
1505   if (DataTree->topLevelItem(index) != item) {
1506     QString warning = "Do you really want to close the overlay : ";
1507     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1508     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1509                        warning, 0, this);
1510     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1511     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1512     if (msgBox.exec() == QMessageBox::AcceptRole) {
1513       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1514       int overlay_index=0;
1515       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1516         if (DataTree->topLevelItem(index)->\
1517             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1518           overlay_index++;
1519         if (DataTree->topLevelItem(index)->child(child) == item) break;
1520       }
1521       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1522       mSlicerManagers[index]->SetColorMap(0);
1523       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1524       mSlicerManagers[index]->Render();
1525     }
1526   } else if (DataTree->topLevelItemCount() <= 1) {
1527     QString warning = "Do you really want to close the image : ";
1528     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1529     warning += "\nThis is the last image, you're about to close vv !!!";
1530     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1531                        warning, 0, this);
1532     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1533     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1534     if (msgBox.exec() == QMessageBox::AcceptRole) {
1535       this->close();
1536     }
1537   } else {
1538     QString warning = "Do you really want to close the image : ";
1539     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1540     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1541                        warning, 0, this);
1542     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1543     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1544     if (msgBox.exec() == QMessageBox::AcceptRole) {
1545
1546       // Tell tools that we close an image
1547       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1548
1549       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1550       DataTree->takeTopLevelItem(index);
1551       for (int i = 0; i < index; i++) {
1552         Manageriter++;
1553       }
1554       linkPanel->removeImage(index);
1555       mSlicerManagers[index]->RemoveActors();
1556       delete mSlicerManagers[index];
1557       mSlicerManagers.erase(Manageriter);
1558
1559       //
1560       InitDisplay();
1561     }
1562   }
1563   ImageInfoChanged();
1564 }
1565 //------------------------------------------------------------------------------
1566
1567 //------------------------------------------------------------------------------
1568 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1569 {
1570   // int index = GetSlicerIndexFromItem(item);
1571   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1572   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1573   //     mSlicerManagers[index]->ReloadVF();
1574   //   else
1575   //     mSlicerManagers[index]->Reload();
1576
1577   //   QApplication::restoreOverrideCursor();
1578   int index = GetSlicerIndexFromItem(item);
1579   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1580   QString role=item->data(1,Qt::UserRole).toString();
1581   if ( role == "vector"){
1582     mSlicerManagers[index]->ReloadVF();
1583   }
1584   else if (role == "overlay"){
1585     mSlicerManagers[index]->ReloadOverlay();
1586   }
1587   else if (role == "fusion"){
1588     mSlicerManagers[index]->ReloadFusion();
1589   }
1590   else{
1591     mSlicerManagers[index]->Reload();
1592   }
1593   // Update view and info
1594   ImageInfoChanged();
1595   mSlicerManagers[index]->Render();
1596   QApplication::restoreOverrideCursor();
1597 }
1598 //------------------------------------------------------------------------------
1599
1600 //------------------------------------------------------------------------------
1601 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1602 {
1603   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1604 }
1605 //------------------------------------------------------------------------------
1606
1607 //------------------------------------------------------------------------------
1608 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1609 {
1610   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1611 }
1612 //------------------------------------------------------------------------------
1613
1614 //------------------------------------------------------------------------------
1615 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1616 {
1617   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1618 }
1619 //------------------------------------------------------------------------------
1620
1621 //------------------------------------------------------------------------------
1622 void vvMainWindow::FusionChanged(int visibility, double value)
1623 {
1624   overlayPanel->getCurrentFusionInfo(visibility,value);
1625 }
1626 //------------------------------------------------------------------------------
1627
1628 //------------------------------------------------------------------------------
1629 void vvMainWindow::WindowsChanged(int window, int view, int slice)
1630 {
1631   infoPanel->setViews(window, view, slice);
1632 }
1633 //------------------------------------------------------------------------------
1634
1635 //------------------------------------------------------------------------------
1636 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap)
1637 {
1638   windowSpinBox->setValue(window);
1639   levelSpinBox->setValue(level);
1640   colorMapComboBox->setCurrentIndex(colormap);
1641   presetComboBox->setCurrentIndex(preset);
1642 }
1643 //------------------------------------------------------------------------------
1644
1645 //------------------------------------------------------------------------------
1646 void vvMainWindow::WindowLevelEdited()
1647 {
1648   presetComboBox->setCurrentIndex(6);
1649   UpdateWindowLevel();
1650 }
1651 //------------------------------------------------------------------------------
1652
1653 //------------------------------------------------------------------------------
1654 void vvMainWindow::UpdateWindowLevel()
1655 {
1656   if (DataTree->selectedItems().size()) {
1657     if (presetComboBox->currentIndex() == 7) //For ventilation
1658       colorMapComboBox->setCurrentIndex(5);
1659     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1660     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1661     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1662     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1663     mSlicerManagers[index]->Render();
1664     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1665     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1666   }
1667 }
1668 //------------------------------------------------------------------------------
1669
1670 //------------------------------------------------------------------------------
1671 void vvMainWindow::UpdateColorMap()
1672 {
