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://oncora1.lyon.fnclcc.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
  25 // VV include
  26 #include "vvMainWindow.h"
  27 #include "vvHelpDialog.h"
  28 #include "vvDocumentation.h"
  29 #include "vvProgressDialog.h"
  30 #include "vvQDicomSeriesSelector.h"
  31 #include "vvSlicerManager.h"
  32 #include "clitkImageCommon.h"
  33 #include "vvSlicer.h"
  34 #include "vvInteractorStyleNavigator.h"
  35 #include "vvImageWriter.h"
  36 #include "vvSegmentationDialog.h"
  37 #include "vvSurfaceViewerDialog.h"
  38 #include "vvDeformationDialog.h"
  39 #include "vvImageWarp.h"
  40 #include "vvUtils.h"
  41 #include "vvMaximumIntensityProjection.h"
  42 #include "vvMidPosition.h"
  43 #include "vvMesh.h"
  44 #include "vvStructSelector.h"
  45 #include "vvMeshReader.h"
  46 #include "vvConstants.h"
  47
  48 #ifdef CLITK_VV_USE_BDCM
  49 #include <bdcmDicomFilesSelectorDialog.h>
  50 #endif
  51
  52 // ITK include
  53 #include "itkImage.h"
  54 #include "itkImageFileReader.h"
  55 #include "itkByteSwapper.h"
  56 #include "itkCommand.h"
  57 #include "itkNumericSeriesFileNames.h"
  58
  59 // VTK include
  60 #include "vtkImageData.h"
  61 #include "vtkImageActor.h"
  62 #include "vtkCornerAnnotation.h"
  63 #include "vtkRenderWindow.h"
  64 #include "vtkRenderWindowInteractor.h"
  65 #include "vtkRenderer.h"
  66 #include "vtkRendererCollection.h"
  67 #include "vtkWindowToImageFilter.h"
  68 #include "vtkBMPWriter.h"
  69 #include "vtkTIFFWriter.h"
  70 #include "vtkPNMWriter.h"
  71 #include "vtkPNGWriter.h"
  72 #include "vtkJPEGWriter.h"
  73
  74 // Standard includes
  75 #include <iostream>
  76
  77 #define COLUMN_TREE 0
  78 #define COLUMN_UL_VIEW 1
  79 #define COLUMN_UR_VIEW 2
  80 #define COLUMN_DL_VIEW 3
  81 #define COLUMN_DR_VIEW 4
  82 #define COLUMN_CLOSE_IMAGE 5
  83 #define COLUMN_RELOAD_IMAGE 6
  84 #define COLUMN_IMAGE_NAME 7
  85
  86 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.hdr *.vox *.his *.xdr)"
  87
  88 /*Data Tree values
  89   0,Qt::UserRole full filename
  90   1,Qt::CheckStateRole checkbutton UL View
  91   1,Qt::UserRole overlay, fusion or vector
  92   2,Qt::CheckStateRole checkbutton UR View
  93   3,Qt::CheckStateRole checkbutton DL View
  94   4,Qt::CheckStateRole checkbutton DR View
  95   5,0  short filename
  96   5,Qt::UserRole mSlicerManager id*/
  97
  98 //------------------------------------------------------------------------------
  99 vvMainWindow::vvMainWindow():vvMainWindowBase() {
 100   setupUi(this); // this sets up the GUI
 101
 102   mInputPathName = "";
 103   mMenuTools = menuTools;
 104   mContextMenu = &contextMenu;
 105   mMenuExperimentalTools = menuExperimental;
 106   mMainWidget = this;
 107   mCurrentTime = -1;
 108
 109   //Init the contextMenu
 110   this->setContextMenuPolicy(Qt::CustomContextMenu);
 111   contextActions.resize(0);
 112   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 113                                                         tr("O&pen new Image"));
 114   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 115   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 116   contextActions.push_back(actionOpen_new_image);
 117   contextMenu.addSeparator();
 118
 119   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 120                                                      tr("Close Current Image"));
 121   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 122   contextActions.push_back(actionClose_Image);
 123
 124   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 125                                                       tr("Reload Current Image"));
 126   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 127   contextActions.push_back(actionReload_image);
 128
 129   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 130                                                     tr("Save Current Image"));
 131   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 132   contextActions.push_back(actionSave_image);
 133
 134   contextMenu.addSeparator();
 135
 136   // QAction* actionCrop_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/crop.png")),
 137   //                                                   tr("Crop Current Image"));
 138   // connect(actionCrop_image,SIGNAL(triggered()),this,SLOT(CropImage()));
 139   // contextActions.push_back(actionCrop_image);
 140
 141   QAction* actionSplit_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/cut.png")),
 142                                                      tr("Split Current Image"));
 143   connect(actionSplit_image,SIGNAL(triggered()),this,SLOT(SplitImage()));
 144   contextActions.push_back(actionSplit_image);
 145
 146   contextMenu.addSeparator();
 147
 148   contextMenu.addAction(actionAdd_VF_to_current_Image);
 149   contextActions.push_back(actionAdd_VF_to_current_Image);
 150
 151   QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 152                                                                        tr("Add overlay image to current image"));
 153   contextMenu.addAction(actionAdd_Overlay_to_current_Image);
 154   contextActions.push_back(actionAdd_Overlay_to_current_Image);
 155
 156   connect(actionAdd_Overlay_to_current_Image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 157
 158   contextMenu.addAction(actionAdd_fusion_image);
 159   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 160   contextActions.push_back(actionAdd_fusion_image);
 161
 162   // TRIAL DS
 163   /*
 164   QMenu * m = new QMenu(menubar);
 165   m->setTitle("TOTO");
 166   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 167   contextMenu.addMenu(m);
 168   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 169                      tr("BIDON"));
 170   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 171                      tr("BIDON2"));
 172   m->addAction(a);
 173   m->addAction(b);
 174   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 175   */
 176
 177   //init the DataTree
 178   mSlicerManagers.resize(0);
 179
 180   QStringList header;
 181   header.append("");
 182   header.append("TL");
 183   header.append("TR");
 184   header.append("BL");
 185   header.append("BR");
 186   header.append("");
 187   header.append("");
 188   header.append("Name");
 189
 190   DataTree->setHeaderLabels(header);
 191   DataTree->resizeColumnToContents(COLUMN_TREE);
 192   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 193   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 194   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 195   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 196   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 197   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 198   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 199
 200   viewMode = 1;
 201   documentation = new vvDocumentation();
 202   help_dialog = new vvHelpDialog();
 203   dicomSeriesSelector = new vvDicomSeriesSelector();
 204
 205   inverseButton->setEnabled(0);
 206   actionAdd_Overlay_to_current_Image->setEnabled(0);
 207   actionSave_As->setEnabled(0);
 208   actionAdd_VF_to_current_Image->setEnabled(0);
 209   actionAdd_fusion_image->setEnabled(0);
 210
 211   //init the sliders
 212   verticalSliders.push_back(NOVerticalSlider);
 213   verticalSliders.push_back(NEVerticalSlider);
 214   verticalSliders.push_back(SOVerticalSlider);
 215   verticalSliders.push_back(SEVerticalSlider);
 216
 217   for (int i =0; i < 4; i++)
 218     verticalSliders[i]->hide();
 219
 220   horizontalSliders.push_back(NOHorizontalSlider);
 221   horizontalSliders.push_back(NEHorizontalSlider);
 222   horizontalSliders.push_back(SOHorizontalSlider);
 223   horizontalSliders.push_back(SEHorizontalSlider);
 224
 225   for (int i =0; i < 4; i++)
 226     horizontalSliders[i]->hide();
 227
 228
 229   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 230   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 231   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 232   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 233
 234   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 235   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 236   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 237   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 238
 239   //connect everything
 240   connect(actionMaximum_Intensity_Projection,SIGNAL(triggered()),this,SLOT(ComputeMIP()));
 241   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 242   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 243   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 244   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 245   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 246   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 247   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 248   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 249   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 250   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 251   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 252   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 253   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 254   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 255   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 256
 257   ///////////////////////////////////////////////
 258   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 259   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 260   ///////////////////////////////////////////////
 261
 262   actionNorth_East_Window->setEnabled(0);
 263   actionNorth_West_Window->setEnabled(0);
 264   actionSouth_East_Window->setEnabled(0);
 265   actionSouth_West_Window->setEnabled(0);
 266
 267   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 268   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 269   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 270   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 271
 272   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 273   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 274           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 275
 276   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 277   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 278   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 279   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 280   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 281   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 282
 283
 284   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 285
 286   connect(linkPanel,SIGNAL(addLink(QString,QString)),this,SLOT(AddLink(QString,QString)));
 287   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 288   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int)),this,SLOT(SetVFProperty(int,int,int)));
 289   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int)),this,SLOT(SetOverlayProperty(int)));
 290   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,double,double)),
 291           this,SLOT(SetFusionProperty(int,int,double,double)));
 292   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 293
 294   playMode = 0;//pause
 295   mFrameRate = 10;
 296   playButton->setEnabled(0);
 297   frameRateLabel->setEnabled(0);
 298   frameRateSpinBox->setEnabled(0);
 299   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 300   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 301
 302   goToCursorPushButton->setEnabled(0);
 303   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 304
 305   NOViewWidget->hide();
 306   NEViewWidget->hide();
 307   SOViewWidget->hide();
 308   SEViewWidget->hide();
 309
 310   //Recently opened files
 311   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 312   if ( !recent_files.empty() )
 313     {
 314       QMenu * rmenu = new QMenu("Recently opened files...");
 315       rmenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 316       menuFile->insertMenu(actionOpen_Image_With_Time,rmenu);
 317       for (std::list<std::string>::iterator i = recent_files.begin();i!=recent_files.end();i++)
 318         {
 319           QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")),
 320                                        (*i).c_str(),this);
 321           rmenu->addAction(current);
 322           connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 323         }
 324     }
 325
