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 "vvSaveState.h"
  49 #include "vvReadState.h"
  50 #include "clitkConfiguration.h"
  51
  52 // ITK include
  53 #include <itkImage.h>
  54 #include <itkImageFileReader.h>
  55 #include <itkByteSwapper.h>
  56 #include <itkCommand.h>
  57 #include <itkNumericSeriesFileNames.h>
  58
  59 // VTK include
  60 #include <vtkImageData.h>
  61 #include <vtkImageActor.h>
  62 #include <vtkCornerAnnotation.h>
  63 #include <vtkRenderWindow.h>
  64 #include <vtkRenderWindowInteractor.h>
  65 #include <vtkRenderer.h>
  66 #include <vtkRendererCollection.h>
  67 #include <vtkWindowToImageFilter.h>
  68 #include <vtkBMPWriter.h>
  69 #include <vtkTIFFWriter.h>
  70 #include <vtkPNMWriter.h>
  71 #include <vtkPNGWriter.h>
  72 #include <vtkJPEGWriter.h>
  73 #ifdef VTK_USE_FFMPEG_ENCODER
  74 #  include <vtkFFMPEGWriter.h>
  75 #endif
  76 #ifdef VTK_USE_MPEG2_ENCODER
  77 #  include <vtkMPEG2Writer.h>
  78 #endif
  79 #include <vtkMatrix4x4.h>
  80 #include <vtkTransform.h>
  81
  82 // Standard includes
  83 #include <iostream>
  84 #include <sstream>
  85 #include <iomanip>
  86
  87 #define COLUMN_TREE 0
  88 #define COLUMN_UL_VIEW 1
  89 #define COLUMN_UR_VIEW 2
  90 #define COLUMN_DL_VIEW 3
  91 #define COLUMN_DR_VIEW 4
  92 #define COLUMN_CLOSE_IMAGE 5
  93 #define COLUMN_RELOAD_IMAGE 6
  94 #define COLUMN_IMAGE_NAME 7
  95
  96 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN )"
  97
  98 /*Data Tree values
  99   0,Qt::UserRole full filename
 100   1,Qt::CheckStateRole checkbutton UL View
 101   1,Qt::UserRole overlay, fusion or vector
 102   2,Qt::CheckStateRole checkbutton UR View
 103   3,Qt::CheckStateRole checkbutton DL View
 104   4,Qt::CheckStateRole checkbutton DR View
 105   5,0  short filename
 106   5,Qt::UserRole mSlicerManager id*/
 107
 108 //------------------------------------------------------------------------------
 109 vvMainWindow::vvMainWindow():vvMainWindowBase()
 110 {
 111   setupUi(this); // this sets up the GUI
 112
 113   mInputPathName = "";
 114   mMenuTools = menuTools;
 115   //  mMenuSegmentation = menuSegmentation;
 116   mContextMenu = &contextMenu;
 117   mMenuExperimentalTools = menuExperimental;
 118   mMainWidget = this;
 119   mCurrentTime = -1;
 120   mCurrentSelectedImageId = "";
 121   mCurrentPickedImageId = "";
 122   mCurrentPickedImageIndex = 0;
 123
 124   //Init the contextMenu
 125   this->setContextMenuPolicy(Qt::CustomContextMenu);
 126   contextActions.resize(0);
 127   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 128                                   tr("O&pen new Image"));
 129   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 130   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 131   contextActions.push_back(actionOpen_new_image);
 132   contextMenu.addSeparator();
 133
 134   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 135                                tr("Close Current Image"));
 136   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 137   contextActions.push_back(actionClose_Image);
 138
 139   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 140                                 tr("Reload Current Image"));
 141   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 142   contextActions.push_back(actionReload_image);
 143
 144   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 145                               tr("Save Current Image"));
 146   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 147   contextActions.push_back(actionSave_image);
 148
 149   QAction* actionSave_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 150                               tr("Save Current State"));
 151   connect(actionSave_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 152   contextActions.push_back(actionSave_state);
 153
 154   QAction* actionRead_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 155                               tr("Read Saved State"));
 156   connect(actionRead_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 157   contextActions.push_back(actionRead_state);
 158
 159   contextMenu.addSeparator();
 160
 161   contextMenu.addAction(actionAdd_VF_to_current_Image);
 162   contextActions.push_back(actionAdd_VF_to_current_Image);
 163
 164   QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 165       tr("Add overlay image to current image"));
 166   contextMenu.addAction(actionAdd_Overlay_to_current_Image);
 167   contextActions.push_back(actionAdd_Overlay_to_current_Image);
 168
 169   connect(actionAdd_Overlay_to_current_Image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 170
 171   contextMenu.addAction(actionAdd_fusion_image);
 172   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 173   contextActions.push_back(actionAdd_fusion_image);
 174
 175   contextMenu.addSeparator();
 176   QAction* actionResetMatrix = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/identity.png")),
 177                                                       tr("Reset transformation to identity"));
 178   connect(actionResetMatrix, SIGNAL(triggered()), this,SLOT(ResetTransformationToIdentity()));
 179
 180   // TRIAL DS
 181   /*
 182   QMenu * m = new QMenu(menubar);
 183   m->setTitle("TOTO");
 184   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 185   contextMenu.addMenu(m);
 186   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 187                      tr("BIDON"));
 188   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 189                      tr("BIDON2"));
 190   m->addAction(a);
 191   m->addAction(b);
 192   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 193   */
 194
 195   //init the DataTree
 196   mSlicerManagers.resize(0);
 197
 198   QStringList header;
 199   header.append("");
 200   header.append("TL");
 201   header.append("TR");
 202   header.append("BL");
 203   header.append("BR");
 204   header.append("");
 205   header.append("");
 206   header.append("Name");
 207
 208   DataTree->setHeaderLabels(header);
 209   DataTree->resizeColumnToContents(COLUMN_TREE);
 210   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 211   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 212   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 213   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 214   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 215   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 216   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 217
 218   viewMode = 1;
 219   documentation = new vvDocumentation();
 220   help_dialog = new vvHelpDialog();
 221   dicomSeriesSelector = new vvDicomSeriesSelector();
 222
 223   inverseButton->setEnabled(0);
 224   actionAdd_Overlay_to_current_Image->setEnabled(0);
 225   actionSave_As->setEnabled(0);
 226   actionAdd_VF_to_current_Image->setEnabled(0);
 227   actionAdd_fusion_image->setEnabled(0);
 228
 229   //init the sliders
 230   verticalSliders.push_back(NOVerticalSlider);
 231   verticalSliders.push_back(NEVerticalSlider);
 232   verticalSliders.push_back(SOVerticalSlider);
 233   verticalSliders.push_back(SEVerticalSlider);
 234
 235   for (int i =0; i < 4; i++)
 236     verticalSliders[i]->hide();
 237
 238   horizontalSliders.push_back(NOHorizontalSlider);
 239   horizontalSliders.push_back(NEHorizontalSlider);
 240   horizontalSliders.push_back(SOHorizontalSlider);
 241   horizontalSliders.push_back(SEHorizontalSlider);
 242
 243   for (int i =0; i < 4; i++)
 244     horizontalSliders[i]->hide();
 245
 246
 247   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 248   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 249   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 250   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 251
 252   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 253   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 254   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 255   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 256
 257   //connect everything
 258   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 259   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 260   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 261   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 262   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 263   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 264   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 265   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 266   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 267   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 268   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 269   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 270   connect(actionSave_current_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 271   connect(actionRead_saved_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 272   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 273   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 274   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 275   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 276   connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
 277
 278   ///////////////////////////////////////////////
 279   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 280   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 281   ///////////////////////////////////////////////
 282
 283   actionNorth_East_Window->setEnabled(0);
 284   actionNorth_West_Window->setEnabled(0);
 285   actionSouth_East_Window->setEnabled(0);
 286   actionSouth_West_Window->setEnabled(0);
 287
 288   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 289   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 290   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 291   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 292   connect(actionSave_all_slices,SIGNAL(triggered()),this,SLOT(SaveScreenshotAllSlices()));
 293
 294   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 295   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 296           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 297
 298   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 299   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 300   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 301   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 302   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 303   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 304   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 305
 306
 307   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 308
 309 #include "vvSaveState.h"
 310   connect(linkPanel,SIGNAL(addLink(QString,QString)),this,SLOT(AddLink(QString,QString)));
 311   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 312   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 313   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int,int,double,double)),
 314           this,SLOT(SetOverlayProperty(int,int,double,double)));
 315   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,int,double,double)),
 316           this,SLOT(SetFusionProperty(int,int,int,double,double)));
 317   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 318
 319   playMode = 0;//pause
 320   mFrameRate = 10;
 321   playButton->setEnabled(0);
 322   frameRateLabel->setEnabled(0);
 323   frameRateSpinBox->setEnabled(0);
 324   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 325   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 326
 327   goToCursorPushButton->setEnabled(0);
 328   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 329
 330   NOViewWidget->hide();
 331   NEViewWidget->hide();
 332   SOViewWidget->hide();
 333   SEViewWidget->hide();
 334
 335   //Recently opened files
 336   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 337   recentlyOpenedFilesMenu=NULL;
 338   if ( !recent_files.empty() ) {
 339     createRecentlyOpenedFilesMenu();
 340     updateRecentlyOpenedFilesMenu(recent_files);
 341   }
 342
 343   // Adding all new tools (insertion in the menu)
 344   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 345   vvToolManager::GetInstance()->EnableToolsInMenu(this, false);
 346
 347   if (!CLITK_EXPERIMENTAL)
 348     menuExperimental->menuAction()->setVisible(false);
 349
 350
 351   QTimer * timerMemory = new QTimer(this);
 352   //timerMemory->setInterval(5);
 353   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 354   timerMemory->start(2000);
 355 }
 356 //------------------------------------------------------------------------------
 357 void vvMainWindow::show()
 358 {
 359   vvMainWindowBase::show();
 360   PopupRegisterForm(true);
 361 }
 362 //------------------------------------------------------------------------------
 363 void vvMainWindow::UpdateMemoryUsage()
 364 {
 365   //  clitk::PrintMemory(true);
 366   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 367   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 368 }
 369 //------------------------------------------------------------------------------
 370
 371
 372 //------------------------------------------------------------------------------
 373 void vvMainWindow::createRecentlyOpenedFilesMenu()
 374 {
 375   recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
 376   recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 377   menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
 378   menuFile->insertSeparator(actionOpen_Image_With_Time);
 379 }
 380 //------------------------------------------------------------------------------
 381
 382
 383 //------------------------------------------------------------------------------
 384
 385 void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
 386 {
 387   if(recentlyOpenedFilesMenu==NULL) {
 388     createRecentlyOpenedFilesMenu();
 389   } else {
 390     recentlyOpenedFilesMenu->clear();
 391   }
 392   for (std::list<std::string>::const_iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 393     QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")), i->c_str(),this);
 394     recentlyOpenedFilesMenu->addAction(current);
 395     connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 396   }
 397 }
 398 //------------------------------------------------------------------------------
 399
 400
 401 //------------------------------------------------------------------------------
 402 void vvMainWindow::ComputeMidPosition()
 403 {
 404   bool ok;
 405   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 406   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 407                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 408   if (ok) {
 409     vvMidPosition midp;
 410     midp.slicer_manager = mSlicerManagers[index];
 411     midp.reference_image_index = ref;
 412     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 413     midp.Update();
 414     if (midp.error)
 415       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 416     else {
 417       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 418       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 419     }
 420     QApplication::restoreOverrideCursor();
 421   }
 422 }
 423 //------------------------------------------------------------------------------
 424
 425
 426 //------------------------------------------------------------------------------
 427 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 428 {
 429   QTreeWidgetItem *item = new QTreeWidgetItem();
 430   item->setData(0,Qt::UserRole,"filename.vtk");
 431   item->setData(1,Qt::UserRole,tr("contour"));
 432   QBrush brush;
 433   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 434   brush.setStyle(Qt::SolidPattern);
 435   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 436   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 437
 438   for (int j = 1; j <= 4; j++)
 439     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 440
 441   QTreePushButton* cButton = new QTreePushButton;
 442   cButton->setItem(item);
 443   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 444   cButton->setToolTip(tr("close image"));
 445   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 446   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 447           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 448
 449   QTreePushButton* rButton = new QTreePushButton;
 450   rButton->setItem(item);
 451   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 452   rButton->setToolTip(tr("reload image"));