1673   if (DataTree->selectedItems().size()) {
1674     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1675     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1676     mSlicerManagers[index]->Render();
1677   }
1678 }
1679 //------------------------------------------------------------------------------
1680 void vvMainWindow::SwitchWindowLevel()
1681 {
1682   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1683   int window = mSlicerManagers[index]->GetColorWindow();
1684   presetComboBox->setCurrentIndex(6);
1685   windowSpinBox->setValue(-window);
1686   UpdateWindowLevel();
1687 }
1688 //------------------------------------------------------------------------------
1689
1690 //------------------------------------------------------------------------------
1691 void vvMainWindow::ApplyWindowLevelToAllImages()
1692 {
1693   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1694     if (mSlicerManagers[i] == NULL)
1695       continue;
1696     mSlicerManagers[i]->SetColorWindow(windowSpinBox->value());
1697     mSlicerManagers[i]->SetColorLevel(levelSpinBox->value());
1698     mSlicerManagers[i]->SetPreset(6);
1699     mSlicerManagers[i]->Render();
1700   }
1701 }
1702 //------------------------------------------------------------------------------
1703
1704 //------------------------------------------------------------------------------
1705 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1706 {
1707   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1708     if (mSlicerManagers[i]->GetId() == id) {
1709       //mSlicerManagers[i]->SetTSlice(temps);
1710       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1711       mSlicerManagers[i]->UpdateViews(0,slicer);
1712       break;
1713     }
1714   }
1715 }
1716 //------------------------------------------------------------------------------
1717
1718 //------------------------------------------------------------------------------
1719 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1720 {
1721   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1722     if (id == mSlicerManagers[i]->GetId()) {
1723       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1724     }
1725   }
1726 }
1727 //------------------------------------------------------------------------------
1728
1729 //------------------------------------------------------------------------------
1730 void vvMainWindow::ShowContextMenu(QPoint point)
1731 {
1732   if (!DataTree->selectedItems().size()) {
1733     contextActions[1]->setEnabled(0);
1734     contextActions[2]->setEnabled(0);
1735     contextActions[3]->setEnabled(0);
1736     contextActions[4]->setEnabled(0);
1737     contextActions[5]->setEnabled(0);
1738     contextActions[6]->setEnabled(0);
1739   } else {
1740     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1741     contextActions[1]->setEnabled(1);
1742     contextActions[2]->setEnabled(
1743       DataTree->itemWidget(DataTree->selectedItems()[0],
1744                            COLUMN_RELOAD_IMAGE)->isEnabled());
1745     contextActions[3]->setEnabled(1);
1746     contextActions[5]->setEnabled(1);
1747     contextActions[6]->setEnabled(1);
1748
1749     if (mSlicerManagers[index]->GetDimension() < 3)
1750       contextActions[4]->setEnabled(0);
1751     else
1752       contextActions[4]->setEnabled(1);
1753   }
1754   contextMenu.exec(QCursor::pos());
1755 }
1756 //------------------------------------------------------------------------------
1757
1758 //------------------------------------------------------------------------------
1759 void vvMainWindow::CloseImage()
1760 {
1761   CloseImage(DataTree->selectedItems()[0],0);
1762 }
1763 //------------------------------------------------------------------------------
1764
1765 //------------------------------------------------------------------------------
1766 void vvMainWindow::ReloadImage()
1767 {
1768   ReloadImage(DataTree->selectedItems()[0],0);
1769 }
1770 //------------------------------------------------------------------------------
1771
1772 //------------------------------------------------------------------------------
1773 void vvMainWindow::SelectOverlayImage()
1774 {
1775   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1776
1777   //check if one overlay image is added
1778   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1779     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1780       QString error = "Cannot add more than one compared image\n";
1781       error += "Please remove first ";
1782       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1783       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1784       return;
1785     }
1786
1787   QString Extensions = EXTENSIONS;
1788   Extensions += ";;All Files (*)";
1789   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1790   if (!file.isEmpty())
1791     AddOverlayImage(index,file);
1792 }
1793 //------------------------------------------------------------------------------
1794
1795 //------------------------------------------------------------------------------
1796 void vvMainWindow::AddOverlayImage(int index, QString file)
1797 {
1798
1799   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1800   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1801                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1802   reader->SetFileName(file.toStdString().c_str());
1803   reader->ReadImageInformation();
1804   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1805   int dimension = reader->GetNumberOfDimensions();
1806   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1807   vvProgressDialog progress("Opening " + file.toStdString());
1808   qApp->processEvents();
1809
1810   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1811   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component)) {
1812     //create an item in the tree with good settings
1813     QTreeWidgetItem *item = new QTreeWidgetItem();
1814     item->setData(0,Qt::UserRole,file.toStdString().c_str());
1815     item->setData(1,Qt::UserRole,tr("overlay"));
1816     QFileInfo fileinfo(file); //Do not show the path
1817     item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1818     item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
1819     qApp->processEvents();
1820
1821     for (int j = 1; j <= 4; j++) {
1822       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1823     }
1824
1825     //Create the buttons for reload and close
1826     qApp->processEvents();
1827     QTreePushButton* cButton = new QTreePushButton;
1828     cButton->setItem(item);
1829     cButton->setColumn(COLUMN_CLOSE_IMAGE);
1830     cButton->setToolTip(tr("close image"));
1831     cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1832     connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1833             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1834
1835     QTreePushButton* rButton = new QTreePushButton;
1836     rButton->setItem(item);
1837     rButton->setColumn(COLUMN_RELOAD_IMAGE);
1838     rButton->setToolTip(tr("reload image"));
1839     rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1840     connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1841             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1842
1843     DataTree->topLevelItem(index)->setExpanded(1);
