vv/vvMainWindow.cxx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://www.centreleonberard.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17 ===========================================================================**/
  18
  19 #include <algorithm>
  20 #include <QMessageBox>
  21 #include <QInputDialog>
  22 #include <QTimer>
  23 #include "QTreePushButton.h"
  24 #include <QUrl>
  25
  26 // VV include
  27 #include "vvMainWindow.h"
  28 #include "vvHelpDialog.h"
  29 #include "vvRegisterForm.h"
  30 #include "vvDocumentation.h"
  31 #include "vvProgressDialog.h"
  32 #include "vvQDicomSeriesSelector.h"
  33 #include "vvSlicerManager.h"
  34 #include "clitkImageCommon.h"
  35 #include "vvSlicer.h"
  36 #include "vvInteractorStyleNavigator.h"
  37 #include "vvImageWriter.h"
  38 #include "vvSegmentationDialog.h"
  39 #include "vvSurfaceViewerDialog.h"
  40 #include "vvDeformationDialog.h"
  41 #include "vvImageWarp.h"
  42 #include "vvUtils.h"
  43 #include "vvMidPosition.h"
  44 #include "vvMesh.h"
  45 #include "vvStructSelector.h"
  46 #include "vvMeshReader.h"
  47 #include "clitkConfiguration.h"
  48
  49 // ITK include
  50 #include <itkImage.h>
  51 #include <itkImageFileReader.h>
  52 #include <itkByteSwapper.h>
  53 #include <itkCommand.h>
  54 #include <itkNumericSeriesFileNames.h>
  55
  56 // VTK include
  57 #include <vtkImageData.h>
  58 #include <vtkImageActor.h>
  59 #include <vtkCornerAnnotation.h>
  60 #include <vtkRenderWindow.h>
  61 #include <vtkRenderWindowInteractor.h>
  62 #include <vtkRenderer.h>
  63 #include <vtkRendererCollection.h>
  64 #include <vtkWindowToImageFilter.h>
  65 #include <vtkBMPWriter.h>
  66 #include <vtkTIFFWriter.h>
  67 #include <vtkPNMWriter.h>
  68 #include <vtkPNGWriter.h>
  69 #include <vtkJPEGWriter.h>
  70 #include <vtkFFMPEGWriter.h>
  71 #ifdef VTK_USE_MPEG2_ENCODER
  72   #include <vtkMPEG2Writer.h>
  73 #endif
  74 #include <vtkMatrix4x4.h>
  75 #include <vtkTransform.h>
  76
  77 // Standard includes
  78 #include <iostream>
  79 #include <sstream>
  80 #include <iomanip>
  81
  82 #define COLUMN_TREE 0
  83 #define COLUMN_UL_VIEW 1
  84 #define COLUMN_UR_VIEW 2
  85 #define COLUMN_DL_VIEW 3
  86 #define COLUMN_DR_VIEW 4
  87 #define COLUMN_CLOSE_IMAGE 5
  88 #define COLUMN_RELOAD_IMAGE 6
  89 #define COLUMN_IMAGE_NAME 7
  90
  91 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN )"
  92
  93 /*Data Tree values
  94   0,Qt::UserRole full filename
  95   1,Qt::CheckStateRole checkbutton UL View
  96   1,Qt::UserRole overlay, fusion or vector
  97   2,Qt::CheckStateRole checkbutton UR View
  98   3,Qt::CheckStateRole checkbutton DL View
  99   4,Qt::CheckStateRole checkbutton DR View
 100   5,0  short filename
 101   5,Qt::UserRole mSlicerManager id*/
 102
 103 //------------------------------------------------------------------------------
 104 vvMainWindow::vvMainWindow():vvMainWindowBase()
 105 {
 106   setupUi(this); // this sets up the GUI
 107
 108   mInputPathName = "";
 109   mMenuTools = menuTools;
 110   //  mMenuSegmentation = menuSegmentation;
 111   mContextMenu = &contextMenu;
 112   mMenuExperimentalTools = menuExperimental;
 113   mMainWidget = this;
 114   mCurrentTime = -1;
 115   mCurrentSelectedImageId = "";
 116   mCurrentPickedImageId = "";
 117   mCurrentPickedImageIndex = 0;
 118
 119   //Init the contextMenu
 120   this->setContextMenuPolicy(Qt::CustomContextMenu);
 121   contextActions.resize(0);
 122   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 123                                   tr("O&pen new Image"));
 124   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 125   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 126   contextActions.push_back(actionOpen_new_image);
 127   contextMenu.addSeparator();
 128
 129   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 130                                tr("Close Current Image"));
 131   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 132   contextActions.push_back(actionClose_Image);
 133
 134   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 135                                 tr("Reload Current Image"));
 136   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 137   contextActions.push_back(actionReload_image);
 138
 139   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 140                               tr("Save Current Image"));
 141   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 142   contextActions.push_back(actionSave_image);
 143
 144   contextMenu.addSeparator();
 145
 146   contextMenu.addAction(actionAdd_VF_to_current_Image);
 147   contextActions.push_back(actionAdd_VF_to_current_Image);
 148
 149   QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 150       tr("Add overlay image to current image"));
 151   contextMenu.addAction(actionAdd_Overlay_to_current_Image);
 152   contextActions.push_back(actionAdd_Overlay_to_current_Image);
 153
 154   connect(actionAdd_Overlay_to_current_Image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 155
 156   contextMenu.addAction(actionAdd_fusion_image);
 157   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 158   contextActions.push_back(actionAdd_fusion_image);
 159
 160   // TRIAL DS
 161   /*
 162   QMenu * m = new QMenu(menubar);
 163   m->setTitle("TOTO");
 164   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 165   contextMenu.addMenu(m);
 166   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 167                      tr("BIDON"));
 168   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 169                      tr("BIDON2"));
 170   m->addAction(a);
 171   m->addAction(b);
 172   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 173   */
 174
 175   //init the DataTree
 176   mSlicerManagers.resize(0);
 177
 178   QStringList header;
 179   header.append("");
 180   header.append("TL");
 181   header.append("TR");
 182   header.append("BL");
 183   header.append("BR");
 184   header.append("");
 185   header.append("");
 186   header.append("Name");
 187
 188   DataTree->setHeaderLabels(header);
 189   DataTree->resizeColumnToContents(COLUMN_TREE);
 190   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 191   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 192   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 193   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 194   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 195   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 196   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 197
 198   viewMode = 1;
 199   documentation = new vvDocumentation();
 200   help_dialog = new vvHelpDialog();
 201   dicomSeriesSelector = new vvDicomSeriesSelector();
 202
 203   inverseButton->setEnabled(0);
 204   actionAdd_Overlay_to_current_Image->setEnabled(0);
 205   actionSave_As->setEnabled(0);
 206   actionAdd_VF_to_current_Image->setEnabled(0);
 207   actionAdd_fusion_image->setEnabled(0);
 208
 209   //init the sliders
 210   verticalSliders.push_back(NOVerticalSlider);
 211   verticalSliders.push_back(NEVerticalSlider);
 212   verticalSliders.push_back(SOVerticalSlider);
 213   verticalSliders.push_back(SEVerticalSlider);
 214
 215   for (int i =0; i < 4; i++)
 216     verticalSliders[i]->hide();
 217
 218   horizontalSliders.push_back(NOHorizontalSlider);
 219   horizontalSliders.push_back(NEHorizontalSlider);
 220   horizontalSliders.push_back(SOHorizontalSlider);
 221   horizontalSliders.push_back(SEHorizontalSlider);
 222
 223   for (int i =0; i < 4; i++)
 224     horizontalSliders[i]->hide();
 225
 226
 227   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 228   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 229   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 230   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 231
 232   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 233   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 234   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 235   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 236
 237   //connect everything
 238   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 239   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 240   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 241   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 242   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 243   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 244   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 245   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 246   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 247   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 248   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 249   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 250   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 251   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 252   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 253   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 254
 255   ///////////////////////////////////////////////
 256   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 257   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 258   ///////////////////////////////////////////////
 259
 260   actionNorth_East_Window->setEnabled(0);
 261   actionNorth_West_Window->setEnabled(0);
 262   actionSouth_East_Window->setEnabled(0);
 263   actionSouth_West_Window->setEnabled(0);
 264
 265   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 266   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 267   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 268   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 269
 270   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 271   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 272           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 273
 274   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 275   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 276   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 277   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 278   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 279   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 280   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 281
 282
 283   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 284
 285   connect(linkPanel,SIGNAL(addLink(QString,QString)),this,SLOT(AddLink(QString,QString)));
 286   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 287   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 288   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int)),this,SLOT(SetOverlayProperty(int)));
 289   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,double,double)),
 290           this,SLOT(SetFusionProperty(int,int,double,double)));
 291   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 292
 293   playMode = 0;//pause
 294   mFrameRate = 10;
 295   playButton->setEnabled(0);
 296   frameRateLabel->setEnabled(0);
 297   frameRateSpinBox->setEnabled(0);
 298   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 299   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 300
 301   goToCursorPushButton->setEnabled(0);
 302   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 303
 304   NOViewWidget->hide();
 305   NEViewWidget->hide();
 306   SOViewWidget->hide();
 307   SEViewWidget->hide();
 308
 309   //Recently opened files
 310   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 311   recentlyOpenedFilesMenu=NULL;
 312   if ( !recent_files.empty() ) {
 313     createRecentlyOpenedFilesMenu();
 314     updateRecentlyOpenedFilesMenu(recent_files);
 315   }
 316
 317   // Adding all new tools (insertion in the menu)
 318   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 319
 320   if (!CLITK_EXPERIMENTAL)
 321     menuExperimental->menuAction()->setVisible(false);
 322
 323
 324   QTimer * timerMemory = new QTimer(this);
 325   //timerMemory->setInterval(5);
 326   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 327   timerMemory->start(2000);
 328 }
 329 //------------------------------------------------------------------------------
 330
 331 void vvMainWindow::show(){
 332  vvMainWindowBase::show();
 333   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://localhost/vvregister/write.php"));
 334   if(registerForm->canPush()){
 335       registerForm->show();
 336       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
 337   }
 338 }
 339 //------------------------------------------------------------------------------
 340 void vvMainWindow::UpdateMemoryUsage()
 341 {
 342   //  clitk::PrintMemory(true);
 343   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 344   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 345 }
 346 //------------------------------------------------------------------------------
 347
 348
 349 //------------------------------------------------------------------------------
 350 void vvMainWindow::createRecentlyOpenedFilesMenu()
 351 {
 352     recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
 353     recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 354     menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
 355     menuFile->insertSeparator(actionOpen_Image_With_Time);
 356 }
 357 //------------------------------------------------------------------------------
 358
 359
 360 //------------------------------------------------------------------------------
 361
 362 void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
 363 {
 364   if(recentlyOpenedFilesMenu==NULL){
 365     createRecentlyOpenedFilesMenu();
 366   }else{
 367     recentlyOpenedFilesMenu->clear();
 368   }
 369   for (std::list<std::string>::const_iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 370     QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")), i->c_str(),this);
 371     recentlyOpenedFilesMenu->addAction(current);
 372     connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 373   }
 374 }
 375 //------------------------------------------------------------------------------
 376
 377
 378 //------------------------------------------------------------------------------
 379 void vvMainWindow::ComputeMidPosition()
 380 {
 381   bool ok;
 382   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 383   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 384                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 385   if (ok) {
 386     vvMidPosition midp;
 387     midp.slicer_manager = mSlicerManagers[index];
 388     midp.reference_image_index = ref;
 389     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 390     midp.Update();
 391     if (midp.error)
 392       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 393     else {
 394       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 395       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 396     }
 397     QApplication::restoreOverrideCursor();
 398   }
 399 }
