vv/vvMainWindow.cxx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://www.centreleonberard.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17 ===========================================================================**/
  18
  19 #include <algorithm>
  20 #include <QMessageBox>
  21 #include <QInputDialog>
  22 #include <QTimer>
  23 #include "QTreePushButton.h"
  24 #include <QUrl>
  25 #include <QSettings>
  26
  27 // VV include
  28 #include "vvMainWindow.h"
  29 #include "vvHelpDialog.h"
  30 #include "vvRegisterForm.h"
  31 #include "vvDocumentation.h"
  32 #include "vvProgressDialog.h"
  33 #include "vvQDicomSeriesSelector.h"
  34 #include "vvSlicerManager.h"
  35 #include "clitkImageCommon.h"
  36 #include "vvSlicer.h"
  37 #include "vvInteractorStyleNavigator.h"
  38 #include "vvImageWriter.h"
  39 #include "vvSegmentationDialog.h"
  40 #include "vvSurfaceViewerDialog.h"
  41 #include "vvDeformationDialog.h"
  42 #include "vvImageWarp.h"
  43 #include "vvUtils.h"
  44 #include "vvMidPosition.h"
  45 #include "vvMesh.h"
  46 #include "vvStructSelector.h"
  47 #include "vvMeshReader.h"
  48 #include "clitkConfiguration.h"
  49
  50 // ITK include
  51 #include <itkImage.h>
  52 #include <itkImageFileReader.h>
  53 #include <itkByteSwapper.h>
  54 #include <itkCommand.h>
  55 #include <itkNumericSeriesFileNames.h>
  56
  57 // VTK include
  58 #include <vtkImageData.h>
  59 #include <vtkImageActor.h>
  60 #include <vtkCornerAnnotation.h>
  61 #include <vtkRenderWindow.h>
  62 #include <vtkRenderWindowInteractor.h>
  63 #include <vtkRenderer.h>
  64 #include <vtkRendererCollection.h>
  65 #include <vtkWindowToImageFilter.h>
  66 #include <vtkBMPWriter.h>
  67 #include <vtkTIFFWriter.h>
  68 #include <vtkPNMWriter.h>
  69 #include <vtkPNGWriter.h>
  70 #include <vtkJPEGWriter.h>
  71 #ifdef VTK_USE_FFMPEG_ENCODER
  72 #  include <vtkFFMPEGWriter.h>
  73 #endif
  74 #ifdef VTK_USE_MPEG2_ENCODER
  75 #  include <vtkMPEG2Writer.h>
  76 #endif
  77 #include <vtkMatrix4x4.h>
  78 #include <vtkTransform.h>
  79
  80 // Standard includes
  81 #include <iostream>
  82 #include <sstream>
  83 #include <iomanip>
  84
  85 #define COLUMN_TREE 0
  86 #define COLUMN_UL_VIEW 1
  87 #define COLUMN_UR_VIEW 2
  88 #define COLUMN_DL_VIEW 3
  89 #define COLUMN_DR_VIEW 4
  90 #define COLUMN_CLOSE_IMAGE 5
  91 #define COLUMN_RELOAD_IMAGE 6
  92 #define COLUMN_IMAGE_NAME 7
  93
  94 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN )"
  95
  96 /*Data Tree values
  97   0,Qt::UserRole full filename
  98   1,Qt::CheckStateRole checkbutton UL View
  99   1,Qt::UserRole overlay, fusion or vector
 100   2,Qt::CheckStateRole checkbutton UR View
 101   3,Qt::CheckStateRole checkbutton DL View
 102   4,Qt::CheckStateRole checkbutton DR View
 103   5,0  short filename
 104   5,Qt::UserRole mSlicerManager id*/
 105
 106 //------------------------------------------------------------------------------
 107 vvMainWindow::vvMainWindow():vvMainWindowBase()
 108 {
 109   setupUi(this); // this sets up the GUI
 110
 111   mInputPathName = "";
 112   mMenuTools = menuTools;
 113   //  mMenuSegmentation = menuSegmentation;
 114   mContextMenu = &contextMenu;
 115   mMenuExperimentalTools = menuExperimental;
 116   mMainWidget = this;
 117   mCurrentTime = -1;
 118   mCurrentSelectedImageId = "";
 119   mCurrentPickedImageId = "";
 120   mCurrentPickedImageIndex = 0;
 121
 122   //Init the contextMenu
 123   this->setContextMenuPolicy(Qt::CustomContextMenu);
 124   contextActions.resize(0);
 125   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 126                                   tr("O&pen new Image"));
 127   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 128   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 129   contextActions.push_back(actionOpen_new_image);
 130   contextMenu.addSeparator();
 131
 132   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 133                                tr("Close Current Image"));
 134   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 135   contextActions.push_back(actionClose_Image);
 136
 137   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 138                                 tr("Reload Current Image"));
 139   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 140   contextActions.push_back(actionReload_image);
 141
 142   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 143                               tr("Save Current Image"));
 144   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 145   contextActions.push_back(actionSave_image);
 146
 147   contextMenu.addSeparator();
 148
 149   contextMenu.addAction(actionAdd_VF_to_current_Image);
 150   contextActions.push_back(actionAdd_VF_to_current_Image);
 151
 152   QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 153       tr("Add overlay image to current image"));
 154   contextMenu.addAction(actionAdd_Overlay_to_current_Image);
 155   contextActions.push_back(actionAdd_Overlay_to_current_Image);
 156
 157   connect(actionAdd_Overlay_to_current_Image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 158
 159   contextMenu.addAction(actionAdd_fusion_image);
 160   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 161   contextActions.push_back(actionAdd_fusion_image);
 162
 163   contextMenu.addSeparator();
 164   QAction* actionResetMatrix = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/identity.png")),
 165                                                       tr("Reset transformation to identity"));
 166   connect(actionResetMatrix, SIGNAL(triggered()), this,SLOT(ResetTransformationToIdentity()));
 167
 168   // TRIAL DS
 169   /*
 170   QMenu * m = new QMenu(menubar);
 171   m->setTitle("TOTO");
 172   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 173   contextMenu.addMenu(m);
 174   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 175                      tr("BIDON"));
 176   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 177                      tr("BIDON2"));
 178   m->addAction(a);
 179   m->addAction(b);
 180   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 181   */
 182
 183   //init the DataTree
 184   mSlicerManagers.resize(0);
 185
 186   QStringList header;
 187   header.append("");
 188   header.append("TL");
 189   header.append("TR");
 190   header.append("BL");
 191   header.append("BR");
 192   header.append("");
 193   header.append("");
 194   header.append("Name");
 195
 196   DataTree->setHeaderLabels(header);
 197   DataTree->resizeColumnToContents(COLUMN_TREE);
 198   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 199   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 200   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 201   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 202   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 203   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 204   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 205
 206   viewMode = 1;
 207   documentation = new vvDocumentation();
 208   help_dialog = new vvHelpDialog();
 209   dicomSeriesSelector = new vvDicomSeriesSelector();
 210
 211   inverseButton->setEnabled(0);
 212   actionAdd_Overlay_to_current_Image->setEnabled(0);
 213   actionSave_As->setEnabled(0);
 214   actionAdd_VF_to_current_Image->setEnabled(0);
 215   actionAdd_fusion_image->setEnabled(0);
 216
 217   //init the sliders
 218   verticalSliders.push_back(NOVerticalSlider);
 219   verticalSliders.push_back(NEVerticalSlider);
 220   verticalSliders.push_back(SOVerticalSlider);
 221   verticalSliders.push_back(SEVerticalSlider);
 222
 223   for (int i =0; i < 4; i++)
 224     verticalSliders[i]->hide();
 225
 226   horizontalSliders.push_back(NOHorizontalSlider);
 227   horizontalSliders.push_back(NEHorizontalSlider);
 228   horizontalSliders.push_back(SOHorizontalSlider);
 229   horizontalSliders.push_back(SEHorizontalSlider);
 230
 231   for (int i =0; i < 4; i++)
 232     horizontalSliders[i]->hide();
 233
 234
 235   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 236   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 237   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 238   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 239
 240   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 241   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 242   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 243   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 244
 245   //connect everything
 246   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 247   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 248   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 249   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 250   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 251   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 252   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 253   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 254   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 255   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 256   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 257   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 258   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 259   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 260   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 261   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 262   connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
 263
 264   ///////////////////////////////////////////////
 265   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 266   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 267   ///////////////////////////////////////////////
 268
 269   actionNorth_East_Window->setEnabled(0);
 270   actionNorth_West_Window->setEnabled(0);
 271   actionSouth_East_Window->setEnabled(0);
 272   actionSouth_West_Window->setEnabled(0);
 273
 274   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 275   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 276   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 277   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 278   connect(actionSave_all_slices,SIGNAL(triggered()),this,SLOT(SaveScreenshotAllSlices()));
 279
 280   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 281   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 282           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 283
 284   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 285   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 286   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 287   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 288   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 289   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 290   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 291
 292
 293   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 294
 295   connect(linkPanel,SIGNAL(addLink(QString,QString)),this,SLOT(AddLink(QString,QString)));
 296   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 297   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 298   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int,int,double,double)),
 299           this,SLOT(SetOverlayProperty(int,int,double,double)));
 300   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,int,double,double)),
 301           this,SLOT(SetFusionProperty(int,int,int,double,double)));
 302   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 303
 304   playMode = 0;//pause
 305   mFrameRate = 10;
 306   playButton->setEnabled(0);
 307   frameRateLabel->setEnabled(0);
 308   frameRateSpinBox->setEnabled(0);
 309   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 310   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 311
 312   goToCursorPushButton->setEnabled(0);
 313   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 314
 315   NOViewWidget->hide();
 316   NEViewWidget->hide();
 317   SOViewWidget->hide();
 318   SEViewWidget->hide();
 319
 320   //Recently opened files
 321   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 322   recentlyOpenedFilesMenu=NULL;
 323   if ( !recent_files.empty() ) {
 324     createRecentlyOpenedFilesMenu();
 325     updateRecentlyOpenedFilesMenu(recent_files);
 326   }
 327
 328   // Adding all new tools (insertion in the menu)
 329   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 330   vvToolManager::GetInstance()->EnableToolsInMenu(this, false);
 331
 332   if (!CLITK_EXPERIMENTAL)
 333     menuExperimental->menuAction()->setVisible(false);
 334
 335
 336   QTimer * timerMemory = new QTimer(this);
 337   //timerMemory->setInterval(5);
 338   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 339   timerMemory->start(2000);
 340 }
 341 //------------------------------------------------------------------------------
 342 void vvMainWindow::show()
 343 {
 344   vvMainWindowBase::show();
 345   PopupRegisterForm(true);
 346 }
 347 //------------------------------------------------------------------------------
 348 void vvMainWindow::UpdateMemoryUsage()
 349 {
 350   //  clitk::PrintMemory(true);
 351   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 352   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 353 }
 354 //------------------------------------------------------------------------------
 355
 356
 357 //------------------------------------------------------------------------------
 358 void vvMainWindow::createRecentlyOpenedFilesMenu()
 359 {
 360   recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
 361   recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 362   menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
 363   menuFile->insertSeparator(actionOpen_Image_With_Time);
 364 }
 365 //------------------------------------------------------------------------------
 366
 367
 368 //------------------------------------------------------------------------------
 369
 370 void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
 371 {
 372   if(recentlyOpenedFilesMenu==NULL) {
 373     createRecentlyOpenedFilesMenu();
 374   } else {
 375     recentlyOpenedFilesMenu->clear();
 376   }
 377   for (std::list<std::string>::const_iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 378     QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")), i->c_str(),this);
 379     recentlyOpenedFilesMenu->addAction(current);
 380     connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 381   }
 382 }
 383 //------------------------------------------------------------------------------
 384
 385
 386 //------------------------------------------------------------------------------
 387 void vvMainWindow::ComputeMidPosition()
 388 {
 389   bool ok;
 390   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 391   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 392                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 393   if (ok) {
 394     vvMidPosition midp;
 395     midp.slicer_manager = mSlicerManagers[index];
 396     midp.reference_image_index = ref;
 397     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 398     midp.Update();
 399     if (midp.error)
 400       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 401     else {
 402       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 403       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 404     }
 405     QApplication::restoreOverrideCursor();
 406   }
 407 }
 408 //------------------------------------------------------------------------------
 409
 410
 411 //------------------------------------------------------------------------------
 412 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 413 {
 414   QTreeWidgetItem *item = new QTreeWidgetItem();
 415   item->setData(0,Qt::UserRole,"filename.vtk");
 416   item->setData(1,Qt::UserRole,tr("contour"));
 417   QBrush brush;
 418   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 419   brush.setStyle(Qt::SolidPattern);
 420   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 421   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 422
 423   for (int j = 1; j <= 4; j++)
 424     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 425
 426   QTreePushButton* cButton = new QTreePushButton;
 427   cButton->setItem(item);
 428   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 429   cButton->setToolTip(tr("close image"));
 430   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 431   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 432           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 433
 434   QTreePushButton* rButton = new QTreePushButton;