 326   // Adding all new tools (insertion in the menu)
 327   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 328
 329   if (!CLITK_EXPERIMENTAL)
 330       menuExperimental->menuAction()->setVisible(false);
 331 }
 332 //------------------------------------------------------------------------------
 333
 334
 335 //------------------------------------------------------------------------------
 336 void vvMainWindow::ComputeMIP()
 337 {
 338   vvMaximumIntensityProjection mip;
 339   vvSlicerManager* selected_slicer = mSlicerManagers[GetSlicerIndexFromItem(DataTree->selectedItems()[0])];
 340   QFileInfo info(selected_slicer->GetFileName().c_str());
 341   mip.Compute(selected_slicer);
 342   if (!mip.error)
 343       AddImage(mip.GetOutput(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_mip.mhd");
 344 }
 345 //------------------------------------------------------------------------------
 346
 347
 348 //------------------------------------------------------------------------------
 349 void vvMainWindow::ComputeMidPosition()
 350 {
 351   bool ok;
 352   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 353   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 354                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 355   if (ok)
 356     {
 357       vvMidPosition midp;
 358       midp.slicer_manager = mSlicerManagers[index];
 359       midp.reference_image_index = ref;
 360       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 361       midp.Update();
 362       if (midp.error)
 363         QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 364       else
 365         {
 366           QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 367           AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 368         }
 369       QApplication::restoreOverrideCursor();
 370     }
 371 }
 372 //------------------------------------------------------------------------------
 373
 374
 375 //------------------------------------------------------------------------------
 376 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 377 {
 378   QTreeWidgetItem *item = new QTreeWidgetItem();
 379   item->setData(0,Qt::UserRole,"filename.vtk");
 380   item->setData(1,Qt::UserRole,tr("contour"));
 381   QBrush brush;
 382   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 383   brush.setStyle(Qt::SolidPattern);
 384   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 385   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 386
 387   for (int j = 1; j <= 4; j++)
 388     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 389
 390   QTreePushButton* cButton = new QTreePushButton;
 391   cButton->setItem(item);
 392   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 393   cButton->setToolTip(tr("close image"));
 394   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 395   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 396           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 397
 398   QTreePushButton* rButton = new QTreePushButton;
 399   rButton->setItem(item);
 400   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 401   rButton->setToolTip(tr("reload image"));
 402   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 403   rButton->setEnabled(false);
 404   //Not implemented
 405   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 406   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 407
 408   DataTree->topLevelItem(image_index)->setExpanded(1);
 409   DataTree->topLevelItem(image_index)->addChild(item);
 410   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 411   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 412   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 413   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 414
 415   UpdateTree();
 416   mSlicerManagers[image_index]->AddContour(contour,propagation);
 417   mSlicerManagers[image_index]->Render();
 418 }
 419 //------------------------------------------------------------------------------
 420
 421
 422 //------------------------------------------------------------------------------
 423 void vvMainWindow::OpenVTKContour()
 424 {
 425   if (mSlicerManagers.size() > 0)
 426     {
 427       QString Extensions = "Images ( *.vtk; *.obj)";
 428       Extensions += ";;All Files (*)";
 429       QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 430       if (file.isNull())
 431         return;
 432       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 433       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 434       vvMeshReader reader;
 435       reader.SetImage(mSlicerManagers[index]->GetImage());
 436       reader.SetModeToVTK();
 437       reader.SetFilename(file.toStdString());
 438       reader.Update();
 439       AddContour(index,reader.GetOutput()[0],false);
 440       QApplication::restoreOverrideCursor();
 441     }
 442 }
 443 //------------------------------------------------------------------------------
 444
 445
 446 //------------------------------------------------------------------------------
 447 void vvMainWindow::OpenDCStructContour()
 448 {
 449   if (mSlicerManagers.size() > 0)
 450     {
 451       QString Extensions = "Dicom Files ( *.dcm; RS*)";
 452       Extensions += ";;All Files (*)";
 453       QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 454       if (file.isNull())
 455         return;
 456       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 457       vvMeshReader reader;
 458       reader.SetFilename(file.toStdString());
 459       vvStructSelector selector;
 460       selector.SetStructures(reader.GetROINames());
 461       if (!mSlicerManagers[index]->GetVF().IsNull())
 462         selector.EnablePropagationCheckBox();
 463       if (selector.exec())
 464         {
 465           QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 466           reader.SetSelectedItems(selector.getSelectedItems());
 467           reader.SetImage(mSlicerManagers[index]->GetImage());
 468           if (selector.PropagationEnabled())
 469             reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 470           reader.Update();
 471           std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 472           for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 473                i!=contours.end();i++)
 474             AddContour(index,*i,selector.PropagationEnabled());
 475           QApplication::restoreOverrideCursor();
 476         }
 477     }
 478 }
 479 //------------------------------------------------------------------------------
 480
 481
 482 //------------------------------------------------------------------------------
 483 void vvMainWindow::ComputeDeformableRegistration()
 484 {
 485   if (mSlicerManagers.size() > 0)
 486     {
 487       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 488       vvDeformationDialog dialog(index,mSlicerManagers);
 489       if (dialog.exec())
 490         {
 491           std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 492           AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 493           WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 494         }
 495       else
 496         std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 497     }
 498   else QMessageBox::information(this, "Need to open image","You must open an image first.");
 499 }
 500 //------------------------------------------------------------------------------
 501
 502
 503 //------------------------------------------------------------------------------
 504 void vvMainWindow::WarpImage()
 505 {
 506   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 507   if (!mSlicerManagers[index]->GetVF().IsNull())
 508     {
 509       bool ok;
 510       int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 511                                          mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 512       if (ok)
 513         {
 514           WarpImage(mSlicerManagers[index],ref);
 515         }
 516     }
 517   else
 518     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 519 }
 520 //------------------------------------------------------------------------------
 521
 522
 523 //------------------------------------------------------------------------------
 524 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 525 {
 526   if (!selected_slicer->GetVF().IsNull())
 527     {
 528       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 529       QFileInfo info(selected_slicer->GetFileName().c_str());
 530       vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 531                        reference_phase,this);
 532       if (warp.ComputeWarpedImage())
 533         {
 534           AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 535           AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 536           AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 537           QApplication::restoreOverrideCursor();
 538         }
 539       else
 540         {
 541           QApplication::restoreOverrideCursor();
 542           QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 543         }
 544     }
 545   else
 546     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 547 }
 548 //------------------------------------------------------------------------------
 549
 550
 551 //------------------------------------------------------------------------------
 552 vvMainWindow::~vvMainWindow() {
 553   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
 554     {
 555       if (mSlicerManagers[i] != NULL)
 556         delete mSlicerManagers[i];
 557     }
 558 }
 559 //------------------------------------------------------------------------------
 560
 561
 562 //------------------------------------------------------------------------------
 563 void vvMainWindow::MergeImages() {
 564   QString Extensions = EXTENSIONS;
 565   Extensions += ";;All Files (*)";
 566   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 567   if (files.isEmpty())
 568     return;
 569   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 570   std::vector<std::string> vector;
 571
 572   unsigned int currentDim = 0;
 573   std::vector<double> currentSpacing;
 574   std::vector<int> currentSize;
 575   std::vector<double> currentOrigin;
 576
 577   for (int i = 0; i < files.size(); i++)
 578     {
 579       itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 580               files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 581       reader->SetFileName(files[i].toStdString().c_str());
 582       reader->ReadImageInformation();
 583       if (reader)        {
 584           //NOViewWidget->hide();
 585           //NEViewWidget->hide();
 586           //SOViewWidget->hide();
 587           //SEViewWidget->hide();
 588           if (i == 0)
 589               currentDim = reader->GetNumberOfDimensions();
 590           bool IsOk = true;
 591           for (unsigned int j = 0;j < currentDim; j++)
 592           {
 593               if (i == 0)
 594               {
 595                   if (j == 0)
 596                   {
 597                       currentSpacing.resize(currentDim);
 598                       currentSize.resize(currentDim);
 599                       currentOrigin.resize(currentDim);
 600                   }
 601                   currentOrigin[j] = reader->GetOrigin(j);
 602                   currentSpacing[j] = reader->GetSpacing(j);
 603                   currentSize[j] = reader->GetDimensions(j);
 604               }
 605               else if (currentDim != reader->GetNumberOfDimensions()
 606                       || currentSpacing[j] != reader->GetSpacing(j)
 607                       || currentSize[j] != (int)reader->GetDimensions(j)
 608                       || currentOrigin[j] != reader->GetOrigin(j))
 609               {
 610                   QString error = "Cannot read file (too different from others ";
 611                   error += files[i].toStdString().c_str();
 612                   QMessageBox::information(this,tr("Reading problem"),error);
 613                   IsOk = false;
 614                   break;
 615               }
 616           }
 617           if (IsOk)
 618               vector.push_back(files[i].toStdString());
 619       }
 620     }
 621   if (vector.size() > 0)
 622     LoadImages(vector, MERGED);
 623 }
 624 //------------------------------------------------------------------------------
 625
 626
 627 //------------------------------------------------------------------------------