 400 //------------------------------------------------------------------------------
 401
 402
 403 //------------------------------------------------------------------------------
 404 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 405 {
 406   QTreeWidgetItem *item = new QTreeWidgetItem();
 407   item->setData(0,Qt::UserRole,"filename.vtk");
 408   item->setData(1,Qt::UserRole,tr("contour"));
 409   QBrush brush;
 410   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 411   brush.setStyle(Qt::SolidPattern);
 412   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 413   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 414
 415   for (int j = 1; j <= 4; j++)
 416     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 417
 418   QTreePushButton* cButton = new QTreePushButton;
 419   cButton->setItem(item);
 420   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 421   cButton->setToolTip(tr("close image"));
 422   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 423   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 424           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 425
 426   QTreePushButton* rButton = new QTreePushButton;
 427   rButton->setItem(item);
 428   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 429   rButton->setToolTip(tr("reload image"));
 430   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 431   rButton->setEnabled(false);
 432   //Not implemented
 433   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 434   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 435
 436   DataTree->topLevelItem(image_index)->setExpanded(1);
 437   DataTree->topLevelItem(image_index)->addChild(item);
 438   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 439   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 440   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 441   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 442
 443   UpdateTree();
 444   mSlicerManagers[image_index]->AddContour(contour,propagation);
 445   mSlicerManagers[image_index]->Render();
 446 }
 447 //------------------------------------------------------------------------------
 448
 449
 450 //------------------------------------------------------------------------------
 451 void vvMainWindow::OpenVTKContour()
 452 {
 453   if (mSlicerManagers.size() > 0) {
 454     QString Extensions = "Images ( *.vtk *.obj)";
 455     Extensions += ";;All Files (*)";
 456     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 457     if (file.isNull())
 458       return;
 459     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 460     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 461     vvMeshReader reader;
 462     reader.SetImage(mSlicerManagers[index]->GetImage());
 463     reader.SetModeToVTK();
 464     reader.SetFilename(file.toStdString());
 465     reader.Update();
 466     AddContour(index,reader.GetOutput()[0],false);
 467     QApplication::restoreOverrideCursor();
 468   }
 469 }
 470 //------------------------------------------------------------------------------
 471
 472
 473 //------------------------------------------------------------------------------
 474 void vvMainWindow::OpenDCStructContour()
 475 {
 476   if (mSlicerManagers.size() > 0) {
 477     QString Extensions = "Dicom Files ( *.dcm RS*)";
 478     Extensions += ";;All Files (*)";
 479     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 480     if (file.isNull())
 481       return;
 482     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 483     vvMeshReader reader;
 484     reader.SetFilename(file.toStdString());
 485     vvStructSelector selector;
 486     selector.SetStructures(reader.GetROINames());
 487     if (!mSlicerManagers[index]->GetVF().IsNull())
 488       selector.EnablePropagationCheckBox();
 489     if (selector.exec()) {
 490       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 491       reader.SetSelectedItems(selector.getSelectedItems());
 492       reader.SetImage(mSlicerManagers[index]->GetImage());
 493       if (selector.PropagationEnabled())
 494         reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 495       reader.Update();
 496       std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 497       for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 498            i!=contours.end(); i++)
 499         AddContour(index,*i,selector.PropagationEnabled());
 500       QApplication::restoreOverrideCursor();
 501     }
 502   }
 503 }
 504 //------------------------------------------------------------------------------
 505
 506
 507 //------------------------------------------------------------------------------
 508 void vvMainWindow::ComputeDeformableRegistration()
 509 {
 510   if (mSlicerManagers.size() > 0) {
 511     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 512     vvDeformationDialog dialog(index,mSlicerManagers);
 513     if (dialog.exec()) {
 514       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 515       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 516       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 517     } else
 518       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 519   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 520 }
 521 //------------------------------------------------------------------------------
 522
 523
 524 //------------------------------------------------------------------------------
 525 void vvMainWindow::WarpImage()
 526 {
 527   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 528   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 529     bool ok;
 530     int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 531                                        mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 532     if (ok) {
 533       WarpImage(mSlicerManagers[index],ref);
 534     }
 535   } else
 536     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 537 }
 538 //------------------------------------------------------------------------------
 539
 540
 541 //------------------------------------------------------------------------------
 542 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 543 {
 544   if (!selected_slicer->GetVF().IsNull()) {
 545     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 546     QFileInfo info(selected_slicer->GetFileName().c_str());
 547     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 548                      reference_phase,this);
 549     if (warp.ComputeWarpedImage()) {
 550       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 551       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 552       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 553       QApplication::restoreOverrideCursor();
 554     } else {
 555       QApplication::restoreOverrideCursor();
 556       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 557     }
 558   } else
 559     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 560 }
 561 //------------------------------------------------------------------------------
 562
 563
 564 //------------------------------------------------------------------------------
 565 vvMainWindow::~vvMainWindow()
 566 {
 567   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 568     if (mSlicerManagers[i] != NULL)
 569       delete mSlicerManagers[i];
 570   }
 571 }
 572 //------------------------------------------------------------------------------
 573
 574 //------------------------------------------------------------------------------
 575 QTabWidget * vvMainWindow::GetTab()
 576 {
 577   return tabWidget;
 578 }
 579 //------------------------------------------------------------------------------
 580
 581
 582 //------------------------------------------------------------------------------
 583 void vvMainWindow::MergeImages()
 584 {
 585   QString Extensions = EXTENSIONS;
 586   Extensions += ";;All Files (*)";
 587   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 588   if (files.isEmpty())
 589     return;
 590   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 591   std::vector<std::string> vector;
 592
 593   unsigned int currentDim = 0;
 594   std::vector<double> currentSpacing;
 595   std::vector<int> currentSize;
 596   std::vector<double> currentOrigin;
 597
 598   for (int i = 0; i < files.size(); i++) {
 599     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 600                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 601     reader->SetFileName(files[i].toStdString().c_str());
 602     reader->ReadImageInformation();
 603     if (reader)        {
 604       //NOViewWidget->hide();
 605       //NEViewWidget->hide();
 606       //SOViewWidget->hide();
 607       //SEViewWidget->hide();
 608       if (i == 0)
 609         currentDim = reader->GetNumberOfDimensions();
 610       bool IsOk = true;
 611       for (unsigned int j = 0; j < currentDim; j++) {
 612         if (i == 0) {
 613           if (j == 0) {
 614             currentSpacing.resize(currentDim);
 615             currentSize.resize(currentDim);
 616             currentOrigin.resize(currentDim);
 617           }
 618           currentOrigin[j] = reader->GetOrigin(j);
 619           currentSpacing[j] = reader->GetSpacing(j);
 620           currentSize[j] = reader->GetDimensions(j);
 621         } else if (currentDim != reader->GetNumberOfDimensions()
 622                    || currentSpacing[j] != reader->GetSpacing(j)
 623                    || currentSize[j] != (int)reader->GetDimensions(j)
 624                    || currentOrigin[j] != reader->GetOrigin(j)) {
 625           QString error = "Cannot read file (too different from others ";
 626           error += files[i].toStdString().c_str();
 627           QMessageBox::information(this,tr("Reading problem"),error);
 628           IsOk = false;
 629           break;
 630         }
 631       }
 632       if (IsOk)
 633         vector.push_back(files[i].toStdString());
 634     }
 635   }
 636   if (vector.size() > 0)
 637     LoadImages(vector, vvImageReader::MERGED);
 638 }
 639 //------------------------------------------------------------------------------
 640
 641 //------------------------------------------------------------------------------
 642 void vvMainWindow::SliceImages()
 643 {
 644   QString Extensions = EXTENSIONS;
 645   Extensions += ";;All Files (*)";
 646
 647   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 648   if (files.isEmpty())
 649     return;
 650   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 651   std::vector<std::string> vector;
 652   for (int i = 0; i < files.size(); i++)
 653     vector.push_back(files[i].toStdString());
 654   LoadImages(vector, vvImageReader::SLICED);
 655 }
 656 //------------------------------------------------------------------------------
 657
 658 //------------------------------------------------------------------------------
 659 void vvMainWindow::MergeImagesWithTime()
 660 {
 661   QString Extensions = EXTENSIONS;
 662   Extensions += ";;All Files (*)";
 663   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 664   if (files.isEmpty())
 665     return;
 666   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 667   std::vector<std::string> vector;
 668
 669   unsigned int currentDim = 0;
 670   std::vector<double> currentSpacing;
 671   std::vector<int> currentSize;
 672   std::vector<double> currentOrigin;
 673
 674   for (int i = 0; i < files.size(); i++) {
 675     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 676                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 677     if (reader) {
 678       reader->SetFileName(files[i].toStdString().c_str());
 679       reader->ReadImageInformation();
 680       if (i == 0)
 681         currentDim = reader->GetNumberOfDimensions();
 682       bool IsOk = true;
 683       for (unsigned int j = 0; j < currentDim; j++) {
 684         if (i == 0) {
 685           if (j == 0) {
 686             currentSpacing.resize(currentDim);
 687             currentSize.resize(currentDim);
 688             currentOrigin.resize(currentDim);
 689           }
 690           currentOrigin[j] = reader->GetOrigin(j);
 691           currentSpacing[j] = reader->GetSpacing(j);
 692           currentSize[j] = reader->GetDimensions(j);
 693         } else if (currentDim != reader->GetNumberOfDimensions()
 694                    || currentSpacing[j] != reader->GetSpacing(j)
 695                    || currentSize[j] != (int)reader->GetDimensions(j)
 696                    || currentOrigin[j] != reader->GetOrigin(j)) {
 697           QString error = "Cannot read file (too different from others ";
 698           error += files[i].toStdString().c_str();
 699           QMessageBox::information(this,tr("Reading problem"),error);
 700           IsOk = false;
 701           break;
 702         }
 703       }
 704       if (IsOk)
 705         vector.push_back(files[i].toStdString());
 706     } else {
 707       QString error = "Cannot read file info for ";
 708       error += files[i].toStdString().c_str();
 709       error += "\n";
 710       error += "Maybe you're trying to open an image in an unsupported format?\n";
 711       QMessageBox::information(this,tr("Reading problem"),error);
 712     }
 713   }
 714   sort(vector.begin(),vector.end());
 715   if (vector.size() > 1)
 716     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 717   else
 718     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.");
 719 }
 720 //------------------------------------------------------------------------------
 721
 722
 723 //------------------------------------------------------------------------------
 724 void vvMainWindow::OpenDicom()
 725 {
 726   std::vector<std::string> files;
 727
 728   std::cout << "dicomSeriesSelector " << std::endl;
 729   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 730     files = *(dicomSeriesSelector->GetFilenames());
 731     LoadImages(files, vvImageReader::DICOM);
 732   }
 733 }
 734 //------------------------------------------------------------------------------
 735
 736 //------------------------------------------------------------------------------
 737 void vvMainWindow::OpenImages()
 738 {
 739   QString Extensions = EXTENSIONS;
 740   Extensions += ";;All Files (*)";
 741
 742   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 743   if (files.isEmpty())
 744     return;
 745   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 746   std::vector<std::string> vector;
 747   for (int i = 0; i < files.size(); i++)
 748     vector.push_back(files[i].toStdString());
 749   LoadImages(vector, vvImageReader::IMAGE);
 750 }
 751 //------------------------------------------------------------------------------
 752 void vvMainWindow::OpenRecentImage()
 753 {
 754   QAction * caller = qobject_cast<QAction*>(sender());
 755   std::vector<std::string> images;
 756   images.push_back(caller->text().toStdString());
 757   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 758   LoadImages(images, vvImageReader::IMAGE);
 759 }