 435   rButton->setItem(item);
 436   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 437   rButton->setToolTip(tr("reload image"));
 438   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 439   rButton->setEnabled(false);
 440   //Not implemented
 441   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 442   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 443
 444   DataTree->topLevelItem(image_index)->setExpanded(1);
 445   DataTree->topLevelItem(image_index)->addChild(item);
 446   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 447   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 448   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 449   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 450
 451   UpdateTree();
 452   mSlicerManagers[image_index]->AddContour(contour,propagation);
 453   mSlicerManagers[image_index]->Render();
 454 }
 455 //------------------------------------------------------------------------------
 456
 457
 458 //------------------------------------------------------------------------------
 459 void vvMainWindow::OpenVTKContour()
 460 {
 461   if (mSlicerManagers.size() > 0) {
 462     QString Extensions = "Images ( *.vtk *.obj)";
 463     Extensions += ";;All Files (*)";
 464     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 465     if (file.isNull())
 466       return;
 467     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 468     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 469     vvMeshReader reader;
 470     reader.SetImage(mSlicerManagers[index]->GetImage());
 471     reader.SetModeToVTK();
 472     reader.SetFilename(file.toStdString());
 473     reader.Update();
 474     AddContour(index,reader.GetOutput()[0],false);
 475     QApplication::restoreOverrideCursor();
 476   }
 477 }
 478 //------------------------------------------------------------------------------
 479
 480
 481 //------------------------------------------------------------------------------
 482 void vvMainWindow::OpenDCStructContour()
 483 {
 484   if (mSlicerManagers.size() > 0) {
 485     QString Extensions = "Dicom Files ( *.dcm RS*)";
 486     Extensions += ";;All Files (*)";
 487     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 488     if (file.isNull())
 489       return;
 490     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 491     vvMeshReader reader;
 492     reader.SetFilename(file.toStdString());
 493     vvStructSelector selector;
 494     selector.SetStructures(reader.GetROINames());
 495     if (!mSlicerManagers[index]->GetVF().IsNull())
 496       selector.EnablePropagationCheckBox();
 497     if (selector.exec()) {
 498       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 499       reader.SetSelectedItems(selector.getSelectedItems());
 500       reader.SetImage(mSlicerManagers[index]->GetImage());
 501       if (selector.PropagationEnabled())
 502         reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 503       reader.Update();
 504       std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 505       for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 506            i!=contours.end(); i++)
 507         AddContour(index,*i,selector.PropagationEnabled());
 508       QApplication::restoreOverrideCursor();
 509     }
 510   }
 511 }
 512 //------------------------------------------------------------------------------
 513
 514
 515 //------------------------------------------------------------------------------
 516 void vvMainWindow::ComputeDeformableRegistration()
 517 {
 518   if (mSlicerManagers.size() > 0) {
 519     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 520     vvDeformationDialog dialog(index,mSlicerManagers);
 521     if (dialog.exec()) {
 522       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 523       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 524       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 525     } else
 526       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 527   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 528 }
 529 //------------------------------------------------------------------------------
 530
 531
 532 //------------------------------------------------------------------------------
 533 void vvMainWindow::WarpImage()
 534 {
 535   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 536   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 537     bool ok;
 538     int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 539                                        mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 540     if (ok) {
 541       WarpImage(mSlicerManagers[index],ref);
 542     }
 543   } else
 544     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 545 }
 546 //------------------------------------------------------------------------------
 547
 548
 549 //------------------------------------------------------------------------------
 550 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 551 {
 552   if (!selected_slicer->GetVF().IsNull()) {
 553     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 554     QFileInfo info(selected_slicer->GetFileName().c_str());
 555     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 556                      reference_phase,this);
 557     if (warp.ComputeWarpedImage()) {
 558       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 559       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 560       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 561       QApplication::restoreOverrideCursor();
 562     } else {
 563       QApplication::restoreOverrideCursor();
 564       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 565     }
 566   } else
 567     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 568 }
 569 //------------------------------------------------------------------------------
 570
 571
 572 //------------------------------------------------------------------------------
 573 vvMainWindow::~vvMainWindow()
 574 {
 575   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 576     if (mSlicerManagers[i] != NULL)
 577       delete mSlicerManagers[i];
 578   }
 579 }
 580 //------------------------------------------------------------------------------
 581
 582 //------------------------------------------------------------------------------
 583 QTabWidget * vvMainWindow::GetTab()
 584 {
 585   return tabWidget;
 586 }
 587 //------------------------------------------------------------------------------
 588
 589
 590 //------------------------------------------------------------------------------
 591 void vvMainWindow::MergeImages()
 592 {
 593   QString Extensions = EXTENSIONS;
 594   Extensions += ";;All Files (*)";
 595   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 596   if (files.isEmpty())
 597     return;
 598   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 599   std::vector<std::string> vector;
 600
 601   unsigned int currentDim = 0;
 602   std::vector<double> currentSpacing;
 603   std::vector<int> currentSize;
 604   std::vector<double> currentOrigin;
 605
 606   for (int i = 0; i < files.size(); i++) {
 607     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 608                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 609     reader->SetFileName(files[i].toStdString().c_str());
 610     reader->ReadImageInformation();
 611     if (reader)        {
 612       //NOViewWidget->hide();
 613       //NEViewWidget->hide();
 614       //SOViewWidget->hide();
 615       //SEViewWidget->hide();
 616       if (i == 0)
 617         currentDim = reader->GetNumberOfDimensions();
 618       bool IsOk = true;
 619       for (unsigned int j = 0; j < currentDim; j++) {
 620         if (i == 0) {
 621           if (j == 0) {
 622             currentSpacing.resize(currentDim);
 623             currentSize.resize(currentDim);
 624             currentOrigin.resize(currentDim);
 625           }
 626           currentOrigin[j] = reader->GetOrigin(j);
 627           currentSpacing[j] = reader->GetSpacing(j);
 628           currentSize[j] = reader->GetDimensions(j);
 629         } else if (currentDim != reader->GetNumberOfDimensions()
 630                    || currentSpacing[j] != reader->GetSpacing(j)
 631                    || currentSize[j] != (int)reader->GetDimensions(j)
 632                    || currentOrigin[j] != reader->GetOrigin(j)) {
 633           QString error = "Cannot read file (too different from others ";
 634           error += files[i].toStdString().c_str();
 635           QMessageBox::information(this,tr("Reading problem"),error);
 636           IsOk = false;
 637           break;
 638         }
 639       }
 640       if (IsOk)
 641         vector.push_back(files[i].toStdString());
 642     }
 643   }
 644   if (vector.size() > 0)
 645     LoadImages(vector, vvImageReader::MERGED);
 646 }
 647 //------------------------------------------------------------------------------
 648
 649 //------------------------------------------------------------------------------
 650 void vvMainWindow::SliceImages()
 651 {
 652   QString Extensions = EXTENSIONS;
 653   Extensions += ";;All Files (*)";
 654
 655   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 656   if (files.isEmpty())
 657     return;
 658   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 659   std::vector<std::string> vector;
 660   for (int i = 0; i < files.size(); i++)
 661     vector.push_back(files[i].toStdString());
 662   LoadImages(vector, vvImageReader::SLICED);
 663 }
 664 //------------------------------------------------------------------------------
 665
 666 //------------------------------------------------------------------------------
 667 void vvMainWindow::MergeImagesWithTime()
 668 {
 669   QString Extensions = EXTENSIONS;
 670   Extensions += ";;All Files (*)";
 671   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 672   if (files.isEmpty())
 673     return;
 674   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 675   std::vector<std::string> vector;
 676
 677   unsigned int currentDim = 0;
 678   std::vector<double> currentSpacing;
 679   std::vector<int> currentSize;
 680   std::vector<double> currentOrigin;
 681
 682   for (int i = 0; i < files.size(); i++) {
 683     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 684                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 685     if (reader) {
 686       reader->SetFileName(files[i].toStdString().c_str());
 687       reader->ReadImageInformation();
 688       if (i == 0)
 689         currentDim = reader->GetNumberOfDimensions();
 690       bool IsOk = true;
 691       for (unsigned int j = 0; j < currentDim; j++) {
 692         if (i == 0) {
 693           if (j == 0) {
 694             currentSpacing.resize(currentDim);
 695             currentSize.resize(currentDim);
 696             currentOrigin.resize(currentDim);
 697           }
 698           currentOrigin[j] = reader->GetOrigin(j);
 699           currentSpacing[j] = reader->GetSpacing(j);
 700           currentSize[j] = reader->GetDimensions(j);
 701         } else if (currentDim != reader->GetNumberOfDimensions()
 702                    || currentSpacing[j] != reader->GetSpacing(j)
 703                    || currentSize[j] != (int)reader->GetDimensions(j)
 704                    || currentOrigin[j] != reader->GetOrigin(j)) {
 705           QString error = "Cannot read file (too different from others ";
 706           error += files[i].toStdString().c_str();
 707           QMessageBox::information(this,tr("Reading problem"),error);
 708           IsOk = false;
 709           break;
 710         }
 711       }
 712       if (IsOk)
 713         vector.push_back(files[i].toStdString());
 714     } else {
 715       QString error = "Cannot read file info for ";
 716       error += files[i].toStdString().c_str();
 717       error += "\n";
 718       error += "Maybe you're trying to open an image in an unsupported format?\n";
 719       QMessageBox::information(this,tr("Reading problem"),error);
 720     }
 721   }
 722   sort(vector.begin(),vector.end());
 723   if (vector.size() > 1)
 724     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 725   else
 726     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.");
 727 }
 728 //------------------------------------------------------------------------------
 729
 730
 731 //------------------------------------------------------------------------------
 732 void vvMainWindow::OpenDicom()
 733 {
 734   std::vector<std::string> files;
 735
 736   std::cout << "dicomSeriesSelector " << std::endl;
 737   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 738     files = *(dicomSeriesSelector->GetFilenames());
 739     LoadImages(files, vvImageReader::DICOM);
 740   }
 741 }
 742 //------------------------------------------------------------------------------
 743
 744 //------------------------------------------------------------------------------
 745 void vvMainWindow::OpenImages()
 746 {
 747   QString Extensions = EXTENSIONS;
 748   Extensions += ";;All Files (*)";
 749
 750   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 751   if (files.isEmpty())
 752     return;
 753   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 754   std::vector<std::string> vector;
 755   for (int i = 0; i < files.size(); i++)
 756     vector.push_back(files[i].toStdString());
 757   LoadImages(vector, vvImageReader::IMAGE);
 758 }
 759 //------------------------------------------------------------------------------
 760 void vvMainWindow::OpenRecentImage()
 761 {
 762   QAction * caller = qobject_cast<QAction*>(sender());
 763   std::vector<std::string> images;
 764   images.push_back(caller->text().toStdString());
 765   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 766   LoadImages(images, vvImageReader::IMAGE);
 767 }
 768 //------------------------------------------------------------------------------
 769
 770
 771 //------------------------------------------------------------------------------
 772 void vvMainWindow::OpenImageWithTime()
 773 {
 774   QString Extensions = EXTENSIONS;
 775   Extensions += ";;All Files (*)";
 776
 777   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 778   if (files.isEmpty())
 779     return;
 780   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 781   std::vector<std::string> vector;
 782   for (int i = 0; i < files.size(); i++) {
 783     vector.push_back(files[i].toStdString());
 784   }
 785   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 786 }
 787 //------------------------------------------------------------------------------
 788
 789
 790 //------------------------------------------------------------------------------
 791 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 792 {
 793   //Separate the way to open images and dicoms
 794   int fileSize;
 795   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 796     fileSize = files.size();
 797   else
 798     fileSize = 1;
 799
 800   // For SLICED, we need the number of slices (ndim and #slices)
 801   std::vector<unsigned int> nSlices;
 802   nSlices.resize(files.size());
 803   std::fill(nSlices.begin(), nSlices.end(), 1);
 804   if (filetype == vvImageReader::SLICED) {
 805     for (int i = 0; i < fileSize; i++) {
 806       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 807       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 808       if (!header) {
 809         nSlices[i] = 0;
 810         QString error = "Cannot open file \n";
 811         error += files[i].c_str();
 812         QMessageBox::information(this,tr("Reading problem"),error);
 813         return;
 814       }
 815       if (header->GetNumberOfDimensions() < 3) {
 816         nSlices[i] = 0;
 817         QString error = "Dimension problem. Cannot slice \n";
 818         error += files[i].c_str();
 819         QMessageBox::information(this,tr("Reading problem"),error);
 820         return;
 821       }
 822       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 823     }
 824   }
 825
 826   //Only add to the list of recently opened files when a single file is opened,
 827   //to avoid polluting the list of recently opened files
 828   if (files.size() == 1) {
 829     QFileInfo finfo=tr(files[0].c_str());
 830     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 831     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 832   }
 833   //init the progress events
 834   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 835   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 836   qApp->processEvents();
 837
 838   int numberofsuccesulreads=0;
 839   //open images as 1 or multiples