 628 void vvMainWindow::MergeImagesWithTime() {
 629   QString Extensions = EXTENSIONS;
 630   Extensions += ";;All Files (*)";
 631   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 632   if (files.isEmpty())
 633     return;
 634   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 635   std::vector<std::string> vector;
 636
 637   unsigned int currentDim = 0;
 638   std::vector<double> currentSpacing;
 639   std::vector<int> currentSize;
 640   std::vector<double> currentOrigin;
 641
 642   for (int i = 0; i < files.size(); i++)
 643     {
 644       itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 645                                                                             files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 646       if (reader)
 647         {
 648           reader->SetFileName(files[i].toStdString().c_str());
 649           reader->ReadImageInformation();
 650           if (i == 0)
 651             currentDim = reader->GetNumberOfDimensions();
 652           bool IsOk = true;
 653           for (unsigned int j = 0;j < currentDim; j++)
 654             {
 655               if (i == 0)
 656                 {
 657                   if (j == 0)
 658                     {
 659                       currentSpacing.resize(currentDim);
 660                       currentSize.resize(currentDim);
 661                       currentOrigin.resize(currentDim);
 662                     }
 663                   currentOrigin[j] = reader->GetOrigin(j);
 664                   currentSpacing[j] = reader->GetSpacing(j);
 665                   currentSize[j] = reader->GetDimensions(j);
 666                 }
 667               else if (currentDim != reader->GetNumberOfDimensions()
 668                        || currentSpacing[j] != reader->GetSpacing(j)
 669                        || currentSize[j] != (int)reader->GetDimensions(j)
 670                        || currentOrigin[j] != reader->GetOrigin(j))
 671                 {
 672                   QString error = "Cannot read file (too different from others ";
 673                   error += files[i].toStdString().c_str();
 674                   QMessageBox::information(this,tr("Reading problem"),error);
 675                   IsOk = false;
 676                   break;
 677                 }
 678             }
 679           if (IsOk)
 680             vector.push_back(files[i].toStdString());
 681         }
 682       else
 683         {
 684           QString error = "Cannot read file info for ";
 685           error += files[i].toStdString().c_str();
 686           error += "\n";
 687           error += "Maybe you're trying to open an image in an unsupported format?\n";
 688           QMessageBox::information(this,tr("Reading problem"),error);
 689         }
 690     }
 691   sort(vector.begin(),vector.end());
 692   if (vector.size() > 1)
 693     LoadImages(vector, MERGEDWITHTIME);
 694   else
 695     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.");
 696 }
 697 //------------------------------------------------------------------------------
 698
 699
 700 //------------------------------------------------------------------------------
 701 void vvMainWindow::OpenDicom() {
 702   std::vector<std::string> files;
 703
 704 #ifdef CLITK_VV_USE_BDCM
 705   bool r = bdcm::OpenDicomFilesSelectorDialog(files,
 706                                               "DicomFilesSelectorDialog test",
 707                                               0,0,800,800,1);
 708
 709   if (r) {
 710     std::cout << "$$$$ main : user clicked 'OK' $$$$"<<std::endl;
 711     std::cout << "$$$$ selected files : "<<std::endl;
 712     std::vector<std::string>::iterator i;
 713     for (i=files.begin();i!=files.end();++i) {
 714       std::cout << *i << std::endl;
 715     }
 716     std::cout << "$$$$ "<<std::endl;
 717
 718     LoadImages(files,DICOM);
 719   }
 720   else {
 721     std::cout << "$$$$ main : user clicked 'CANCEL' $$$$"<<std::endl;
 722   }
 723 #else
 724   std::cout << "dicomSeriesSelector " << std::endl;
 725   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 726     files = *(dicomSeriesSelector->GetFilenames());
 727     LoadImages(files,DICOM);
 728   }
 729 #endif
 730
 731 }
 732 //------------------------------------------------------------------------------
 733
 734 //------------------------------------------------------------------------------
 735 void vvMainWindow::OpenImages() {
 736   QString Extensions = EXTENSIONS;
 737   Extensions += ";;All Files (*)";
 738
 739   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 740   if (files.isEmpty())
 741     return;
 742   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 743   std::vector<std::string> vector;
 744   for (int i = 0; i < files.size(); i++)
 745     vector.push_back(files[i].toStdString());
 746   LoadImages(vector, IMAGE);
 747 }
 748 //------------------------------------------------------------------------------
 749 void vvMainWindow::OpenRecentImage()
 750 {
 751   QAction * caller = qobject_cast<QAction*>(sender());
 752   std::vector<std::string> images;
 753   images.push_back(caller->text().toStdString());
 754   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 755   LoadImages(images,IMAGE);
 756 }
 757 //------------------------------------------------------------------------------
 758
 759
 760 //------------------------------------------------------------------------------
 761 void vvMainWindow::OpenImageWithTime() {
 762   QString Extensions = EXTENSIONS;
 763   Extensions += ";;All Files (*)";
 764
 765   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 766   if (files.isEmpty())
 767     return;
 768   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 769   std::vector<std::string> vector;
 770   for (int i = 0; i < files.size(); i++)
 771     {
 772       vector.push_back(files[i].toStdString());
 773     }
 774   LoadImages(vector, IMAGEWITHTIME);
 775 }
 776 //------------------------------------------------------------------------------
 777
 778
 779 //------------------------------------------------------------------------------
 780 void vvMainWindow::LoadImages(std::vector<std::string> files, LoadedImageType filetype) {
 781   //Separate the way to open images and dicoms
 782   int fileSize;
 783   if (filetype == IMAGE || filetype == IMAGEWITHTIME)
 784     fileSize = files.size();
 785   else
 786     fileSize = 1;
 787
 788   //Only add to the list of recently opened files when a single file is opened,
 789   //to avoid polluting the list of recently opened files
 790   if (files.size() == 1)
 791     {
 792       QFileInfo finfo=tr(files[0].c_str());
 793       AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 794     }
 795   //init the progress events
 796   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 797   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 798   qApp->processEvents();
 799
 800   int numberofsuccesulreads=0;
 801   //open images as 1 or multiples
 802   for (int i = 0; i < fileSize; i++) {
 803
 804     progress.Update("Opening " + files[i]);
 805     progress.SetProgress(i,fileSize);
 806     qApp->processEvents();
 807
 808     //read the image and put it in mSlicerManagers
 809     vvSlicerManager* imageManager = new vvSlicerManager(4);
 810     qApp->processEvents();
 811
 812     bool SetImageSucceed=false;
 813
 814     // Change filename if an image with the same already exist
 815     //    DD(files[i]);
 816     int number=0;
 817     for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
 818       vvSlicerManager * v = mSlicerManagers[l];
 819       //      DD(v->GetBaseFileName());
 820       // DD(v->GetFileName());
 821       if (v->GetBaseFileName() ==
 822           vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(files[i]))) {
 823         number = std::max(number, v->GetBaseFileNameNumber()+1);
 824       }
 825     }
 826
 827
 828     if (filetype == IMAGE || filetype == IMAGEWITHTIME)
 829       SetImageSucceed = imageManager->SetImage(files[i],filetype, number);
 830     else
 831       {
 832         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 833       }
 834     if (SetImageSucceed == false)
 835       {
 836         QApplication::restoreOverrideCursor();
 837         QString error = "Cannot open file \n";
 838         error += imageManager->GetLastError().c_str();
 839         QMessageBox::information(this,tr("Reading problem"),error);
 840         delete imageManager;
 841       }
 842     else
 843       {
 844         mSlicerManagers.push_back(imageManager);
 845
 846         //create an item in the tree with good settings
 847         QTreeWidgetItem *item = new QTreeWidgetItem();
 848         item->setData(0,Qt::UserRole,files[i].c_str());
 849         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 850         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 851         qApp->processEvents();
 852
 853         //Create the buttons for reload and close
 854         qApp->processEvents();
 855         QTreePushButton* cButton = new QTreePushButton;
 856         cButton->setItem(item);
 857         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 858         cButton->setToolTip(tr("close image"));
 859         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 860         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 861                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 862
 863         QTreePushButton* rButton = new QTreePushButton;
 864         rButton->setItem(item);
 865         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 866         rButton->setToolTip(tr("reload image"));
 867         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 868         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 869                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 870
 871         DataTree->addTopLevelItem(item);
 872         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 873         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 874
 875         //set the id of the image
 876         QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 877         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 878         mSlicerManagers.back()->SetId(id.toStdString());
 879
 880         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 881
 882         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 883                 this,SLOT(CurrentImageChanged(std::string)));
 884         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 885              this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 886         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 887                 this, SLOT(VectorChanged(int,double,double,double, double)));
 888         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 889                 this, SLOT(OverlayChanged(int,double,double)));
 890         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 891                 this, SLOT(FusionChanged(int,double)));
 892         connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
 893                 this,SLOT(WindowsChanged(int, int, int)));
 894         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
 895                 this,SLOT(WindowLevelChanged(double, double, int, int)));
 896         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 897                 this,SLOT(UpdateSlice(int,int)));
 898         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 899                 this,SLOT(UpdateTSlice(int, int)));
 900         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 901                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 902         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 903                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 904         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 905                 this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 906         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 907         InitSlicers();
 908         numberofsuccesulreads++;
 909       }
 910   }
 911   if (numberofsuccesulreads)
 912     {
 913       NOViewWidget->show();
 914       NEViewWidget->show();
 915       SOViewWidget->show();
 916       SEViewWidget->show();
 917       UpdateTree();
 918       InitDisplay();
 919       ShowLastImage();
 920     }
 921   QApplication::restoreOverrideCursor();
 922
 923   // Try to guess default WindowLevel