 453   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 454   rButton->setEnabled(false);
 455   //Not implemented
 456   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 457   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 458
 459   DataTree->topLevelItem(image_index)->setExpanded(1);
 460   DataTree->topLevelItem(image_index)->addChild(item);
 461   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 462   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 463   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 464   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 465
 466   UpdateTree();
 467   mSlicerManagers[image_index]->AddContour(contour,propagation);
 468   mSlicerManagers[image_index]->Render();
 469 }
 470 //------------------------------------------------------------------------------
 471
 472
 473 //------------------------------------------------------------------------------
 474 void vvMainWindow::OpenVTKContour()
 475 {
 476   if (mSlicerManagers.size() > 0) {
 477     QString Extensions = "Images ( *.vtk *.obj)";
 478     Extensions += ";;All Files (*)";
 479     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 480     if (file.isNull())
 481       return;
 482     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 483     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 484     vvMeshReader reader;
 485     reader.SetImage(mSlicerManagers[index]->GetImage());
 486     reader.SetModeToVTK();
 487     reader.SetFilename(file.toStdString());
 488     reader.Update();
 489     AddContour(index,reader.GetOutput()[0],false);
 490     QApplication::restoreOverrideCursor();
 491   }
 492 }
 493 //------------------------------------------------------------------------------
 494
 495
 496 //------------------------------------------------------------------------------
 497 void vvMainWindow::OpenDCStructContour()
 498 {
 499   if (mSlicerManagers.size() > 0) {
 500     QString Extensions = "Dicom Files ( *.dcm RS*)";
 501     Extensions += ";;All Files (*)";
 502     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 503     if (file.isNull())
 504       return;
 505     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 506     vvMeshReader reader;
 507     reader.SetFilename(file.toStdString());
 508     vvStructSelector selector;
 509     selector.SetStructures(reader.GetROINames());
 510     if (!mSlicerManagers[index]->GetVF().IsNull())
 511       selector.EnablePropagationCheckBox();
 512     if (selector.exec()) {
 513       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 514       reader.SetSelectedItems(selector.getSelectedItems());
 515       reader.SetImage(mSlicerManagers[index]->GetImage());
 516       if (selector.PropagationEnabled())
 517         reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 518       reader.Update();
 519       std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 520       for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 521            i!=contours.end(); i++)
 522         AddContour(index,*i,selector.PropagationEnabled());
 523       QApplication::restoreOverrideCursor();
 524     }
 525   }
 526 }
 527 //------------------------------------------------------------------------------
 528
 529
 530 //------------------------------------------------------------------------------
 531 void vvMainWindow::ComputeDeformableRegistration()
 532 {
 533   if (mSlicerManagers.size() > 0) {
 534     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 535     vvDeformationDialog dialog(index,mSlicerManagers);
 536     if (dialog.exec()) {
 537       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 538       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 539       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 540     } else
 541       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 542   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 543 }
 544 //------------------------------------------------------------------------------
 545
 546
 547 //------------------------------------------------------------------------------
 548 void vvMainWindow::WarpImage()
 549 {
 550   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 551   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 552     bool ok;
 553     int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 554                                        mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 555     if (ok) {
 556       WarpImage(mSlicerManagers[index],ref);
 557     }
 558   } else
 559     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 560 }
 561 //------------------------------------------------------------------------------
 562
 563
 564 //------------------------------------------------------------------------------
 565 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 566 {
 567   if (!selected_slicer->GetVF().IsNull()) {
 568     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 569     QFileInfo info(selected_slicer->GetFileName().c_str());
 570     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 571                      reference_phase,this);
 572     if (warp.ComputeWarpedImage()) {
 573       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 574       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 575       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 576       QApplication::restoreOverrideCursor();
 577     } else {
 578       QApplication::restoreOverrideCursor();
 579       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 580     }
 581   } else
 582     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 583 }
 584 //------------------------------------------------------------------------------
 585
 586
 587 //------------------------------------------------------------------------------
 588 vvMainWindow::~vvMainWindow()
 589 {
 590   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 591     if (mSlicerManagers[i] != NULL)
 592       delete mSlicerManagers[i];
 593   }
 594 }
 595 //------------------------------------------------------------------------------
 596
 597 //------------------------------------------------------------------------------
 598 QTabWidget * vvMainWindow::GetTab()
 599 {
 600   return tabWidget;
 601 }
 602 //------------------------------------------------------------------------------
 603
 604
 605 //------------------------------------------------------------------------------
 606 void vvMainWindow::MergeImages()
 607 {
 608   QString Extensions = EXTENSIONS;
 609   Extensions += ";;All Files (*)";
 610   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 611   if (files.isEmpty())
 612     return;
 613   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 614   std::vector<std::string> vector;
 615
 616   unsigned int currentDim = 0;
 617   std::vector<double> currentSpacing;
 618   std::vector<int> currentSize;
 619   std::vector<double> currentOrigin;
 620
 621   for (int i = 0; i < files.size(); i++) {
 622     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 623                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 624     reader->SetFileName(files[i].toStdString().c_str());
 625     reader->ReadImageInformation();
 626     if (reader)        {
 627       //NOViewWidget->hide();
 628       //NEViewWidget->hide();
 629       //SOViewWidget->hide();
 630       //SEViewWidget->hide();
 631       if (i == 0)
 632         currentDim = reader->GetNumberOfDimensions();
 633       bool IsOk = true;
 634       for (unsigned int j = 0; j < currentDim; j++) {
 635         if (i == 0) {
 636           if (j == 0) {
 637             currentSpacing.resize(currentDim);
 638             currentSize.resize(currentDim);
 639             currentOrigin.resize(currentDim);
 640           }
 641           currentOrigin[j] = reader->GetOrigin(j);
 642           currentSpacing[j] = reader->GetSpacing(j);
 643           currentSize[j] = reader->GetDimensions(j);
 644         } else if (currentDim != reader->GetNumberOfDimensions()
 645                    || currentSpacing[j] != reader->GetSpacing(j)
 646                    || currentSize[j] != (int)reader->GetDimensions(j)
 647                    || currentOrigin[j] != reader->GetOrigin(j)) {
 648           QString error = "Cannot read file (too different from others ";
 649           error += files[i].toStdString().c_str();
 650           QMessageBox::information(this,tr("Reading problem"),error);
 651           IsOk = false;
 652           break;
 653         }
 654       }
 655       if (IsOk)
 656         vector.push_back(files[i].toStdString());
 657     }
 658   }
 659   if (vector.size() > 0)
 660     LoadImages(vector, vvImageReader::MERGED);
 661 }
 662 //------------------------------------------------------------------------------
 663
 664 //------------------------------------------------------------------------------
 665 void vvMainWindow::SliceImages()
 666 {
 667   QString Extensions = EXTENSIONS;
 668   Extensions += ";;All Files (*)";
 669
 670   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 671   if (files.isEmpty())
 672     return;
 673   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 674   std::vector<std::string> vector;
 675   for (int i = 0; i < files.size(); i++)
 676     vector.push_back(files[i].toStdString());
 677   LoadImages(vector, vvImageReader::SLICED);
 678 }
 679 //------------------------------------------------------------------------------
 680
 681 //------------------------------------------------------------------------------
 682 void vvMainWindow::MergeImagesWithTime()
 683 {
 684   QString Extensions = EXTENSIONS;
 685   Extensions += ";;All Files (*)";
 686   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 687   if (files.isEmpty())
 688     return;
 689   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 690   std::vector<std::string> vector;
 691
 692   unsigned int currentDim = 0;
 693   std::vector<double> currentSpacing;
 694   std::vector<int> currentSize;
 695   std::vector<double> currentOrigin;
 696
 697   for (int i = 0; i < files.size(); i++) {
 698     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 699                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 700     if (reader) {
 701       reader->SetFileName(files[i].toStdString().c_str());
 702       reader->ReadImageInformation();
 703       if (i == 0)
 704         currentDim = reader->GetNumberOfDimensions();
 705       bool IsOk = true;
 706       for (unsigned int j = 0; j < currentDim; j++) {
 707         if (i == 0) {
 708           if (j == 0) {
 709             currentSpacing.resize(currentDim);
 710             currentSize.resize(currentDim);
 711             currentOrigin.resize(currentDim);
 712           }
 713           currentOrigin[j] = reader->GetOrigin(j);
 714           currentSpacing[j] = reader->GetSpacing(j);
 715           currentSize[j] = reader->GetDimensions(j);
 716         } else if (currentDim != reader->GetNumberOfDimensions()
 717                    || currentSpacing[j] != reader->GetSpacing(j)
 718                    || currentSize[j] != (int)reader->GetDimensions(j)
 719                    || currentOrigin[j] != reader->GetOrigin(j)) {
 720           QString error = "Cannot read file (too different from others ";
 721           error += files[i].toStdString().c_str();
 722           QMessageBox::information(this,tr("Reading problem"),error);
 723           IsOk = false;
 724           break;
 725         }
 726       }
 727       if (IsOk)
 728         vector.push_back(files[i].toStdString());
 729     } else {
 730       QString error = "Cannot read file info for ";
 731       error += files[i].toStdString().c_str();
 732       error += "\n";
 733       error += "Maybe you're trying to open an image in an unsupported format?\n";
 734       QMessageBox::information(this,tr("Reading problem"),error);
 735     }
 736   }
 737   sort(vector.begin(),vector.end());
 738   if (vector.size() > 1)
 739     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 740   else
 741     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.");
 742 }
 743 //------------------------------------------------------------------------------
 744
 745
 746 //------------------------------------------------------------------------------
 747 void vvMainWindow::OpenDicom()
 748 {
 749   std::vector<std::string> files;
 750
 751   std::cout << "dicomSeriesSelector " << std::endl;
 752   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 753     files = *(dicomSeriesSelector->GetFilenames());
 754     LoadImages(files, vvImageReader::DICOM);
 755   }
 756 }
 757 //------------------------------------------------------------------------------
 758
 759 //------------------------------------------------------------------------------
 760 void vvMainWindow::OpenImages()
 761 {
 762   QString Extensions = EXTENSIONS;
 763   Extensions += ";;All Files (*)";
 764
 765   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 766   if (files.isEmpty())
 767     return;
 768   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 769   std::vector<std::string> vector;
 770   for (int i = 0; i < files.size(); i++)
 771     vector.push_back(files[i].toStdString());
 772   LoadImages(vector, vvImageReader::IMAGE);
 773 }
 774 //------------------------------------------------------------------------------
 775 void vvMainWindow::OpenRecentImage()
 776 {
 777   QAction * caller = qobject_cast<QAction*>(sender());
 778   std::vector<std::string> images;
 779   images.push_back(caller->text().toStdString());
 780   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 781   LoadImages(images, vvImageReader::IMAGE);
 782 }
 783 //------------------------------------------------------------------------------
 784
 785
 786 //------------------------------------------------------------------------------
 787 void vvMainWindow::OpenImageWithTime()
 788 {
 789   QString Extensions = EXTENSIONS;
 790   Extensions += ";;All Files (*)";
 791
 792   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 793   if (files.isEmpty())
 794     return;
 795   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 796   std::vector<std::string> vector;
 797   for (int i = 0; i < files.size(); i++) {
 798     vector.push_back(files[i].toStdString());
 799   }
 800   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 801 }
 802 //------------------------------------------------------------------------------
 803
 804
 805 //------------------------------------------------------------------------------
 806 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 807 {
 808   //Separate the way to open images and dicoms
 809   int fileSize;
 810   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 811     fileSize = files.size();
 812   else
 813     fileSize = 1;
 814
 815   // For SLICED, we need the number of slices (ndim and #slices)
 816   std::vector<unsigned int> nSlices;
 817   nSlices.resize(files.size());
 818   std::fill(nSlices.begin(), nSlices.end(), 1);
 819   if (filetype == vvImageReader::SLICED) {
 820     for (int i = 0; i < fileSize; i++) {
 821       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 822       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 823       if (!header) {
 824         nSlices[i] = 0;
 825         QString error = "Cannot open file \n";
 826         error += files[i].c_str();
 827         QMessageBox::information(this,tr("Reading problem"),error);
 828         return;
 829       }
 830       if (header->GetNumberOfDimensions() < 3) {
 831         nSlices[i] = 0;
 832         QString error = "Dimension problem. Cannot slice \n";
 833         error += files[i].c_str();
 834         QMessageBox::information(this,tr("Reading problem"),error);
 835         return;
 836       }
 837       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 838     }
 839   }
 840
 841   //Only add to the list of recently opened files when a single file is opened,
 842   //to avoid polluting the list of recently opened files
 843   if (files.size() == 1) {
 844     QFileInfo finfo=tr(files[0].c_str());
 845     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 846     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 847   }
 848   //init the progress events
 849   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 850   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 851   qApp->processEvents();
 852
 853   int numberofsuccesulreads=0;
 854   //open images as 1 or multiples
 855   for (int i = 0; i < fileSize; i++) {
 856
 857     progress.SetText("Opening " + files[i]);