 840   for (int i = 0; i < fileSize; i++) {
 841
 842     progress.SetText("Opening " + files[i]);
 843     progress.SetProgress(i,fileSize);
 844     qApp->processEvents();
 845
 846     for (unsigned int j = 0; j < nSlices[i]; j++) {
 847       //read the image and put it in mSlicerManagers
 848       vvSlicerManager* imageManager = new vvSlicerManager(4);
 849       qApp->processEvents();
 850
 851       bool SetImageSucceed=false;
 852
 853       // Change filename if an image with the same already exist
 854       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 855
 856       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED)
 857         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 858       else {
 859         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 860       }
 861       if (!SetImageSucceed) {
 862         QApplication::restoreOverrideCursor();
 863         QString error = "Cannot open file \n";
 864         error += imageManager->GetLastError().c_str();
 865         QMessageBox::information(this,tr("Reading problem"),error);
 866         delete imageManager;
 867       } else {
 868         mSlicerManagers.push_back(imageManager);
 869
 870         //create an item in the tree with good settings
 871         QTreeWidgetItem *item = new QTreeWidgetItem();
 872         item->setData(0,Qt::UserRole,files[i].c_str());
 873         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 874         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 875         item->setData(1,Qt::UserRole,tr("image"));
 876         item->setToolTip(COLUMN_IMAGE_NAME, imageManager->GetListOfAbsoluteFilePathInOneString("image").c_str());
 877         qApp->processEvents();
 878
 879         //Create the buttons for reload and close
 880         qApp->processEvents();
 881         QTreePushButton* cButton = new QTreePushButton;
 882         cButton->setItem(item);
 883         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 884         cButton->setToolTip(tr("close image"));
 885         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 886         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 887                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 888
 889         QTreePushButton* rButton = new QTreePushButton;
 890         rButton->setItem(item);
 891         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 892         rButton->setToolTip(tr("reload image"));
 893         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 894         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 895                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 896
 897         DataTree->addTopLevelItem(item);
 898         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 899         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 900
 901         //set the id of the image
 902         QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 903         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 904         mSlicerManagers.back()->SetId(id.toStdString());
 905
 906         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 907
 908         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 909                 this,SLOT(CurrentImageChanged(std::string)));
 910         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 911                 this, SLOT(CurrentPickedImageChanged(std::string)));
 912         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 913                 this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 914         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 915                 this, SLOT(VectorChanged(int,double,double,double, double)));
 916         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 917                 this, SLOT(OverlayChanged(int,double,double)));
 918         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 919                 this, SLOT(FusionChanged(int,double)));
 920         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
 921                 this,SLOT(WindowLevelChanged()));
 922         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 923                 this,SLOT(UpdateSlice(int,int)));
 924         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 925                 this,SLOT(UpdateTSlice(int, int)));
 926         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 927                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 928         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 929                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 930         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 931                 this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 932         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 933                 this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 934         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 935         InitSlicers();
 936         numberofsuccesulreads++;
 937       }
 938     }
 939   }
 940   if (numberofsuccesulreads) {
 941     NOViewWidget->show();
 942     NEViewWidget->show();
 943     SOViewWidget->show();
 944     SEViewWidget->show();
 945     UpdateTree();
 946     InitDisplay();
 947     ShowLastImage();
 948
 949     // Try to guess default WindowLevel
 950     double range[2];
 951     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 952     if ((range[0] == 0) && (range[1] == 1)) {
 953       presetComboBox->setCurrentIndex(5);// binary
 954     } else {
 955       // TODO
 956     }
 957   }
 958   QApplication::restoreOverrideCursor();
 959 }
 960 //------------------------------------------------------------------------------
 961
 962 //------------------------------------------------------------------------------
 963 void vvMainWindow::UpdateTree()
 964 {
 965   DataTree->resizeColumnToContents(COLUMN_TREE);
 966   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 967   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 968   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 969   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 970   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 971   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 972   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 973 }
 974 //------------------------------------------------------------------------------
 975
 976 //------------------------------------------------------------------------------
 977 void vvMainWindow::CurrentImageChanged(std::string id)
 978 {
 979   if (id == mCurrentSelectedImageId) return; // Do nothing
 980   int selected = 0;
 981   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 982     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 983       selected = i;
 984     } else {
 985       DataTree->topLevelItem(i)->setSelected(0);
 986     }
 987     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 988       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 989
 990   }
 991   DataTree->topLevelItem(selected)->setSelected(1);
 992   mCurrentSelectedImageId = id;
 993   emit SelectedImageHasChanged(mSlicerManagers[selected]);
 994 }
 995 //------------------------------------------------------------------------------
 996
 997 //------------------------------------------------------------------------------
 998 void vvMainWindow::CurrentPickedImageChanged(std::string id)
 999 {
1000   if (id == mCurrentPickedImageId) return; // Do nothing
1001   int selected = 0;
1002   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1003     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1004       selected = i;
1005     } else {
1006       DataTree->topLevelItem(i)->setSelected(0);
1007     }
1008     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1009       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1010
1011   }
1012   DataTree->topLevelItem(selected)->setSelected(1);
1013   mCurrentPickedImageId = id;
1014   mCurrentPickedImageIndex = selected;
1015 }
1016 //------------------------------------------------------------------------------
1017
1018 //------------------------------------------------------------------------------
1019 void vvMainWindow::ImageInfoChanged()
1020 {
1021   contextActions[6]->setEnabled(1);
1022   contextActions[5]->setEnabled(1);
1023   actionSave_As->setEnabled(1);
1024   actionAdd_VF_to_current_Image->setEnabled(1);
1025   actionAdd_fusion_image->setEnabled(1);
1026   actionNorth_East_Window->setEnabled(1);
1027   actionNorth_West_Window->setEnabled(1);
1028   actionSouth_East_Window->setEnabled(1);
1029   actionSouth_West_Window->setEnabled(1);
1030   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1031   inverseButton->setEnabled(1);
1032
1033   goToCursorPushButton->setEnabled(1);
1034
1035   if (DataTree->selectedItems().size()) {
1036     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1037
1038     colorMapComboBox->setEnabled(1);
1039     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1040       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1041           DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion") {
1042         colorMapComboBox->setEnabled(0);
1043         break;
1044       }
1045     }
1046
1047     std::vector<double> origin;
1048     std::vector<double> inputSpacing;
1049     std::vector<int> inputSize;
1050     std::vector<double> sizeMM;
1051     vtkSmartPointer<vtkMatrix4x4> transformation;
1052     int dimension=0;
1053     QString pixelType;
1054     QString inputSizeInBytes;
1055     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1056
1057     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1) {
1058       playButton->setEnabled(1);
1059       frameRateLabel->setEnabled(1);
1060       frameRateSpinBox->setEnabled(1);
1061     } else {
1062       playButton->setEnabled(0);
1063       frameRateLabel->setEnabled(0);
1064       frameRateSpinBox->setEnabled(0);
1065     }
1066
1067     //read image header
1068     int NPixel = 1;
1069
1070     vvImage::Pointer imageSelected;
1071     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1072       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1073     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1074       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1075     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1076       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1077     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1078       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1079     }
1080     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "contour") {
1081       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1082     }
1083     else {
1084       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1085     }
1086
1087     dimension = imageSelected->GetNumberOfDimensions();
1088     origin.resize(dimension);
1089     inputSpacing.resize(dimension);
1090     inputSize.resize(dimension);
1091     sizeMM.resize(dimension);
1092     pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1093     for (int i = 0; i < dimension; i++) {
1094       origin[i] = imageSelected->GetOrigin()[i];
1095       inputSpacing[i] = imageSelected->GetSpacing()[i];
1096       inputSize[i] = imageSelected->GetSize()[i];
1097       sizeMM[i] = inputSize[i]*inputSpacing[i];
1098       NPixel *= inputSize[i];
1099     }
1100     inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1101
1102     QString dim = QString::number(dimension) + " (";
1103     dim += pixelType + ")";
1104
1105     infoPanel->setFileName(image);
1106     infoPanel->setDimension(dim);
1107     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1108     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1109     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1110     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1111     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1112     transformation = imageSelected->GetTransform()->GetMatrix();
1113     infoPanel->setTransformation(Get4x4MatrixDoubleAsString(transformation));
1114
1115     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1116                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1117     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1118     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1119
1120     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1121     for (int i = 0; i < 4; i++) {
1122       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1123         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1124         break;
1125       }
1126     }
1127
1128     infoPanel->setFileName(image);
1129     infoPanel->setDimension(dim);
1130     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1131     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1132     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1133     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1134     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1135
1136     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1137                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1138     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1139     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1140
1141     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1142     for (int i = 0; i < 4; i++) {
1143       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1144         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1145         break;
1146       }
1147     }
1148     WindowLevelChanged();
1149
1150     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1151       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1152       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1153                                   mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1154                                   mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1155     } else {
1156       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1157       overlayPanel->getVFProperty(-1,-1,-1);
1158     }
1159     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1160       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1161     } else {
1162       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1163     }
1164
1165     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1166       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1167     } else {
1168       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1169     }
1170   }
1171 }
1172 //------------------------------------------------------------------------------
1173
1174 //------------------------------------------------------------------------------
1175 void vvMainWindow::ShowDocumentation()
1176 {
1177   documentation->show();
1178 }
1179 //------------------------------------------------------------------------------
1180
1181 //------------------------------------------------------------------------------
1182 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1183 {
1184   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1185   if(!checkCanPush) {
1186     registerForm->show();
1187   } else {
1188     if(registerForm->canPush()) {
1189       registerForm->show();
1190       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1191     }
1192   }
1193 }
1194 //------------------------------------------------------------------------------
1195
1196 //------------------------------------------------------------------------------
1197 void vvMainWindow::ShowHelpDialog()
1198 {
1199   help_dialog->show();
1200 }
1201 //------------------------------------------------------------------------------
1202
1203 //------------------------------------------------------------------------------
1204 void vvMainWindow::ChangeViewMode()
1205 {
1206   QList<int> size;
1207   if (viewMode == 1) {
1208     viewMode = 0;
1209     size.push_back(1);
1210     size.push_back(0);
1211     splitter_3->setSizes(size);
1212     OSplitter->setSizes(size);
1213     DataTree->setColumnHidden(2,1);
1214     DataTree->setColumnHidden(3,1);
1215     DataTree->setColumnHidden(4,1);
1216   } else {
1217     viewMode = 1;
1218     size.push_back(1);
1219     size.push_back(1);
1220     splitter_3->setSizes(size);
1221     OSplitter->setSizes(size);
1222     DataTree->setColumnHidden(2,0);
1223     DataTree->setColumnHidden(3,0);
1224     DataTree->setColumnHidden(4,0);
1225   }
1226   UpdateRenderWindows();
1227   /*
1228   ** I don't know why but for both resized QVTKWidget we also need to render
1229   ** the associated Slicer to redraw crosses.