 924   double range[2];
 925   mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 926   // DD(range[0]);
 927   //   DD(range[1]);
 928   if ((range[0] == 0) && (range[1] == 1)) {
 929     presetComboBox->setCurrentIndex(5);// binary
 930   }
 931   else {
 932     // TODO
 933   }
 934 }
 935 //------------------------------------------------------------------------------
 936
 937 //------------------------------------------------------------------------------
 938 void vvMainWindow::UpdateTree() {
 939   DataTree->resizeColumnToContents(COLUMN_TREE);
 940   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 941   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 942   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 943   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 944   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 945   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 946   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 947 }
 948 //------------------------------------------------------------------------------
 949
 950 //------------------------------------------------------------------------------
 951 void vvMainWindow::CurrentImageChanged(std::string id) {
 952   int selected = 0;
 953   for (int i = 0; i < DataTree->topLevelItemCount(); i++)
 954     {
 955       if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id)
 956         {
 957           selected = i;
 958         }
 959       else
 960         {
 961           DataTree->topLevelItem(i)->setSelected(0);
 962         }
 963       for (int child = 0; child < DataTree->topLevelItem(i)->childCount();child++)
 964         DataTree->topLevelItem(i)->child(child)->setSelected(0);
 965
 966     }
 967   DataTree->topLevelItem(selected)->setSelected(1);
 968 }
 969 //------------------------------------------------------------------------------
 970
 971 //------------------------------------------------------------------------------
 972 void vvMainWindow::ImageInfoChanged() {
 973   contextActions[7]->setEnabled(1);
 974   contextActions[6]->setEnabled(1);
 975   actionSave_As->setEnabled(1);
 976   actionAdd_VF_to_current_Image->setEnabled(1);
 977   actionAdd_fusion_image->setEnabled(1);
 978   actionNorth_East_Window->setEnabled(1);
 979   actionNorth_West_Window->setEnabled(1);
 980   actionSouth_East_Window->setEnabled(1);
 981   actionSouth_West_Window->setEnabled(1);
 982   inverseButton->setEnabled(1);
 983
 984   goToCursorPushButton->setEnabled(1);
 985
 986   if (DataTree->selectedItems().size()) {
 987     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 988
 989     colorMapComboBox->setEnabled(1);
 990     for (int i = 0; i < DataTree->topLevelItem(index)->childCount();i++)
 991       {
 992         if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
 993             DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion")
 994           {
 995             colorMapComboBox->setEnabled(0);
 996             break;
 997           }
 998       }
 999
1000     std::vector<double> origin;
1001     std::vector<double> inputSpacing;
1002     std::vector<int> inputSize;
1003     std::vector<double> sizeMM;
1004     int dimension=0;
1005     QString pixelType;
1006     QString inputSizeInBytes;
1007     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1008
1009     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1)
1010       {
1011         playButton->setEnabled(1);
1012         frameRateLabel->setEnabled(1);
1013         frameRateSpinBox->setEnabled(1);
1014       }
1015     else
1016       {
1017         playButton->setEnabled(0);
1018         frameRateLabel->setEnabled(0);
1019         frameRateSpinBox->setEnabled(0);
1020       }
1021
1022     //read image header
1023     int NPixel = 1;
1024
1025     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0])
1026       {
1027         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1028         dimension = imageSelected->GetNumberOfDimensions();
1029         origin.resize(dimension);
1030         inputSpacing.resize(dimension);
1031         inputSize.resize(dimension);
1032         sizeMM.resize(dimension);
1033         pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
1034         for (int i = 0;i < dimension;i++)
1035           {
1036             origin[i] = imageSelected->GetOrigin()[i];
1037             inputSpacing[i] = imageSelected->GetSpacing()[i];
1038             inputSize[i] = imageSelected->GetSize()[i];
1039             sizeMM[i] = inputSize[i]*inputSpacing[i];
1040             NPixel *= inputSize[i];
1041           }
1042         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1043       }
1044     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector")
1045       {
1046         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1047         dimension = imageSelected->GetNumberOfDimensions();
1048         origin.resize(dimension);
1049         inputSpacing.resize(dimension);
1050         inputSize.resize(dimension);
1051         sizeMM.resize(dimension);
1052         pixelType = mSlicerManagers[index]->GetVF()->GetScalarTypeAsString().c_str();
1053         for (int i = 0;i < dimension;i++)
1054           {
1055             origin[i] = imageSelected->GetOrigin()[i];
1056             inputSpacing[i] = imageSelected->GetSpacing()[i];
1057             inputSize[i] = imageSelected->GetSize()[i];
1058             sizeMM[i] = inputSize[i]*inputSpacing[i];
1059             NPixel *= inputSize[i];
1060           }
1061         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1062       }
1063     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay")
1064       {
1065         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1066         dimension = imageSelected->GetNumberOfDimensions();
1067         origin.resize(dimension);
1068         inputSpacing.resize(dimension);
1069         inputSize.resize(dimension);
1070         sizeMM.resize(dimension);
1071         pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
1072         for (int i = 0;i < dimension;i++)
1073           {
1074             origin[i] = imageSelected->GetOrigin()[i];
1075             inputSpacing[i] = imageSelected->GetSpacing()[i];
1076             inputSize[i] = imageSelected->GetSize()[i];
1077             sizeMM[i] = inputSize[i]*inputSpacing[i];
1078             NPixel *= inputSize[i];
1079           }
1080         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1081       }
1082     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion")
1083       {
1084         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1085         dimension = imageSelected->GetNumberOfDimensions();
1086         origin.resize(dimension);
1087         inputSpacing.resize(dimension);
1088         inputSize.resize(dimension);
1089         sizeMM.resize(dimension);
1090         pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
1091         for (int i = 0;i < dimension;i++)
1092           {
1093             origin[i] = imageSelected->GetOrigin()[i];
1094             inputSpacing[i] = imageSelected->GetSpacing()[i];
1095             inputSize[i] = imageSelected->GetSize()[i];
1096             sizeMM[i] = inputSize[i]*inputSpacing[i];
1097             NPixel *= inputSize[i];
1098           }
1099         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1100       }
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
1113     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1114                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1115     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1116     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1117
1118     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1119     for (int i = 0; i < 4;i++)
1120       {
1121         if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3)
1122           {
1123             mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1124             break;
1125           }
1126       }
1127     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1128     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1129     // DD(mSlicerManagers[index]->GetColorMap());
1130     // DD(mSlicerManagers[index]->GetPreset());
1131     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1132     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1133
1134     infoPanel->setFileName(image);
1135     infoPanel->setDimension(dim);
1136     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1137     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1138     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1139     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1140     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1141
1142     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1143                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1144     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1145     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1146
1147     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1148     for (int i = 0; i < 4;i++)
1149       {
1150         if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3)
1151           {
1152             mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1153             break;
1154           }
1155       }
1156     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1157     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1158     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1159     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1160
1161     if (mSlicerManagers[index]->GetSlicer(0)->GetVF())
1162       {
1163         overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1164         overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1165                                     mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1166                                     mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1167       }
1168     else
1169       {
1170         overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1171         overlayPanel->getVFProperty(-1,-1,-1);
1172       }
1173     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1174       {
1175         overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1176         overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1177       }
1178     else
1179       {
1180         overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1181         overlayPanel->getOverlayProperty(-1);
1182       }
1183     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion())
1184       {
1185         overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1186         overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1187                                         mSlicerManagers[index]->GetFusionColorMap(),
1188                                         mSlicerManagers[index]->GetFusionWindow(),
1189                                         mSlicerManagers[index]->GetFusionLevel());
1190       }
1191     else
1192       {
1193         overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1194         overlayPanel->getFusionProperty(-1, -1,-1,-1);
1195       }
1196   }
1197 }
1198 //------------------------------------------------------------------------------
1199
1200 //------------------------------------------------------------------------------
1201 void vvMainWindow::ShowDocumentation() {
1202   documentation->show();
1203 }
1204 //------------------------------------------------------------------------------
1205 void vvMainWindow::ShowHelpDialog() {
1206   help_dialog->show();
1207 }
1208 //------------------------------------------------------------------------------
1209
1210 //------------------------------------------------------------------------------
1211 void vvMainWindow::ChangeViewMode() {
1212   QListIterator<int> it0(splitter_3->sizes());
1213   QListIterator<int> it1(splitter_3->sizes());
1214   int max0 = 0;
1215   int max1 = 1;
1216   while (it0.hasNext())
1217     {
1218       max0 += it0.next();
1219     }
1220   while (it1.hasNext())
1221     {
1222       max1 += it1.next();
1223     }
1224   QList<int> size0;
1225   QList<int> size1;
1226   if (viewMode == 1)
1227     {
1228       viewMode = 0;
1229       size0.push_back(max0);
1230       size0.push_back(0);
1231       size1.push_back(max1);
1232       size1.push_back(0);
1233       splitter_3->setSizes(size0);
1234       OSplitter->setSizes(size1);
1235       DataTree->setColumnHidden(2,1);