 858     progress.SetProgress(i,fileSize);
 859     qApp->processEvents();
 860
 861     for (unsigned int j = 0; j < nSlices[i]; j++) {
 862       //read the image and put it in mSlicerManagers
 863       vvSlicerManager* imageManager = new vvSlicerManager(4);
 864       qApp->processEvents();
 865
 866       bool SetImageSucceed=false;
 867
 868       // Change filename if an image with the same already exist
 869       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 870
 871       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED)
 872         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 873       else {
 874         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 875       }
 876       if (!SetImageSucceed) {
 877         QApplication::restoreOverrideCursor();
 878         QString error = "Cannot open file \n";
 879         error += imageManager->GetLastError().c_str();
 880         QMessageBox::information(this,tr("Reading problem"),error);
 881         delete imageManager;
 882       } else {
 883         mSlicerManagers.push_back(imageManager);
 884
 885         //create an item in the tree with good settings
 886         QTreeWidgetItem *item = new QTreeWidgetItem();
 887         item->setData(0,Qt::UserRole,files[i].c_str());
 888         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 889         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 890         item->setData(1,Qt::UserRole,tr("image"));
 891         item->setToolTip(COLUMN_IMAGE_NAME, imageManager->GetListOfAbsoluteFilePathInOneString("image").c_str());
 892         qApp->processEvents();
 893
 894         //Create the buttons for reload and close
 895         qApp->processEvents();
 896         QTreePushButton* cButton = new QTreePushButton;
 897         cButton->setItem(item);
 898         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 899         cButton->setToolTip(tr("close image"));
 900         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 901         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 902                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 903
 904         QTreePushButton* rButton = new QTreePushButton;
 905         rButton->setItem(item);
 906         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 907         rButton->setToolTip(tr("reload image"));
 908         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 909         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 910                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 911
 912         DataTree->addTopLevelItem(item);
 913         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 914         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 915
 916         //set the id of the image
 917         QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 918         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 919         mSlicerManagers.back()->SetId(id.toStdString());
 920
 921         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 922
 923         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 924                 this,SLOT(CurrentImageChanged(std::string)));
 925         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 926                 this, SLOT(CurrentPickedImageChanged(std::string)));
 927         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 928                 this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 929         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 930                 this, SLOT(VectorChanged(int,double,double,double, double)));
 931         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 932                 this, SLOT(OverlayChanged(int,double,double)));
 933         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 934                 this, SLOT(FusionChanged(int,double)));
 935         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
 936                 this,SLOT(WindowLevelChanged()));
 937         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 938                 this,SLOT(UpdateSlice(int,int)));
 939         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 940                 this,SLOT(UpdateTSlice(int, int)));
 941         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 942                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 943         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 944                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 945         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 946                 this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 947         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 948                 this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 949         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 950         InitSlicers();
 951         numberofsuccesulreads++;
 952       }
 953     }
 954   }
 955   if (numberofsuccesulreads) {
 956     NOViewWidget->show();
 957     NEViewWidget->show();
 958     SOViewWidget->show();
 959     SEViewWidget->show();
 960     UpdateTree();
 961     InitDisplay();
 962     ShowLastImage();
 963
 964     // Try to guess default WindowLevel
 965     double range[2];
 966     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 967     if ((range[0] == 0) && (range[1] == 1)) {
 968       presetComboBox->setCurrentIndex(5);// binary
 969     } else {
 970       // TODO
 971     }
 972   }
 973   QApplication::restoreOverrideCursor();
 974 }
 975 //------------------------------------------------------------------------------
 976
 977 //------------------------------------------------------------------------------
 978 void vvMainWindow::UpdateTree()
 979 {
 980   DataTree->resizeColumnToContents(COLUMN_TREE);
 981   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 982   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 983   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 984   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 985   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 986   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 987   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 988 }
 989 //------------------------------------------------------------------------------
 990
 991 //------------------------------------------------------------------------------
 992 void vvMainWindow::CurrentImageChanged(std::string id)
 993 {
 994   if (id == mCurrentSelectedImageId) return; // Do nothing
 995   int selected = 0;
 996   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 997     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 998       selected = i;
 999     } else {
1000       DataTree->topLevelItem(i)->setSelected(0);
1001     }
1002     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1003       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1004
1005   }
1006   DataTree->topLevelItem(selected)->setSelected(1);
1007   mCurrentSelectedImageId = id;
1008   emit SelectedImageHasChanged(mSlicerManagers[selected]);
1009 }
1010 //------------------------------------------------------------------------------
1011
1012 //------------------------------------------------------------------------------
1013 void vvMainWindow::CurrentPickedImageChanged(std::string id)
1014 {
1015   if (id == mCurrentPickedImageId) return; // Do nothing
1016   int selected = 0;
1017   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1018     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1019       selected = i;
1020     } else {
1021       DataTree->topLevelItem(i)->setSelected(0);
1022     }
1023     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1024       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1025
1026   }
1027   DataTree->topLevelItem(selected)->setSelected(1);
1028   mCurrentPickedImageId = id;
1029   mCurrentPickedImageIndex = selected;
1030 }
1031 //------------------------------------------------------------------------------
1032
1033 //------------------------------------------------------------------------------
1034 void vvMainWindow::ImageInfoChanged()
1035 {
1036   contextActions[6]->setEnabled(1);
1037   contextActions[5]->setEnabled(1);
1038   actionSave_As->setEnabled(1);
1039   actionAdd_VF_to_current_Image->setEnabled(1);
1040   actionAdd_fusion_image->setEnabled(1);
1041   actionNorth_East_Window->setEnabled(1);
1042   actionNorth_West_Window->setEnabled(1);
1043   actionSouth_East_Window->setEnabled(1);
1044   actionSouth_West_Window->setEnabled(1);
1045   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1046   inverseButton->setEnabled(1);
1047
1048   goToCursorPushButton->setEnabled(1);
1049
1050   if (DataTree->selectedItems().size()) {
1051     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1052
1053     colorMapComboBox->setEnabled(1);
1054     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1055       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1056           DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion") {
1057         colorMapComboBox->setEnabled(0);
1058         break;
1059       }
1060     }
1061
1062     std::vector<double> origin;
1063     std::vector<double> inputSpacing;
1064     std::vector<int> inputSize;
1065     std::vector<double> sizeMM;
1066     vtkSmartPointer<vtkMatrix4x4> transformation;
1067     int dimension=0;
1068     QString pixelType;
1069     QString inputSizeInBytes;
1070     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1071
1072     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1) {
1073       playButton->setEnabled(1);
1074       frameRateLabel->setEnabled(1);
1075       frameRateSpinBox->setEnabled(1);
1076     } else {
1077       playButton->setEnabled(0);
1078       frameRateLabel->setEnabled(0);
1079       frameRateSpinBox->setEnabled(0);
1080     }
1081
1082     //read image header
1083     int NPixel = 1;
1084
1085     vvImage::Pointer imageSelected;
1086     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1087       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1088     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1089       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1090     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1091       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1092     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1093       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1094     }
1095     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "contour") {
1096       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1097     }
1098     else {
1099       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1100     }
1101
1102     dimension = imageSelected->GetNumberOfDimensions();
1103     origin.resize(dimension);
1104     inputSpacing.resize(dimension);
1105     inputSize.resize(dimension);
1106     sizeMM.resize(dimension);
1107     pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1108     for (int i = 0; i < dimension; i++) {
1109       origin[i] = imageSelected->GetOrigin()[i];
1110       inputSpacing[i] = imageSelected->GetSpacing()[i];
1111       inputSize[i] = imageSelected->GetSize()[i];
1112       sizeMM[i] = inputSize[i]*inputSpacing[i];
1113       NPixel *= inputSize[i];
1114     }
1115     inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1116
1117     QString dim = QString::number(dimension) + " (";
1118     dim += pixelType + ")";
1119
1120     infoPanel->setFileName(image);
1121     infoPanel->setDimension(dim);
1122     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1123     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1124     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1125     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1126     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1127     transformation = imageSelected->GetTransform()->GetMatrix();
1128     infoPanel->setTransformation(Get4x4MatrixDoubleAsString(transformation));
1129
1130     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1131                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1132     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1133     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1134
1135     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1136     for (int i = 0; i < 4; i++) {
1137       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1138         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1139         break;
1140       }
1141     }
1142
1143     infoPanel->setFileName(image);
1144     infoPanel->setDimension(dim);
1145     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1146     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1147     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1148     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1149     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1150
1151     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1152                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1153     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1154     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1155
1156     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1157     for (int i = 0; i < 4; i++) {
1158       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1159         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1160         break;
1161       }
1162     }
1163     WindowLevelChanged();
1164
1165     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1166       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1167       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1168                                   mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1169                                   mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1170     } else {
1171       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1172       overlayPanel->getVFProperty(-1,-1,-1);
1173     }
1174     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1175       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1176     } else {
1177       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1178     }
1179
1180     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1181       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1182     } else {
1183       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1184     }
1185   }
1186 }
1187 //------------------------------------------------------------------------------
1188
1189 //------------------------------------------------------------------------------
1190 void vvMainWindow::ShowDocumentation()
1191 {
1192   documentation->show();
1193 }
1194 //------------------------------------------------------------------------------
1195
1196 //------------------------------------------------------------------------------
1197 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1198 {
1199   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1200   if(!checkCanPush) {
1201     registerForm->show();
1202   } else {
1203     if(registerForm->canPush()) {
1204       registerForm->show();
1205       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1206     }
1207   }
1208 }
1209 //------------------------------------------------------------------------------
1210
1211 //------------------------------------------------------------------------------
1212 void vvMainWindow::ShowHelpDialog()
1213 {
1214   help_dialog->show();
1215 }
1216 //------------------------------------------------------------------------------
1217
1218 //------------------------------------------------------------------------------
1219 void vvMainWindow::ChangeViewMode()
1220 {
1221   QList<int> size;
1222   if (viewMode == 1) {
1223     viewMode = 0;
1224     size.push_back(1);
1225     size.push_back(0);
1226     splitter_3->setSizes(size);
1227     OSplitter->setSizes(size);
1228     DataTree->setColumnHidden(2,1);
1229     DataTree->setColumnHidden(3,1);
1230     DataTree->setColumnHidden(4,1);
1231   } else {
1232     viewMode = 1;
1233     size.push_back(1);
1234     size.push_back(1);
1235     splitter_3->setSizes(size);
1236     OSplitter->setSizes(size);
1237     DataTree->setColumnHidden(2,0);
1238     DataTree->setColumnHidden(3,0);
1239     DataTree->setColumnHidden(4,0);
1240   }
1241   UpdateRenderWindows();
1242   /*
1243   ** I don't know why but for both resized QVTKWidget we also need to render
1244   ** the associated Slicer to redraw crosses.