1230   */
1231   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1232     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1233       mSlicerManagers[i]->GetSlicer(0)->Render();
1234     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1235       mSlicerManagers[i]->GetSlicer(2)->Render();
1236   }
1237 }
1238 //------------------------------------------------------------------------------
1239
1240 //------------------------------------------------------------------------------
1241 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1242 {
1243   QString result = "";// QString::number(size);
1244   //result += " bytes (";
1245   if (size > 1000000000) {
1246     size /= 1000000000;
1247     result += QString::number(size);
1248     result += "Gb";//)";
1249   } else if (size > 1000000) {
1250     size /= 1000000;
1251     result += QString::number(size);
1252     result += "Mb";//)";
1253   } else if (size > 1000) {
1254     size /= 1000;
1255     result += QString::number(size);
1256     result += "kb";//)";
1257   }
1258   return result;
1259 }
1260 //------------------------------------------------------------------------------
1261
1262 //------------------------------------------------------------------------------
1263 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix)
1264 {
1265   std::ostringstream strmatrix;
1266
1267   for (unsigned int i = 0; i < 4; i++) {
1268     for (unsigned int j = 0; j < 4; j++) {
1269       strmatrix.flags(ios::showpos);
1270       strmatrix.width(10);
1271       strmatrix.precision(3);
1272       strmatrix.setf(ios::fixed,ios::floatfield);
1273       strmatrix.fill(' ');
1274       strmatrix << std::left << matrix->GetElement(i, j);
1275       //strmatrix.width(10);
1276       strmatrix << " ";
1277     }
1278     strmatrix << std::endl;
1279   }
1280   QString result = strmatrix.str().c_str();
1281   return result;
1282 }
1283 //------------------------------------------------------------------------------
1284
1285 //------------------------------------------------------------------------------
1286 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1287 {
1288   QString result;
1289   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1290     if (i != 0)
1291       result += " ";
1292     result += QString::number(vectorDouble[i]);
1293   }
1294   return result;
1295 }
1296 //------------------------------------------------------------------------------
1297
1298 //------------------------------------------------------------------------------
1299 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1300 {
1301   QString result;
1302   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1303     if (i != 0)
1304       result += " ";
1305     result += QString::number(vectorInt[i]);
1306   }
1307   return result;
1308 }
1309 //------------------------------------------------------------------------------
1310
1311 //------------------------------------------------------------------------------
1312 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1313 {
1314   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1315   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1316     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1317       return i;
1318   }
1319   return -1;
1320 }
1321 //------------------------------------------------------------------------------
1322
1323 //------------------------------------------------------------------------------
1324 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1325 {
1326   QString id = sm->GetId().c_str();
1327   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1328     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1329       return DataTree->topLevelItem(i);
1330   }
1331   return NULL;
1332 }
1333 //------------------------------------------------------------------------------
1334
1335 //------------------------------------------------------------------------------
1336 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clickedItem, int column)
1337 {
1338   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1339     return;
1340
1341   // Get parent information (might be the same item)
1342   int slicerManagerIndex = GetSlicerIndexFromItem(clickedItem);
1343   QTreeWidgetItem* clickedParentItem = DataTree->topLevelItem(slicerManagerIndex);
1344   vvSlicer* clickedSlicer = mSlicerManagers[slicerManagerIndex]->GetSlicer(column-1);
1345
1346   // Go over the complete item tree (only 2 levels, parents and children)
1347   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1348     // Trick to avoid redoing twice the job for a key (sr)
1349     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()->GetInteractor()->SetKeySym("Crap");
1350
1351     QTreeWidgetItem* currentParentItem = DataTree->topLevelItem(i);
1352     if(currentParentItem != clickedParentItem) {
1353       // Not the branch of the clicked item, uncheck all
1354
1355       // Parent
1356       currentParentItem->setData(column,Qt::CheckStateRole, 0);
1357       mSlicerManagers[i]->UpdateSlicer(column-1, false);
1358
1359       // Children
1360       for (int iChild = 0; iChild < currentParentItem->childCount(); iChild++) {
1361         currentParentItem->child(iChild)->setData(column,Qt::CheckStateRole, 0);
1362       }
1363     }
1364     else {
1365       // Branch of the clicked one: get check status from actor visibility in slicer
1366       // and toggle the clicked one
1367
1368       // Parent
1369       bool vis = clickedSlicer->GetActorVisibility("image", 0);
1370       bool draw = clickedSlicer->GetRenderer()->GetDraw();
1371
1372       // Update slicer (after getting visibility)
1373       mSlicerManagers[slicerManagerIndex]->UpdateSlicer(column-1, true);
1374       mSlicerManagers[slicerManagerIndex]->UpdateInfoOnCursorPosition(column-1);
1375       DisplaySliders(slicerManagerIndex, column-1);
1376       if(clickedParentItem == clickedItem) {
1377         // Toggle
1378         vis = !draw || !vis;
1379       }
1380       clickedSlicer->SetActorVisibility("image", 0, vis);
1381       clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
1382
1383       // Children
1384       std::map<std::string, int> actorTypeCounts;
1385       for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
1386         QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
1387         std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
1388         vis = clickedSlicer->GetActorVisibility(actorType, actorTypeCounts[actorType]);
1389         if(currentChildItem == clickedItem) {
1390           // Toggle or force visibility if it was not on this branch so far
1391           vis = !draw || !vis;
1392           clickedSlicer->SetActorVisibility(actorType, actorTypeCounts[actorType], vis);
1393         }
1394         currentChildItem->setData(column, Qt::CheckStateRole, vis?2:0);
1395         actorTypeCounts[actorType]++;
1396       }
1397     }
1398   }
1399
1400   clickedSlicer->Render();
1401 }
1402 //------------------------------------------------------------------------------
1403
1404 void vvMainWindow::InitSlicers()
1405 {
1406   if (mSlicerManagers.size()) {
1407     mSlicerManagers.back()->GenerateDefaultLookupTable();
1408
1409     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1410     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1411     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1412     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1413   }
1414 }
1415
1416 //------------------------------------------------------------------------------
1417 void vvMainWindow::InitDisplay()
1418 {
1419   if (mSlicerManagers.size()) {
1420     //BE CAREFUL : this is absolutely necessary to set the interactor style
1421     //in order to have the same style instanciation for all SlicerManagers in
1422     // a same window
1423     for (int j = 0; j < 4; j++) {
1424       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1425       style->SetAutoAdjustCameraClippingRange(1);
1426       bool AlreadySelected = false;
1427       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1428         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1429
1430         //select the image only if previous are not selected
1431         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1432           mSlicerManagers[i]->UpdateSlicer(j,1);
1433           AlreadySelected = true;
1434         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1435           if (DataTree->selectedItems().size() == 0)
1436             DataTree->topLevelItem(i)->setSelected(1);
1437           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1438           mSlicerManagers[i]->UpdateSlicer(j,1);
1439           DisplaySliders(i,j);
1440         } else {
1441           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1442           mSlicerManagers[i]->UpdateSlicer(j,0);
1443         }
1444       }
1445       style->Delete();
1446     }
1447   }
1448 }
1449 //------------------------------------------------------------------------------
1450
1451 //------------------------------------------------------------------------------
1452 void vvMainWindow::DisplaySliders(int slicer, int window)
1453 {
1454   int range[2];
1455   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1456   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1457
1458   int tRange[2];
1459   tRange[0] = 0;
1460   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1461   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1462   bool showHorizontal = false;
1463   bool showVertical = false;
1464   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1465       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1466           && mSlicerManagers[slicer]->GetType() != vvImageReader::IMAGEWITHTIME
1467           && mSlicerManagers[slicer]->GetType() != vvImageReader::MERGEDWITHTIME))
1468     showVertical = true;
1469   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1470       || mSlicerManagers[slicer]->GetType() == vvImageReader::IMAGEWITHTIME
1471       || mSlicerManagers[slicer]->GetType() == vvImageReader::MERGEDWITHTIME)
1472     showHorizontal = true;
1473
1474   if (showVertical)
1475     verticalSliders[window]->show();
1476   else
1477     verticalSliders[window]->hide();
1478   verticalSliders[window]->setRange(range[0],range[1]);
1479   verticalSliders[window]->setValue(position);
1480
1481   if (showHorizontal)
1482     horizontalSliders[window]->show();
1483   else
1484     horizontalSliders[window]->hide();
1485   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1486   horizontalSliders[window]->setValue(tPosition);
1487 }
1488 //------------------------------------------------------------------------------
1489
1490 //------------------------------------------------------------------------------
1491 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1492 {
1493   int index = GetSlicerIndexFromItem(item);
1494
1495   if (DataTree->topLevelItem(index) != item) {
1496     QString warning = "Do you really want to close the overlay : ";
1497     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1498     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1499                        warning, 0, this);
1500     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1501     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1502     if (msgBox.exec() == QMessageBox::AcceptRole) {
1503       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1504       int overlay_index=0;
1505       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1506         if (DataTree->topLevelItem(index)->\
1507             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1508           overlay_index++;
1509         if (DataTree->topLevelItem(index)->child(child) == item) break;
1510       }
1511       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1512       mSlicerManagers[index]->SetColorMap(0);
1513       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1514       mSlicerManagers[index]->Render();
1515     }
1516   } else if (DataTree->topLevelItemCount() <= 1) {
1517     QString warning = "Do you really want to close the image : ";
1518     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1519     warning += "\nThis is the last image, you're about to close vv !!!";
1520     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1521                        warning, 0, this);
1522     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1523     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1524     if (msgBox.exec() == QMessageBox::AcceptRole) {
1525       this->close();
1526     }
1527   } else {
1528     QString warning = "Do you really want to close the image : ";
1529     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1530     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1531                        warning, 0, this);
1532     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1533     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1534     if (msgBox.exec() == QMessageBox::AcceptRole) {
1535
1536       // Tell tools that we close an image
1537       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1538
1539       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1540       DataTree->takeTopLevelItem(index);
1541       for (int i = 0; i < index; i++) {
1542         Manageriter++;
1543       }
1544       linkPanel->removeImage(index);
1545       mSlicerManagers[index]->RemoveActors();
1546       delete mSlicerManagers[index];
1547       mSlicerManagers.erase(Manageriter);
1548
1549       //
1550       InitDisplay();
1551     }
1552   }
1553   ImageInfoChanged();
1554 }
1555 //------------------------------------------------------------------------------
1556
1557 //------------------------------------------------------------------------------
1558 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1559 {
1560   // int index = GetSlicerIndexFromItem(item);
1561   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1562   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1563   //     mSlicerManagers[index]->ReloadVF();
1564   //   else
1565   //     mSlicerManagers[index]->Reload();
1566
1567   //   QApplication::restoreOverrideCursor();
1568   int index = GetSlicerIndexFromItem(item);