1236       DataTree->setColumnHidden(3,1);
1237       DataTree->setColumnHidden(4,1);
1238     }
1239   else
1240     {
1241       viewMode = 1;
1242       size0.push_back(int(max0/2));
1243       size0.push_back(int(max0/2));
1244       size1.push_back(int(max1/2));
1245       size1.push_back(int(max1/2));
1246       splitter_3->setSizes(size0);
1247       OSplitter->setSizes(size1);
1248       DataTree->setColumnHidden(2,0);
1249       DataTree->setColumnHidden(3,0);
1250       DataTree->setColumnHidden(4,0);
1251     }
1252 }
1253 //------------------------------------------------------------------------------
1254
1255 //------------------------------------------------------------------------------
1256 QString vvMainWindow::GetSizeInBytes(unsigned long size) {
1257   QString result = "";// QString::number(size);
1258   //result += " bytes (";
1259   if (size > 1000000000)
1260     {
1261       size /= 1000000000;
1262       result += QString::number(size);
1263       result += "Gb";//)";
1264     }
1265   else if (size > 1000000)
1266     {
1267       size /= 1000000;
1268       result += QString::number(size);
1269       result += "Mb";//)";
1270     }
1271   else if (size > 1000)
1272     {
1273       size /= 1000;
1274       result += QString::number(size);
1275       result += "kb";//)";
1276     }
1277   return result;
1278 }
1279 //------------------------------------------------------------------------------
1280
1281 //------------------------------------------------------------------------------
1282 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble) {
1283   QString result;
1284   for (unsigned int i= 0; i < vectorDouble.size(); i++)
1285     {
1286       if (i != 0)
1287         result += " ";
1288       result += QString::number(vectorDouble[i]);
1289     }
1290   return result;
1291 }
1292 //------------------------------------------------------------------------------
1293
1294 //------------------------------------------------------------------------------
1295 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt) {
1296   QString result;
1297   for (unsigned int i= 0; i < vectorInt.size(); i++)
1298     {
1299       if (i != 0)
1300         result += " ";
1301       result += QString::number(vectorInt[i]);
1302     }
1303   return result;
1304 }
1305 //------------------------------------------------------------------------------
1306
1307 //------------------------------------------------------------------------------
1308 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item) {
1309   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1310   for (int i = 0; i < DataTree->topLevelItemCount(); i++)
1311     {
1312       if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1313         return i;
1314     }
1315   return -1;
1316 }
1317 //------------------------------------------------------------------------------
1318
1319 //------------------------------------------------------------------------------
1320 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm) {
1321     QString id = sm->GetId().c_str();
1322     for (int i = 0; i < DataTree->topLevelItemCount(); i++)
1323     {
1324         if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1325             return DataTree->topLevelItem(i);
1326     }
1327     return NULL;
1328 }
1329 //------------------------------------------------------------------------------
1330
1331 //------------------------------------------------------------------------------
1332 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clicked_item, int column) {
1333   int index = GetSlicerIndexFromItem(clicked_item);
1334   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1335     return;
1336   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
1337     {
1338      //Trick to avoid redoing twice the job for a key (sr)
1339       mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()-> GetInteractor()->SetKeySym("Crap");
1340
1341       QTreeWidgetItem* current_row=DataTree->topLevelItem(i);
1342       if (DataTree->topLevelItem(index) == current_row)
1343         {
1344           vvSlicer* clicked_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1345           if (current_row == clicked_item)
1346             {
1347               //If we just activated a slicer
1348               if (current_row->data(column,Qt::CheckStateRole).toInt() > 0)
1349                 {
1350                   mSlicerManagers[i]->UpdateSlicer(column-1,clicked_item->data(column,Qt::CheckStateRole).toInt());
1351                   mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1352                   DisplaySliders(i,column-1);
1353                   std::map<std::string,int> overlay_counts;
1354                   for (int child = 0; child < current_row->childCount(); child++)
1355                     {
1356                       std::string overlay_type =
1357                         current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1358                       overlay_counts[overlay_type]++;
1359                       current_row->child(child)->setData(column,Qt::CheckStateRole,
1360                                                          current_row->data(column,Qt::CheckStateRole));
1361                       clicked_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,true);
1362                     }
1363                 }
1364               else //We don't allow simply desactivating a slicer
1365                 {
1366                   clicked_item->setData(column,Qt::CheckStateRole,2);
1367                   return;
1368                 }
1369             }
1370           //if we clicked on the vector(or overlay) and not the image
1371           else
1372             {
1373               if (clicked_item->data(column,Qt::CheckStateRole).toInt())
1374                 {
1375                   current_row->setData(column,Qt::CheckStateRole,2);
1376                   mSlicerManagers[i]->UpdateSlicer(column-1,2);
1377                   mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1378                   DisplaySliders(i,column-1);
1379                 }
1380               int vis = clicked_item->data(column,Qt::CheckStateRole).toInt();
1381               std::string overlay_type = clicked_item->data(1,Qt::UserRole).toString().toStdString();
1382               int overlay_index=0;
1383               for (int child = 0; child < current_row->childCount(); child++)
1384                 {
1385                   if (current_row->child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1386                     overlay_index++;
1387                   if (current_row->child(child) == clicked_item) break;
1388                 }
1389               clicked_slicer->SetActorVisibility(
1390                                                  clicked_item->data(1,Qt::UserRole).toString().toStdString(), overlay_index-1,vis);
1391             }
1392         }
1393       else if (current_row->data(column,Qt::CheckStateRole).toInt() > 0)
1394         {
1395           current_row->setData(column,Qt::CheckStateRole,0);
1396           mSlicerManagers[i]->UpdateSlicer(column-1,0);
1397           std::map<std::string,int> overlay_counts;
1398           for (int child = 0; child < current_row->childCount(); child++)
1399             {
1400               std::string overlay_type =
1401                 current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1402               overlay_counts[overlay_type]++;
1403               current_row->child(child)->setData(column,Qt::CheckStateRole,0);
1404               vvSlicer * current_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1405               current_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,false);
1406             }
1407         }
1408       //mSlicerManagers[i]->SetColorMap(-1);
1409       mSlicerManagers[i]->SetColorMap();
1410     }
1411   mSlicerManagers[index]->GetSlicer(column-1)->Render();
1412 }
1413 //------------------------------------------------------------------------------
1414
1415 void vvMainWindow::InitSlicers()
1416 {
1417   if (mSlicerManagers.size())
1418     {
1419       mSlicerManagers.back()->GenerateDefaultLookupTable();
1420
1421       mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1422       mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1423       mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1424       mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1425     }
1426 }
1427
1428 //------------------------------------------------------------------------------
1429 void vvMainWindow::InitDisplay() {
1430   if (mSlicerManagers.size())
1431     {
1432       //BE CAREFUL : this is absolutely necessary to set the interactor style
1433       //in order to have the same style instanciation for all SlicerManagers in
1434       // a same window
1435       for (int j = 0; j < 4; j++)
1436         {
1437           vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1438           style->SetAutoAdjustCameraClippingRange(1);
1439           bool AlreadySelected = false;
1440           for (int i = 0; i < DataTree->topLevelItemCount(); i++)
1441             {
1442               mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1443
1444               //select the image only if previous are not selected
1445               if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1)
1446                 {
1447                   mSlicerManagers[i]->UpdateSlicer(j,1);
1448                   AlreadySelected = true;
1449                 }
1450               else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected)
1451                 {
1452                   if (DataTree->selectedItems().size() == 0)
1453                     DataTree->topLevelItem(i)->setSelected(1);
1454                   DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1455                   mSlicerManagers[i]->UpdateSlicer(j,1);
1456                   DisplaySliders(i,j);
1457                 }
1458               else
1459                 {
1460                   DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1461                   mSlicerManagers[i]->UpdateSlicer(j,0);
1462                 }
1463             }
1464           style->Delete();
1465         }
1466     }
1467 }
1468 //------------------------------------------------------------------------------
1469
1470 //------------------------------------------------------------------------------
1471 void vvMainWindow::DisplaySliders(int slicer, int window) {
1472   int range[2];
1473   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1474   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1475
1476   int tRange[2];
1477   tRange[0] = 0;
1478   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1479   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1480   bool showHorizontal = false;
1481   bool showVertical = false;
1482   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1483       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1484           && mSlicerManagers[slicer]->GetType() != IMAGEWITHTIME
1485           && mSlicerManagers[slicer]->GetType() != MERGEDWITHTIME))
1486     showVertical = true;
1487   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1488       || mSlicerManagers[slicer]->GetType() == IMAGEWITHTIME
1489       || mSlicerManagers[slicer]->GetType() == MERGEDWITHTIME)
1490     showHorizontal = true;
1491
1492   if (showVertical)
1493     verticalSliders[window]->show();
1494   else
1495     verticalSliders[window]->hide();
1496   verticalSliders[window]->setRange(range[0],range[1]);
1497   verticalSliders[window]->setValue(position);
1498
1499   if (showHorizontal)
1500     horizontalSliders[window]->show();
1501   else
1502     horizontalSliders[window]->hide();
1503   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1504   horizontalSliders[window]->setValue(tPosition);
1505 }
1506 //------------------------------------------------------------------------------
1507
1508 //------------------------------------------------------------------------------
1509 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column) {
1510   int index = GetSlicerIndexFromItem(item);
1511
1512   if (DataTree->topLevelItem(index) != item)
1513     {
1514       QString warning = "Do you really want to close the overlay : ";
1515       warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1516       QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1517                          warning, 0, this);