1245   */
1246   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1247     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1248       mSlicerManagers[i]->GetSlicer(0)->Render();
1249     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1250       mSlicerManagers[i]->GetSlicer(2)->Render();
1251   }
1252 }
1253 //------------------------------------------------------------------------------
1254
1255 //------------------------------------------------------------------------------
1256 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1257 {
1258   QString result = "";// QString::number(size);
1259   //result += " bytes (";
1260   if (size > 1000000000) {
1261     size /= 1000000000;
1262     result += QString::number(size);
1263     result += "Gb";//)";
1264   } else if (size > 1000000) {
1265     size /= 1000000;
1266     result += QString::number(size);
1267     result += "Mb";//)";
1268   } else if (size > 1000) {
1269     size /= 1000;
1270     result += QString::number(size);
1271     result += "kb";//)";
1272   }
1273   return result;
1274 }
1275 //------------------------------------------------------------------------------
1276
1277 //------------------------------------------------------------------------------
1278 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix)
1279 {
1280   std::ostringstream strmatrix;
1281
1282   for (unsigned int i = 0; i < 4; i++) {
1283     for (unsigned int j = 0; j < 4; j++) {
1284       strmatrix.flags(ios::showpos);
1285       strmatrix.width(10);
1286       strmatrix.precision(3);
1287       strmatrix.setf(ios::fixed,ios::floatfield);
1288       strmatrix.fill(' ');
1289       strmatrix << std::left << matrix->GetElement(i, j);
1290       //strmatrix.width(10);
1291       strmatrix << " ";
1292     }
1293     strmatrix << std::endl;
1294   }
1295   QString result = strmatrix.str().c_str();
1296   return result;
1297 }
1298 //------------------------------------------------------------------------------
1299
1300 //------------------------------------------------------------------------------
1301 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1302 {
1303   QString result;
1304   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1305     if (i != 0)
1306       result += " ";
1307     result += QString::number(vectorDouble[i]);
1308   }
1309   return result;
1310 }
1311 //------------------------------------------------------------------------------
1312
1313 //------------------------------------------------------------------------------
1314 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1315 {
1316   QString result;
1317   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1318     if (i != 0)
1319       result += " ";
1320     result += QString::number(vectorInt[i]);
1321   }
1322   return result;
1323 }
1324 //------------------------------------------------------------------------------
1325
1326 //------------------------------------------------------------------------------
1327 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1328 {
1329   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1330   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1331     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1332       return i;
1333   }
1334   return -1;
1335 }
1336 //------------------------------------------------------------------------------
1337
1338 //------------------------------------------------------------------------------
1339 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1340 {
1341   QString id = sm->GetId().c_str();
1342   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1343     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1344       return DataTree->topLevelItem(i);
1345   }
1346   return NULL;
1347 }
1348 //------------------------------------------------------------------------------
1349
1350 //------------------------------------------------------------------------------
1351 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clickedItem, int column)
1352 {
1353   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1354     return;
1355
1356   // Get parent information (might be the same item)
1357   int slicerManagerIndex = GetSlicerIndexFromItem(clickedItem);
1358   QTreeWidgetItem* clickedParentItem = DataTree->topLevelItem(slicerManagerIndex);
1359   vvSlicer* clickedSlicer = mSlicerManagers[slicerManagerIndex]->GetSlicer(column-1);
1360
1361   // Go over the complete item tree (only 2 levels, parents and children)
1362   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1363     // Trick to avoid redoing twice the job for a key (sr)
1364     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()->GetInteractor()->SetKeySym("Crap");
1365
1366     QTreeWidgetItem* currentParentItem = DataTree->topLevelItem(i);
1367     if(currentParentItem != clickedParentItem) {
1368       // Not the branch of the clicked item, uncheck all
1369
1370       // Parent
1371       currentParentItem->setData(column,Qt::CheckStateRole, 0);
1372       mSlicerManagers[i]->UpdateSlicer(column-1, false);
1373
1374       // Children
1375       for (int iChild = 0; iChild < currentParentItem->childCount(); iChild++) {
1376         currentParentItem->child(iChild)->setData(column,Qt::CheckStateRole, 0);
1377       }
1378     }
1379     else {
1380       // Branch of the clicked one: get check status from actor visibility in slicer
1381       // and toggle the clicked one
1382
1383       // Parent
1384       bool vis = clickedSlicer->GetActorVisibility("image", 0);
1385       bool draw = clickedSlicer->GetRenderer()->GetDraw();
1386
1387       // Update slicer (after getting visibility)
1388       mSlicerManagers[slicerManagerIndex]->UpdateSlicer(column-1, true);
1389       mSlicerManagers[slicerManagerIndex]->UpdateInfoOnCursorPosition(column-1);
1390       DisplaySliders(slicerManagerIndex, column-1);
1391       if(clickedParentItem == clickedItem) {
1392         // Toggle
1393         vis = !draw || !vis;
1394       }
1395       clickedSlicer->SetActorVisibility("image", 0, vis);
1396       clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
1397
1398       // Children
1399       std::map<std::string, int> actorTypeCounts;
1400       for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
1401         QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
1402         std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
1403         vis = clickedSlicer->GetActorVisibility(actorType, actorTypeCounts[actorType]);
1404         if(currentChildItem == clickedItem) {
1405           // Toggle or force visibility if it was not on this branch so far
1406           vis = !draw || !vis;
1407           clickedSlicer->SetActorVisibility(actorType, actorTypeCounts[actorType], vis);
1408         }
1409         currentChildItem->setData(column, Qt::CheckStateRole, vis?2:0);
1410         actorTypeCounts[actorType]++;
1411       }
1412     }
1413   }
1414
1415   clickedSlicer->Render();
1416 }
1417 //------------------------------------------------------------------------------
1418
1419 void vvMainWindow::InitSlicers()
1420 {
1421   if (mSlicerManagers.size()) {
1422     mSlicerManagers.back()->GenerateDefaultLookupTable();
1423
1424     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1425     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1426     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1427     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1428   }
1429 }
1430
1431 //------------------------------------------------------------------------------
1432 void vvMainWindow::InitDisplay()
1433 {
1434   if (mSlicerManagers.size()) {
1435     //BE CAREFUL : this is absolutely necessary to set the interactor style
1436     //in order to have the same style instanciation for all SlicerManagers in
1437     // a same window
1438     for (int j = 0; j < 4; j++) {
1439       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1440       style->SetAutoAdjustCameraClippingRange(1);
1441       bool AlreadySelected = false;
1442       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1443         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1444
1445         //select the image only if previous are not selected
1446         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1447           mSlicerManagers[i]->UpdateSlicer(j,1);
1448           AlreadySelected = true;
1449         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1450           if (DataTree->selectedItems().size() == 0)
1451             DataTree->topLevelItem(i)->setSelected(1);
1452           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1453           mSlicerManagers[i]->UpdateSlicer(j,1);
1454           DisplaySliders(i,j);
1455         } else {
1456           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1457           mSlicerManagers[i]->UpdateSlicer(j,0);
1458         }
1459       }
1460       style->Delete();
1461     }
1462   }
1463 }
1464 //------------------------------------------------------------------------------
1465
1466 //------------------------------------------------------------------------------
1467 void vvMainWindow::DisplaySliders(int slicer, int window)
1468 {
1469   int range[2];
1470   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1471   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1472
1473   int tRange[2];
1474   tRange[0] = 0;
1475   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1476   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1477   bool showHorizontal = false;
1478   bool showVertical = false;
1479   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1480       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1481           && mSlicerManagers[slicer]->GetType() != vvImageReader::IMAGEWITHTIME
1482           && mSlicerManagers[slicer]->GetType() != vvImageReader::MERGEDWITHTIME))
1483     showVertical = true;
1484   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1485       || mSlicerManagers[slicer]->GetType() == vvImageReader::IMAGEWITHTIME
1486       || mSlicerManagers[slicer]->GetType() == vvImageReader::MERGEDWITHTIME)
1487     showHorizontal = true;
1488
1489   if (showVertical)
1490     verticalSliders[window]->show();
1491   else
1492     verticalSliders[window]->hide();
1493   verticalSliders[window]->setRange(range[0],range[1]);
1494   verticalSliders[window]->setValue(position);
1495
1496   if (showHorizontal)
1497     horizontalSliders[window]->show();
1498   else
1499     horizontalSliders[window]->hide();
1500   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1501   horizontalSliders[window]->setValue(tPosition);
1502 }
1503 //------------------------------------------------------------------------------
1504
1505 //------------------------------------------------------------------------------
1506 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1507 {
1508   int index = GetSlicerIndexFromItem(item);
1509
1510   if (DataTree->topLevelItem(index) != item) {
1511     QString warning = "Do you really want to close the overlay : ";
1512     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1513     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1514                        warning, 0, this);
1515     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1516     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1517     if (msgBox.exec() == QMessageBox::AcceptRole) {
1518       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1519       int overlay_index=0;
1520       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1521         if (DataTree->topLevelItem(index)->\
1522             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1523           overlay_index++;
1524         if (DataTree->topLevelItem(index)->child(child) == item) break;
1525       }
1526       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1527       mSlicerManagers[index]->SetColorMap(0);
1528       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1529       mSlicerManagers[index]->Render();
1530     }
1531   } else if (DataTree->topLevelItemCount() <= 1) {
1532     QString warning = "Do you really want to close the image : ";
1533     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1534     warning += "\nThis is the last image, you're about to close vv !!!";
1535     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1536                        warning, 0, this);
1537     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1538     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1539     if (msgBox.exec() == QMessageBox::AcceptRole) {
1540       this->close();
1541     }
1542   } else {
1543     QString warning = "Do you really want to close the image : ";
1544     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1545     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1546                        warning, 0, this);
1547     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1548     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1549     if (msgBox.exec() == QMessageBox::AcceptRole) {
1550
1551       // Tell tools that we close an image
1552       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1553
1554       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1555       DataTree->takeTopLevelItem(index);
1556       for (int i = 0; i < index; i++) {
1557         Manageriter++;
1558       }
1559       linkPanel->removeImage(index);
1560       mSlicerManagers[index]->RemoveActors();
1561       delete mSlicerManagers[index];
1562       mSlicerManagers.erase(Manageriter);
1563
1564       //
1565       InitDisplay();
1566     }
1567   }
1568   ImageInfoChanged();
1569 }
1570 //------------------------------------------------------------------------------
1571
1572 //------------------------------------------------------------------------------
1573 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1574 {
1575   // int index = GetSlicerIndexFromItem(item);
1576   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1577   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1578   //     mSlicerManagers[index]->ReloadVF();
1579   //   else
1580   //     mSlicerManagers[index]->Reload();
1581
1582   //   QApplication::restoreOverrideCursor();
1583   int index = GetSlicerIndexFromItem(item);
1584   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1585   QString role=item->data(1,Qt::UserRole).toString();
1586   if ( role == "vector"){
1587     mSlicerManagers[index]->ReloadVF();
1588   }
1589   else if (role == "overlay"){
1590     mSlicerManagers[index]->ReloadOverlay();
1591   }
1592   else if (role == "fusion"){
1593     mSlicerManagers[index]->ReloadFusion();
1594   }
1595   else{
1596     mSlicerManagers[index]->Reload();
1597   }