1844     DataTree->topLevelItem(index)->addChild(item);
1845     DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1846     DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1847
1848     //set the id of the image
1849     QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1850     item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1851     UpdateTree();
1852     qApp->processEvents();
1853     ImageInfoChanged();
1854     QApplication::restoreOverrideCursor();
1855   } else {
1856     QApplication::restoreOverrideCursor();
1857     QString error = "Cannot import the new image.\n";
1858     error += mSlicerManagers[index]->GetLastError().c_str();
1859     QMessageBox::information(this,tr("Problem reading image !"),error);
1860   }
1861 }
1862 //------------------------------------------------------------------------------
1863
1864
1865 //------------------------------------------------------------------------------
1866 void vvMainWindow::AddROI(int index, QString file)
1867 {
1868   /*
1869   // Get slice manager
1870
1871   // Load image
1872
1873   vvImageReader * mReader = new vvImageReader;
1874   mReader->SetInputFilename(filename.toStdString());
1875   mReader->Update(IMAGE);
1876   if (mReader->GetLastError().size() != 0) {
1877     std::cerr << "Error while reading " << filename.toStdString() << std::endl;
1878     QString error = "Cannot open file \n";
1879     error += mReader->GetLastError().c_str();
1880     QMessageBox::information(this,tr("Reading problem"),error);
1881     delete mReader;
1882     return;
1883   }
1884   vvImage::Pointer roi = mReader->GetOutput();
1885
1886   // Create roi in new tool
1887   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
1888   */
1889 }
1890 //------------------------------------------------------------------------------
1891
1892 //------------------------------------------------------------------------------
1893 void vvMainWindow::SelectFusionImage()
1894 {
1895   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1896
1897   //check if one fusion image is added
1898   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1899     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
1900       QString error = "Cannot add more than one fusion image\n";
1901       error += "Please remove first ";
1902       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1903       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1904       return;
1905     }
1906
1907   QString Extensions = EXTENSIONS;
1908   Extensions += ";;All Files (*)";
1909   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1910   if (!file.isEmpty())
1911     AddFusionImage(index,file);
1912 }
1913 //------------------------------------------------------------------------------
1914
1915 //------------------------------------------------------------------------------
1916 void vvMainWindow::AddFusionImage(int index, QString file)
1917 {
1918   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1919   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1920                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1921   reader->SetFileName(file.toStdString().c_str());
1922   reader->ReadImageInformation();
1923   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1924   if (reader) {
1925     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1926     vvProgressDialog progress("Opening fusion");
1927     qApp->processEvents();
1928
1929     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1930     if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1931                                           reader->GetNumberOfDimensions(), component)) {
1932       //create an item in the tree with good settings
1933       QTreeWidgetItem *item = new QTreeWidgetItem();
1934       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1935       item->setData(1,Qt::UserRole,tr("fusion"));
1936       QFileInfo fileinfo(filename.c_str()); //Do not show the path
1937       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1938       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
1939       qApp->processEvents();
1940
1941       for (int j = 1; j <= 4; j++) {
1942         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1943       }
1944
1945       //Create the buttons for reload and close
1946       qApp->processEvents();
1947       QTreePushButton* cButton = new QTreePushButton;
1948       cButton->setItem(item);
1949       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1950       cButton->setToolTip(tr("close image"));
1951       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1952       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1953               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1954
1955       QTreePushButton* rButton = new QTreePushButton;
1956       rButton->setItem(item);
1957       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1958       rButton->setToolTip(tr("reload image"));
1959       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1960       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1961               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1962
1963       DataTree->topLevelItem(index)->setExpanded(1);
1964       DataTree->topLevelItem(index)->addChild(item);
1965       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1966       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1967
1968       //set the id of the image
1969       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1970       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1971       UpdateTree();
1972       qApp->processEvents();
1973       ImageInfoChanged();
1974       QApplication::restoreOverrideCursor();
1975     } else {
1976       QApplication::restoreOverrideCursor();
1977       QString error = "Cannot import the new image.\n";
1978       error += mSlicerManagers[index]->GetLastError().c_str();
1979       QMessageBox::information(this,tr("Problem reading image !"),error);
1980     }
1981   } else {
1982     QString error = "Cannot import the new image.\n";
1983     QMessageBox::information(this,tr("Problem reading image !"),error);
1984   }
1985 }
1986 //------------------------------------------------------------------------------
1987
1988
1989 //------------------------------------------------------------------------------
1990 void vvMainWindow::OpenField()
1991 {
1992   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1993   //check if a vector field has already been added
1994   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1995     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
1996       QString error = "Cannot add more than one vector field\n";
1997       error += "Please remove first ";
1998       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1999       QMessageBox::information(this,tr("Problem adding vector field!"),error);
2000       return;
2001     }
2002
2003   QString Extensions = "Images ( *.mhd)";
2004   Extensions += ";;Images ( *.vf)";
2005   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2006   if (!file.isEmpty())
2007     AddField(file,index);
2008 }
2009 //------------------------------------------------------------------------------
2010
2011
2012 //------------------------------------------------------------------------------