1518       msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1519       msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1520       if (msgBox.exec() == QMessageBox::AcceptRole)
1521         {
1522           std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1523           int overlay_index=0;
1524           for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1525             {
1526               if (DataTree->topLevelItem(index)->\
1527                   child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1528                 overlay_index++;
1529               if (DataTree->topLevelItem(index)->child(child) == item) break;
1530             }
1531           mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1532           mSlicerManagers[index]->SetColorMap(0);
1533           DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1534           mSlicerManagers[index]->Render();
1535         }
1536     }
1537   else if (DataTree->topLevelItemCount() <= 1)
1538     {
1539       QString warning = "Do you really want to close the image : ";
1540       warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1541       warning += "\nThis is the last image, you're about to close vv !!!";
1542       QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1543                          warning, 0, this);
1544       msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1545       msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1546       if (msgBox.exec() == QMessageBox::AcceptRole)
1547         {
1548           this->close();
1549         }
1550     }
1551   else
1552     {
1553       QString warning = "Do you really want to close the image : ";
1554       warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1555       QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1556                          warning, 0, this);
1557       msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1558       msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1559       if (msgBox.exec() == QMessageBox::AcceptRole)
1560         {
1561
1562           // Tell tools that we close an image
1563           emit AnImageIsBeingClosed(mSlicerManagers[index]);
1564
1565           std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1566           DataTree->takeTopLevelItem(index);
1567           for (int i = 0; i < index; i++)
1568             {
1569               Manageriter++;
1570             }
1571           linkPanel->removeImage(index);
1572           mSlicerManagers[index]->RemoveActors();
1573           delete mSlicerManagers[index];
1574           mSlicerManagers.erase(Manageriter);
1575
1576           //
1577           InitDisplay();
1578         }
1579     }
1580 }
1581 //------------------------------------------------------------------------------
1582
1583 //------------------------------------------------------------------------------
1584 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column) {
1585   // int index = GetSlicerIndexFromItem(item);
1586   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1587   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1588   //     mSlicerManagers[index]->ReloadVF();
1589   //   else
1590   //     mSlicerManagers[index]->Reload();
1591
1592   //   QApplication::restoreOverrideCursor();
1593   int index = GetSlicerIndexFromItem(item);
1594   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1595   QString role=item->data(1,Qt::UserRole).toString();
1596   if ( role == "vector")
1597     mSlicerManagers[index]->ReloadVF();
1598   else if (role == "overlay")
1599     mSlicerManagers[index]->ReloadOverlay();
1600   else if (role == "fusion")
1601     mSlicerManagers[index]->ReloadFusion();
1602   else
1603     mSlicerManagers[index]->Reload();
1604   QApplication::restoreOverrideCursor();
1605 }
1606 //------------------------------------------------------------------------------
1607
1608 // void vvMainWindow::CropImage()
1609 // {
1610 //   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1611 //   vvCropDialog crop(mSlicerManagers,index);
1612 //   if(crop.exec())
1613 //     AddImage(crop.GetOutput(),"cropped.mhd");
1614 // }
1615
1616 //------------------------------------------------------------------------------
1617 void vvMainWindow::SplitImage() {
1618   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1619   int dim = mSlicerManagers[index]->GetDimension();
1620   QString warning = "Do you really want to split the ";
1621   warning += QString::number(dim) + "D image ";
1622   warning += DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString() + " into ";
1623   warning += QString::number(mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetSize()[dim-1]) + " ";
1624   warning += QString::number(dim-1) + "D images.";
1625   QMessageBox msgBox(QMessageBox::Warning, tr("Split Image"),
1626                      warning, 0, this);
1627   msgBox.addButton(tr("Split"), QMessageBox::AcceptRole);
1628   msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1629   if (msgBox.exec() == QMessageBox::AcceptRole)
1630     {
1631       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1632       if (dim > 2)
1633         {
1634           std::string filename = DataTree->selectedItems()[0]->data(0,Qt::UserRole).toString().toStdString();
1635           int numberOfSlice = mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetSize()[dim-1];
1636           std::string path = itksys::SystemTools::GetFilenamePath(
1637                                                                   filename);
1638           path += "/";
1639           path += DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString().toStdString();
1640           path += "%03d";
1641           path += itksys::SystemTools::GetFilenameLastExtension(
1642                                                                 filename).c_str();
1643
1644           typedef itk::NumericSeriesFileNames NameGeneratorType;
1645           NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
1646           nameGenerator->SetSeriesFormat(path.c_str());
1647           nameGenerator->SetStartIndex(0);
1648           nameGenerator->SetEndIndex(numberOfSlice-1);
1649           nameGenerator->SetIncrementIndex(1);
1650
1651           for (int i = 0; i < numberOfSlice; i++)
1652             {
1653               vvSlicerManager* imageManager = new vvSlicerManager(4);
1654               imageManager->SetExtractedImage(nameGenerator->GetFileNames()[i],
1655                                               mSlicerManagers[index]->GetSlicer(0)->GetImage(), i);
1656               mSlicerManagers.push_back(imageManager);
1657
1658               //create an item in the tree with good settings
1659               QTreeWidgetItem *item = new QTreeWidgetItem();
1660               item->setData(0,Qt::UserRole,nameGenerator->GetFileNames()[i].c_str());
1661               std::string fileI = itksys::SystemTools::GetFilenameWithoutLastExtension(
1662                                                                                        nameGenerator->GetFileNames()[i]).c_str();
1663               item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileI.c_str());
1664               for (int j = 1; j <= 4; j++)
1665                 {
1666                   for (int i = 0; i < DataTree->topLevelItemCount(); i++)
1667                     {
1668                       DataTree->topLevelItem(i)->setData(j,Qt::CheckStateRole,0);
1669                     }
1670                   item->setData(j,Qt::CheckStateRole,2);
1671                 }
1672
1673               //Create the buttons for reload and close
1674               QTreePushButton* cButton = new QTreePushButton;
1675               cButton->setItem(item);
1676               cButton->setColumn(COLUMN_CLOSE_IMAGE);
1677               cButton->setToolTip(tr("close image"));
1678               cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1679               connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1680                       this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1681
1682               QTreePushButton* rButton = new QTreePushButton;
1683               rButton->setItem(item);
1684               rButton->setColumn(COLUMN_RELOAD_IMAGE);
1685               rButton->setToolTip(tr("reload image"));
1686               rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1687               rButton->setEnabled(false);
1688               connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1689                       this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1690
1691               DataTree->addTopLevelItem(item);
1692               DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1693               DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1694
1695               //set the id of the image
1696               QString id = nameGenerator->GetFileNames()[i].c_str() + QString::number(mSlicerManagers.size()-1);
1697               item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1698               mSlicerManagers.back()->SetId(id.toStdString());
1699               linkPanel->addImage(fileI, id.toStdString());
1700               connect(mSlicerManagers.back(),SIGNAL(currentImageChanged(std::string)),
1701                       this,SLOT(CurrentImageChanged(std::string)));
1702               connect(mSlicerManagers.back(),SIGNAL(
1703                                                     UpdatePosition(int, double, double, double, double, double, double, double)),this,
1704                       SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
1705               connect(mSlicerManagers.back(),SIGNAL(UpdateVector(int, double, double, double, double)),
1706                       this, SLOT(VectorChanged(int,double,double,double, double)));
1707               connect(mSlicerManagers.back(),SIGNAL(UpdateOverlay(int, double, double)),
1708                       this, SLOT(OverlayChanged(int,double,double)));
1709               connect(mSlicerManagers.back(),SIGNAL(UpdateFusion(int, double)),
1710                       this, SLOT(FusionChanged(int,double)));
1711               connect(mSlicerManagers.back(),SIGNAL(UpdateWindows(int, int, int)),
1712                       this,SLOT(WindowsChanged(int, int, int)));
1713               connect(mSlicerManagers.back(),SIGNAL(WindowLevelChanged(double, double,int, int)),
1714                       this,SLOT(WindowLevelChanged(double, double, int, int)));
1715               connect(mSlicerManagers.back(),SIGNAL(UpdateSlice(int,int)),
1716                       this,SLOT(UpdateSlice(int,int)));
1717               connect(mSlicerManagers.back(),SIGNAL(UpdateTSlice(int, int)),
1718                       this,SLOT(UpdateTSlice(int, int)));
1719               connect(mSlicerManagers.back(),SIGNAL(UpdateSliceRange(int,int,int,int,int)),
1720                       this,SLOT(UpdateSliceRange(int,int,int,int,int)));
1721               connect(mSlicerManagers.back(),SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
1722                       this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
1723               connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
1724               UpdateTree();
1725               qApp->processEvents();
1726               InitSlicers();
1727               InitDisplay();
1728               qApp->processEvents();
1729             }
1730           QApplication::restoreOverrideCursor();
1731         }
1732       else
1733         {
1734           QApplication::restoreOverrideCursor();
1735           QString error = "Cannot split file (dimensions must be greater than 2) ";
1736           QMessageBox::information(this,tr("Splitting problem"),error);
1737         }
1738     }
1739 }
1740 //------------------------------------------------------------------------------
1741
1742 //------------------------------------------------------------------------------
1743 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value) {
1744   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1745 }
1746 //------------------------------------------------------------------------------
1747
1748 //------------------------------------------------------------------------------
1749 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value) {
1750   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1751 }
1752 //------------------------------------------------------------------------------
1753