 760 //------------------------------------------------------------------------------
 761
 762
 763 //------------------------------------------------------------------------------
 764 void vvMainWindow::OpenImageWithTime()
 765 {
 766   QString Extensions = EXTENSIONS;
 767   Extensions += ";;All Files (*)";
 768
 769   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 770   if (files.isEmpty())
 771     return;
 772   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 773   std::vector<std::string> vector;
 774   for (int i = 0; i < files.size(); i++) {
 775     vector.push_back(files[i].toStdString());
 776   }
 777   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 778 }
 779 //------------------------------------------------------------------------------
 780
 781
 782 //------------------------------------------------------------------------------
 783 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 784 {
 785   //Separate the way to open images and dicoms
 786   int fileSize;
 787   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 788     fileSize = files.size();
 789   else
 790     fileSize = 1;
 791
 792   // For SLICED, we need the number of slices (ndim and #slices)
 793   std::vector<unsigned int> nSlices;
 794   nSlices.resize(files.size());
 795   std::fill(nSlices.begin(), nSlices.end(), 1);
 796   if (filetype == vvImageReader::SLICED) {
 797     for (int i = 0; i < fileSize; i++) {
 798       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 799       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 800       if (!header) {
 801         nSlices[i] = 0;
 802         QString error = "Cannot open file \n";
 803         error += files[i].c_str();
 804         QMessageBox::information(this,tr("Reading problem"),error);
 805         return;
 806       }
 807       if (header->GetNumberOfDimensions() < 3) {
 808         nSlices[i] = 0;
 809         QString error = "Dimension problem. Cannot slice \n";
 810         error += files[i].c_str();
 811         QMessageBox::information(this,tr("Reading problem"),error);
 812         return;
 813       }
 814       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 815     }
 816   }
 817
 818   //Only add to the list of recently opened files when a single file is opened,
 819   //to avoid polluting the list of recently opened files
 820   if (files.size() == 1) {
 821     QFileInfo finfo=tr(files[0].c_str());
 822     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 823     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 824   }
 825   //init the progress events
 826   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 827   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 828   qApp->processEvents();
 829
 830   int numberofsuccesulreads=0;
 831   //open images as 1 or multiples
 832   for (int i = 0; i < fileSize; i++) {
 833
 834     progress.SetText("Opening " + files[i]);
 835     progress.SetProgress(i,fileSize);
 836     qApp->processEvents();
 837
 838     for (unsigned int j = 0; j < nSlices[i]; j++) {
 839       //read the image and put it in mSlicerManagers
 840       vvSlicerManager* imageManager = new vvSlicerManager(4);
 841       qApp->processEvents();
 842
 843       bool SetImageSucceed=false;
 844
 845       // Change filename if an image with the same already exist
 846       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 847
 848       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED)
 849         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 850       else {
 851         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 852       }
 853       if (!SetImageSucceed) {
 854         QApplication::restoreOverrideCursor();
 855         QString error = "Cannot open file \n";
 856         error += imageManager->GetLastError().c_str();
 857         QMessageBox::information(this,tr("Reading problem"),error);
 858         delete imageManager;
 859       } else {
 860         mSlicerManagers.push_back(imageManager);
 861
 862         //create an item in the tree with good settings
 863         QTreeWidgetItem *item = new QTreeWidgetItem();
 864         item->setData(0,Qt::UserRole,files[i].c_str());
 865         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 866         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 867         item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
 868         qApp->processEvents();
 869
 870         //Create the buttons for reload and close
 871         qApp->processEvents();
 872         QTreePushButton* cButton = new QTreePushButton;
 873         cButton->setItem(item);
 874         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 875         cButton->setToolTip(tr("close image"));
 876         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 877         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 878                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 879
 880         QTreePushButton* rButton = new QTreePushButton;
 881         rButton->setItem(item);
 882         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 883         rButton->setToolTip(tr("reload image"));
 884         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 885         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 886                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 887
 888         DataTree->addTopLevelItem(item);
 889         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 890         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 891
 892         //set the id of the image
 893         QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 894         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 895         mSlicerManagers.back()->SetId(id.toStdString());
 896
 897         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 898
 899         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 900                 this,SLOT(CurrentImageChanged(std::string)));
 901         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 902                 this, SLOT(CurrentPickedImageChanged(std::string)));
 903         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 904                 this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 905         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 906                 this, SLOT(VectorChanged(int,double,double,double, double)));
 907         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 908                 this, SLOT(OverlayChanged(int,double,double)));
 909         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 910                 this, SLOT(FusionChanged(int,double)));
 911         connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
 912                 this,SLOT(WindowsChanged(int, int, int)));
 913         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
 914                 this,SLOT(WindowLevelChanged(double, double, int, int)));
 915         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 916                 this,SLOT(UpdateSlice(int,int)));
 917         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 918                 this,SLOT(UpdateTSlice(int, int)));
 919         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 920                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 921         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 922                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 923         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 924                 this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 925         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 926                 this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 927         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 928         InitSlicers();
 929         numberofsuccesulreads++;
 930       }
 931     }
 932   }
 933   if (numberofsuccesulreads) {
 934     NOViewWidget->show();
 935     NEViewWidget->show();
 936     SOViewWidget->show();
 937     SEViewWidget->show();
 938     UpdateTree();
 939     InitDisplay();
 940     ShowLastImage();
 941
 942     // Try to guess default WindowLevel
 943     double range[2];
 944     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 945     if ((range[0] == 0) && (range[1] == 1)) {
 946       presetComboBox->setCurrentIndex(5);// binary
 947     } else {
 948       // TODO
 949     }
 950   }
 951   QApplication::restoreOverrideCursor();
 952 }
 953 //------------------------------------------------------------------------------
 954
 955 //------------------------------------------------------------------------------
 956 void vvMainWindow::UpdateTree()
 957 {
 958   DataTree->resizeColumnToContents(COLUMN_TREE);
 959   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 960   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 961   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 962   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 963   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 964   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 965   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 966 }
 967 //------------------------------------------------------------------------------
 968
 969 //------------------------------------------------------------------------------
 970 void vvMainWindow::CurrentImageChanged(std::string id)
 971 {
 972   if (id == mCurrentSelectedImageId) return; // Do nothing
 973   int selected = 0;
 974   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 975     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 976       selected = i;
 977     } else {
 978       DataTree->topLevelItem(i)->setSelected(0);
 979     }
 980     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 981       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 982
 983   }
 984   DataTree->topLevelItem(selected)->setSelected(1);
 985   mCurrentSelectedImageId = id;
 986   emit SelectedImageHasChanged(mSlicerManagers[selected]);
 987 }
 988 //------------------------------------------------------------------------------
 989
 990 //------------------------------------------------------------------------------
 991 void vvMainWindow::CurrentPickedImageChanged(std::string id)
 992 {
 993   if (id == mCurrentPickedImageId) return; // Do nothing
 994   int selected = 0;
 995   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 996     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 997       selected = i;
 998     } else {
 999       DataTree->topLevelItem(i)->setSelected(0);
1000     }
1001     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1002       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1003
1004   }
1005   DataTree->topLevelItem(selected)->setSelected(1);
1006   mCurrentPickedImageId = id;
1007   mCurrentPickedImageIndex = selected;
1008 }
1009 //------------------------------------------------------------------------------
1010
1011 //------------------------------------------------------------------------------
1012 void vvMainWindow::ImageInfoChanged()
1013 {
1014   contextActions[6]->setEnabled(1);
1015   contextActions[5]->setEnabled(1);
1016   actionSave_As->setEnabled(1);
1017   actionAdd_VF_to_current_Image->setEnabled(1);
1018   actionAdd_fusion_image->setEnabled(1);
1019   actionNorth_East_Window->setEnabled(1);
1020   actionNorth_West_Window->setEnabled(1);
1021   actionSouth_East_Window->setEnabled(1);
1022   actionSouth_West_Window->setEnabled(1);
1023   inverseButton->setEnabled(1);
1024
1025   goToCursorPushButton->setEnabled(1);
1026
1027   if (DataTree->selectedItems().size()) {
1028     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1029
1030     colorMapComboBox->setEnabled(1);
1031     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1032       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1033           DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion") {
1034         colorMapComboBox->setEnabled(0);
1035         break;
1036       }
1037     }
1038
1039     std::vector<double> origin;
1040     std::vector<double> inputSpacing;
1041     std::vector<int> inputSize;
1042     std::vector<double> sizeMM;
1043     vtkSmartPointer<vtkMatrix4x4> transformation;
1044     int dimension=0;
1045     QString pixelType;
1046     QString inputSizeInBytes;
1047     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1048
1049     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1) {
1050       playButton->setEnabled(1);
1051       frameRateLabel->setEnabled(1);
1052       frameRateSpinBox->setEnabled(1);
1053     } else {
1054       playButton->setEnabled(0);
1055       frameRateLabel->setEnabled(0);
1056       frameRateSpinBox->setEnabled(0);
1057     }
1058
1059     //read image header
1060     int NPixel = 1;
1061
1062     vvImage::Pointer imageSelected;
1063     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1064       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1065       dimension = imageSelected->GetNumberOfDimensions();
1066       origin.resize(dimension);
1067       inputSpacing.resize(dimension);
1068       inputSize.resize(dimension);
1069       sizeMM.resize(dimension);
1070       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1071       for (int i = 0; i < dimension; i++) {
1072         origin[i] = imageSelected->GetOrigin()[i];
1073         inputSpacing[i] = imageSelected->GetSpacing()[i];
1074         inputSize[i] = imageSelected->GetSize()[i];
1075         sizeMM[i] = inputSize[i]*inputSpacing[i];
1076         NPixel *= inputSize[i];
1077       }
1078       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1079     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1080       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1081       dimension = imageSelected->GetNumberOfDimensions();
1082       origin.resize(dimension);
1083       inputSpacing.resize(dimension);
1084       inputSize.resize(dimension);
1085       sizeMM.resize(dimension);
1086       pixelType = mSlicerManagers[index]->GetVF()->GetScalarTypeAsITKString().c_str();
1087       for (int i = 0; i < dimension; i++) {
1088         origin[i] = imageSelected->GetOrigin()[i];
1089         inputSpacing[i] = imageSelected->GetSpacing()[i];
1090         inputSize[i] = imageSelected->GetSize()[i];
1091         sizeMM[i] = inputSize[i]*inputSpacing[i];
1092         NPixel *= inputSize[i];
1093       }
1094       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1095     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1096       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1097       dimension = imageSelected->GetNumberOfDimensions();
1098       origin.resize(dimension);
1099       inputSpacing.resize(dimension);
1100       inputSize.resize(dimension);
1101       sizeMM.resize(dimension);
1102       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1103       for (int i = 0; i < dimension; i++) {
1104         origin[i] = imageSelected->GetOrigin()[i];
1105         inputSpacing[i] = imageSelected->GetSpacing()[i];