2013 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2014 {
2015   //create an item in the tree with good settings
2016   QTreeWidgetItem *item = new QTreeWidgetItem();
2017   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2018   item->setData(1,Qt::UserRole,tr("vector"));
2019   QFileInfo fileinfo(filename); //Do not show the path
2020   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2021   item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("vector").c_str());
2022   qApp->processEvents();
2023
2024   for (int j = 1; j <= 4; j++) {
2025     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2026   }
2027
2028   //Create the buttons for reload and close
2029   qApp->processEvents();
2030   QTreePushButton* cButton = new QTreePushButton;
2031   cButton->setItem(item);
2032   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2033   cButton->setToolTip(tr("close vector field"));
2034   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2035   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2036           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2037
2038   QTreePushButton* rButton = new QTreePushButton;
2039   rButton->setItem(item);
2040   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2041   rButton->setToolTip(tr("reload vector field"));
2042   rButton->setEnabled(from_disk);
2043   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2044   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2045           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2046
2047   DataTree->topLevelItem(index)->setExpanded(1);
2048   DataTree->topLevelItem(index)->addChild(item);
2049   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2050   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2051
2052   //set the id of the image
2053   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2054   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2055   UpdateTree();
2056   qApp->processEvents();
2057   ImageInfoChanged();
2058   QApplication::restoreOverrideCursor();
2059 }
2060 //------------------------------------------------------------------------------
2061
2062
2063 //------------------------------------------------------------------------------
2064 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2065 {
2066   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2067   vvSlicerManager* imageManager = mSlicerManagers[index];
2068   if (imageManager->SetVF(vf,file.toStdString())) {
2069     AddFieldEntry(file,index,false);
2070   } else {
2071     QString error = "Cannot import the vector field for this image.\n";
2072     error += imageManager->GetLastError().c_str();
2073     QMessageBox::information(this,tr("Problem reading VF !"),error);
2074   }
2075   QApplication::restoreOverrideCursor();
2076 }
2077 //------------------------------------------------------------------------------
2078
2079
2080 //------------------------------------------------------------------------------
2081 void vvMainWindow::AddField(QString file,int index)
2082 {
2083   if (QFile::exists(file)) {
2084     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2085
2086     //init the progress events
2087     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2088     vvProgressDialog progress("Opening " + file.toStdString());
2089     qApp->processEvents();
2090
2091     //read the vector and put it in the current mSlicerManager
2092     vvSlicerManager* imageManager = mSlicerManagers[index];
2093     qApp->processEvents();
2094
2095     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2096     if (imageManager->SetVF(file.toStdString())) {
2097       imageManager->Render();
2098       AddFieldEntry(file,index,true);
2099     } else {
2100       QApplication::restoreOverrideCursor();
2101       QString error = "Cannot import the vector field for this image.\n";
2102       error += imageManager->GetLastError().c_str();
2103       QMessageBox::information(this,tr("Problem reading VF !"),error);
2104     }
2105   } else
2106     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2107
2108 }
2109 //------------------------------------------------------------------------------
2110
2111
2112 //------------------------------------------------------------------------------
2113 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2114 {
2115   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2116   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2117     for (int i = 0; i < 4; i++) {
2118       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2119       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2120       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2121       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2122       if (log > 0)
2123         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2124       else
2125         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2126     }
2127   }
2128 }
2129 //------------------------------------------------------------------------------
2130
2131
2132 //------------------------------------------------------------------------------
2133 void vvMainWindow::SetOverlayProperty(int color)
2134 {
2135   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2136   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2137     mSlicerManagers[index]->SetOverlayColor(color);
2138     mSlicerManagers[index]->SetColorMap(0);
2139     mSlicerManagers[index]->Render();
2140   }
2141 }
2142 //------------------------------------------------------------------------------
2143
2144 //------------------------------------------------------------------------------
2145 void vvMainWindow::SetFusionProperty(int opacity, int thresOpacity, int colormap,double window, double level)
2146 {
2147   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2148   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2149     mSlicerManagers[index]->SetFusionColorMap(colormap);
2150     mSlicerManagers[index]->SetFusionOpacity(opacity);
2151     mSlicerManagers[index]->SetFusionThresholdOpacity(thresOpacity);
2152     mSlicerManagers[index]->SetFusionWindow(window);
2153     mSlicerManagers[index]->SetFusionLevel(level);
2154     mSlicerManagers[index]->SetColorMap(0);
2155     mSlicerManagers[index]->Render();
2156   }
2157 }
2158 //------------------------------------------------------------------------------
2159
2160 //------------------------------------------------------------------------------
2161 void vvMainWindow::SaveAs()
2162 {
2163   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2164     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2165     return;
2166   }
2167
2168   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2169   int dimension = mSlicerManagers[index]->GetDimension();
2170   QStringList OutputListeFormat;
2171   OutputListeFormat.clear();
2172   if (dimension == 1) {
2173     OutputListeFormat.push_back(".mhd");
2174   }
2175   if (dimension == 2) {
2176     OutputListeFormat.push_back(".bmp");
2177     OutputListeFormat.push_back(".png");
2178     OutputListeFormat.push_back(".jpeg");
2179     OutputListeFormat.push_back(".tif");
2180     OutputListeFormat.push_back(".mhd");
2181     OutputListeFormat.push_back(".hdr");