1754 //------------------------------------------------------------------------------
1755 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef) {
1756   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1757 }
1758 //------------------------------------------------------------------------------
1759
1760 //------------------------------------------------------------------------------
1761 void vvMainWindow::FusionChanged(int visibility, double value) {
1762   overlayPanel->getCurrentFusionInfo(visibility,value);
1763 }
1764 //------------------------------------------------------------------------------
1765
1766 //------------------------------------------------------------------------------
1767 void vvMainWindow::WindowsChanged(int window, int view, int slice) {
1768   infoPanel->setViews(window, view, slice);
1769 }
1770 //------------------------------------------------------------------------------
1771
1772 //------------------------------------------------------------------------------
1773 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap) {
1774   windowSpinBox->setValue(window);
1775   levelSpinBox->setValue(level);
1776   colorMapComboBox->setCurrentIndex(colormap);
1777   presetComboBox->setCurrentIndex(preset);
1778 }
1779 //------------------------------------------------------------------------------
1780
1781 //------------------------------------------------------------------------------
1782 void vvMainWindow::WindowLevelEdited() {
1783   presetComboBox->setCurrentIndex(6);
1784   UpdateWindowLevel();
1785 }
1786 //------------------------------------------------------------------------------
1787
1788 //------------------------------------------------------------------------------
1789 void vvMainWindow::UpdateWindowLevel() {
1790   if (DataTree->selectedItems().size())
1791     {
1792       if (presetComboBox->currentIndex() == 7) //For ventilation
1793         colorMapComboBox->setCurrentIndex(5);
1794       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1795       mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1796       mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1797       mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1798       mSlicerManagers[index]->Render();
1799     }
1800 }
1801 //------------------------------------------------------------------------------
1802
1803 //------------------------------------------------------------------------------
1804 void vvMainWindow::UpdateColorMap() {
1805   if (DataTree->selectedItems().size())
1806     {
1807       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1808       mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1809       mSlicerManagers[index]->Render();
1810     }
1811 }
1812 //------------------------------------------------------------------------------
1813 void vvMainWindow::SwitchWindowLevel() {
1814   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1815   int window = mSlicerManagers[index]->GetColorWindow();
1816   presetComboBox->setCurrentIndex(6);
1817   windowSpinBox->setValue(-window);
1818   UpdateWindowLevel();
1819 }
1820 //------------------------------------------------------------------------------
1821
1822 //------------------------------------------------------------------------------
1823 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps) {
1824   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
1825     {
1826       if (mSlicerManagers[i]->GetId() == id)
1827         {
1828           //mSlicerManagers[i]->SetTSlice(temps);
1829           mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1830           mSlicerManagers[i]->UpdateViews(0,slicer);
1831           break;
1832         }
1833     }
1834 }
1835 //------------------------------------------------------------------------------
1836
1837 //------------------------------------------------------------------------------
1838 void vvMainWindow::ShowContextMenu(QPoint point) {
1839   if (!DataTree->selectedItems().size())
1840     {
1841       contextActions[1]->setEnabled(0);
1842       contextActions[2]->setEnabled(0);
1843       contextActions[3]->setEnabled(0);
1844       contextActions[4]->setEnabled(0);
1845       contextActions[5]->setEnabled(0);
1846       contextActions[6]->setEnabled(0);
1847       contextActions[7]->setEnabled(0);
1848     }
1849   else
1850     {
1851       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1852       contextActions[1]->setEnabled(1);
1853       contextActions[2]->setEnabled(
1854                                     DataTree->itemWidget(DataTree->selectedItems()[0],
1855                                                          COLUMN_RELOAD_IMAGE)->isEnabled());
1856       contextActions[3]->setEnabled(1);
1857       contextActions[5]->setEnabled(1);
1858       contextActions[6]->setEnabled(1);
1859       contextActions[7]->setEnabled(1);
1860
1861       if (mSlicerManagers[index]->GetDimension() < 3)
1862         contextActions[4]->setEnabled(0);
1863       else
1864         contextActions[4]->setEnabled(1);
1865     }
1866   contextMenu.exec(QCursor::pos());
1867 }
1868 //------------------------------------------------------------------------------
1869
1870 //------------------------------------------------------------------------------
1871 void vvMainWindow::CloseImage() {
1872   CloseImage(DataTree->selectedItems()[0],0);
1873 }
1874 //------------------------------------------------------------------------------
1875
1876 //------------------------------------------------------------------------------
1877 void vvMainWindow::ReloadImage() {
1878   ReloadImage(DataTree->selectedItems()[0],0);
1879 }
1880 //------------------------------------------------------------------------------
1881
1882 //------------------------------------------------------------------------------
1883 void vvMainWindow::SelectOverlayImage() {
1884   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1885
1886   //check if one overlay image is added
1887   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1888     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay")
1889       {
1890         QString error = "Cannot add more than one compared image\n";
1891         error += "Please remove first ";
1892         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1893         QMessageBox::information(this,tr("Problem adding compared image !"),error);
1894         return;
1895       }
1896
1897   QString Extensions = EXTENSIONS;
1898   Extensions += ";;All Files (*)";
1899   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1900   if (!file.isEmpty())
1901     AddOverlayImage(index,file);
1902 }
1903 //------------------------------------------------------------------------------
1904
1905 //------------------------------------------------------------------------------
1906 void vvMainWindow::AddOverlayImage(int index, QString file) {
1907
1908   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1909   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1910                                                                         file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1911   reader->SetFileName(file.toStdString().c_str());
1912   reader->ReadImageInformation();
1913   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1914   int dimension = reader->GetNumberOfDimensions();
1915   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1916   vvProgressDialog progress("Opening " + file.toStdString());
1917   qApp->processEvents();
1918
1919   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1920   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component))
1921     {
1922       //create an item in the tree with good settings
1923       QTreeWidgetItem *item = new QTreeWidgetItem();
1924       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1925       item->setData(1,Qt::UserRole,tr("overlay"));
1926       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
1927       qApp->processEvents();
1928
1929       for (int j = 1; j <= 4; j++)
1930         {
1931           item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1932           mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("overlay",0,
1933                                                                     DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1934         }
1935
1936       //Create the buttons for reload and close
1937       qApp->processEvents();
1938       QTreePushButton* cButton = new QTreePushButton;
1939       cButton->setItem(item);
1940       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1941       cButton->setToolTip(tr("close image"));
1942       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1943       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1944               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1945
1946       QTreePushButton* rButton = new QTreePushButton;
1947       rButton->setItem(item);
1948       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1949       rButton->setToolTip(tr("reload image"));
1950       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1951       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1952               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1953
1954       DataTree->topLevelItem(index)->setExpanded(1);
1955       DataTree->topLevelItem(index)->addChild(item);
1956       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1957       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1958
1959       //set the id of the image
1960       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1961       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1962       UpdateTree();
1963       qApp->processEvents();
1964       ImageInfoChanged();
1965       QApplication::restoreOverrideCursor();
1966     }
1967   else
1968     {
1969       QApplication::restoreOverrideCursor();
1970       QString error = "Cannot import the new image.\n";
1971       error += mSlicerManagers[index]->GetLastError().c_str();
1972       QMessageBox::information(this,tr("Problem reading image !"),error);
1973     }
1974 }
1975
1976 void vvMainWindow::AddFusionImage()
1977 {
1978   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1979
1980   //check if one fusion image is added
1981   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1982     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion")
1983       {
1984         QString error = "Cannot add more than one fusion image\n";
1985         error += "Please remove first ";
1986         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1987         QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1988         return;
1989       }
1990
1991   QString Extensions = EXTENSIONS;
1992   Extensions += ";;All Files (*)";
1993   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1994   if (!file.isEmpty())
1995     {
1996       mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1997       itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1998                                                                             file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1999       reader->SetFileName(file.toStdString().c_str());
2000       reader->ReadImageInformation();
2001       std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2002       if (reader)
2003         {
2004           QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2005           vvProgressDialog progress("Opening fusion");
2006           qApp->processEvents();
2007
2008           std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2009           if (mSlicerManagers[index]->SetFusion(file.toStdString(),
2010                                                 reader->GetNumberOfDimensions(), component))
2011             {
2012               //create an item in the tree with good settings
2013               QTreeWidgetItem *item = new QTreeWidgetItem();
2014               item->setData(0,Qt::UserRole,file.toStdString().c_str());
2015               item->setData(1,Qt::UserRole,tr("fusion"));
2016               item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
2017               qApp->processEvents();
2018
2019               for (int j = 1; j <= 4; j++)
2020                 {
2021                   item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2022                   mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("fusion",0,
2023                                                                              DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