1106         inputSize[i] = imageSelected->GetSize()[i];
1107         sizeMM[i] = inputSize[i]*inputSpacing[i];
1108         NPixel *= inputSize[i];
1109       }
1110       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1111     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1112       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1113       dimension = imageSelected->GetNumberOfDimensions();
1114       origin.resize(dimension);
1115       inputSpacing.resize(dimension);
1116       inputSize.resize(dimension);
1117       sizeMM.resize(dimension);
1118       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1119       for (int i = 0; i < dimension; i++) {
1120         origin[i] = imageSelected->GetOrigin()[i];
1121         inputSpacing[i] = imageSelected->GetSpacing()[i];
1122         inputSize[i] = imageSelected->GetSize()[i];
1123         sizeMM[i] = inputSize[i]*inputSpacing[i];
1124         NPixel *= inputSize[i];
1125       }
1126       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1127     }
1128
1129     QString dim = QString::number(dimension) + " (";
1130     dim += pixelType + ")";
1131
1132     infoPanel->setFileName(image);
1133     infoPanel->setDimension(dim);
1134     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1135     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1136     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1137     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1138     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1139     transformation = imageSelected->GetTransform()->GetMatrix();
1140     infoPanel->setTransformation(Get4x4MatrixDoubleAsString(transformation));
1141
1142     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1143                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1144     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1145     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1146
1147     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1148     for (int i = 0; i < 4; i++) {
1149       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1150         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1151         break;
1152       }
1153     }
1154     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1155     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1156     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1157     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1158
1159     infoPanel->setFileName(image);
1160     infoPanel->setDimension(dim);
1161     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1162     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1163     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1164     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1165     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1166
1167     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1168                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1169     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1170     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1171
1172     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1173     for (int i = 0; i < 4; i++) {
1174       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1175         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1176         break;
1177       }
1178     }
1179     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1180     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1181     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1182     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1183
1184     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1185       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1186       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1187                                   mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1188                                   mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1189     } else {
1190       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1191       overlayPanel->getVFProperty(-1,-1,-1);
1192     }
1193     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1194       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1195       overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1196     } else {
1197       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1198       overlayPanel->getOverlayProperty(-1);
1199     }
1200     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1201       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1202       overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1203                                       mSlicerManagers[index]->GetFusionColorMap(),
1204                                       mSlicerManagers[index]->GetFusionWindow(),
1205                                       mSlicerManagers[index]->GetFusionLevel());
1206     } else {
1207       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1208       overlayPanel->getFusionProperty(-1, -1,-1,-1);
1209     }
1210   }
1211 }
1212 //------------------------------------------------------------------------------
1213
1214 //------------------------------------------------------------------------------
1215 void vvMainWindow::ShowDocumentation()
1216 {
1217   documentation->show();
1218 }
1219 //------------------------------------------------------------------------------
1220 void vvMainWindow::ShowHelpDialog()
1221 {
1222   help_dialog->show();
1223 }
1224 //------------------------------------------------------------------------------
1225
1226 //------------------------------------------------------------------------------
1227 void vvMainWindow::ChangeViewMode()
1228 {
1229   QListIterator<int> it0(splitter_3->sizes());
1230   QListIterator<int> it1(splitter_3->sizes());
1231   int max0 = 0;
1232   int max1 = 1;
1233   while (it0.hasNext()) {
1234     max0 += it0.next();
1235   }
1236   while (it1.hasNext()) {
1237     max1 += it1.next();
1238   }
1239   QList<int> size0;
1240   QList<int> size1;
1241   if (viewMode == 1) {
1242     viewMode = 0;
1243     size0.push_back(max0);
1244     size0.push_back(0);
1245     size1.push_back(max1);
1246     size1.push_back(0);
1247     splitter_3->setSizes(size0);
1248     OSplitter->setSizes(size1);
1249     DataTree->setColumnHidden(2,1);
1250     DataTree->setColumnHidden(3,1);
1251     DataTree->setColumnHidden(4,1);
1252   } else {
1253     viewMode = 1;
1254     size0.push_back(int(max0/2));
1255     size0.push_back(int(max0/2));
1256     size1.push_back(int(max1/2));
1257     size1.push_back(int(max1/2));
1258     splitter_3->setSizes(size0);
1259     OSplitter->setSizes(size1);
1260     DataTree->setColumnHidden(2,0);
1261     DataTree->setColumnHidden(3,0);
1262     DataTree->setColumnHidden(4,0);
1263   }
1264 }
1265 //------------------------------------------------------------------------------
1266
1267 //------------------------------------------------------------------------------
1268 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1269 {
1270   QString result = "";// QString::number(size);
1271   //result += " bytes (";
1272   if (size > 1000000000) {
1273     size /= 1000000000;
1274     result += QString::number(size);
1275     result += "Gb";//)";
1276   } else if (size > 1000000) {
1277     size /= 1000000;
1278     result += QString::number(size);
1279     result += "Mb";//)";
1280   } else if (size > 1000) {
1281     size /= 1000;
1282     result += QString::number(size);
1283     result += "kb";//)";
1284   }
1285   return result;
1286 }
1287 //------------------------------------------------------------------------------
1288
1289 //------------------------------------------------------------------------------
1290 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix)
1291 {
1292   std::ostringstream strmatrix;
1293
1294   for (unsigned int i = 0; i < 4; i++) {
1295     for (unsigned int j = 0; j < 4; j++) {
1296       strmatrix.flags(ios::showpos);
1297       strmatrix.width(10);
1298       strmatrix.precision(3);
1299       strmatrix.setf(ios::fixed,ios::floatfield);
1300       strmatrix.fill(' ');
1301       strmatrix << std::left << matrix->GetElement(i, j);
1302       //strmatrix.width(10);
1303       strmatrix << " ";
1304     }
1305     strmatrix << std::endl;
1306   }
1307   QString result = strmatrix.str().c_str();
1308   return result;
1309 }
1310 //------------------------------------------------------------------------------
1311
1312 //------------------------------------------------------------------------------
1313 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1314 {
1315   QString result;
1316   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1317     if (i != 0)
1318       result += " ";
1319     result += QString::number(vectorDouble[i]);
1320   }
1321   return result;
1322 }
1323 //------------------------------------------------------------------------------
1324
1325 //------------------------------------------------------------------------------
1326 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1327 {
1328   QString result;
1329   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1330     if (i != 0)
1331       result += " ";
1332     result += QString::number(vectorInt[i]);
1333   }
1334   return result;
1335 }
1336 //------------------------------------------------------------------------------
1337
1338 //------------------------------------------------------------------------------
1339 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1340 {
1341   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1342   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1343     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1344       return i;
1345   }
1346   return -1;
1347 }
1348 //------------------------------------------------------------------------------
1349
1350 //------------------------------------------------------------------------------
1351 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1352 {
1353   QString id = sm->GetId().c_str();
1354   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1355     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1356       return DataTree->topLevelItem(i);
1357   }
1358   return NULL;
1359 }
1360 //------------------------------------------------------------------------------
1361
1362 //------------------------------------------------------------------------------
1363 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clicked_item, int column)
1364 {
1365   int index = GetSlicerIndexFromItem(clicked_item);
1366   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1367     return;
1368   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1369     //Trick to avoid redoing twice the job for a key (sr)
1370     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()-> GetInteractor()->SetKeySym("Crap");
1371
1372     QTreeWidgetItem* current_row=DataTree->topLevelItem(i);
1373     if (DataTree->topLevelItem(index) == current_row) {
1374       vvSlicer* clicked_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1375       if (current_row == clicked_item) {
1376         //If we just activated a slicer
1377         if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1378           mSlicerManagers[i]->UpdateSlicer(column-1,clicked_item->data(column,Qt::CheckStateRole).toInt());
1379           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1380           DisplaySliders(i,column-1);
1381           std::map<std::string,int> overlay_counts;
1382           for (int child = 0; child < current_row->childCount(); child++) {
1383             std::string overlay_type =
1384               current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1385             overlay_counts[overlay_type]++;
1386             current_row->child(child)->setData(column,Qt::CheckStateRole,
1387                                                current_row->data(column,Qt::CheckStateRole));
1388             clicked_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,true);
1389           }
1390         } else { //We don't allow simply desactivating a slicer
1391           clicked_item->setData(column,Qt::CheckStateRole,2);
1392           return;
1393         }
1394       }
1395       //if we clicked on the vector(or overlay) and not the image
1396       else {
1397         if (clicked_item->data(column,Qt::CheckStateRole).toInt()) {
1398           current_row->setData(column,Qt::CheckStateRole,2);
1399           mSlicerManagers[i]->UpdateSlicer(column-1,2);
1400           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1401           DisplaySliders(i,column-1);
1402         }
1403         int vis = clicked_item->data(column,Qt::CheckStateRole).toInt();
1404         std::string overlay_type = clicked_item->data(1,Qt::UserRole).toString().toStdString();
1405         int overlay_index=0;
1406         for (int child = 0; child < current_row->childCount(); child++) {
1407           if (current_row->child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1408             overlay_index++;
1409           if (current_row->child(child) == clicked_item) break;
1410         }
1411         clicked_slicer->SetActorVisibility(
1412           clicked_item->data(1,Qt::UserRole).toString().toStdString(), overlay_index-1,vis);
1413       }
1414     } else if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1415       current_row->setData(column,Qt::CheckStateRole,0);
1416       mSlicerManagers[i]->UpdateSlicer(column-1,0);
1417       std::map<std::string,int> overlay_counts;
1418       for (int child = 0; child < current_row->childCount(); child++) {
1419         std::string overlay_type =
1420           current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1421         overlay_counts[overlay_type]++;
1422         current_row->child(child)->setData(column,Qt::CheckStateRole,0);
1423         vvSlicer * current_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1424         current_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,false);
1425       }
1426     }
1427     //mSlicerManagers[i]->SetColorMap(-1);
1428     mSlicerManagers[i]->SetColorMap();
1429   }
1430   mSlicerManagers[index]->GetSlicer(column-1)->Render();
1431 }
1432 //------------------------------------------------------------------------------
1433
1434 void vvMainWindow::InitSlicers()
1435 {
1436   if (mSlicerManagers.size()) {
1437     mSlicerManagers.back()->GenerateDefaultLookupTable();
1438
1439     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1440     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1441     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1442     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1443   }
1444 }
1445
1446 //------------------------------------------------------------------------------
1447 void vvMainWindow::InitDisplay()
1448 {
1449   if (mSlicerManagers.size()) {