2182     OutputListeFormat.push_back(".vox");
2183   } else if (dimension == 3) {
2184     OutputListeFormat.push_back(".mhd");
2185     OutputListeFormat.push_back(".hdr");
2186     OutputListeFormat.push_back(".vox");
2187   } else if (dimension == 4) {
2188     OutputListeFormat.push_back(".mhd");
2189   }
2190   QString Extensions = "AllFiles(*.*)";
2191   for (int i = 0; i < OutputListeFormat.count(); i++) {
2192     Extensions += ";;Images ( *";
2193     Extensions += OutputListeFormat[i];
2194     Extensions += ")";
2195   }
2196   QString fileName = QFileDialog::getSaveFileName(this,
2197                      tr("Save As"),
2198                      mSlicerManagers[index]->GetFileName().c_str(),
2199                      Extensions);
2200   if (!fileName.isEmpty()) {
2201     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2202     if (OutputListeFormat.contains(
2203           fileformat.c_str())) {
2204       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2205       std::string action = "Saving";
2206       vvProgressDialog progress("Saving "+fileName.toStdString());
2207       qApp->processEvents();
2208       vvImageWriter::Pointer writer = vvImageWriter::New();
2209       writer->SetOutputFileName(fileName.toStdString());
2210       writer->SetInput(mSlicerManagers[index]->GetImage());
2211       writer->Update();
2212       QApplication::restoreOverrideCursor();
2213       if (writer->GetLastError().size()) {
2214         QString error = "Saving did not succeed\n";
2215         error += writer->GetLastError().c_str();
2216         QMessageBox::information(this,tr("Saving Problem"),error);
2217         SaveAs();
2218       }
2219     } else {
2220       QString error = fileformat.c_str();
2221       if (error.isEmpty())
2222         error += "no file format specified !";
2223       else
2224         error += " format unknown !!!\n";
2225       QMessageBox::information(this,tr("Saving Problem"),error);
2226       SaveAs();
2227     }
2228   }
2229 }
2230 //------------------------------------------------------------------------------
2231
2232
2233 //------------------------------------------------------------------------------
2234 void vvMainWindow::AddLink(QString image1,QString image2)
2235 {
2236   unsigned int sm1 = 0;
2237   unsigned int sm2 = 0;
2238
2239   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2240     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2241       mSlicerManagers[i]->AddLink(image2.toStdString());
2242       sm1 = i;
2243     }
2244     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2245       mSlicerManagers[i]->AddLink(image1.toStdString());
2246       sm2 = i;
2247     }
2248   }
2249
2250   if (linkPanel->isLinkAll())   {
2251     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2252     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2253   } else {
2254     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2255   }
2256 }
2257
2258 //------------------------------------------------------------------------------
2259
2260
2261 //------------------------------------------------------------------------------
2262 void vvMainWindow::RemoveLink(QString image1,QString image2)
2263 {
2264   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2265     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2266       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2267     }
2268     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2269       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2270     }
2271   }
2272 }
2273 //------------------------------------------------------------------------------
2274
2275 //------------------------------------------------------------------------------
2276 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2277 {
2278   int index = 0;
2279   while(sm != mSlicerManagers[index])
2280     index++;
2281   index = (index+offset) % mSlicerManagers.size();
2282
2283   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2284   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2285   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2286   DisplayChanged(item,slicer+1);
2287 }
2288 //------------------------------------------------------------------------------
2289
2290 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2291 {
2292   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2293     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2294       for (int j = 0; j < 4; j++) {
2295         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2296         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2297         //UpdateTSlice(j,value);
2298       }
2299       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2300       break;
2301     }
2302   }
2303 }
2304 //------------------------------------------------------------------------------
2305
2306
2307 //------------------------------------------------------------------------------
2308 void vvMainWindow::NOHorizontalSliderMoved()
2309 {
2310   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2311   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2312 //  mCurrentTime = NOHorizontalSlider->value();
2313 }
2314 //------------------------------------------------------------------------------
2315
2316
2317 //------------------------------------------------------------------------------
2318 void vvMainWindow::NEHorizontalSliderMoved()
2319 {
2320   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2321   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2322 //  mCurrentTime = NEHorizontalSlider->value();
2323 }
2324 //------------------------------------------------------------------------------
2325
2326
2327 //------------------------------------------------------------------------------
2328 void vvMainWindow::SOHorizontalSliderMoved()
2329 {
2330   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2331   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2332   // mCurrentTime = SOHorizontalSlider->value();
2333 }
2334 //------------------------------------------------------------------------------
2335
2336
2337 //------------------------------------------------------------------------------
2338 void vvMainWindow::SEHorizontalSliderMoved()
2339 {
2340   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2341   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2342   // mCurrentTime = SEHorizontalSlider->value();
2343 }
2344 //------------------------------------------------------------------------------
2345
2346 //------------------------------------------------------------------------------
2347 void vvMainWindow::NOVerticalSliderChanged()
2348 {
2349   static int value=-1;
2350   if (value == NOVerticalSlider->value()) return;
2351   else value = NOVerticalSlider->value();
2352   //  int value = NOVerticalSlider->value();
2353   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2354     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2355       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2356         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2357         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2358
2359         // If nor Update/Render -> slider not work
2360         // only render = ok navigation, but for contour Update needed but slower ?