1598   // Update view and info
1599   ImageInfoChanged();
1600   mSlicerManagers[index]->Render();
1601   QApplication::restoreOverrideCursor();
1602 }
1603 //------------------------------------------------------------------------------
1604
1605 //------------------------------------------------------------------------------
1606 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1607 {
1608   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1609 }
1610 //------------------------------------------------------------------------------
1611
1612 //------------------------------------------------------------------------------
1613 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1614 {
1615   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1616 }
1617 //------------------------------------------------------------------------------
1618
1619 //------------------------------------------------------------------------------
1620 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1621 {
1622   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1623 }
1624 //------------------------------------------------------------------------------
1625
1626 //------------------------------------------------------------------------------
1627 void vvMainWindow::FusionChanged(int visibility, double value)
1628 {
1629   overlayPanel->getCurrentFusionInfo(visibility,value);
1630 }
1631 //------------------------------------------------------------------------------
1632
1633 //------------------------------------------------------------------------------
1634 void vvMainWindow::WindowLevelChanged()
1635 {
1636   // Base image
1637   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1638   if(index==-1) return;
1639   windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1640   levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1641   colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1642   presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1643
1644   // Overlay image
1645   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1646     overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor(),
1647                                      mSlicerManagers[index]->GetLinkOverlayWindowLevel(),
1648                                      mSlicerManagers[index]->GetOverlayColorWindow(),
1649                                      mSlicerManagers[index]->GetOverlayColorLevel());
1650   else
1651     overlayPanel->getOverlayProperty(-1,0,0.,0.);
1652
1653   // Fusion image
1654   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion())
1655     overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1656                                     mSlicerManagers[index]->GetFusionThresholdOpacity(),
1657                                     mSlicerManagers[index]->GetFusionColorMap(),
1658                                     mSlicerManagers[index]->GetFusionWindow(),
1659                                     mSlicerManagers[index]->GetFusionLevel());
1660   else
1661     overlayPanel->getFusionProperty(-1, -1, -1, -1, -1);
1662 }
1663 //------------------------------------------------------------------------------
1664
1665 //------------------------------------------------------------------------------
1666 void vvMainWindow::WindowLevelEdited()
1667 {
1668   presetComboBox->setCurrentIndex(6);
1669   UpdateWindowLevel();
1670 }
1671 //------------------------------------------------------------------------------
1672
1673 //------------------------------------------------------------------------------
1674 void vvMainWindow::SetWindowLevel(double w, double l)
1675 {
1676   windowSpinBox->setValue(w);
1677   levelSpinBox->setValue(l);
1678   presetComboBox->setCurrentIndex(6);
1679   colorMapComboBox->setCurrentIndex(0);
1680   UpdateWindowLevel();
1681 }
1682 //------------------------------------------------------------------------------
1683
1684 //------------------------------------------------------------------------------
1685 void vvMainWindow::UpdateWindowLevel()
1686 {
1687   if (DataTree->selectedItems().size()) {
1688     if (presetComboBox->currentIndex() == 7) //For ventilation
1689       colorMapComboBox->setCurrentIndex(5);
1690     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1691     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1692     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1693     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1694     mSlicerManagers[index]->Render();
1695     WindowLevelChanged();
1696   }
1697 }
1698 //------------------------------------------------------------------------------
1699
1700 //------------------------------------------------------------------------------
1701 void vvMainWindow::UpdateColorMap()
1702 {
1703   if (DataTree->selectedItems().size()) {
1704     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1705     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1706     mSlicerManagers[index]->Render();
1707   }
1708 }
1709 //------------------------------------------------------------------------------
1710 void vvMainWindow::SwitchWindowLevel()
1711 {
1712   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1713   int window = mSlicerManagers[index]->GetColorWindow();
1714   presetComboBox->setCurrentIndex(6);
1715   windowSpinBox->setValue(-window);
1716   UpdateWindowLevel();
1717 }
1718 //------------------------------------------------------------------------------
1719
1720 //------------------------------------------------------------------------------
1721 void vvMainWindow::ApplyWindowLevelToAllImages()
1722 {
1723   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1724     if (mSlicerManagers[i] == NULL)
1725       continue;
1726     mSlicerManagers[i]->SetColorWindow(windowSpinBox->value());
1727     mSlicerManagers[i]->SetColorLevel(levelSpinBox->value());
1728     mSlicerManagers[i]->SetPreset(6);
1729     mSlicerManagers[i]->Render();
1730   }
1731 }
1732 //------------------------------------------------------------------------------
1733
1734 //------------------------------------------------------------------------------
1735 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1736 {
1737   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1738     if (mSlicerManagers[i]->GetId() == id) {
1739       //mSlicerManagers[i]->SetTSlice(temps);
1740       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1741       mSlicerManagers[i]->UpdateViews(0,slicer);
1742       break;
1743     }
1744   }
1745 }
1746 //------------------------------------------------------------------------------
1747
1748 //------------------------------------------------------------------------------
1749 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1750 {
1751   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1752     if (id == mSlicerManagers[i]->GetId()) {
1753       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1754     }
1755   }
1756 }
1757 //------------------------------------------------------------------------------
1758
1759 //------------------------------------------------------------------------------
1760 void vvMainWindow::ShowContextMenu(QPoint point)
1761 {
1762   if (!DataTree->selectedItems().size()) {
1763     contextActions[1]->setEnabled(0);
1764     contextActions[2]->setEnabled(0);
1765     contextActions[3]->setEnabled(0);
1766     contextActions[4]->setEnabled(0);
1767     contextActions[5]->setEnabled(0);
1768     contextActions[6]->setEnabled(0);
1769   } else {
1770     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1771     contextActions[1]->setEnabled(1);
1772     contextActions[2]->setEnabled(
1773       DataTree->itemWidget(DataTree->selectedItems()[0],
1774                            COLUMN_RELOAD_IMAGE)->isEnabled());
1775     contextActions[3]->setEnabled(1);
1776     contextActions[5]->setEnabled(1);
1777     contextActions[6]->setEnabled(1);
1778
1779     if (mSlicerManagers[index]->GetDimension() < 3)
1780       contextActions[4]->setEnabled(0);
1781     else
1782       contextActions[4]->setEnabled(1);
1783   }
1784   contextMenu.exec(QCursor::pos());
1785 }
1786 //------------------------------------------------------------------------------
1787
1788 //------------------------------------------------------------------------------
1789 void vvMainWindow::CloseImage()
1790 {
1791   CloseImage(DataTree->selectedItems()[0],0);
1792 }
1793 //------------------------------------------------------------------------------
1794
1795 //------------------------------------------------------------------------------
1796 void vvMainWindow::ReloadImage()
1797 {
1798   ReloadImage(DataTree->selectedItems()[0],0);
1799 }
1800 //------------------------------------------------------------------------------
1801
1802 //------------------------------------------------------------------------------
1803 void vvMainWindow::SelectOverlayImage()
1804 {
1805   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1806
1807   //check if one overlay image is added
1808   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1809     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1810       QString error = "Cannot add more than one compared image\n";
1811       error += "Please remove first ";
1812       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1813       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1814       return;
1815     }
1816
1817   QString Extensions = EXTENSIONS;
1818   Extensions += ";;All Files (*)";
1819   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1820   if (!file.isEmpty())
1821     AddOverlayImage(index,file);
1822 }
1823 //------------------------------------------------------------------------------
1824
1825 //------------------------------------------------------------------------------
1826 void vvMainWindow::AddOverlayImage(int index, QString file)
1827 {
1828
1829   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1830   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1831                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1832   reader->SetFileName(file.toStdString().c_str());
1833   reader->ReadImageInformation();
1834   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1835   int dimension = reader->GetNumberOfDimensions();
1836   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1837   vvProgressDialog progress("Opening " + file.toStdString());
1838   qApp->processEvents();
1839
1840   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1841   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component)) {
1842     //create an item in the tree with good settings
1843     QTreeWidgetItem *item = new QTreeWidgetItem();
1844     item->setData(0,Qt::UserRole,file.toStdString().c_str());
1845     item->setData(1,Qt::UserRole,tr("overlay"));
1846     QFileInfo fileinfo(file); //Do not show the path
1847     item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1848     item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
1849     qApp->processEvents();
1850
1851     for (int j = 1; j <= 4; j++) {
1852       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1853     }
1854
1855     //Create the buttons for reload and close
1856     qApp->processEvents();
1857     QTreePushButton* cButton = new QTreePushButton;
1858     cButton->setItem(item);
1859     cButton->setColumn(COLUMN_CLOSE_IMAGE);
1860     cButton->setToolTip(tr("close image"));
1861     cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1862     connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1863             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1864
1865     QTreePushButton* rButton = new QTreePushButton;
1866     rButton->setItem(item);
1867     rButton->setColumn(COLUMN_RELOAD_IMAGE);
1868     rButton->setToolTip(tr("reload image"));
1869     rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1870     connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1871             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1872
1873     DataTree->topLevelItem(index)->setExpanded(1);
1874     DataTree->topLevelItem(index)->addChild(item);
1875     DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1876     DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1877
1878     //set the id of the image
1879     QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1880     item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1881     UpdateTree();
1882     qApp->processEvents();
1883     ImageInfoChanged();
1884     QApplication::restoreOverrideCursor();
1885   } else {
1886     QApplication::restoreOverrideCursor();
1887     QString error = "Cannot import the new image.\n";
1888     error += mSlicerManagers[index]->GetLastError().c_str();
1889     QMessageBox::information(this,tr("Problem reading image !"),error);
1890   }
1891   WindowLevelChanged();
1892 }
1893 //------------------------------------------------------------------------------
1894
1895
1896 //------------------------------------------------------------------------------
1897 void vvMainWindow::AddROI(int index, QString file)
1898 {
1899   /*
1900   // Get slice manager
1901
1902   // Load image
1903
1904   vvImageReader * mReader = new vvImageReader;
1905   mReader->SetInputFilename(filename.toStdString());
1906   mReader->Update(IMAGE);
1907   if (mReader->GetLastError().size() != 0) {
1908     std::cerr << "Error while reading " << filename.toStdString() << std::endl;
1909     QString error = "Cannot open file \n";
1910     error += mReader->GetLastError().c_str();
1911     QMessageBox::information(this,tr("Reading problem"),error);
1912     delete mReader;
1913     return;
1914   }
1915   vvImage::Pointer roi = mReader->GetOutput();
1916
1917   // Create roi in new tool
1918   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
1919   */
1920 }
1921 //------------------------------------------------------------------------------
1922
1923 //------------------------------------------------------------------------------
1924 void vvMainWindow::SelectFusionImage()
1925 {
1926   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1927
1928   //check if one fusion image is added
1929   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1930     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
1931       QString error = "Cannot add more than one fusion image\n";
1932       error += "Please remove first ";
1933       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1934       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1935       return;
1936     }
1937
1938   QString Extensions = EXTENSIONS;
1939   Extensions += ";;All Files (*)";
1940   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1941   if (!file.isEmpty())
1942     AddFusionImage(index,file);
1943 }