1450     //BE CAREFUL : this is absolutely necessary to set the interactor style
1451     //in order to have the same style instanciation for all SlicerManagers in
1452     // a same window
1453     for (int j = 0; j < 4; j++) {
1454       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1455       style->SetAutoAdjustCameraClippingRange(1);
1456       bool AlreadySelected = false;
1457       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1458         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1459
1460         //select the image only if previous are not selected
1461         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1462           mSlicerManagers[i]->UpdateSlicer(j,1);
1463           AlreadySelected = true;
1464         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1465           if (DataTree->selectedItems().size() == 0)
1466             DataTree->topLevelItem(i)->setSelected(1);
1467           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1468           mSlicerManagers[i]->UpdateSlicer(j,1);
1469           DisplaySliders(i,j);
1470         } else {
1471           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1472           mSlicerManagers[i]->UpdateSlicer(j,0);
1473         }
1474       }
1475       style->Delete();
1476     }
1477   }
1478 }
1479 //------------------------------------------------------------------------------
1480
1481 //------------------------------------------------------------------------------
1482 void vvMainWindow::DisplaySliders(int slicer, int window)
1483 {
1484   int range[2];
1485   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1486   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1487
1488   int tRange[2];
1489   tRange[0] = 0;
1490   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1491   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1492   bool showHorizontal = false;
1493   bool showVertical = false;
1494   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1495       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1496           && mSlicerManagers[slicer]->GetType() != vvImageReader::IMAGEWITHTIME
1497           && mSlicerManagers[slicer]->GetType() != vvImageReader::MERGEDWITHTIME))
1498     showVertical = true;
1499   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1500       || mSlicerManagers[slicer]->GetType() == vvImageReader::IMAGEWITHTIME
1501       || mSlicerManagers[slicer]->GetType() == vvImageReader::MERGEDWITHTIME)
1502     showHorizontal = true;
1503
1504   if (showVertical)
1505     verticalSliders[window]->show();
1506   else
1507     verticalSliders[window]->hide();
1508   verticalSliders[window]->setRange(range[0],range[1]);
1509   verticalSliders[window]->setValue(position);
1510
1511   if (showHorizontal)
1512     horizontalSliders[window]->show();
1513   else
1514     horizontalSliders[window]->hide();
1515   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1516   horizontalSliders[window]->setValue(tPosition);
1517 }
1518 //------------------------------------------------------------------------------
1519
1520 //------------------------------------------------------------------------------
1521 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1522 {
1523   int index = GetSlicerIndexFromItem(item);
1524
1525   if (DataTree->topLevelItem(index) != item) {
1526     QString warning = "Do you really want to close the overlay : ";
1527     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1528     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1529                        warning, 0, this);
1530     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1531     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1532     if (msgBox.exec() == QMessageBox::AcceptRole) {
1533       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1534       int overlay_index=0;
1535       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1536         if (DataTree->topLevelItem(index)->\
1537             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1538           overlay_index++;
1539         if (DataTree->topLevelItem(index)->child(child) == item) break;
1540       }
1541       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1542       mSlicerManagers[index]->SetColorMap(0);
1543       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1544       mSlicerManagers[index]->Render();
1545     }
1546   } else if (DataTree->topLevelItemCount() <= 1) {
1547     QString warning = "Do you really want to close the image : ";
1548     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1549     warning += "\nThis is the last image, you're about to close vv !!!";
1550     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1551                        warning, 0, this);
1552     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1553     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1554     if (msgBox.exec() == QMessageBox::AcceptRole) {
1555       this->close();
1556     }
1557   } else {
1558     QString warning = "Do you really want to close the image : ";
1559     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1560     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1561                        warning, 0, this);
1562     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1563     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1564     if (msgBox.exec() == QMessageBox::AcceptRole) {
1565
1566       // Tell tools that we close an image
1567       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1568
1569       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1570       DataTree->takeTopLevelItem(index);
1571       for (int i = 0; i < index; i++) {
1572         Manageriter++;
1573       }
1574       linkPanel->removeImage(index);
1575       mSlicerManagers[index]->RemoveActors();
1576       delete mSlicerManagers[index];
1577       mSlicerManagers.erase(Manageriter);
1578
1579       //
1580       InitDisplay();
1581     }
1582   }
1583   ImageInfoChanged();
1584 }
1585 //------------------------------------------------------------------------------
1586
1587 //------------------------------------------------------------------------------
1588 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1589 {
1590   // int index = GetSlicerIndexFromItem(item);
1591   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1592   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1593   //     mSlicerManagers[index]->ReloadVF();
1594   //   else
1595   //     mSlicerManagers[index]->Reload();
1596
1597   //   QApplication::restoreOverrideCursor();
1598   int index = GetSlicerIndexFromItem(item);
1599   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1600   QString role=item->data(1,Qt::UserRole).toString();
1601   if ( role == "vector")
1602     mSlicerManagers[index]->ReloadVF();
1603   else if (role == "overlay")
1604     mSlicerManagers[index]->ReloadOverlay();
1605   else if (role == "fusion")
1606     mSlicerManagers[index]->ReloadFusion();
1607   else
1608     mSlicerManagers[index]->Reload();
1609
1610   // Update view and info
1611   ImageInfoChanged();
1612   mSlicerManagers[index]->Render();
1613   QApplication::restoreOverrideCursor();
1614 }
1615 //------------------------------------------------------------------------------
1616
1617 //------------------------------------------------------------------------------
1618 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1619 {
1620   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1621 }
1622 //------------------------------------------------------------------------------
1623
1624 //------------------------------------------------------------------------------
1625 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1626 {
1627   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1628 }
1629 //------------------------------------------------------------------------------
1630
1631 //------------------------------------------------------------------------------
1632 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1633 {
1634   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1635 }
1636 //------------------------------------------------------------------------------
1637
1638 //------------------------------------------------------------------------------
1639 void vvMainWindow::FusionChanged(int visibility, double value)
1640 {
1641   overlayPanel->getCurrentFusionInfo(visibility,value);
1642 }
1643 //------------------------------------------------------------------------------
1644
1645 //------------------------------------------------------------------------------
1646 void vvMainWindow::WindowsChanged(int window, int view, int slice)
1647 {
1648   infoPanel->setViews(window, view, slice);
1649 }
1650 //------------------------------------------------------------------------------
1651
1652 //------------------------------------------------------------------------------
1653 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap)
1654 {
1655   windowSpinBox->setValue(window);
1656   levelSpinBox->setValue(level);
1657   colorMapComboBox->setCurrentIndex(colormap);
1658   presetComboBox->setCurrentIndex(preset);
1659 }
1660 //------------------------------------------------------------------------------
1661
1662 //------------------------------------------------------------------------------
1663 void vvMainWindow::WindowLevelEdited()
1664 {
1665   presetComboBox->setCurrentIndex(6);
1666   UpdateWindowLevel();
1667 }
1668 //------------------------------------------------------------------------------
1669
1670 //------------------------------------------------------------------------------
1671 void vvMainWindow::UpdateWindowLevel()
1672 {
1673   if (DataTree->selectedItems().size()) {
1674     if (presetComboBox->currentIndex() == 7) //For ventilation
1675       colorMapComboBox->setCurrentIndex(5);
1676     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1677     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1678     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1679     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1680     mSlicerManagers[index]->Render();
1681     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1682     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1683   }
1684 }
1685 //------------------------------------------------------------------------------
1686
1687 //------------------------------------------------------------------------------
1688 void vvMainWindow::UpdateColorMap()
1689 {
1690   if (DataTree->selectedItems().size()) {
1691     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1692     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1693     mSlicerManagers[index]->Render();
1694   }
1695 }
1696 //------------------------------------------------------------------------------
1697 void vvMainWindow::SwitchWindowLevel()
1698 {
1699   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1700   int window = mSlicerManagers[index]->GetColorWindow();
1701   presetComboBox->setCurrentIndex(6);
1702   windowSpinBox->setValue(-window);
1703   UpdateWindowLevel();
1704 }
1705 //------------------------------------------------------------------------------
1706
1707 //------------------------------------------------------------------------------
1708 void vvMainWindow::ApplyWindowLevelToAllImages()
1709 {
1710   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1711     if (mSlicerManagers[i] == NULL)
1712       continue;
1713     mSlicerManagers[i]->SetColorWindow(windowSpinBox->value());
1714     mSlicerManagers[i]->SetColorLevel(levelSpinBox->value());
1715     mSlicerManagers[i]->SetPreset(6);
1716     mSlicerManagers[i]->Render();
1717   }
1718 }
1719 //------------------------------------------------------------------------------
1720
1721 //------------------------------------------------------------------------------
1722 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1723 {
1724   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1725     if (mSlicerManagers[i]->GetId() == id) {
1726       //mSlicerManagers[i]->SetTSlice(temps);
1727       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1728       mSlicerManagers[i]->UpdateViews(0,slicer);
1729       break;
1730     }
1731   }
1732 }
1733 //------------------------------------------------------------------------------
1734
1735 //------------------------------------------------------------------------------
1736 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1737 {
1738   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1739     if (id == mSlicerManagers[i]->GetId()) {
1740       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1741     }
1742   }
1743 }
1744 //------------------------------------------------------------------------------
1745
1746 //------------------------------------------------------------------------------
1747 void vvMainWindow::ShowContextMenu(QPoint point)
1748 {
1749   if (!DataTree->selectedItems().size()) {
1750     contextActions[1]->setEnabled(0);
1751     contextActions[2]->setEnabled(0);
1752     contextActions[3]->setEnabled(0);
1753     contextActions[4]->setEnabled(0);
1754     contextActions[5]->setEnabled(0);
1755     contextActions[6]->setEnabled(0);
1756   } else {
1757     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1758     contextActions[1]->setEnabled(1);
1759     contextActions[2]->setEnabled(
1760       DataTree->itemWidget(DataTree->selectedItems()[0],
1761                            COLUMN_RELOAD_IMAGE)->isEnabled());
1762     contextActions[3]->setEnabled(1);
1763     contextActions[5]->setEnabled(1);
1764     contextActions[6]->setEnabled(1);
1765
1766     if (mSlicerManagers[index]->GetDimension() < 3)
1767       contextActions[4]->setEnabled(0);
1768     else
1769       contextActions[4]->setEnabled(1);
1770   }
1771   contextMenu.exec(QCursor::pos());
1772 }
1773 //------------------------------------------------------------------------------
1774
1775 //------------------------------------------------------------------------------
1776 void vvMainWindow::CloseImage()
1777 {
1778   CloseImage(DataTree->selectedItems()[0],0);
1779 }
1780 //------------------------------------------------------------------------------
1781
1782 //------------------------------------------------------------------------------
1783 void vvMainWindow::ReloadImage()
1784 {
1785   ReloadImage(DataTree->selectedItems()[0],0);
1786 }
1787 //------------------------------------------------------------------------------
1788
1789 //------------------------------------------------------------------------------
1790 void vvMainWindow::SelectOverlayImage()
1791 {
1792   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1793
1794   //check if one overlay image is added
1795   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1796     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1797       QString error = "Cannot add more than one compared image\n";
1798       error += "Please remove first ";