2361
2362         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2363         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2364       }
2365       break;
2366     }
2367   }
2368 }
2369 //------------------------------------------------------------------------------
2370
2371
2372 //------------------------------------------------------------------------------
2373 void vvMainWindow::NEVerticalSliderChanged()
2374 {
2375   static int value=-1;
2376   if (value == NEVerticalSlider->value()) return;
2377   else value = NEVerticalSlider->value();
2378   //  int value = NEVerticalSlider->value();
2379   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2380     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2381       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2382         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2383         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2384         mSlicerManagers[i]->UpdateSlice(1);
2385         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2386       }
2387       break;
2388     }
2389   }
2390 }
2391 //------------------------------------------------------------------------------
2392
2393
2394 //------------------------------------------------------------------------------
2395 void vvMainWindow::SOVerticalSliderChanged()
2396 {
2397   static int value=-1;
2398   if (value == SOVerticalSlider->value()) return;
2399   else value = SOVerticalSlider->value();
2400   //int value = SOVerticalSlider->value();
2401   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2402     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2403       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2404         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2405         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2406         mSlicerManagers[i]->UpdateSlice(2);
2407         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2408       }
2409       // else { DD("avoid SOVerticalSlider slicer update"); }
2410       break;
2411     }
2412   }
2413 }
2414 //------------------------------------------------------------------------------
2415
2416
2417 //------------------------------------------------------------------------------
2418 void vvMainWindow::SEVerticalSliderChanged()
2419 {
2420   static int value=-1;
2421   if (value == SEVerticalSlider->value()) return;
2422   else value = SEVerticalSlider->value();
2423   // int value = SEVerticalSlider->value();
2424   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2425     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2426       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2427         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2428         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2429         mSlicerManagers[i]->UpdateSlice(3);
2430         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2431       }
2432       break;
2433     }
2434   }
2435 }
2436 //------------------------------------------------------------------------------
2437
2438
2439 //------------------------------------------------------------------------------
2440 void vvMainWindow::UpdateSlice(int slicer, int slice)
2441 {
2442   // DD("vvMainWindow::UpdateSlice");
2443 //   DD(slicer);
2444 //   DD(slice);
2445   if (slicer == 0) {
2446     //    if (slice != NOVerticalSlider->value())
2447     NOVerticalSlider->setValue(slice);
2448   } else {
2449     if (slicer == 1)
2450       NEVerticalSlider->setValue(slice);
2451     else {
2452       if (slicer == 2)
2453         SOVerticalSlider->setValue(slice);
2454       else {
2455         if (slicer == 3)
2456           SEVerticalSlider->setValue(slice);
2457       }
2458     }
2459   }
2460   // DD("vvMainWindow:UpdateSlice END");
2461 }
2462 //------------------------------------------------------------------------------
2463
2464
2465 //------------------------------------------------------------------------------
2466 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2467 {
2468   switch (slicer) {
2469   case 0:
2470     NOHorizontalSlider->setValue(slice);
2471     break;
2472   case 1:
2473     NEHorizontalSlider->setValue(slice);
2474     break;
2475   case 2:
2476     SOHorizontalSlider->setValue(slice);
2477     break;
2478   case 3:
2479     SEHorizontalSlider->setValue(slice);
2480     break;
2481   }
2482 }
2483 //------------------------------------------------------------------------------
2484
2485
2486 //------------------------------------------------------------------------------
2487 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2488 {
2489   int position = int((min+max)/2);
2490   int tPosition = int((tmin+tmax)/2);
2491   if (slicer == 0) {
2492     NOVerticalSlider->setValue(position);
2493     NOVerticalSlider->setRange(min,max);
2494     NOHorizontalSlider->setRange(tmin,tmax);
2495     NOHorizontalSlider->setValue(tPosition);
2496   } else if (slicer == 1) {
2497     NEVerticalSlider->setValue(position);
2498     NEVerticalSlider->setRange(min,max);
2499     NEHorizontalSlider->setRange(tmin,tmax);
2500     NEHorizontalSlider->setValue(tPosition);
2501   } else if (slicer == 2) {
2502     SOVerticalSlider->setValue(position);
2503     SOVerticalSlider->setRange(min,max);
2504     SOHorizontalSlider->setRange(tmin,tmax);
2505     SOHorizontalSlider->setValue(tPosition);
2506   } else if (slicer == 3) {
2507     SEVerticalSlider->setValue(position);
2508     SEVerticalSlider->setRange(min,max);
2509     SEHorizontalSlider->setRange(tmin,tmax);
2510     SEHorizontalSlider->setValue(tPosition);
2511   }
2512 }
2513 //------------------------------------------------------------------------------
2514
2515
2516 //------------------------------------------------------------------------------
2517 void vvMainWindow::SaveNOScreenshot()
2518 {
2519   SaveScreenshot(NOViewWidget);
2520 }
2521 //------------------------------------------------------------------------------
2522
2523
2524 //------------------------------------------------------------------------------
2525 void vvMainWindow::SaveNEScreenshot()
2526 {
2527   SaveScreenshot(NEViewWidget);
2528 }
2529 //------------------------------------------------------------------------------
2530
2531
2532 //------------------------------------------------------------------------------
2533 void vvMainWindow::SaveSOScreenshot()
2534 {
2535   SaveScreenshot(SOViewWidget);
2536 }
2537 //------------------------------------------------------------------------------
2538
2539
2540 //------------------------------------------------------------------------------
2541 void vvMainWindow::SaveSEScreenshot()
2542 {
2543   SaveScreenshot(SEViewWidget);
2544 }
