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