1799       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1800       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1801       return;
1802     }
1803
1804   QString Extensions = EXTENSIONS;
1805   Extensions += ";;All Files (*)";
1806   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1807   if (!file.isEmpty())
1808     AddOverlayImage(index,file);
1809 }
1810 //------------------------------------------------------------------------------
1811
1812 //------------------------------------------------------------------------------
1813 void vvMainWindow::AddOverlayImage(int index, QString file)
1814 {
1815
1816   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1817   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1818                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1819   reader->SetFileName(file.toStdString().c_str());
1820   reader->ReadImageInformation();
1821   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1822   int dimension = reader->GetNumberOfDimensions();
1823   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1824   vvProgressDialog progress("Opening " + file.toStdString());
1825   qApp->processEvents();
1826
1827   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1828   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component)) {
1829     //create an item in the tree with good settings
1830     QTreeWidgetItem *item = new QTreeWidgetItem();
1831     item->setData(0,Qt::UserRole,file.toStdString().c_str());
1832     item->setData(1,Qt::UserRole,tr("overlay"));
1833     QFileInfo fileinfo(file); //Do not show the path
1834     item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1835     item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1836     qApp->processEvents();
1837
1838     for (int j = 1; j <= 4; j++) {
1839       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1840       mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("overlay",0,
1841           DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1842     }
1843
1844     //Create the buttons for reload and close
1845     qApp->processEvents();
1846     QTreePushButton* cButton = new QTreePushButton;
1847     cButton->setItem(item);
1848     cButton->setColumn(COLUMN_CLOSE_IMAGE);
1849     cButton->setToolTip(tr("close image"));
1850     cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1851     connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1852             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1853
1854     QTreePushButton* rButton = new QTreePushButton;
1855     rButton->setItem(item);
1856     rButton->setColumn(COLUMN_RELOAD_IMAGE);
1857     rButton->setToolTip(tr("reload image"));
1858     rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1859     connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1860             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1861
1862     DataTree->topLevelItem(index)->setExpanded(1);
1863     DataTree->topLevelItem(index)->addChild(item);
1864     DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1865     DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1866
1867     //set the id of the image
1868     QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1869     item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1870     UpdateTree();
1871     qApp->processEvents();
1872     ImageInfoChanged();
1873     QApplication::restoreOverrideCursor();
1874   } else {
1875     QApplication::restoreOverrideCursor();
1876     QString error = "Cannot import the new image.\n";
1877     error += mSlicerManagers[index]->GetLastError().c_str();
1878     QMessageBox::information(this,tr("Problem reading image !"),error);
1879   }
1880 }
1881 //------------------------------------------------------------------------------
1882
1883
1884 //------------------------------------------------------------------------------
1885 void vvMainWindow::AddROI(int index, QString file)
1886 {
1887   /*
1888   // Get slice manager
1889
1890   // Load image
1891
1892   vvImageReader * mReader = new vvImageReader;
1893   mReader->SetInputFilename(filename.toStdString());
1894   mReader->Update(IMAGE);
1895   if (mReader->GetLastError().size() != 0) {
1896     std::cerr << "Error while reading " << filename.toStdString() << std::endl;
1897     QString error = "Cannot open file \n";
1898     error += mReader->GetLastError().c_str();
1899     QMessageBox::information(this,tr("Reading problem"),error);
1900     delete mReader;
1901     return;
1902   }
1903   vvImage::Pointer roi = mReader->GetOutput();
1904
1905   // Create roi in new tool
1906   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
1907   */
1908 }
1909 //------------------------------------------------------------------------------
1910
1911 //------------------------------------------------------------------------------
1912 void vvMainWindow::SelectFusionImage()
1913 {
1914   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1915
1916   //check if one fusion image is added
1917   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1918     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
1919       QString error = "Cannot add more than one fusion image\n";
1920       error += "Please remove first ";
1921       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1922       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1923       return;
1924     }
1925
1926   QString Extensions = EXTENSIONS;
1927   Extensions += ";;All Files (*)";
1928   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1929   if (!file.isEmpty())
1930     AddFusionImage(index,file);
1931 }
1932 //------------------------------------------------------------------------------
1933
1934 //------------------------------------------------------------------------------
1935 void vvMainWindow::AddFusionImage(int index, QString file)
1936 {
1937   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1938   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1939                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1940   reader->SetFileName(file.toStdString().c_str());
1941   reader->ReadImageInformation();
1942   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1943   if (reader) {
1944     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1945     vvProgressDialog progress("Opening fusion");
1946     qApp->processEvents();
1947
1948     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1949     if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1950                                           reader->GetNumberOfDimensions(), component)) {
1951       //create an item in the tree with good settings
1952       QTreeWidgetItem *item = new QTreeWidgetItem();
1953       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1954       item->setData(1,Qt::UserRole,tr("fusion"));
1955       QFileInfo fileinfo(filename.c_str()); //Do not show the path
1956       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1957       item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1958       qApp->processEvents();
1959
1960       for (int j = 1; j <= 4; j++) {
1961         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1962         mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("fusion",0,
1963             DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1964       }
1965
1966       //Create the buttons for reload and close
1967       qApp->processEvents();
1968       QTreePushButton* cButton = new QTreePushButton;
1969       cButton->setItem(item);
1970       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1971       cButton->setToolTip(tr("close image"));
1972       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1973       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1974               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1975
1976       QTreePushButton* rButton = new QTreePushButton;
1977       rButton->setItem(item);
1978       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1979       rButton->setToolTip(tr("reload image"));
1980       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1981       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1982               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1983
1984       DataTree->topLevelItem(index)->setExpanded(1);
1985       DataTree->topLevelItem(index)->addChild(item);
1986       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1987       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1988
1989       //set the id of the image
1990       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1991       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1992       UpdateTree();
1993       qApp->processEvents();
1994       ImageInfoChanged();
1995       QApplication::restoreOverrideCursor();
1996     } else {
1997       QApplication::restoreOverrideCursor();
1998       QString error = "Cannot import the new image.\n";
1999       error += mSlicerManagers[index]->GetLastError().c_str();
2000       QMessageBox::information(this,tr("Problem reading image !"),error);
2001     }
2002   } else {
2003     QString error = "Cannot import the new image.\n";
2004     QMessageBox::information(this,tr("Problem reading image !"),error);
2005   }
2006 }
2007 //------------------------------------------------------------------------------
2008
2009
2010 //------------------------------------------------------------------------------
2011 void vvMainWindow::OpenField()
2012 {
2013   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2014   //check if a vector field has already been added
2015   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2016     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
2017       QString error = "Cannot add more than one vector field\n";
2018       error += "Please remove first ";
2019       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2020       QMessageBox::information(this,tr("Problem adding vector field!"),error);
2021       return;
2022     }
2023
2024   QString Extensions = "Images ( *.mhd)";
2025   Extensions += ";;Images ( *.vf)";
2026   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2027   if (!file.isEmpty())
2028     AddField(file,index);
2029 }
2030 //------------------------------------------------------------------------------
2031
2032
2033 //------------------------------------------------------------------------------
2034 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2035 {
2036   //create an item in the tree with good settings
2037   QTreeWidgetItem *item = new QTreeWidgetItem();
2038   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2039   item->setData(1,Qt::UserRole,tr("vector"));
2040   QFileInfo fileinfo(filename); //Do not show the path
2041   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2042   item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
2043   qApp->processEvents();
2044
2045   for (int j = 1; j <= 4; j++) {
2046     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2047     mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("vector",0,
2048         DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
2049   }
2050
2051   //Create the buttons for reload and close
2052   qApp->processEvents();
2053   QTreePushButton* cButton = new QTreePushButton;
2054   cButton->setItem(item);
2055   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2056   cButton->setToolTip(tr("close vector field"));
2057   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2058   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2059           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2060
2061   QTreePushButton* rButton = new QTreePushButton;
2062   rButton->setItem(item);
2063   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2064   rButton->setToolTip(tr("reload vector field"));
2065   rButton->setEnabled(from_disk);
2066   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2067   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2068           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2069
2070   DataTree->topLevelItem(index)->setExpanded(1);
2071   DataTree->topLevelItem(index)->addChild(item);
2072   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2073   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2074
2075   //set the id of the image
2076   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2077   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2078   UpdateTree();
2079   qApp->processEvents();
2080   ImageInfoChanged();
2081   QApplication::restoreOverrideCursor();
2082 }
2083 //------------------------------------------------------------------------------
2084
2085
2086 //------------------------------------------------------------------------------
2087 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2088 {
2089   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2090   vvSlicerManager* imageManager = mSlicerManagers[index];
2091   if (imageManager->SetVF(vf,file.toStdString())) {
2092     AddFieldEntry(file,index,false);
2093   } else {
2094     QString error = "Cannot import the vector field for this image.\n";
2095     error += imageManager->GetLastError().c_str();
2096     QMessageBox::information(this,tr("Problem reading VF !"),error);
2097   }
2098   QApplication::restoreOverrideCursor();
2099 }
2100 //------------------------------------------------------------------------------
2101
2102
2103 //------------------------------------------------------------------------------
2104 void vvMainWindow::AddField(QString file,int index)
2105 {
2106   if (QFile::exists(file)) {
2107     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2108
2109     //init the progress events
2110     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2111     vvProgressDialog progress("Opening " + file.toStdString());
2112     qApp->processEvents();
2113
2114     //read the vector and put it in the current mSlicerManager
2115     vvSlicerManager* imageManager = mSlicerManagers[index];
2116     qApp->processEvents();
2117
2118     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2119     if (imageManager->SetVF(file.toStdString())) {
2120       imageManager->Render();
2121       AddFieldEntry(file,index,true);
2122     } else {
2123       QApplication::restoreOverrideCursor();
2124       QString error = "Cannot import the vector field for this image.\n";
2125       error += imageManager->GetLastError().c_str();
2126       QMessageBox::information(this,tr("Problem reading VF !"),error);
2127     }
2128   } else
2129     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2130
2131 }
2132 //------------------------------------------------------------------------------
2133
2134
2135 //------------------------------------------------------------------------------
2136 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2137 {
2138   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2139   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2140     for (int i = 0; i < 4; i++) {