1569   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1570   QString role=item->data(1,Qt::UserRole).toString();
1571   if ( role == "vector"){
1572     mSlicerManagers[index]->ReloadVF();
1573   }
1574   else if (role == "overlay"){
1575     mSlicerManagers[index]->ReloadOverlay();
1576   }
1577   else if (role == "fusion"){
1578     mSlicerManagers[index]->ReloadFusion();
1579   }
1580   else{
1581     mSlicerManagers[index]->Reload();
1582   }
1583   // Update view and info
1584   ImageInfoChanged();
1585   mSlicerManagers[index]->Render();
1586   QApplication::restoreOverrideCursor();
1587 }
1588 //------------------------------------------------------------------------------
1589
1590 //------------------------------------------------------------------------------
1591 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1592 {
1593   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1594 }
1595 //------------------------------------------------------------------------------
1596
1597 //------------------------------------------------------------------------------
1598 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1599 {
1600   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1601 }
1602 //------------------------------------------------------------------------------
1603
1604 //------------------------------------------------------------------------------
1605 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1606 {
1607   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1608 }
1609 //------------------------------------------------------------------------------
1610
1611 //------------------------------------------------------------------------------
1612 void vvMainWindow::FusionChanged(int visibility, double value)
1613 {
1614   overlayPanel->getCurrentFusionInfo(visibility,value);
1615 }
1616 //------------------------------------------------------------------------------
1617
1618 //------------------------------------------------------------------------------
1619 void vvMainWindow::WindowLevelChanged()
1620 {
1621   // Base image
1622   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1623   if(index==-1) return;
1624   windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1625   levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1626   colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1627   presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1628
1629   // Overlay image
1630   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1631     overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor(),
1632                                      mSlicerManagers[index]->GetLinkOverlayWindowLevel(),
1633                                      mSlicerManagers[index]->GetOverlayColorWindow(),
1634                                      mSlicerManagers[index]->GetOverlayColorLevel());
1635   else
1636     overlayPanel->getOverlayProperty(-1,0,0.,0.);
1637
1638   // Fusion image
1639   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion())
1640     overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1641                                     mSlicerManagers[index]->GetFusionThresholdOpacity(),
1642                                     mSlicerManagers[index]->GetFusionColorMap(),
1643                                     mSlicerManagers[index]->GetFusionWindow(),
1644                                     mSlicerManagers[index]->GetFusionLevel());
1645   else
1646     overlayPanel->getFusionProperty(-1, -1, -1, -1, -1);
1647 }
1648 //------------------------------------------------------------------------------
1649
1650 //------------------------------------------------------------------------------
1651 void vvMainWindow::WindowLevelEdited()
1652 {
1653   presetComboBox->setCurrentIndex(6);
1654   UpdateWindowLevel();
1655 }
1656 //------------------------------------------------------------------------------
1657
1658 //------------------------------------------------------------------------------
1659 void vvMainWindow::SetWindowLevel(double w, double l)
1660 {
1661   windowSpinBox->setValue(w);
1662   levelSpinBox->setValue(l);
1663   presetComboBox->setCurrentIndex(6);
1664   colorMapComboBox->setCurrentIndex(0);
1665   UpdateWindowLevel();
1666 }
1667 //------------------------------------------------------------------------------
1668
1669 //------------------------------------------------------------------------------
1670 void vvMainWindow::UpdateWindowLevel()
1671 {
1672   if (DataTree->selectedItems().size()) {
1673     if (presetComboBox->currentIndex() == 7) //For ventilation
1674       colorMapComboBox->setCurrentIndex(5);
1675     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1676     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1677     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1678     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1679     mSlicerManagers[index]->Render();
1680     WindowLevelChanged();
1681   }
1682 }
1683 //------------------------------------------------------------------------------
1684
1685 //------------------------------------------------------------------------------
1686 void vvMainWindow::UpdateColorMap()
1687 {
1688   if (DataTree->selectedItems().size()) {
1689     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1690     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1691     mSlicerManagers[index]->Render();
1692   }
1693 }
1694 //------------------------------------------------------------------------------
1695 void vvMainWindow::SwitchWindowLevel()
1696 {
1697   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1698   int window = mSlicerManagers[index]->GetColorWindow();
1699   presetComboBox->setCurrentIndex(6);
1700   windowSpinBox->setValue(-window);
1701   UpdateWindowLevel();
1702 }
1703 //------------------------------------------------------------------------------
1704
1705 //------------------------------------------------------------------------------
1706 void vvMainWindow::ApplyWindowLevelToAllImages()
1707 {
1708   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1709     if (mSlicerManagers[i] == NULL)
1710       continue;
1711     mSlicerManagers[i]->SetColorWindow(windowSpinBox->value());
1712     mSlicerManagers[i]->SetColorLevel(levelSpinBox->value());
1713     mSlicerManagers[i]->SetPreset(6);
1714     mSlicerManagers[i]->Render();
1715   }
1716 }
1717 //------------------------------------------------------------------------------
1718
1719 //------------------------------------------------------------------------------
1720 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1721 {
1722   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1723     if (mSlicerManagers[i]->GetId() == id) {
1724       //mSlicerManagers[i]->SetTSlice(temps);
1725       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1726       mSlicerManagers[i]->UpdateViews(0,slicer);
1727       break;
1728     }
1729   }
1730 }
1731 //------------------------------------------------------------------------------
1732
1733 //------------------------------------------------------------------------------
1734 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1735 {
1736   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1737     if (id == mSlicerManagers[i]->GetId()) {
1738       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1739     }
1740   }
1741 }
1742 //------------------------------------------------------------------------------
1743
1744 //------------------------------------------------------------------------------
1745 void vvMainWindow::ShowContextMenu(QPoint point)
1746 {
1747   if (!DataTree->selectedItems().size()) {
1748     contextActions[1]->setEnabled(0);
1749     contextActions[2]->setEnabled(0);
1750     contextActions[3]->setEnabled(0);
1751     contextActions[4]->setEnabled(0);
1752     contextActions[5]->setEnabled(0);
1753     contextActions[6]->setEnabled(0);
1754   } else {
1755     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1756     contextActions[1]->setEnabled(1);
1757     contextActions[2]->setEnabled(
1758       DataTree->itemWidget(DataTree->selectedItems()[0],
1759                            COLUMN_RELOAD_IMAGE)->isEnabled());
1760     contextActions[3]->setEnabled(1);
1761     contextActions[5]->setEnabled(1);
1762     contextActions[6]->setEnabled(1);
1763
1764     if (mSlicerManagers[index]->GetDimension() < 3)
1765       contextActions[4]->setEnabled(0);
1766     else
1767       contextActions[4]->setEnabled(1);
1768   }
1769   contextMenu.exec(QCursor::pos());
1770 }
1771 //------------------------------------------------------------------------------
1772
1773 //------------------------------------------------------------------------------
1774 void vvMainWindow::CloseImage()
1775 {
1776   CloseImage(DataTree->selectedItems()[0],0);
1777 }
1778 //------------------------------------------------------------------------------
1779
1780 //------------------------------------------------------------------------------
1781 void vvMainWindow::ReloadImage()
1782 {
1783   ReloadImage(DataTree->selectedItems()[0],0);
1784 }
1785 //------------------------------------------------------------------------------
1786
1787 //------------------------------------------------------------------------------
1788 void vvMainWindow::SelectOverlayImage()
1789 {
1790   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1791
1792   //check if one overlay image is added
1793   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1794     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1795       QString error = "Cannot add more than one compared image\n";
1796       error += "Please remove first ";
1797       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1798       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1799       return;
1800     }
1801
1802   QString Extensions = EXTENSIONS;
1803   Extensions += ";;All Files (*)";
1804   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1805   if (!file.isEmpty())
1806     AddOverlayImage(index,file);
1807 }
1808 //------------------------------------------------------------------------------
1809
1810 //------------------------------------------------------------------------------
1811 void vvMainWindow::AddOverlayImage(int index, QString file)
1812 {
1813
1814   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1815   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1816                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1817   reader->SetFileName(file.toStdString().c_str());
1818   reader->ReadImageInformation();
1819   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1820   int dimension = reader->GetNumberOfDimensions();
1821   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1822   vvProgressDialog progress("Opening " + file.toStdString());
1823   qApp->processEvents();
1824
1825   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1826   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component)) {
1827     //create an item in the tree with good settings
1828     QTreeWidgetItem *item = new QTreeWidgetItem();
1829     item->setData(0,Qt::UserRole,file.toStdString().c_str());
1830     item->setData(1,Qt::UserRole,tr("overlay"));
1831     QFileInfo fileinfo(file); //Do not show the path
1832     item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1833     item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
1834     qApp->processEvents();
1835
1836     for (int j = 1; j <= 4; j++) {
1837       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1838     }
1839
1840     //Create the buttons for reload and close
1841     qApp->processEvents();
1842     QTreePushButton* cButton = new QTreePushButton;
1843     cButton->setItem(item);
1844     cButton->setColumn(COLUMN_CLOSE_IMAGE);
1845     cButton->setToolTip(tr("close image"));
1846     cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1847     connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1848             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1849
1850     QTreePushButton* rButton = new QTreePushButton;
1851     rButton->setItem(item);
1852     rButton->setColumn(COLUMN_RELOAD_IMAGE);
1853     rButton->setToolTip(tr("reload image"));
1854     rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1855     connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1856             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1857
1858     DataTree->topLevelItem(index)->setExpanded(1);
1859     DataTree->topLevelItem(index)->addChild(item);
1860     DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1861     DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1862
1863     //set the id of the image
1864     QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1865     item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1866     UpdateTree();
1867     qApp->processEvents();
1868     ImageInfoChanged();
1869     QApplication::restoreOverrideCursor();
1870   } else {
1871     QApplication::restoreOverrideCursor();
1872     QString error = "Cannot import the new image.\n";
1873     error += mSlicerManagers[index]->GetLastError().c_str();
1874     QMessageBox::information(this,tr("Problem reading image !"),error);
1875   }
1876   WindowLevelChanged();
1877 }
1878 //------------------------------------------------------------------------------
1879
1880
1881 //------------------------------------------------------------------------------
1882 void vvMainWindow::AddROI(int index, QString file)
1883 {
1884   /*
1885   // Get slice manager
1886
1887   // Load image
1888
1889   vvImageReader * mReader = new vvImageReader;
1890   mReader->SetInputFilename(filename.toStdString());
1891   mReader->Update(IMAGE);
1892   if (mReader->GetLastError().size() != 0) {
1893     std::cerr << "Error while reading " << filename.toStdString() << std::endl;
1894     QString error = "Cannot open file \n";
1895     error += mReader->GetLastError().c_str();
1896     QMessageBox::information(this,tr("Reading problem"),error);
1897     delete mReader;
1898     return;
1899   }
1900   vvImage::Pointer roi = mReader->GetOutput();
1901
1902   // Create roi in new tool
1903   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
1904   */
1905 }
