vv/vvMainWindow.cxx

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