2141       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2142       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2143       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2144       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2145       if (log > 0)
2146         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2147       else
2148         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2149     }
2150   }
2151 }
2152 //------------------------------------------------------------------------------
2153
2154
2155 //------------------------------------------------------------------------------
2156 void vvMainWindow::SetOverlayProperty(int color)
2157 {
2158   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2159   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2160     mSlicerManagers[index]->SetOverlayColor(color);
2161     mSlicerManagers[index]->SetColorMap(0);
2162     mSlicerManagers[index]->Render();
2163   }
2164 }
2165 //------------------------------------------------------------------------------
2166
2167 //------------------------------------------------------------------------------
2168 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level)
2169 {
2170   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2171   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2172     mSlicerManagers[index]->SetFusionOpacity(opacity);
2173     mSlicerManagers[index]->SetFusionColorMap(colormap);
2174     mSlicerManagers[index]->SetFusionWindow(window);
2175     mSlicerManagers[index]->SetFusionLevel(level);
2176     mSlicerManagers[index]->SetColorMap(0);
2177     mSlicerManagers[index]->Render();
2178   }
2179 }
2180 //------------------------------------------------------------------------------
2181
2182 //------------------------------------------------------------------------------
2183 void vvMainWindow::SaveAs()
2184 {
2185   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2186     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2187     return;
2188   }
2189
2190   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2191   int dimension = mSlicerManagers[index]->GetDimension();
2192   QStringList OutputListeFormat;
2193   OutputListeFormat.clear();
2194   if (dimension == 1) {
2195     OutputListeFormat.push_back(".mhd");
2196   }
2197   if (dimension == 2) {
2198     OutputListeFormat.push_back(".bmp");
2199     OutputListeFormat.push_back(".png");
2200     OutputListeFormat.push_back(".jpeg");
2201     OutputListeFormat.push_back(".tif");
2202     OutputListeFormat.push_back(".mhd");
2203     OutputListeFormat.push_back(".hdr");
2204     OutputListeFormat.push_back(".vox");
2205   } else if (dimension == 3) {
2206     OutputListeFormat.push_back(".mhd");
2207     OutputListeFormat.push_back(".hdr");
2208     OutputListeFormat.push_back(".vox");
2209   } else if (dimension == 4) {
2210     OutputListeFormat.push_back(".mhd");
2211   }
2212   QString Extensions = "AllFiles(*.*)";
2213   for (int i = 0; i < OutputListeFormat.count(); i++) {
2214     Extensions += ";;Images ( *";
2215     Extensions += OutputListeFormat[i];
2216     Extensions += ")";
2217   }
2218   QString fileName = QFileDialog::getSaveFileName(this,
2219                      tr("Save As"),
2220                      mSlicerManagers[index]->GetFileName().c_str(),
2221                      Extensions);
2222   if (!fileName.isEmpty()) {
2223     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2224     if (OutputListeFormat.contains(
2225           fileformat.c_str())) {
2226       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2227       std::string action = "Saving";
2228       vvProgressDialog progress("Saving "+fileName.toStdString());
2229       qApp->processEvents();
2230       vvImageWriter::Pointer writer = vvImageWriter::New();
2231       writer->SetOutputFileName(fileName.toStdString());
2232       writer->SetInput(mSlicerManagers[index]->GetImage());
2233       writer->Update();
2234       QApplication::restoreOverrideCursor();
2235       if (writer->GetLastError().size()) {
2236         QString error = "Saving did not succeed\n";
2237         error += writer->GetLastError().c_str();
2238         QMessageBox::information(this,tr("Saving Problem"),error);
2239         SaveAs();
2240       }
2241     } else {
2242       QString error = fileformat.c_str();
2243       if (error.isEmpty())
2244         error += "no file format specified !";
2245       else
2246         error += " format unknown !!!\n";
2247       QMessageBox::information(this,tr("Saving Problem"),error);
2248       SaveAs();
2249     }
2250   }
2251 }
2252 //------------------------------------------------------------------------------
2253
2254
2255 //------------------------------------------------------------------------------
2256 void vvMainWindow::AddLink(QString image1,QString image2)
2257 {
2258   unsigned int sm1 = 0;
2259   unsigned int sm2 = 0;
2260
2261   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2262     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2263       mSlicerManagers[i]->AddLink(image2.toStdString());
2264       sm1 = i;
2265     }
2266     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2267       mSlicerManagers[i]->AddLink(image1.toStdString());
2268       sm2 = i;
2269     }
2270   }
2271
2272   if (linkPanel->isLinkAll())   {
2273     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2274     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2275   }
2276   else {
2277     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2278   }
2279 }
2280
2281 //------------------------------------------------------------------------------
2282
2283
2284 //------------------------------------------------------------------------------
2285 void vvMainWindow::RemoveLink(QString image1,QString image2)
2286 {
2287   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2288     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2289       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2290     }
2291     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2292       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2293     }
2294   }
2295 }
2296 //------------------------------------------------------------------------------
2297
2298 //------------------------------------------------------------------------------
2299 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2300 {
2301   int index = 0;
2302   while(sm != mSlicerManagers[index])
2303     index++;
2304   index = (index+offset) % mSlicerManagers.size();
2305
2306   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2307   //CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2308   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2309   DisplayChanged(item,slicer+1);
2310 }
2311 //------------------------------------------------------------------------------
2312
2313 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2314 {
2315   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2316     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2317       for (int j = 0; j < 4; j++) {
2318         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2319         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2320         //UpdateTSlice(j,value);
2321       }
2322       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2323       break;
2324     }
2325   }
2326 }
2327 //------------------------------------------------------------------------------
2328
2329
2330 //------------------------------------------------------------------------------
2331 void vvMainWindow::NOHorizontalSliderMoved()
2332 {
2333   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2334   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2335 //  mCurrentTime = NOHorizontalSlider->value();
2336 }
2337 //------------------------------------------------------------------------------
2338
2339
2340 //------------------------------------------------------------------------------
2341 void vvMainWindow::NEHorizontalSliderMoved()
2342 {
2343   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2344   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2345 //  mCurrentTime = NEHorizontalSlider->value();
2346 }
2347 //------------------------------------------------------------------------------
2348
2349
2350 //------------------------------------------------------------------------------
2351 void vvMainWindow::SOHorizontalSliderMoved()
2352 {
2353   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2354   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2355   // mCurrentTime = SOHorizontalSlider->value();
2356 }
2357 //------------------------------------------------------------------------------
2358
2359
2360 //------------------------------------------------------------------------------
2361 void vvMainWindow::SEHorizontalSliderMoved()
2362 {
2363   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2364   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2365   // mCurrentTime = SEHorizontalSlider->value();
2366 }
2367 //------------------------------------------------------------------------------
2368
2369 //------------------------------------------------------------------------------
2370 void vvMainWindow::NOVerticalSliderChanged()
2371 {
2372   static int value=-1;
2373   if (value == NOVerticalSlider->value()) return;
2374   else value = NOVerticalSlider->value();
2375   //  int value = NOVerticalSlider->value();
2376   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2377     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2378       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2379         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2380         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2381
2382         // If nor Update/Render -> slider not work
2383         // only render = ok navigation, but for contour Update needed but slower ?
2384
2385         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2386         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2387       }
2388       break;
2389     }
2390   }
2391 }
2392 //------------------------------------------------------------------------------
2393
2394
2395 //------------------------------------------------------------------------------
2396 void vvMainWindow::NEVerticalSliderChanged()
2397 {
2398   static int value=-1;
2399   if (value == NEVerticalSlider->value()) return;
2400   else value = NEVerticalSlider->value();
2401   //  int value = NEVerticalSlider->value();
2402   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2403     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2404       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2405         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2406         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2407         mSlicerManagers[i]->UpdateSlice(1);
2408         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2409       }
2410       break;
2411     }
2412   }
2413 }
2414 //------------------------------------------------------------------------------
2415
2416
2417 //------------------------------------------------------------------------------
2418 void vvMainWindow::SOVerticalSliderChanged()
2419 {
2420   static int value=-1;
2421   if (value == SOVerticalSlider->value()) return;
2422   else value = SOVerticalSlider->value();
2423   //int value = SOVerticalSlider->value();
2424   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2425     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2426       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2427         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2428         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2429         mSlicerManagers[i]->UpdateSlice(2);
2430         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2431       }
2432       // else { DD("avoid SOVerticalSlider slicer update"); }
2433       break;
2434     }
2435   }
2436 }
2437 //------------------------------------------------------------------------------
2438
2439
2440 //------------------------------------------------------------------------------
2441 void vvMainWindow::SEVerticalSliderChanged()
2442 {
2443   static int value=-1;
2444   if (value == SEVerticalSlider->value()) return;
2445   else value = SEVerticalSlider->value();
2446   // int value = SEVerticalSlider->value();
2447   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2448     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2449       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2450         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2451         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2452         mSlicerManagers[i]->UpdateSlice(3);
2453         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2454       }
2455       break;
2456     }
2457   }
2458 }
2459 //------------------------------------------------------------------------------
2460
2461
2462 //------------------------------------------------------------------------------
2463 void vvMainWindow::UpdateSlice(int slicer, int slice)
2464 {
2465   // DD("vvMainWindow::UpdateSlice");
2466 //   DD(slicer);
2467 //   DD(slice);
2468   if (slicer == 0) {
2469     //    if (slice != NOVerticalSlider->value())
2470     NOVerticalSlider->setValue(slice);
2471   } else {
2472     if (slicer == 1)
2473       NEVerticalSlider->setValue(slice);
2474     else {
2475       if (slicer == 2)
2476         SOVerticalSlider->setValue(slice);
2477       else {
2478         if (slicer == 3)
2479           SEVerticalSlider->setValue(slice);
2480       }
2481     }
2482   }
2483   // DD("vvMainWindow:UpdateSlice END");
2484 }
2485 //------------------------------------------------------------------------------
2486
2487
2488 //------------------------------------------------------------------------------
2489 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2490 {
2491   switch (slicer) {
2492   case 0:
2493     NOHorizontalSlider->setValue(slice);
2494     break;
2495   case 1:
2496     NEHorizontalSlider->setValue(slice);
2497     break;
2498   case 2:
2499     SOHorizontalSlider->setValue(slice);
2500     break;
2501   case 3:
2502     SEHorizontalSlider->setValue(slice);
2503     break;
2504   }
2505 }
2506 //------------------------------------------------------------------------------
2507
2508
2509 //------------------------------------------------------------------------------
2510 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2511 {
2512   int position = int((min+max)/2);
2513   int tPosition = int((tmin+tmax)/2);
2514   if (slicer == 0) {
2515     NOVerticalSlider->setValue(position);
2516     NOVerticalSlider->setRange(min,max);
2517     NOHorizontalSlider->setRange(tmin,tmax);
2518     NOHorizontalSlider->setValue(tPosition);
2519   } else if (slicer == 1) {
2520     NEVerticalSlider->setValue(position);
2521     NEVerticalSlider->setRange(min,max);
2522     NEHorizontalSlider->setRange(tmin,tmax);