1906 //------------------------------------------------------------------------------
1907
1908 //------------------------------------------------------------------------------
1909 void vvMainWindow::SelectFusionImage()
1910 {
1911   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1912
1913   //check if one fusion image is added
1914   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1915     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
1916       QString error = "Cannot add more than one fusion image\n";
1917       error += "Please remove first ";
1918       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1919       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1920       return;
1921     }
1922
1923   QString Extensions = EXTENSIONS;
1924   Extensions += ";;All Files (*)";
1925   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1926   if (!file.isEmpty())
1927     AddFusionImage(index,file);
1928 }
1929 //------------------------------------------------------------------------------
1930
1931 //------------------------------------------------------------------------------
1932 void vvMainWindow::ResetTransformationToIdentity()
1933 {
1934   std::string actorType = DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString().toStdString();
1935   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1936   mSlicerManagers[index]->ResetTransformationToIdentity(actorType);
1937   ImageInfoChanged();
1938 }
1939 //------------------------------------------------------------------------------
1940
1941 //------------------------------------------------------------------------------
1942 void vvMainWindow::AddFusionImage(int index, QString file)
1943 {
1944   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1945   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1946                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1947   reader->SetFileName(file.toStdString().c_str());
1948   reader->ReadImageInformation();
1949   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1950   if (reader) {
1951     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1952     vvProgressDialog progress("Opening fusion");
1953     qApp->processEvents();
1954
1955     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1956     if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1957                                           reader->GetNumberOfDimensions(), component)) {
1958       //create an item in the tree with good settings
1959       QTreeWidgetItem *item = new QTreeWidgetItem();
1960       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1961       item->setData(1,Qt::UserRole,tr("fusion"));
1962       QFileInfo fileinfo(filename.c_str()); //Do not show the path
1963       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1964       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
1965       qApp->processEvents();
1966
1967       for (int j = 1; j <= 4; j++) {
1968         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1969       }
1970
1971       //Create the buttons for reload and close
1972       qApp->processEvents();
1973       QTreePushButton* cButton = new QTreePushButton;
1974       cButton->setItem(item);
1975       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1976       cButton->setToolTip(tr("close image"));
1977       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1978       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1979               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1980
1981       QTreePushButton* rButton = new QTreePushButton;
1982       rButton->setItem(item);
1983       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1984       rButton->setToolTip(tr("reload image"));
1985       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1986       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1987               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1988
1989       DataTree->topLevelItem(index)->setExpanded(1);
1990       DataTree->topLevelItem(index)->addChild(item);
1991       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1992       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1993
1994       //set the id of the image
1995       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1996       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1997       UpdateTree();
1998       qApp->processEvents();
1999       ImageInfoChanged();
2000       QApplication::restoreOverrideCursor();
2001     } else {
2002       QApplication::restoreOverrideCursor();
2003       QString error = "Cannot import the new image.\n";
2004       error += mSlicerManagers[index]->GetLastError().c_str();
2005       QMessageBox::information(this,tr("Problem reading image !"),error);
2006     }
2007   } else {
2008     QString error = "Cannot import the new image.\n";
2009     QMessageBox::information(this,tr("Problem reading image !"),error);
2010   }
2011 }
2012 //------------------------------------------------------------------------------
2013
2014
2015 //------------------------------------------------------------------------------
2016 void vvMainWindow::OpenField()
2017 {
2018   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2019   //check if a vector field has already been added
2020   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2021     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
2022       QString error = "Cannot add more than one vector field\n";
2023       error += "Please remove first ";
2024       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2025       QMessageBox::information(this,tr("Problem adding vector field!"),error);
2026       return;
2027     }
2028
2029   QString Extensions = "Images ( *.mhd)";
2030   Extensions += ";;Images ( *.mha)";
2031   Extensions += ";;Images ( *.vf)";
2032   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2033   if (!file.isEmpty())
2034     AddField(file,index);
2035 }
2036 //------------------------------------------------------------------------------
2037
2038
2039 //------------------------------------------------------------------------------
2040 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2041 {
2042   //create an item in the tree with good settings
2043   QTreeWidgetItem *item = new QTreeWidgetItem();
2044   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2045   item->setData(1,Qt::UserRole,tr("vector"));
2046   QFileInfo fileinfo(filename); //Do not show the path
2047   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2048   item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("vector").c_str());
2049   qApp->processEvents();
2050
2051   for (int j = 1; j <= 4; j++) {
2052     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2053   }
2054
2055   //Create the buttons for reload and close
2056   qApp->processEvents();
2057   QTreePushButton* cButton = new QTreePushButton;
2058   cButton->setItem(item);
2059   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2060   cButton->setToolTip(tr("close vector field"));
2061   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2062   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2063           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2064
2065   QTreePushButton* rButton = new QTreePushButton;
2066   rButton->setItem(item);
2067   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2068   rButton->setToolTip(tr("reload vector field"));
2069   rButton->setEnabled(from_disk);
2070   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2071   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2072           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2073
2074   DataTree->topLevelItem(index)->setExpanded(1);
2075   DataTree->topLevelItem(index)->addChild(item);
2076   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2077   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2078
2079   //set the id of the image
2080   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2081   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2082   UpdateTree();
2083   qApp->processEvents();
2084   ImageInfoChanged();
2085   QApplication::restoreOverrideCursor();
2086 }
2087 //------------------------------------------------------------------------------
2088
2089
2090 //------------------------------------------------------------------------------
2091 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2092 {
2093   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2094   vvSlicerManager* imageManager = mSlicerManagers[index];
2095   if (imageManager->SetVF(vf,file.toStdString())) {
2096     AddFieldEntry(file,index,false);
2097   } else {
2098     QString error = "Cannot import the vector field for this image.\n";
2099     error += imageManager->GetLastError().c_str();
2100     QMessageBox::information(this,tr("Problem reading VF !"),error);
2101   }
2102   QApplication::restoreOverrideCursor();
2103 }
2104 //------------------------------------------------------------------------------
2105
2106
2107 //------------------------------------------------------------------------------
2108 void vvMainWindow::AddField(QString file,int index)
2109 {
2110   if (QFile::exists(file)) {
2111     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2112
2113     //init the progress events
2114     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2115     vvProgressDialog progress("Opening " + file.toStdString());
2116     qApp->processEvents();
2117
2118     //read the vector and put it in the current mSlicerManager
2119     vvSlicerManager* imageManager = mSlicerManagers[index];
2120     qApp->processEvents();
2121
2122     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2123     if (imageManager->SetVF(file.toStdString())) {
2124       imageManager->Render();
2125       AddFieldEntry(file,index,true);
2126     } else {
2127       QApplication::restoreOverrideCursor();
2128       QString error = "Cannot import the vector field for this image.\n";
2129       error += imageManager->GetLastError().c_str();
2130       QMessageBox::information(this,tr("Problem reading VF !"),error);
2131     }
2132   } else
2133     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2134
2135 }
2136 //------------------------------------------------------------------------------
2137
2138
2139 //------------------------------------------------------------------------------
2140 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2141 {
2142   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2143   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2144     for (int i = 0; i < 4; i++) {
2145       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2146       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2147       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2148       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2149       if (log > 0)
2150         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2151       else
2152         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2153     }
2154   }
2155 }
2156 //------------------------------------------------------------------------------
2157
2158
2159 //------------------------------------------------------------------------------
2160 void vvMainWindow::SetOverlayProperty(int color, int linked, double window, double level)
2161 {
2162   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2163   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2164     mSlicerManagers[index]->SetOverlayColor(color);
2165     mSlicerManagers[index]->SetColorMap(0);
2166     mSlicerManagers[index]->SetLinkOverlayWindowLevel(linked);
2167     mSlicerManagers[index]->SetOverlayColorWindow(window);
2168     mSlicerManagers[index]->SetOverlayColorLevel(level);
2169     mSlicerManagers[index]->Render();
2170   }
2171 }
2172 //------------------------------------------------------------------------------
2173
2174 //------------------------------------------------------------------------------
2175 void vvMainWindow::SetFusionProperty(int opacity, int thresOpacity, int colormap,double window, double level)
2176 {
2177   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2178   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2179     mSlicerManagers[index]->SetFusionColorMap(colormap);
2180     mSlicerManagers[index]->SetFusionOpacity(opacity);
2181     mSlicerManagers[index]->SetFusionThresholdOpacity(thresOpacity);
2182     mSlicerManagers[index]->SetFusionWindow(window);
2183     mSlicerManagers[index]->SetFusionLevel(level);
2184     mSlicerManagers[index]->SetColorMap(0);
2185     mSlicerManagers[index]->Render();
2186   }
2187 }
2188 //------------------------------------------------------------------------------
2189
2190 //------------------------------------------------------------------------------
2191 void vvMainWindow::SaveAs()
2192 {
2193   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2194     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2195     return;
2196   }
2197
2198   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2199   int dimension = mSlicerManagers[index]->GetDimension();
2200   QStringList OutputListeFormat;
2201   OutputListeFormat.clear();
2202   if (dimension == 1) {
2203     OutputListeFormat.push_back(".mhd");
2204     OutputListeFormat.push_back(".mha");
2205   }
2206   if (dimension == 2) {
2207     OutputListeFormat.push_back(".bmp");
2208     OutputListeFormat.push_back(".png");
2209     OutputListeFormat.push_back(".jpeg");
2210     OutputListeFormat.push_back(".tif");
2211     OutputListeFormat.push_back(".mhd");
2212     OutputListeFormat.push_back(".mha");
2213     OutputListeFormat.push_back(".hdr");
2214     OutputListeFormat.push_back(".vox");
2215   } else if (dimension == 3) {
2216     OutputListeFormat.push_back(".mhd");
2217     OutputListeFormat.push_back(".mha");
2218     OutputListeFormat.push_back(".hdr");
2219     OutputListeFormat.push_back(".vox");
2220   } else if (dimension == 4) {
2221     OutputListeFormat.push_back(".mhd");
2222     OutputListeFormat.push_back(".mha");
2223   }
2224   QString Extensions = "AllFiles(*.*)";
2225   for (int i = 0; i < OutputListeFormat.count(); i++) {
2226     Extensions += ";;Images ( *";
2227     Extensions += OutputListeFormat[i];
2228     Extensions += ")";
2229   }