1944 //------------------------------------------------------------------------------
1945
1946 //------------------------------------------------------------------------------
1947 void vvMainWindow::ResetTransformationToIdentity()
1948 {
1949   std::string actorType = DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString().toStdString();
1950   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1951   mSlicerManagers[index]->ResetTransformationToIdentity(actorType);
1952   ImageInfoChanged();
1953 }
1954 //------------------------------------------------------------------------------
1955
1956 //------------------------------------------------------------------------------
1957 void vvMainWindow::AddFusionImage(int index, QString file)
1958 {
1959   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1960   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1961                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1962   reader->SetFileName(file.toStdString().c_str());
1963   reader->ReadImageInformation();
1964   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1965   if (reader) {
1966     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1967     vvProgressDialog progress("Opening fusion");
1968     qApp->processEvents();
1969
1970     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1971     if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1972                                           reader->GetNumberOfDimensions(), component)) {
1973       //create an item in the tree with good settings
1974       QTreeWidgetItem *item = new QTreeWidgetItem();
1975       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1976       item->setData(1,Qt::UserRole,tr("fusion"));
1977       QFileInfo fileinfo(filename.c_str()); //Do not show the path
1978       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1979       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
1980       qApp->processEvents();
1981
1982       for (int j = 1; j <= 4; j++) {
1983         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1984       }
1985
1986       //Create the buttons for reload and close
1987       qApp->processEvents();
1988       QTreePushButton* cButton = new QTreePushButton;
1989       cButton->setItem(item);
1990       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1991       cButton->setToolTip(tr("close image"));
1992       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1993       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1994               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1995
1996       QTreePushButton* rButton = new QTreePushButton;
1997       rButton->setItem(item);
1998       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1999       rButton->setToolTip(tr("reload image"));
2000       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2001       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2002               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2003
2004       DataTree->topLevelItem(index)->setExpanded(1);
2005       DataTree->topLevelItem(index)->addChild(item);
2006       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2007       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2008
2009       //set the id of the image
2010       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2011       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2012       UpdateTree();
2013       qApp->processEvents();
2014       ImageInfoChanged();
2015       QApplication::restoreOverrideCursor();
2016     } else {
2017       QApplication::restoreOverrideCursor();
2018       QString error = "Cannot import the new image.\n";
2019       error += mSlicerManagers[index]->GetLastError().c_str();
2020       QMessageBox::information(this,tr("Problem reading image !"),error);
2021     }
2022   } else {
2023     QString error = "Cannot import the new image.\n";
2024     QMessageBox::information(this,tr("Problem reading image !"),error);
2025   }
2026 }
2027 //------------------------------------------------------------------------------
2028
2029
2030 //------------------------------------------------------------------------------
2031 void vvMainWindow::OpenField()
2032 {
2033   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2034   //check if a vector field has already been added
2035   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2036     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
2037       QString error = "Cannot add more than one vector field\n";
2038       error += "Please remove first ";
2039       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2040       QMessageBox::information(this,tr("Problem adding vector field!"),error);
2041       return;
2042     }
2043
2044   QString Extensions = "Images ( *.mhd)";
2045   Extensions += ";;Images ( *.mha)";
2046   Extensions += ";;Images ( *.vf)";
2047   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2048   if (!file.isEmpty())
2049     AddField(file,index);
2050 }
2051 //------------------------------------------------------------------------------
2052
2053
2054 //------------------------------------------------------------------------------
2055 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2056 {
2057   //create an item in the tree with good settings
2058   QTreeWidgetItem *item = new QTreeWidgetItem();
2059   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2060   item->setData(1,Qt::UserRole,tr("vector"));
2061   QFileInfo fileinfo(filename); //Do not show the path
2062   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2063   item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("vector").c_str());
2064   qApp->processEvents();
2065
2066   for (int j = 1; j <= 4; j++) {
2067     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2068   }
2069
2070   //Create the buttons for reload and close
2071   qApp->processEvents();
2072   QTreePushButton* cButton = new QTreePushButton;
2073   cButton->setItem(item);
2074   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2075   cButton->setToolTip(tr("close vector field"));
2076   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2077   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2078           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2079
2080   QTreePushButton* rButton = new QTreePushButton;
2081   rButton->setItem(item);
2082   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2083   rButton->setToolTip(tr("reload vector field"));
2084   rButton->setEnabled(from_disk);
2085   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2086   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2087           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2088
2089   DataTree->topLevelItem(index)->setExpanded(1);
2090   DataTree->topLevelItem(index)->addChild(item);
2091   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2092   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2093
2094   //set the id of the image
2095   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2096   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2097   UpdateTree();
2098   qApp->processEvents();
2099   ImageInfoChanged();
2100   QApplication::restoreOverrideCursor();
2101 }
2102 //------------------------------------------------------------------------------
2103
2104
2105 //------------------------------------------------------------------------------
2106 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2107 {
2108   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2109   vvSlicerManager* imageManager = mSlicerManagers[index];
2110   if (imageManager->SetVF(vf,file.toStdString())) {
2111     AddFieldEntry(file,index,false);
2112   } else {
2113     QString error = "Cannot import the vector field for this image.\n";
2114     error += imageManager->GetLastError().c_str();
2115     QMessageBox::information(this,tr("Problem reading VF !"),error);
2116   }
2117   QApplication::restoreOverrideCursor();
2118 }
2119 //------------------------------------------------------------------------------
2120
2121
2122 //------------------------------------------------------------------------------
2123 void vvMainWindow::AddField(QString file,int index)
2124 {
2125   if (QFile::exists(file)) {
2126     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2127
2128     //init the progress events
2129     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2130     vvProgressDialog progress("Opening " + file.toStdString());
2131     qApp->processEvents();
2132
2133     //read the vector and put it in the current mSlicerManager
2134     vvSlicerManager* imageManager = mSlicerManagers[index];
2135     qApp->processEvents();
2136
2137     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2138     if (imageManager->SetVF(file.toStdString())) {
2139       imageManager->Render();
2140       AddFieldEntry(file,index,true);
2141     } else {
2142       QApplication::restoreOverrideCursor();
2143       QString error = "Cannot import the vector field for this image.\n";
2144       error += imageManager->GetLastError().c_str();
2145       QMessageBox::information(this,tr("Problem reading VF !"),error);
2146     }
2147   } else
2148     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2149
2150 }
2151 //------------------------------------------------------------------------------
2152
2153
2154 //------------------------------------------------------------------------------
2155 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2156 {
2157   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2158   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2159     for (int i = 0; i < 4; i++) {
2160       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2161       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2162       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2163       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2164       if (log > 0)
2165         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2166       else
2167         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2168     }
2169   }
2170 }
2171 //------------------------------------------------------------------------------
2172
2173
2174 //------------------------------------------------------------------------------
2175 void vvMainWindow::SetOverlayProperty(int color, int linked, double window, double level)
2176 {
2177   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2178   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2179     mSlicerManagers[index]->SetOverlayColor(color);
2180     mSlicerManagers[index]->SetColorMap(0);
2181     mSlicerManagers[index]->SetLinkOverlayWindowLevel(linked);
2182     mSlicerManagers[index]->SetOverlayColorWindow(window);
2183     mSlicerManagers[index]->SetOverlayColorLevel(level);
2184     mSlicerManagers[index]->Render();
2185   }
2186 }
2187 //------------------------------------------------------------------------------
2188
2189 //------------------------------------------------------------------------------
2190 void vvMainWindow::SetFusionProperty(int opacity, int thresOpacity, int colormap,double window, double level)
2191 {
2192   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2193   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2194     mSlicerManagers[index]->SetFusionColorMap(colormap);
2195     mSlicerManagers[index]->SetFusionOpacity(opacity);
2196     mSlicerManagers[index]->SetFusionThresholdOpacity(thresOpacity);
2197     mSlicerManagers[index]->SetFusionWindow(window);
2198     mSlicerManagers[index]->SetFusionLevel(level);
2199     mSlicerManagers[index]->SetColorMap(0);
2200     mSlicerManagers[index]->Render();
2201   }
2202 }
2203 //------------------------------------------------------------------------------
2204
2205 //------------------------------------------------------------------------------
2206 void vvMainWindow::SaveAs()
2207 {
2208   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2209     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2210     return;
2211   }
2212
2213   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2214   int dimension = mSlicerManagers[index]->GetDimension();
2215   QStringList OutputListeFormat;
2216   OutputListeFormat.clear();
2217   if (dimension == 1) {
2218     OutputListeFormat.push_back(".mhd");
2219     OutputListeFormat.push_back(".mha");
2220   }
2221   if (dimension == 2) {
2222     OutputListeFormat.push_back(".bmp");
2223     OutputListeFormat.push_back(".png");
2224     OutputListeFormat.push_back(".jpeg");
2225     OutputListeFormat.push_back(".tif");
2226     OutputListeFormat.push_back(".mhd");
2227     OutputListeFormat.push_back(".mha");
2228     OutputListeFormat.push_back(".hdr");
2229     OutputListeFormat.push_back(".vox");
2230   } else if (dimension == 3) {
2231     OutputListeFormat.push_back(".mhd");
2232     OutputListeFormat.push_back(".mha");
2233     OutputListeFormat.push_back(".hdr");
2234     OutputListeFormat.push_back(".vox");
2235   } else if (dimension == 4) {
2236     OutputListeFormat.push_back(".mhd");
2237     OutputListeFormat.push_back(".mha");
2238   }
2239   QString Extensions = "AllFiles(*.*)";
2240   for (int i = 0; i < OutputListeFormat.count(); i++) {
2241     Extensions += ";;Images ( *";
2242     Extensions += OutputListeFormat[i];
2243     Extensions += ")";
2244   }
2245   QString fileName = QFileDialog::getSaveFileName(this,
2246                      tr("Save As"),
2247                      mSlicerManagers[index]->GetFileName().c_str(),
2248                      Extensions);
2249   if (!fileName.isEmpty()) {
2250     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2251     if (OutputListeFormat.contains(
2252           fileformat.c_str())) {
2253       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2254       std::string action = "Saving";
2255       vvProgressDialog progress("Saving "+fileName.toStdString());
2256       qApp->processEvents();
2257       vvImageWriter::Pointer writer = vvImageWriter::New();
2258       writer->SetOutputFileName(fileName.toStdString());
2259       writer->SetInput(mSlicerManagers[index]->GetImage());
2260       writer->Update();
2261       QApplication::restoreOverrideCursor();
2262       if (writer->GetLastError().size()) {
2263         QString error = "Saving did not succeed\n";
2264         error += writer->GetLastError().c_str();
2265         QMessageBox::information(this,tr("Saving Problem"),error);
2266         SaveAs();
2267       }
2268     } else {
2269       QString error = fileformat.c_str();
2270       if (error.isEmpty())
2271         error += "no file format specified !";
2272       else
2273         error += " format unknown !!!\n";
2274       QMessageBox::information(this,tr("Saving Problem"),error);