2523     NEHorizontalSlider->setValue(tPosition);
2524   } else if (slicer == 2) {
2525     SOVerticalSlider->setValue(position);
2526     SOVerticalSlider->setRange(min,max);
2527     SOHorizontalSlider->setRange(tmin,tmax);
2528     SOHorizontalSlider->setValue(tPosition);
2529   } else if (slicer == 3) {
2530     SEVerticalSlider->setValue(position);
2531     SEVerticalSlider->setRange(min,max);
2532     SEHorizontalSlider->setRange(tmin,tmax);
2533     SEHorizontalSlider->setValue(tPosition);
2534   }
2535 }
2536 //------------------------------------------------------------------------------
2537
2538
2539 //------------------------------------------------------------------------------
2540 void vvMainWindow::SaveNOScreenshot()
2541 {
2542   SaveScreenshot(NOViewWidget);
2543 }
2544 //------------------------------------------------------------------------------
2545
2546
2547 //------------------------------------------------------------------------------
2548 void vvMainWindow::SaveNEScreenshot()
2549 {
2550   SaveScreenshot(NEViewWidget);
2551 }
2552 //------------------------------------------------------------------------------
2553
2554
2555 //------------------------------------------------------------------------------
2556 void vvMainWindow::SaveSOScreenshot()
2557 {
2558   SaveScreenshot(SOViewWidget);
2559 }
2560 //------------------------------------------------------------------------------
2561
2562
2563 //------------------------------------------------------------------------------
2564 void vvMainWindow::SaveSEScreenshot()
2565 {
2566   SaveScreenshot(SEViewWidget);
2567 }
2568 //------------------------------------------------------------------------------
2569
2570
2571 //------------------------------------------------------------------------------
2572 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
2573 {
2574   QString Extensions = "Images( *.png);;";
2575   Extensions += "Images( *.jpg);;";
2576   Extensions += "Images( *.bmp);;";
2577   Extensions += "Images( *.tif);;";
2578   Extensions += "Images( *.ppm)";
2579 #ifdef VTK_USE_FFMPEG_ENCODER
2580   Extensions += "Images( *.avi)";
2581 #endif
2582 #ifdef VTK_USE_MPEG2_ENCODER
2583   Extensions += "Images( *.mpg)";
2584 #endif
2585
2586   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2587   QString fileName = QFileDialog::getSaveFileName(this,
2588                      tr("Save As"),
2589                      itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
2590                      Extensions);
2591
2592   if (!fileName.isEmpty()) {
2593     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2594     w2i->SetInput(widget->GetRenderWindow());
2595     w2i->Update();
2596     vtkImageData *image = w2i->GetOutput();
2597
2598     const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2599     if (!strcmp(ext, ".bmp")) {
2600       vtkBMPWriter *bmp = vtkBMPWriter::New();
2601       bmp->SetInput(image);
2602       bmp->SetFileName(fileName.toStdString().c_str());
2603       bmp->Write();
2604       bmp->Delete();
2605     } else if (!strcmp(ext, ".tif")) {
2606       vtkTIFFWriter *tif = vtkTIFFWriter::New();
2607       tif->SetInput(image);
2608       tif->SetFileName(fileName.toStdString().c_str());
2609       tif->Write();
2610       tif->Delete();
2611     } else if (!strcmp(ext, ".ppm")) {
2612       vtkPNMWriter *pnm = vtkPNMWriter::New();
2613       pnm->SetInput(image);
2614       pnm->SetFileName(fileName.toStdString().c_str());
2615       pnm->Write();
2616       pnm->Delete();
2617     } else if (!strcmp(ext, ".png")) {
2618       vtkPNGWriter *png = vtkPNGWriter::New();
2619       png->SetInput(image);
2620       png->SetFileName(fileName.toStdString().c_str());
2621       png->Write();
2622       png->Delete();
2623     } else if (!strcmp(ext, ".jpg")) {
2624       vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2625       jpg->SetInput(image);
2626       jpg->SetFileName(fileName.toStdString().c_str());
2627       jpg->Write();
2628       jpg->Delete();
2629 #ifdef VTK_USE_FFMPEG_ENCODER
2630     } else if (!strcmp(ext, ".avi")) {
2631       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
2632       mpg->SetInput(image);
2633       mpg->SetFileName(fileName.toStdString().c_str());
2634       mpg->SetQuality(2);
2635       mpg->SetRate(5);
2636       mpg->Start();
2637
2638       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2639       int nSlice = vvImg->GetVTKImages().size();
2640       for(int i=0; i<nSlice; i++)
2641       {
2642         mSlicerManagers[smIndex]->SetNextTSlice(0);
2643         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2644         w2i->SetInput(widget->GetRenderWindow());
2645         w2i->Update();
2646         mpg->SetInput(w2i->GetOutput());
2647         mpg->Write();
2648       }
2649       mpg->End();
2650       mpg->Delete();
2651 #endif
2652 #ifdef VTK_USE_MPEG2_ENCODER
2653     } else if (!strcmp(ext, ".mpg")) {
2654       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
2655       mpg->SetInput(image);
2656       mpg->SetFileName(fileName.toStdString().c_str());
2657       mpg->Start();
2658
2659       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2660       int nSlice = vvImg->GetVTKImages().size();
2661       for(int i=0; i<nSlice; i++)
2662       {
2663         mSlicerManagers[smIndex]->SetNextTSlice(0);
2664         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2665         w2i->SetInput(widget->GetRenderWindow());
2666         w2i->Update();
2667         mpg->SetInput(w2i->GetOutput());
2668         mpg->Write();
2669       }
2670       mpg->End();
2671       mpg->Delete();
2672 #endif
2673     } else {
2674       QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2675     }
2676   }
2677 }
2678 //------------------------------------------------------------------------------
2679
2680
2681 //------------------------------------------------------------------------------
2682 void vvMainWindow::GoToCursor()
2683 {
2684   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2685   for (int column = 1; column < 5; column++) {
2686     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
2687       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2688       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2689         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2690       mSlicerManagers[index]->UpdateViews(1,column-1);
2691       mSlicerManagers[index]->UpdateLinked(column-1);
2692       break;
2693     }
2694   }
2695 }
2696 //------------------------------------------------------------------------------
2697
2698 //------------------------------------------------------------------------------
2699 void vvMainWindow::PlayPause()
2700 {
2701   if (playMode) {
2702     playMode = 0;
2703     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2704     ImageInfoChanged();
2705     return;
2706   } else {
2707     int image_number=DataTree->topLevelItemCount();
2708     bool has_temporal;
2709     for (int i=0; i<image_number; i++)
2710       if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1) {
2711         has_temporal=true;
2712         break;
2713       }
2714     if (has_temporal) {
2715       playMode = 1;
2716       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2717       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2718     }
2719   }
2720 }
2721 //------------------------------------------------------------------------------
2722
2723 //------------------------------------------------------------------------------
2724 void vvMainWindow::PlayNext()
2725 {
2726   if (playMode && !this->isHidden()) {
2727     int image_number=DataTree->topLevelItemCount();
2728     ///Only play one slicer per SM, and only if the SM is being displayed
2729     for (int i=0; i<image_number; i++)
2730       for (int j=0; j<4; j++)
2731         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2732             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
2733           mSlicerManagers[i]->SetNextTSlice(j);
2734           break;
2735         }
2736     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2737   }
2738 }
2739 //------------------------------------------------------------------------------
2740
2741 void vvMainWindow::ShowLastImage()
2742 {
2743   if (mSlicerManagers.size() > 1) {
2744     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2745     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2746     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2747     DisplayChanged(item,1);
2748   }
2749 }
2750
2751 //------------------------------------------------------------------------------
2752 void vvMainWindow::UpdateRenderWindows()
2753 {
2754   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2755   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2756   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2757   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2758 }
2759 //------------------------------------------------------------------------------
2760
2761 //------------------------------------------------------------------------------
2762 void vvMainWindow::SegmentationOnCurrentImage()
2763 {
2764   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2765
2766   vvSegmentationDialog segmentation;
2767   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2768   segmentation.exec();
2769 }
2770 //------------------------------------------------------------------------------
2771
2772 void vvMainWindow::SurfaceViewerLaunch()
2773 {
2774   vvSurfaceViewerDialog surfaceViewer;
2775   surfaceViewer.exec();
2776 }
2777 //------------------------------------------------------------------------------
2778
2779
2780 //------------------------------------------------------------------------------
2781 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
2782 {
2783   int number=0;
2784   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
2785     vvSlicerManager * v = mSlicerManagers[l];
2786     if (v->GetBaseFileName() ==
2787         vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
2788       number = std::max(number, v->GetBaseFileNameNumber()+1);
2789     }
2790   }
2791   return number;
2792 }
2793 //------------------------------------------------------------------------------
2794
2795
2796 //------------------------------------------------------------------------------
2797 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2798 {
2799   // Change filename if another image exist with the same name
2800   int number = GetImageDuplicateFilenameNumber(filename);
2801
2802   // Create new SliceManager
2803   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
2804   slicer_manager->SetImage(image);//, IMAGE, number);
2805   //  filename = filename+"_"+clitk::toString(number);
2806   slicer_manager->SetFilename(filename, number);
2807   mSlicerManagers.push_back(slicer_manager);
2808
2809   //create an item in the tree with good settings
2810   QTreeWidgetItem *item = new QTreeWidgetItem();
2811   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2812   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
2813   qApp->processEvents();
2814
2815   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2816
2817   //Create the buttons for reload and close
2818   qApp->processEvents();
2819   QTreePushButton* cButton = new QTreePushButton;
2820   cButton->setItem(item);
2821   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2822   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2823   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2824           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2825
2826   QTreePushButton* rButton = new QTreePushButton;
2827   rButton->setItem(item);
2828   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2829   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2830   rButton->setEnabled(0);
2831   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2832           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2833
2834   DataTree->addTopLevelItem(item);
2835   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2836   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2837
2838   //set the id of the image
2839   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2840   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2841   mSlicerManagers.back()->SetId(id.toStdString());
2842
2843   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
2844                       , id.toStdString());
2845
2846   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
2847           this, SLOT(CurrentImageChanged(std::string)));
2848   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
2849           this, SLOT(CurrentPickedImageChanged(std::string)));
2850   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
2851           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2852   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
2853           this, SLOT(VectorChanged(int,double,double,double, double)));
2854   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
2855           this, SLOT(OverlayChanged(int,double,double)));
2856   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
2857           this, SLOT(FusionChanged(int,double)));
2858   connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
2859           this,SLOT(WindowsChanged(int, int, int)));
2860   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
2861           this,SLOT(WindowLevelChanged(double, double, int, int)));
2862   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
2863           this,SLOT(UpdateSlice(int,int)));
2864   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
2865           this,SLOT(UpdateTSlice(int, int)));
2866   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2867           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2868   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2869           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2870   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
2871           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
2872   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
2873           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
2874   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2875   UpdateTree();
2876   qApp->processEvents();
2877   InitSlicers();
2878   ShowLastImage();
2879   InitDisplay();
2880   qApp->processEvents();
2881
2882   // End
2883   ImageInfoChanged();
2884   return slicer_manager;
2885 }
2886 //------------------------------------------------------------------------------
2887
2888
2889 //------------------------------------------------------------------------------
2890 void vvMainWindow::UpdateCurrentSlicer()
2891 {
2892   int index = -1;
2893   if (DataTree->selectedItems().size() > 0) {
2894     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2895   }
2896   mSlicerManagerCurrentIndex = index;
2897 }
2898 //------------------------------------------------------------------------------
2899