2230   QString fileName = QFileDialog::getSaveFileName(this,
2231                      tr("Save As"),
2232                      mSlicerManagers[index]->GetFileName().c_str(),
2233                      Extensions);
2234   if (!fileName.isEmpty()) {
2235     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2236     if (OutputListeFormat.contains(
2237           fileformat.c_str())) {
2238       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2239       std::string action = "Saving";
2240       vvProgressDialog progress("Saving "+fileName.toStdString());
2241       qApp->processEvents();
2242       vvImageWriter::Pointer writer = vvImageWriter::New();
2243       writer->SetOutputFileName(fileName.toStdString());
2244       writer->SetInput(mSlicerManagers[index]->GetImage());
2245       writer->Update();
2246       QApplication::restoreOverrideCursor();
2247       if (writer->GetLastError().size()) {
2248         QString error = "Saving did not succeed\n";
2249         error += writer->GetLastError().c_str();
2250         QMessageBox::information(this,tr("Saving Problem"),error);
2251         SaveAs();
2252       }
2253     } else {
2254       QString error = fileformat.c_str();
2255       if (error.isEmpty())
2256         error += "no file format specified !";
2257       else
2258         error += " format unknown !!!\n";
2259       QMessageBox::information(this,tr("Saving Problem"),error);
2260       SaveAs();
2261     }
2262   }
2263 }
2264 //------------------------------------------------------------------------------
2265
2266
2267 //------------------------------------------------------------------------------
2268 void vvMainWindow::AddLink(QString image1,QString image2)
2269 {
2270   unsigned int sm1 = 0;
2271   unsigned int sm2 = 0;
2272
2273   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2274     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2275       mSlicerManagers[i]->AddLink(image2.toStdString());
2276       sm1 = i;
2277     }
2278     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2279       mSlicerManagers[i]->AddLink(image1.toStdString());
2280       sm2 = i;
2281     }
2282   }
2283
2284   if (linkPanel->isLinkAll())   {
2285     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2286     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2287   } else {
2288     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2289   }
2290 }
2291
2292 //------------------------------------------------------------------------------
2293
2294
2295 //------------------------------------------------------------------------------
2296 void vvMainWindow::RemoveLink(QString image1,QString image2)
2297 {
2298   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2299     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2300       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2301     }
2302     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2303       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2304     }
2305   }
2306 }
2307 //------------------------------------------------------------------------------
2308
2309 //------------------------------------------------------------------------------
2310 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2311 {
2312   int index = 0;
2313   while(sm != mSlicerManagers[index])
2314     index++;
2315   index = (index+offset) % mSlicerManagers.size();
2316
2317   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2318   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2319   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2320   DisplayChanged(item,slicer+1);
2321 }
2322 //------------------------------------------------------------------------------
2323
2324 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2325 {
2326   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2327     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2328       for (int j = 0; j < 4; j++) {
2329         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2330         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2331         //UpdateTSlice(j,value);
2332       }
2333       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2334       break;
2335     }
2336   }
2337 }
2338 //------------------------------------------------------------------------------
2339
2340
2341 //------------------------------------------------------------------------------
2342 void vvMainWindow::NOHorizontalSliderMoved()
2343 {
2344   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2345   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2346 //  mCurrentTime = NOHorizontalSlider->value();
2347 }
2348 //------------------------------------------------------------------------------
2349
2350
2351 //------------------------------------------------------------------------------
2352 void vvMainWindow::NEHorizontalSliderMoved()
2353 {
2354   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2355   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2356 //  mCurrentTime = NEHorizontalSlider->value();
2357 }
2358 //------------------------------------------------------------------------------
2359
2360
2361 //------------------------------------------------------------------------------
2362 void vvMainWindow::SOHorizontalSliderMoved()
2363 {
2364   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2365   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2366   // mCurrentTime = SOHorizontalSlider->value();
2367 }
2368 //------------------------------------------------------------------------------
2369
2370
2371 //------------------------------------------------------------------------------
2372 void vvMainWindow::SEHorizontalSliderMoved()
2373 {
2374   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2375   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2376   // mCurrentTime = SEHorizontalSlider->value();
2377 }
2378 //------------------------------------------------------------------------------
2379
2380 //------------------------------------------------------------------------------
2381 void vvMainWindow::NOVerticalSliderChanged()
2382 {
2383   static int value=-1;
2384   if (value == NOVerticalSlider->value()) return;
2385   else value = NOVerticalSlider->value();
2386   //  int value = NOVerticalSlider->value();
2387   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2388     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2389       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2390         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2391         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2392
2393         // If nor Update/Render -> slider not work
2394         // only render = ok navigation, but for contour Update needed but slower ?
2395
2396         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2397         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2398       }
2399       break;
2400     }
2401   }
2402 }
2403 //------------------------------------------------------------------------------
2404
2405
2406 //------------------------------------------------------------------------------
2407 void vvMainWindow::NEVerticalSliderChanged()
2408 {
2409   static int value=-1;
2410   if (value == NEVerticalSlider->value()) return;
2411   else value = NEVerticalSlider->value();
2412   //  int value = NEVerticalSlider->value();
2413   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2414     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2415       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2416         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2417         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2418         mSlicerManagers[i]->UpdateSlice(1);
2419         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2420       }
2421       break;
2422     }
2423   }
2424 }
2425 //------------------------------------------------------------------------------
2426
2427
2428 //------------------------------------------------------------------------------
2429 void vvMainWindow::SOVerticalSliderChanged()
2430 {
2431   static int value=-1;
2432   if (value == SOVerticalSlider->value()) return;
2433   else value = SOVerticalSlider->value();
2434   //int value = SOVerticalSlider->value();
2435   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2436     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2437       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2438         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2439         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2440         mSlicerManagers[i]->UpdateSlice(2);
2441         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2442       }
2443       // else { DD("avoid SOVerticalSlider slicer update"); }
2444       break;
2445     }
2446   }
2447 }
2448 //------------------------------------------------------------------------------
2449
2450
2451 //------------------------------------------------------------------------------
2452 void vvMainWindow::SEVerticalSliderChanged()
2453 {
2454   static int value=-1;
2455   if (value == SEVerticalSlider->value()) return;
2456   else value = SEVerticalSlider->value();
2457   // int value = SEVerticalSlider->value();
2458   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2459     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2460       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2461         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2462         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2463         mSlicerManagers[i]->UpdateSlice(3);
2464         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2465       }
2466       break;
2467     }
2468   }
2469 }
2470 //------------------------------------------------------------------------------
2471
2472
2473 //------------------------------------------------------------------------------
2474 void vvMainWindow::UpdateSlice(int slicer, int slice)
2475 {
2476   // DD("vvMainWindow::UpdateSlice");
2477 //   DD(slicer);
2478 //   DD(slice);
2479   if (slicer == 0) {
2480     //    if (slice != NOVerticalSlider->value())
2481     NOVerticalSlider->setValue(slice);
2482   } else {
2483     if (slicer == 1)
2484       NEVerticalSlider->setValue(slice);
2485     else {
2486       if (slicer == 2)
2487         SOVerticalSlider->setValue(slice);
2488       else {
2489         if (slicer == 3)
2490           SEVerticalSlider->setValue(slice);
2491       }
2492     }
2493   }
2494   // DD("vvMainWindow:UpdateSlice END");
2495 }
2496 //------------------------------------------------------------------------------
2497
2498
2499 //------------------------------------------------------------------------------
2500 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2501 {
2502   switch (slicer) {
2503   case 0:
2504     NOHorizontalSlider->setValue(slice);
2505     break;
2506   case 1:
2507     NEHorizontalSlider->setValue(slice);
2508     break;
2509   case 2:
2510     SOHorizontalSlider->setValue(slice);
2511     break;
2512   case 3:
2513     SEHorizontalSlider->setValue(slice);
2514     break;
2515   }
2516 }
2517 //------------------------------------------------------------------------------
2518
2519
2520 //------------------------------------------------------------------------------
2521 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2522 {
2523   int position = int((min+max)/2);
2524   if (slicer == 0) {
2525     NOVerticalSlider->setValue(position);
2526     NOVerticalSlider->setRange(min,max);
2527     NOHorizontalSlider->setRange(tmin,tmax);
2528   } else if (slicer == 1) {
2529     NEVerticalSlider->setValue(position);
2530     NEVerticalSlider->setRange(min,max);
2531     NEHorizontalSlider->setRange(tmin,tmax);
2532   } else if (slicer == 2) {
2533     SOVerticalSlider->setValue(position);
2534     SOVerticalSlider->setRange(min,max);
2535     SOHorizontalSlider->setRange(tmin,tmax);
2536   } else if (slicer == 3) {
2537     SEVerticalSlider->setValue(position);
2538     SEVerticalSlider->setRange(min,max);
2539     SEHorizontalSlider->setRange(tmin,tmax);
2540   }
2541 }
2542 //------------------------------------------------------------------------------
2543
2544
2545 //------------------------------------------------------------------------------
2546 void vvMainWindow::SaveNOScreenshot()
2547 {
2548   SaveScreenshot(NOViewWidget);
2549 }
2550 //------------------------------------------------------------------------------
2551
2552
2553 //------------------------------------------------------------------------------
2554 void vvMainWindow::SaveNEScreenshot()
2555 {
2556   SaveScreenshot(NEViewWidget);
2557 }
2558 //------------------------------------------------------------------------------
2559
2560
2561 //------------------------------------------------------------------------------
2562 void vvMainWindow::SaveSOScreenshot()
2563 {
2564   SaveScreenshot(SOViewWidget);
2565 }
2566 //------------------------------------------------------------------------------
2567
2568
2569 //------------------------------------------------------------------------------
2570 void vvMainWindow::SaveSEScreenshot()
2571 {
2572   SaveScreenshot(SEViewWidget);
2573 }
2574 //------------------------------------------------------------------------------
2575
2576
2577 //------------------------------------------------------------------------------
2578 void vvMainWindow::SaveScreenshotAllSlices()
2579 {
2580   QVTKWidget *widget = NOViewWidget;
2581   vtkSmartPointer<vtkRenderWindow>  renderWindow = widget->GetRenderWindow();
2582
2583   int index = 0;// GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2584   vvSlicerManager * SM = mSlicerManagers[index];
2585   vvImage * image = SM->GetImage();
2586   vvSlicer * slicer = SM->GetSlicer(0);
2587   int orientation = slicer->GetOrientation();
2588   int nbSlices = image->GetSize()[orientation];
2589
2590   // Select filename base
2591   QString filename = QFileDialog::getSaveFileName(this,
2592                                                   tr("Save As (filename will be completed by slice number)"),
2593                                                   itksys::SystemTools::GetFilenamePath(mSlicerManagers[index]->GetFileName()).c_str(),
2594                                                   "Images( *.png);;");