2275       SaveAs();
2276     }
2277   }
2278 }
2279 //------------------------------------------------------------------------------
2280
2281 //------------------------------------------------------------------------------
2282 void vvMainWindow::SaveCurrentState()
2283 {
2284   QString Extensions = "XML Files(*.xml)";
2285   QString fileName = QFileDialog::getSaveFileName(this,
2286                      tr("Save Current Window State"),
2287                      "",
2288                      Extensions);
2289
2290   SaveCurrentStateAs(fileName.toStdString());
2291 }
2292 //------------------------------------------------------------------------------
2293
2294 //------------------------------------------------------------------------------
2295 void vvMainWindow::SaveCurrentStateAs(const std::string& stateFile)
2296 {
2297   vvSaveState save_state;
2298   save_state.Run(this, stateFile);
2299
2300   std::cout << "void vvMainWindow::SaveCurrentState()" << std::endl;
2301 }
2302
2303 //------------------------------------------------------------------------------
2304 void vvMainWindow::ReadSavedState()
2305 {
2306   QString Extensions = "XML Files(*.xml)";
2307   QString fileName = QFileDialog::getOpenFileName(this,
2308                      tr("Load Window State"),
2309                      "",
2310                      Extensions);
2311
2312   ReadSavedStateFile(fileName.toStdString());
2313 }
2314 //------------------------------------------------------------------------------
2315
2316 //------------------------------------------------------------------------------
2317 void vvMainWindow::ReadSavedStateFile(const std::string& stateFile)
2318 {
2319   vvReadState read_state;
2320   read_state.Run(this, stateFile);
2321 }
2322 //------------------------------------------------------------------------------
2323
2324 //------------------------------------------------------------------------------
2325 void vvMainWindow::LinkAllImages()
2326 {
2327         linkPanel->linkAll();
2328 }
2329
2330 //------------------------------------------------------------------------------
2331 void vvMainWindow::AddLink(QString image1,QString image2)
2332 {
2333   unsigned int sm1 = 0;
2334   unsigned int sm2 = 0;
2335
2336   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2337     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2338       mSlicerManagers[i]->AddLink(image2.toStdString());
2339       sm1 = i;
2340     }
2341     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2342       mSlicerManagers[i]->AddLink(image1.toStdString());
2343       sm2 = i;
2344     }
2345   }
2346
2347   if (linkPanel->isLinkAll())   {
2348     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2349     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2350   } else {
2351     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2352   }
2353 }
2354
2355 //------------------------------------------------------------------------------
2356
2357
2358 //------------------------------------------------------------------------------
2359 void vvMainWindow::RemoveLink(QString image1,QString image2)
2360 {
2361   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2362     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2363       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2364     }
2365     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2366       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2367     }
2368   }
2369 }
2370 //------------------------------------------------------------------------------
2371
2372 //------------------------------------------------------------------------------
2373 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2374 {
2375   int index = 0;
2376   while(sm != mSlicerManagers[index])
2377     index++;
2378   index = (index+offset) % mSlicerManagers.size();
2379
2380   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2381   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2382   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2383   DisplayChanged(item,slicer+1);
2384 }
2385 //------------------------------------------------------------------------------
2386
2387 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2388 {
2389   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2390     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2391       for (int j = 0; j < 4; j++) {
2392         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2393         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2394         //UpdateTSlice(j,value);
2395       }
2396       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2397       break;
2398     }
2399   }
2400 }
2401 //------------------------------------------------------------------------------
2402
2403
2404 //------------------------------------------------------------------------------
2405 void vvMainWindow::NOHorizontalSliderMoved()
2406 {
2407   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2408   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2409 //  mCurrentTime = NOHorizontalSlider->value();
2410 }
2411 //------------------------------------------------------------------------------
2412
2413
2414 //------------------------------------------------------------------------------
2415 void vvMainWindow::NEHorizontalSliderMoved()
2416 {
2417   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2418   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2419 //  mCurrentTime = NEHorizontalSlider->value();
2420 }
2421 //------------------------------------------------------------------------------
2422
2423
2424 //------------------------------------------------------------------------------
2425 void vvMainWindow::SOHorizontalSliderMoved()
2426 {
2427   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2428   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2429   // mCurrentTime = SOHorizontalSlider->value();
2430 }
2431 //------------------------------------------------------------------------------
2432
2433
2434 //------------------------------------------------------------------------------
2435 void vvMainWindow::SEHorizontalSliderMoved()
2436 {
2437   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2438   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2439   // mCurrentTime = SEHorizontalSlider->value();
2440 }
2441 //------------------------------------------------------------------------------
2442
2443 //------------------------------------------------------------------------------
2444 void vvMainWindow::NOVerticalSliderChanged()
2445 {
2446   static int value=-1;
2447   if (value == NOVerticalSlider->value()) return;
2448   else value = NOVerticalSlider->value();
2449   //  int value = NOVerticalSlider->value();
2450   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2451     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2452       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2453         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2454         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2455
2456         // If nor Update/Render -> slider not work
2457         // only render = ok navigation, but for contour Update needed but slower ?
2458
2459         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2460         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2461       }
2462       break;
2463     }
2464   }
2465 }
2466 //------------------------------------------------------------------------------
2467
2468
2469 //------------------------------------------------------------------------------
2470 void vvMainWindow::NEVerticalSliderChanged()
2471 {
2472   static int value=-1;
2473   if (value == NEVerticalSlider->value()) return;
2474   else value = NEVerticalSlider->value();
2475   //  int value = NEVerticalSlider->value();
2476   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2477     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2478       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2479         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2480         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2481         mSlicerManagers[i]->UpdateSlice(1);
2482         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2483       }
2484       break;
2485     }
2486   }
2487 }
2488 //------------------------------------------------------------------------------
2489
2490
2491 //------------------------------------------------------------------------------
2492 void vvMainWindow::SOVerticalSliderChanged()
2493 {
2494   static int value=-1;
2495   if (value == SOVerticalSlider->value()) return;
2496   else value = SOVerticalSlider->value();
2497   //int value = SOVerticalSlider->value();
2498   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2499     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2500       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2501         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2502         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2503         mSlicerManagers[i]->UpdateSlice(2);
2504         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2505       }
2506       // else { DD("avoid SOVerticalSlider slicer update"); }
2507       break;
2508     }
2509   }
2510 }
2511 //------------------------------------------------------------------------------
2512
2513
2514 //------------------------------------------------------------------------------
2515 void vvMainWindow::SEVerticalSliderChanged()
2516 {
2517   static int value=-1;
2518   if (value == SEVerticalSlider->value()) return;
2519   else value = SEVerticalSlider->value();
2520   // int value = SEVerticalSlider->value();
2521   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2522     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2523       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2524         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2525         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2526         mSlicerManagers[i]->UpdateSlice(3);
2527         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2528       }
2529       break;
2530     }
2531   }
2532 }
2533 //------------------------------------------------------------------------------
2534
2535
2536 //------------------------------------------------------------------------------
2537 void vvMainWindow::UpdateSlice(int slicer, int slice)
2538 {
2539   // DD("vvMainWindow::UpdateSlice");
2540 //   DD(slicer);
2541 //   DD(slice);
2542   if (slicer == 0) {
2543     //    if (slice != NOVerticalSlider->value())
2544     NOVerticalSlider->setValue(slice);
2545   } else {
2546     if (slicer == 1)
2547       NEVerticalSlider->setValue(slice);
2548     else {
2549       if (slicer == 2)
2550         SOVerticalSlider->setValue(slice);
2551       else {
2552         if (slicer == 3)
2553           SEVerticalSlider->setValue(slice);
2554       }
2555     }
2556   }
2557   // DD("vvMainWindow:UpdateSlice END");
2558 }
2559 //------------------------------------------------------------------------------
2560
2561
2562 //------------------------------------------------------------------------------
2563 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2564 {
2565   switch (slicer) {
2566   case 0:
2567     NOHorizontalSlider->setValue(slice);
2568     break;
2569   case 1:
2570     NEHorizontalSlider->setValue(slice);
2571     break;
2572   case 2:
2573     SOHorizontalSlider->setValue(slice);
2574     break;
2575   case 3:
2576     SEHorizontalSlider->setValue(slice);
2577     break;
2578   }
2579 }
2580 //------------------------------------------------------------------------------
2581
2582
2583 //------------------------------------------------------------------------------
2584 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2585 {
2586   int position = int((min+max)/2);
2587   if (slicer == 0) {
2588     NOVerticalSlider->setValue(position);
2589     NOVerticalSlider->setRange(min,max);
2590     NOHorizontalSlider->setRange(tmin,tmax);
2591   } else if (slicer == 1) {
2592     NEVerticalSlider->setValue(position);
2593     NEVerticalSlider->setRange(min,max);
2594     NEHorizontalSlider->setRange(tmin,tmax);
2595   } else if (slicer == 2) {
2596     SOVerticalSlider->setValue(position);
2597     SOVerticalSlider->setRange(min,max);
2598     SOHorizontalSlider->setRange(tmin,tmax);
2599   } else if (slicer == 3) {
2600     SEVerticalSlider->setValue(position);
2601     SEVerticalSlider->setRange(min,max);
2602     SEHorizontalSlider->setRange(tmin,tmax);
2603   }
2604 }
2605 //------------------------------------------------------------------------------
2606
2607
2608 //------------------------------------------------------------------------------
2609 void vvMainWindow::SaveNOScreenshot()
2610 {
2611   SaveScreenshot(NOViewWidget);
2612 }
2613 //------------------------------------------------------------------------------
2614
2615
2616 //------------------------------------------------------------------------------
2617 void vvMainWindow::SaveNEScreenshot()
2618 {
2619   SaveScreenshot(NEViewWidget);
2620 }
2621 //------------------------------------------------------------------------------
2622
2623
2624 //------------------------------------------------------------------------------
2625 void vvMainWindow::SaveSOScreenshot()
2626 {
2627   SaveScreenshot(SOViewWidget);
2628 }
2629 //------------------------------------------------------------------------------
2630
2631
2632 //------------------------------------------------------------------------------
2633 void vvMainWindow::SaveSEScreenshot()
2634 {
2635   SaveScreenshot(SEViewWidget);
2636 }
2637 //------------------------------------------------------------------------------
2638
2639
2640 //------------------------------------------------------------------------------
2641 void vvMainWindow::SaveScreenshotAllSlices()
2642 {
2643   QVTKWidget *widget = NOViewWidget;
2644
2645   int index = 0;// GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2646   vvSlicerManager * SM = mSlicerManagers[index];
2647   vvImage * image = SM->GetImage();
2648   vvSlicer * slicer = SM->GetSlicer(0);
2649   int orientation = slicer->GetOrientation();
2650   int nbSlices = image->GetSize()[orientation];
2651   vtkSmartPointer<vtkRenderWindow>  renderWindow = widget->GetRenderWindow();
2652
2653   // Select filename base
2654   QString filename = QFileDialog::getSaveFileName(this,
2655                                                   tr("Save As (filename will be completed by slice number)"),
2656                                                   itksys::SystemTools::GetFilenamePath(mSlicerManagers[index]->GetFileName()).c_str(),