2545 //------------------------------------------------------------------------------
2546
2547
2548 //------------------------------------------------------------------------------
2549 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
2550 {
2551   QString Extensions = "Images( *.png);;";
2552   Extensions += "Images( *.jpg);;";
2553   Extensions += "Images( *.bmp);;";
2554   Extensions += "Images( *.tif);;";
2555   Extensions += "Images( *.ppm)";
2556 #ifdef VTK_USE_FFMPEG_ENCODER
2557   Extensions += "Images( *.avi)";
2558 #endif
2559 #ifdef VTK_USE_MPEG2_ENCODER
2560   Extensions += "Images( *.mpg)";
2561 #endif
2562
2563   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2564   QString fileName = QFileDialog::getSaveFileName(this,
2565                      tr("Save As"),
2566                      itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
2567                      Extensions);
2568
2569   if (!fileName.isEmpty()) {
2570     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2571     w2i->SetInput(widget->GetRenderWindow());
2572     w2i->Update();
2573     vtkImageData *image = w2i->GetOutput();
2574
2575     const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2576     if (!strcmp(ext, ".bmp")) {
2577       vtkBMPWriter *bmp = vtkBMPWriter::New();
2578       bmp->SetInput(image);
2579       bmp->SetFileName(fileName.toStdString().c_str());
2580       bmp->Write();
2581       bmp->Delete();
2582     } else if (!strcmp(ext, ".tif")) {
2583       vtkTIFFWriter *tif = vtkTIFFWriter::New();
2584       tif->SetInput(image);
2585       tif->SetFileName(fileName.toStdString().c_str());
2586       tif->Write();
2587       tif->Delete();
2588     } else if (!strcmp(ext, ".ppm")) {
2589       vtkPNMWriter *pnm = vtkPNMWriter::New();
2590       pnm->SetInput(image);
2591       pnm->SetFileName(fileName.toStdString().c_str());
2592       pnm->Write();
2593       pnm->Delete();
2594     } else if (!strcmp(ext, ".png")) {
2595       vtkPNGWriter *png = vtkPNGWriter::New();
2596       png->SetInput(image);
2597       png->SetFileName(fileName.toStdString().c_str());
2598       png->Write();
2599       png->Delete();
2600     } else if (!strcmp(ext, ".jpg")) {
2601       vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2602       jpg->SetInput(image);
2603       jpg->SetFileName(fileName.toStdString().c_str());
2604       jpg->Write();
2605       jpg->Delete();
2606 #ifdef VTK_USE_FFMPEG_ENCODER
2607     } else if (!strcmp(ext, ".avi")) {
2608       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
2609       mpg->SetInput(image);
2610       mpg->SetFileName(fileName.toStdString().c_str());
2611       mpg->SetQuality(2);
2612       mpg->SetRate(5);
2613       mpg->Start();
2614
2615       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2616       int nSlice = vvImg->GetVTKImages().size();
2617       for(int i=0; i<nSlice; i++) {
2618         mSlicerManagers[smIndex]->SetNextTSlice(0);
2619         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2620         w2i->SetInput(widget->GetRenderWindow());
2621         w2i->Update();
2622         mpg->SetInput(w2i->GetOutput());
2623         mpg->Write();
2624       }
2625       mpg->End();
2626       mpg->Delete();
2627 #endif
2628 #ifdef VTK_USE_MPEG2_ENCODER
2629     } else if (!strcmp(ext, ".mpg")) {
2630       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
2631       mpg->SetInput(image);
2632       mpg->SetFileName(fileName.toStdString().c_str());
2633       mpg->Start();
2634
2635       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2636       int nSlice = vvImg->GetVTKImages().size();
2637       for(int i=0; i<nSlice; i++) {
2638         mSlicerManagers[smIndex]->SetNextTSlice(0);
2639         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2640         w2i->SetInput(widget->GetRenderWindow());
2641         w2i->Update();
2642         mpg->SetInput(w2i->GetOutput());
2643         mpg->Write();
2644       }
2645       mpg->End();
2646       mpg->Delete();
2647 #endif
2648     } else {
2649       QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2650     }
2651   }
2652 }
2653 //------------------------------------------------------------------------------
2654
2655
2656 //------------------------------------------------------------------------------
2657 void vvMainWindow::GoToCursor()
2658 {
2659   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2660   for (int column = 1; column < 5; column++) {
2661     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
2662       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2663       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2664         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2665       mSlicerManagers[index]->UpdateViews(1,column-1);
2666       mSlicerManagers[index]->UpdateLinked(column-1);
2667       break;
2668     }
2669   }
2670 }
2671 //------------------------------------------------------------------------------
2672
2673 //------------------------------------------------------------------------------
2674 void vvMainWindow::PlayPause()
2675 {
2676   if (playMode) {
2677     playMode = 0;
2678     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2679     ImageInfoChanged();
2680     return;
2681   } else {
2682     int image_number=DataTree->topLevelItemCount();
2683     bool has_temporal;
2684     for (int i=0; i<image_number; i++)
2685       if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1) {
2686         has_temporal=true;
2687         break;
2688       }
2689     if (has_temporal) {
2690       playMode = 1;
2691       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2692       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2693     }
2694   }
2695 }
2696 //------------------------------------------------------------------------------
2697
2698 //------------------------------------------------------------------------------
2699 void vvMainWindow::PlayNext()
2700 {
2701   if (playMode && !this->isHidden()) {
2702     int image_number=DataTree->topLevelItemCount();
2703     ///Only play one slicer per SM, and only if the SM is being displayed
2704     for (int i=0; i<image_number; i++)
2705       for (int j=0; j<4; j++)
2706         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2707             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
2708           mSlicerManagers[i]->SetNextTSlice(j);
2709           break;
2710         }
2711     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2712   }
2713 }
2714 //------------------------------------------------------------------------------
2715
2716 void vvMainWindow::ShowLastImage()
2717 {
2718   if (mSlicerManagers.size() > 1) {