2595
2596   // Loop on slices
2597   for(uint i=0; i<nbSlices; i++) {
2598     // Change the slice
2599     slicer->SetSlice(i);
2600
2601     // Screenshot
2602     vtkSmartPointer<vtkWindowToImageFilter> windowToImageFilter = vtkSmartPointer<vtkWindowToImageFilter>::New();
2603     windowToImageFilter->SetInput(renderWindow);
2604     windowToImageFilter->SetMagnification(1);
2605     windowToImageFilter->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
2606     windowToImageFilter->Update();
2607
2608     vtkSmartPointer<vtkPNGWriter> writer = vtkSmartPointer<vtkPNGWriter>::New();
2609     std::string fn = itksys::SystemTools::GetFilenameWithoutLastExtension(filename.toStdString());
2610     fn = fn + "_" + clitk::toString(i) + itksys::SystemTools::GetFilenameLastExtension(filename.toStdString());
2611     writer->SetFileName(fn.c_str());
2612     writer->SetInput(windowToImageFilter->GetOutput());
2613     writer->Write();
2614   }
2615 }
2616 //------------------------------------------------------------------------------
2617
2618
2619 //------------------------------------------------------------------------------
2620 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
2621 {
2622   QString Extensions = "Images( *.png);;";
2623   Extensions += "Images( *.jpg);;";
2624   Extensions += "Images( *.bmp);;";
2625   Extensions += "Images( *.tif);;";
2626   Extensions += "Images( *.ppm)";
2627 #ifdef VTK_USE_FFMPEG_ENCODER
2628   Extensions += "Images( *.avi)";
2629 #endif
2630 #ifdef VTK_USE_MPEG2_ENCODER
2631   Extensions += "Images( *.mpg)";
2632 #endif
2633
2634   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2635   QString fileName = QFileDialog::getSaveFileName(this,
2636                      tr("Save As"),
2637                      itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
2638                      Extensions);
2639
2640   if (!fileName.isEmpty()) {
2641     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2642     w2i->SetInput(widget->GetRenderWindow());
2643     w2i->Update();
2644     vtkImageData *image = w2i->GetOutput();
2645
2646     const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2647     if (!strcmp(ext, ".bmp")) {
2648       vtkBMPWriter *bmp = vtkBMPWriter::New();
2649       bmp->SetInput(image);
2650       bmp->SetFileName(fileName.toStdString().c_str());
2651       bmp->Write();
2652       bmp->Delete();
2653     } else if (!strcmp(ext, ".tif")) {
2654       vtkTIFFWriter *tif = vtkTIFFWriter::New();
2655       tif->SetInput(image);
2656       tif->SetFileName(fileName.toStdString().c_str());
2657       tif->Write();
2658       tif->Delete();
2659     } else if (!strcmp(ext, ".ppm")) {
2660       vtkPNMWriter *pnm = vtkPNMWriter::New();
2661       pnm->SetInput(image);
2662       pnm->SetFileName(fileName.toStdString().c_str());
2663       pnm->Write();
2664       pnm->Delete();
2665     } else if (!strcmp(ext, ".png")) {
2666       vtkPNGWriter *png = vtkPNGWriter::New();
2667       png->SetInput(image);
2668       png->SetFileName(fileName.toStdString().c_str());
2669       png->Write();
2670       png->Delete();
2671     } else if (!strcmp(ext, ".jpg")) {
2672       vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2673       jpg->SetInput(image);
2674       jpg->SetFileName(fileName.toStdString().c_str());
2675       jpg->Write();
2676       jpg->Delete();
2677 #ifdef VTK_USE_FFMPEG_ENCODER
2678     } else if (!strcmp(ext, ".avi")) {
2679       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
2680       mpg->SetInput(image);
2681       mpg->SetFileName(fileName.toStdString().c_str());
2682       mpg->SetQuality(2);
2683       mpg->SetRate(5);
2684       mpg->Start();
2685
2686       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2687       int nSlice = vvImg->GetVTKImages().size();
2688       for(int i=0; i<nSlice; i++) {
2689         mSlicerManagers[smIndex]->SetNextTSlice(0);
2690         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2691         w2i->SetInput(widget->GetRenderWindow());
2692         w2i->Update();
2693         mpg->SetInput(w2i->GetOutput());
2694         mpg->Write();
2695       }
2696       mpg->End();
2697       mpg->Delete();
2698 #endif
2699 #ifdef VTK_USE_MPEG2_ENCODER
2700     } else if (!strcmp(ext, ".mpg")) {
2701       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
2702       mpg->SetInput(image);
2703       mpg->SetFileName(fileName.toStdString().c_str());
2704       mpg->Start();
2705
2706       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2707       int nSlice = vvImg->GetVTKImages().size();
2708       for(int i=0; i<nSlice; i++) {
2709         mSlicerManagers[smIndex]->SetNextTSlice(0);
2710         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2711         w2i->SetInput(widget->GetRenderWindow());
2712         w2i->Update();
2713         mpg->SetInput(w2i->GetOutput());
2714         mpg->Write();
2715       }
2716       mpg->End();
2717       mpg->Delete();
2718 #endif
2719     } else {
2720       QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2721     }
2722   }
2723 }
2724 //------------------------------------------------------------------------------
2725
2726
2727 //------------------------------------------------------------------------------
2728 void vvMainWindow::GoToCursor()
2729 {
2730   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2731   for (int column = 1; column < 5; column++) {
2732     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
2733       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2734       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2735         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2736       mSlicerManagers[index]->UpdateViews(1,column-1);
2737       mSlicerManagers[index]->UpdateLinked(column-1);
2738       break;
2739     }
2740   }
2741 }
2742 //------------------------------------------------------------------------------
2743
2744 //------------------------------------------------------------------------------
2745 void vvMainWindow::PlayPause()
2746 {
2747   if (playMode) {
2748     playMode = 0;
2749     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2750     ImageInfoChanged();
2751     return;
2752   } else {
2753     int image_number=DataTree->topLevelItemCount();
2754     bool has_temporal;
2755     for (int i=0; i<image_number; i++)
2756       if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1) {
2757         has_temporal=true;
2758         break;
2759       }
2760     if (has_temporal) {
2761       playMode = 1;
2762       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2763       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2764     }
2765   }
2766 }
2767 //------------------------------------------------------------------------------
2768
2769 //------------------------------------------------------------------------------
2770 void vvMainWindow::PlayNext()
2771 {
2772   if (playMode && !this->isHidden()) {
2773     int image_number=DataTree->topLevelItemCount();
2774     ///Only play one slicer per SM, and only if the SM is being displayed
2775     for (int i=0; i<image_number; i++)
2776       for (int j=0; j<4; j++)
2777         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2778             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
2779           mSlicerManagers[i]->SetNextTSlice(j);
2780           break;
2781         }
2782     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2783   }
2784 }
2785 //------------------------------------------------------------------------------
2786
2787 void vvMainWindow::ShowLastImage()
2788 {
2789   if (mSlicerManagers.size() > 1) {
2790     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2791     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2792     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2793     DisplayChanged(item,1);
2794   }
2795 }
2796
2797 //------------------------------------------------------------------------------
2798 void vvMainWindow::UpdateRenderWindows()
2799 {
2800   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2801   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2802   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2803   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2804 }
2805 //------------------------------------------------------------------------------
2806
2807 //------------------------------------------------------------------------------
2808 void vvMainWindow::SegmentationOnCurrentImage()
2809 {
2810   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2811
2812   vvSegmentationDialog segmentation;
2813   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2814   segmentation.exec();
2815 }
2816 //------------------------------------------------------------------------------
2817
2818 void vvMainWindow::SurfaceViewerLaunch()
2819 {
2820   vvSurfaceViewerDialog surfaceViewer;
2821   surfaceViewer.exec();
2822 }
2823 //------------------------------------------------------------------------------
2824
2825
2826 //------------------------------------------------------------------------------
2827 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
2828 {
2829   int number=0;
2830   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
2831     vvSlicerManager * v = mSlicerManagers[l];
2832     if (v->GetBaseFileName() ==
2833         vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
2834       number = std::max(number, v->GetBaseFileNameNumber()+1);
2835     }
2836   }
2837   return number;
2838 }
2839 //------------------------------------------------------------------------------
2840
2841
2842 //------------------------------------------------------------------------------
2843 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2844 {
2845   // Change filename if another image exist with the same name
2846   int number = GetImageDuplicateFilenameNumber(filename);
2847
2848   // Create new SliceManager
2849   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
2850   slicer_manager->SetImage(image);//, IMAGE, number);
2851   //  filename = filename+"_"+clitk::toString(number);
2852   slicer_manager->SetFilename(filename, number);
2853   mSlicerManagers.push_back(slicer_manager);
2854
2855   //create an item in the tree with good settings
2856   QTreeWidgetItem *item = new QTreeWidgetItem();
2857   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2858   item->setData(1,Qt::UserRole,tr("image"));
2859   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
2860   qApp->processEvents();
2861
2862   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2863
2864   //Create the buttons for reload and close
2865   qApp->processEvents();
2866   QTreePushButton* cButton = new QTreePushButton;
2867   cButton->setItem(item);
2868   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2869   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2870   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2871           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2872
2873   QTreePushButton* rButton = new QTreePushButton;
2874   rButton->setItem(item);
2875   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2876   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2877   rButton->setEnabled(0);
2878   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2879           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2880
2881   DataTree->addTopLevelItem(item);
2882   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2883   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2884
2885   //set the id of the image
2886   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2887   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2888   mSlicerManagers.back()->SetId(id.toStdString());
2889
2890   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
2891                       , id.toStdString());
2892
2893   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
2894           this, SLOT(CurrentImageChanged(std::string)));
2895   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
2896           this, SLOT(CurrentPickedImageChanged(std::string)));
2897   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
2898           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2899   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
2900           this, SLOT(VectorChanged(int,double,double,double, double)));
2901   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
2902           this, SLOT(OverlayChanged(int,double,double)));
2903   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
2904           this, SLOT(FusionChanged(int,double)));
2905   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
2906           this,SLOT(WindowLevelChanged()));
2907   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
2908           this,SLOT(UpdateSlice(int,int)));
2909   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
2910           this,SLOT(UpdateTSlice(int, int)));
2911   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2912           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2913   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2914           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2915   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
2916           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
2917   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
2918           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
2919   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2920   UpdateTree();
2921   qApp->processEvents();
2922   InitSlicers();
2923   ShowLastImage();
2924   InitDisplay();
2925   qApp->processEvents();
2926
2927   // End
2928   ImageInfoChanged();
2929   return slicer_manager;
2930 }
2931 //------------------------------------------------------------------------------
2932
2933
2934 //------------------------------------------------------------------------------
2935 void vvMainWindow::UpdateCurrentSlicer()
2936 {
2937   int index = -1;
2938   if (DataTree->selectedItems().size() > 0) {
2939     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2940   }
2941   mSlicerManagerCurrentIndex = index;
2942 }
2943 //------------------------------------------------------------------------------
2944