2657                                                   "Images( *.png);;Images( *.jpg)");
2658
2659   // Loop on slices
2660   for(uint i=0; i<nbSlices; i++) {
2661     // Change the slice
2662     slicer->SetSlice(i); // -> change the slice of the current slicer
2663     SM->UpdateSlice(0); // --> this one emit UpdateSlice
2664     QCoreApplication::flush(); // -> needed to force display of contours
2665
2666     // Screenshot
2667     vtkSmartPointer<vtkWindowToImageFilter> windowToImageFilter = vtkSmartPointer<vtkWindowToImageFilter>::New();
2668     windowToImageFilter->SetInput(renderWindow);
2669     windowToImageFilter->SetMagnification(1);
2670     windowToImageFilter->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
2671     windowToImageFilter->Update();
2672
2673     vtkSmartPointer<vtkPNGWriter> writer = vtkSmartPointer<vtkPNGWriter>::New();
2674     std::string fn = itksys::SystemTools::GetFilenameWithoutLastExtension(filename.toStdString());
2675     std::string num = clitk::toString(i);
2676     if (i<10) num = "0"+num;
2677     if (i<100) num = "0"+num;
2678     if (i<1000) num = "0"+num;
2679
2680     fn = itksys::SystemTools::GetFilenamePath(filename.toStdString()) + "/"+ fn
2681       + "_" + num + itksys::SystemTools::GetFilenameLastExtension(filename.toStdString());
2682     writer->SetFileName(fn.c_str());
2683     writer->SetInput(windowToImageFilter->GetOutput());
2684     writer->Write();
2685   }
2686 }
2687 //------------------------------------------------------------------------------
2688
2689
2690 //------------------------------------------------------------------------------
2691 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
2692 {
2693   QString Extensions = "Images( *.png);;";
2694   Extensions += "Images( *.jpg);;";
2695   Extensions += "Images( *.bmp);;";
2696   Extensions += "Images( *.tif);;";
2697   Extensions += "Images( *.ppm)";
2698 #ifdef VTK_USE_FFMPEG_ENCODER
2699   Extensions += "Images( *.avi)";
2700 #endif
2701 #ifdef VTK_USE_MPEG2_ENCODER
2702   Extensions += "Images( *.mpg)";
2703 #endif
2704
2705   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2706   QString fileName = QFileDialog::getSaveFileName(this,
2707                      tr("Save As"),
2708                      itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
2709                      Extensions);
2710
2711   if (!fileName.isEmpty()) {
2712     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2713     w2i->SetInput(widget->GetRenderWindow());
2714     w2i->Update();
2715     vtkImageData *image = w2i->GetOutput();
2716
2717     const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2718     if (!strcmp(ext, ".bmp")) {
2719       vtkBMPWriter *bmp = vtkBMPWriter::New();
2720       bmp->SetInput(image);
2721       bmp->SetFileName(fileName.toStdString().c_str());
2722       bmp->Write();
2723       bmp->Delete();
2724     } else if (!strcmp(ext, ".tif")) {
2725       vtkTIFFWriter *tif = vtkTIFFWriter::New();
2726       tif->SetInput(image);
2727       tif->SetFileName(fileName.toStdString().c_str());
2728       tif->Write();
2729       tif->Delete();
2730     } else if (!strcmp(ext, ".ppm")) {
2731       vtkPNMWriter *pnm = vtkPNMWriter::New();
2732       pnm->SetInput(image);
2733       pnm->SetFileName(fileName.toStdString().c_str());
2734       pnm->Write();
2735       pnm->Delete();
2736     } else if (!strcmp(ext, ".png")) {
2737       vtkPNGWriter *png = vtkPNGWriter::New();
2738       png->SetInput(image);
2739       png->SetFileName(fileName.toStdString().c_str());
2740       png->Write();
2741       png->Delete();
2742     } else if (!strcmp(ext, ".jpg")) {
2743       vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2744       jpg->SetInput(image);
2745       jpg->SetFileName(fileName.toStdString().c_str());
2746       jpg->Write();
2747       jpg->Delete();
2748 #ifdef VTK_USE_FFMPEG_ENCODER
2749     } else if (!strcmp(ext, ".avi")) {
2750       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
2751       mpg->SetInput(image);
2752       mpg->SetFileName(fileName.toStdString().c_str());
2753       mpg->SetQuality(2);
2754       mpg->SetRate(5);
2755       mpg->Start();
2756
2757       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2758       int nSlice = vvImg->GetVTKImages().size();
2759       for(int i=0; i<nSlice; i++) {
2760         mSlicerManagers[smIndex]->SetNextTSlice(0);
2761         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2762         w2i->SetInput(widget->GetRenderWindow());
2763         w2i->Update();
2764         mpg->SetInput(w2i->GetOutput());
2765         mpg->Write();
2766       }
2767       mpg->End();
2768       mpg->Delete();
2769 #endif
2770 #ifdef VTK_USE_MPEG2_ENCODER
2771     } else if (!strcmp(ext, ".mpg")) {
2772       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
2773       mpg->SetInput(image);
2774       mpg->SetFileName(fileName.toStdString().c_str());
2775       mpg->Start();
2776
2777       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2778       int nSlice = vvImg->GetVTKImages().size();
2779       for(int i=0; i<nSlice; i++) {
2780         mSlicerManagers[smIndex]->SetNextTSlice(0);
2781         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2782         w2i->SetInput(widget->GetRenderWindow());
2783         w2i->Update();
2784         mpg->SetInput(w2i->GetOutput());
2785         mpg->Write();
2786       }
2787       mpg->End();
2788       mpg->Delete();
2789 #endif
2790     } else {
2791       QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2792     }
2793   }
2794 }
2795 //------------------------------------------------------------------------------
2796
2797
2798 //------------------------------------------------------------------------------
2799 void vvMainWindow::GoToCursor()
2800 {
2801   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2802   for (int column = 1; column < 5; column++) {
2803     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
2804       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2805       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2806         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2807       mSlicerManagers[index]->UpdateViews(1,column-1);
2808       mSlicerManagers[index]->UpdateLinked(column-1);
2809       break;
2810     }
2811   }
2812 }
2813 //------------------------------------------------------------------------------
2814
2815 //------------------------------------------------------------------------------
2816 void vvMainWindow::PlayPause()
2817 {
2818   if (playMode) {
2819     playMode = 0;
2820     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2821     ImageInfoChanged();
2822     return;
2823   } else {
2824     int image_number=DataTree->topLevelItemCount();
2825     bool has_temporal;
2826     for (int i=0; i<image_number; i++)
2827       if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1) {
2828         has_temporal=true;
2829         break;
2830       }
2831     if (has_temporal) {
2832       playMode = 1;
2833       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2834       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2835     }
2836   }
2837 }
2838 //------------------------------------------------------------------------------
2839
2840 //------------------------------------------------------------------------------
2841 void vvMainWindow::PlayNext()
2842 {
2843   if (playMode && !this->isHidden()) {
2844     int image_number=DataTree->topLevelItemCount();
2845     ///Only play one slicer per SM, and only if the SM is being displayed
2846     for (int i=0; i<image_number; i++)
2847       for (int j=0; j<4; j++)
2848         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2849             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
2850           mSlicerManagers[i]->SetNextTSlice(j);
2851           break;
2852         }
2853     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2854   }
2855 }
2856 //------------------------------------------------------------------------------
2857
2858 void vvMainWindow::ShowLastImage()
2859 {
2860   if (mSlicerManagers.size() > 1) {
2861     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2862     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2863     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2864     DisplayChanged(item,1);
2865   }
2866 }
2867
2868 //------------------------------------------------------------------------------
2869 void vvMainWindow::UpdateRenderWindows()
2870 {
2871   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2872   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2873   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2874   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2875 }
2876 //------------------------------------------------------------------------------
2877
2878 //------------------------------------------------------------------------------
2879 void vvMainWindow::SegmentationOnCurrentImage()
2880 {
2881   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2882
2883   vvSegmentationDialog segmentation;
2884   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2885   segmentation.exec();
2886 }
2887 //------------------------------------------------------------------------------
2888
2889 void vvMainWindow::SurfaceViewerLaunch()
2890 {
2891   vvSurfaceViewerDialog surfaceViewer;
2892   surfaceViewer.exec();
2893 }
2894 //------------------------------------------------------------------------------
2895
2896
2897 //------------------------------------------------------------------------------
2898 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
2899 {
2900   int number=0;
2901   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
2902     vvSlicerManager * v = mSlicerManagers[l];
2903     if (v->GetBaseFileName() ==
2904         vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
2905       number = std::max(number, v->GetBaseFileNameNumber()+1);
2906     }
2907   }
2908   return number;
2909 }
2910 //------------------------------------------------------------------------------
2911
2912
2913 //------------------------------------------------------------------------------
2914 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2915 {
2916   // Change filename if another image exist with the same name
2917   int number = GetImageDuplicateFilenameNumber(filename);
2918
2919   // Create new SliceManager
2920   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
2921   slicer_manager->SetImage(image);//, IMAGE, number);
2922   //  filename = filename+"_"+clitk::toString(number);
2923   slicer_manager->SetFilename(filename, number);
2924   mSlicerManagers.push_back(slicer_manager);
2925
2926   //create an item in the tree with good settings
2927   QTreeWidgetItem *item = new QTreeWidgetItem();
2928   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2929   item->setData(1,Qt::UserRole,tr("image"));
2930   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
2931   qApp->processEvents();
2932
2933   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2934
2935   //Create the buttons for reload and close
2936   qApp->processEvents();
2937   QTreePushButton* cButton = new QTreePushButton;
2938   cButton->setItem(item);
2939   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2940   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2941   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2942           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2943
2944   QTreePushButton* rButton = new QTreePushButton;
2945   rButton->setItem(item);
2946   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2947   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2948   rButton->setEnabled(0);
2949   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2950           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2951
2952   DataTree->addTopLevelItem(item);
2953   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2954   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2955
2956   //set the id of the image
2957   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2958   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2959   mSlicerManagers.back()->SetId(id.toStdString());
2960
2961   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
2962                       , id.toStdString());
2963
2964   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
2965           this, SLOT(CurrentImageChanged(std::string)));
2966   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
2967           this, SLOT(CurrentPickedImageChanged(std::string)));
2968   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
2969           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2970   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
2971           this, SLOT(VectorChanged(int,double,double,double, double)));
2972   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
2973           this, SLOT(OverlayChanged(int,double,double)));
2974   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
2975           this, SLOT(FusionChanged(int,double)));
2976   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
2977           this,SLOT(WindowLevelChanged()));
2978   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
2979           this,SLOT(UpdateSlice(int,int)));
2980   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
2981           this,SLOT(UpdateTSlice(int, int)));
2982   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2983           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2984   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2985           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2986   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
2987           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
2988   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
2989           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
2990   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2991   UpdateTree();
2992   qApp->processEvents();
2993   InitSlicers();
2994   ShowLastImage();
2995   InitDisplay();
2996   qApp->processEvents();
2997
2998   // End
2999   ImageInfoChanged();
3000   return slicer_manager;
3001 }
3002 //------------------------------------------------------------------------------
3003
3004
3005 //------------------------------------------------------------------------------
3006 void vvMainWindow::UpdateCurrentSlicer()
3007 {
3008   int index = -1;
3009   if (DataTree->selectedItems().size() > 0) {
3010     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3011   }
3012   mSlicerManagerCurrentIndex = index;
3013 }
3014 //------------------------------------------------------------------------------
3015