2719     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2720     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2721     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2722     DisplayChanged(item,1);
2723   }
2724 }
2725
2726 //------------------------------------------------------------------------------
2727 void vvMainWindow::UpdateRenderWindows()
2728 {
2729   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2730   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2731   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2732   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2733 }
2734 //------------------------------------------------------------------------------
2735
2736 //------------------------------------------------------------------------------
2737 void vvMainWindow::SegmentationOnCurrentImage()
2738 {
2739   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2740
2741   vvSegmentationDialog segmentation;
2742   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2743   segmentation.exec();
2744 }
2745 //------------------------------------------------------------------------------
2746
2747 void vvMainWindow::SurfaceViewerLaunch()
2748 {
2749   vvSurfaceViewerDialog surfaceViewer;
2750   surfaceViewer.exec();
2751 }
2752 //------------------------------------------------------------------------------
2753
2754
2755 //------------------------------------------------------------------------------
2756 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
2757 {
2758   int number=0;
2759   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
2760     vvSlicerManager * v = mSlicerManagers[l];
2761     if (v->GetBaseFileName() ==
2762         vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
2763       number = std::max(number, v->GetBaseFileNameNumber()+1);
2764     }
2765   }
2766   return number;
2767 }
2768 //------------------------------------------------------------------------------
2769
2770
2771 //------------------------------------------------------------------------------
2772 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2773 {
2774   // Change filename if another image exist with the same name
2775   int number = GetImageDuplicateFilenameNumber(filename);
2776
2777   // Create new SliceManager
2778   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
2779   slicer_manager->SetImage(image);//, IMAGE, number);
2780   //  filename = filename+"_"+clitk::toString(number);
2781   slicer_manager->SetFilename(filename, number);
2782   mSlicerManagers.push_back(slicer_manager);
2783
2784   //create an item in the tree with good settings
2785   QTreeWidgetItem *item = new QTreeWidgetItem();
2786   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2787   item->setData(1,Qt::UserRole,tr("image"));
2788   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
2789   qApp->processEvents();
2790
2791   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2792
2793   //Create the buttons for reload and close
2794   qApp->processEvents();
2795   QTreePushButton* cButton = new QTreePushButton;
2796   cButton->setItem(item);
2797   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2798   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2799   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2800           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2801
2802   QTreePushButton* rButton = new QTreePushButton;
2803   rButton->setItem(item);
2804   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2805   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2806   rButton->setEnabled(0);
2807   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2808           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2809
2810   DataTree->addTopLevelItem(item);
2811   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2812   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2813
2814   //set the id of the image
2815   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2816   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2817   mSlicerManagers.back()->SetId(id.toStdString());
2818
2819   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
2820                       , id.toStdString());
2821
2822   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
2823           this, SLOT(CurrentImageChanged(std::string)));
2824   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
2825           this, SLOT(CurrentPickedImageChanged(std::string)));
2826   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
2827           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2828   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
2829           this, SLOT(VectorChanged(int,double,double,double, double)));
2830   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
2831           this, SLOT(OverlayChanged(int,double,double)));
2832   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
2833           this, SLOT(FusionChanged(int,double)));
2834   connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
2835           this,SLOT(WindowsChanged(int, int, int)));
2836   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
2837           this,SLOT(WindowLevelChanged(double, double, int, int)));
2838   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
2839           this,SLOT(UpdateSlice(int,int)));
2840   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
2841           this,SLOT(UpdateTSlice(int, int)));
2842   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2843           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2844   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2845           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2846   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
2847           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
2848   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
2849           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
2850   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2851   UpdateTree();
2852   qApp->processEvents();
2853   InitSlicers();
2854   ShowLastImage();
2855   InitDisplay();
2856   qApp->processEvents();
2857
2858   // End
2859   ImageInfoChanged();
2860   return slicer_manager;
2861 }
2862 //------------------------------------------------------------------------------
2863
2864
2865 //------------------------------------------------------------------------------
2866 void vvMainWindow::UpdateCurrentSlicer()
2867 {
2868   int index = -1;
2869   if (DataTree->selectedItems().size() > 0) {
2870     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2871   }
2872   mSlicerManagerCurrentIndex = index;
2873 }
2874 //------------------------------------------------------------------------------
2875