2024                 }
2025
2026               //Create the buttons for reload and close
2027               qApp->processEvents();
2028               QTreePushButton* cButton = new QTreePushButton;
2029               cButton->setItem(item);
2030               cButton->setColumn(COLUMN_CLOSE_IMAGE);
2031               cButton->setToolTip(tr("close image"));
2032               cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2033               connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2034                       this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2035
2036               QTreePushButton* rButton = new QTreePushButton;
2037               rButton->setItem(item);
2038               rButton->setColumn(COLUMN_RELOAD_IMAGE);
2039               rButton->setToolTip(tr("reload image"));
2040               rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2041               connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2042                       this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2043
2044               DataTree->topLevelItem(index)->setExpanded(1);
2045               DataTree->topLevelItem(index)->addChild(item);
2046               DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2047               DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2048
2049               //set the id of the image
2050               QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2051               item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2052               UpdateTree();
2053               qApp->processEvents();
2054               ImageInfoChanged();
2055               QApplication::restoreOverrideCursor();
2056             }
2057           else
2058             {
2059               QApplication::restoreOverrideCursor();
2060               QString error = "Cannot import the new image.\n";
2061               error += mSlicerManagers[index]->GetLastError().c_str();
2062               QMessageBox::information(this,tr("Problem reading image !"),error);
2063             }
2064         }
2065       else
2066         {
2067           QString error = "Cannot import the new image.\n";
2068           QMessageBox::information(this,tr("Problem reading image !"),error);
2069         }
2070     }
2071 }
2072 //------------------------------------------------------------------------------
2073
2074
2075 //------------------------------------------------------------------------------
2076 void vvMainWindow::OpenField()
2077 {
2078   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2079   //check if a vector field has already been added
2080   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2081     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector")
2082       {
2083         QString error = "Cannot add more than one vector field\n";
2084         error += "Please remove first ";
2085         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2086         QMessageBox::information(this,tr("Problem adding vector field!"),error);
2087         return;
2088       }
2089
2090   QString Extensions = "Images ( *.mhd)";
2091   Extensions += ";;Images ( *.vf)";
2092   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2093   if (!file.isEmpty())
2094     AddField(file,index);
2095 }
2096 //------------------------------------------------------------------------------
2097
2098
2099 //------------------------------------------------------------------------------
2100 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2101 {
2102   //create an item in the tree with good settings
2103   QTreeWidgetItem *item = new QTreeWidgetItem();
2104   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2105   item->setData(1,Qt::UserRole,tr("vector"));
2106   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename);
2107   qApp->processEvents();
2108
2109   for (int j = 1; j <= 4; j++)
2110     {
2111       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2112       mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("vector",0,
2113                                                                  DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
2114     }
2115
2116   //Create the buttons for reload and close
2117   qApp->processEvents();
2118   QTreePushButton* cButton = new QTreePushButton;
2119   cButton->setItem(item);
2120   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2121   cButton->setToolTip(tr("close vector field"));
2122   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2123   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2124           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2125
2126   QTreePushButton* rButton = new QTreePushButton;
2127   rButton->setItem(item);
2128   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2129   rButton->setToolTip(tr("reload vector field"));
2130   rButton->setEnabled(from_disk);
2131   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2132   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2133           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2134
2135   DataTree->topLevelItem(index)->setExpanded(1);
2136   DataTree->topLevelItem(index)->addChild(item);
2137   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2138   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2139
2140   //set the id of the image
2141   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2142   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2143   UpdateTree();
2144   qApp->processEvents();
2145   ImageInfoChanged();
2146   QApplication::restoreOverrideCursor();
2147 }
2148 //------------------------------------------------------------------------------
2149
2150
2151 //------------------------------------------------------------------------------
2152 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2153 {
2154   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2155   vvSlicerManager* imageManager = mSlicerManagers[index];
2156   if (imageManager->SetVF(vf,file.toStdString()))
2157     {
2158       AddFieldEntry(file,index,false);
2159     }
2160   else
2161     {
2162       QString error = "Cannot import the vector field for this image.\n";
2163       error += imageManager->GetLastError().c_str();
2164       QMessageBox::information(this,tr("Problem reading VF !"),error);
2165     }
2166   QApplication::restoreOverrideCursor();
2167 }
2168 //------------------------------------------------------------------------------
2169
2170
2171 //------------------------------------------------------------------------------
2172 void vvMainWindow::AddField(QString file,int index)
2173 {
2174   if (QFile::exists(file))
2175     {
2176       mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2177
2178       //init the progress events
2179       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2180       vvProgressDialog progress("Opening " + file.toStdString());
2181       qApp->processEvents();
2182
2183       //read the vector and put it in the current mSlicerManager
2184       vvSlicerManager* imageManager = mSlicerManagers[index];
2185       qApp->processEvents();
2186
2187       std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2188       if (imageManager->SetVF(file.toStdString()))
2189         {
2190           imageManager->Render();
2191           AddFieldEntry(file,index,true);
2192         }
2193       else
2194         {
2195           QApplication::restoreOverrideCursor();
2196           QString error = "Cannot import the vector field for this image.\n";
2197           error += imageManager->GetLastError().c_str();
2198           QMessageBox::information(this,tr("Problem reading VF !"),error);
2199         }
2200     }
2201   else
2202     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2203
2204 }
2205 //------------------------------------------------------------------------------
2206
2207
2208 //------------------------------------------------------------------------------
2209 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log) {
2210   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2211   if (mSlicerManagers[index]->GetSlicer(0)->GetVF())
2212     {
2213       for (int i = 0; i < 4; i++)
2214         {
2215           mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2216           mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2217           if (log > 0)
2218             mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2219           else
2220             mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2221         }
2222     }
2223 }
2224 //------------------------------------------------------------------------------
2225
2226
2227 //------------------------------------------------------------------------------
2228 void vvMainWindow::SetOverlayProperty(int color) {
2229   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2230   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
2231     {
2232       mSlicerManagers[index]->SetOverlayColor(color);
2233       mSlicerManagers[index]->SetColorMap(0);
2234       mSlicerManagers[index]->Render();
2235     }
2236 }
2237 //------------------------------------------------------------------------------
2238
2239 //------------------------------------------------------------------------------
2240 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level) {
2241   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2242   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion())
2243     {
2244       mSlicerManagers[index]->SetFusionOpacity(opacity);
2245       mSlicerManagers[index]->SetFusionColorMap(colormap);
2246       mSlicerManagers[index]->SetFusionWindow(window);
2247       mSlicerManagers[index]->SetFusionLevel(level);
2248       mSlicerManagers[index]->SetColorMap(0);
2249       mSlicerManagers[index]->Render();
2250     }
2251 }
2252 //------------------------------------------------------------------------------
2253
2254 //------------------------------------------------------------------------------
2255 void vvMainWindow::SaveAs() {
2256   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector")
2257     {
2258       QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2259       return;
2260     }
2261
2262   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2263   int dimension = mSlicerManagers[index]->GetDimension();
2264   QStringList OutputListeFormat;
2265   OutputListeFormat.clear();
2266   if (dimension == 1)
2267     {
2268       OutputListeFormat.push_back(".mhd");
2269     }
2270   if (dimension == 2)
2271     {
2272       OutputListeFormat.push_back(".bmp");
2273       OutputListeFormat.push_back(".png");
2274       OutputListeFormat.push_back(".jpeg");
2275       OutputListeFormat.push_back(".tif");
2276       OutputListeFormat.push_back(".mhd");
2277       OutputListeFormat.push_back(".hdr");
2278       OutputListeFormat.push_back(".vox");
2279     }
2280   else if (dimension == 3)
2281     {
2282       OutputListeFormat.push_back(".mhd");
2283       OutputListeFormat.push_back(".hdr");
2284       OutputListeFormat.push_back(".vox");
2285     }
2286   else if (dimension == 4)
2287     {
2288       OutputListeFormat.push_back(".mhd");
2289     }
2290   QString Extensions = "AllFiles(*.*)";
2291   for (int i = 0; i < OutputListeFormat.count(); i++)
2292     {
2293       Extensions += ";;Images ( *";
2294       Extensions += OutputListeFormat[i];
2295       Extensions += ")";
2296     }
2297   QString fileName = QFileDialog::getSaveFileName(this,
2298                                                   tr("Save As"),
2299                                                   mSlicerManagers[index]->GetFileName().c_str(),
2300                                                   Extensions);
2301   if (!fileName.isEmpty())
2302     {
2303       std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2304       if (OutputListeFormat.contains(
2305                                      fileformat.c_str()))
2306         {
2307           QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2308           std::string action = "Saving";
2309           vvProgressDialog progress("Saving "+fileName.toStdString());
2310           qApp->processEvents();
2311           vvImageWriter *writer = new vvImageWriter;
2312           writer->SetOutputFileName(fileName.toStdString());
2313           writer->SetInput(mSlicerManagers[index]->GetImage());
2314           writer->Update();
2315           QApplication::restoreOverrideCursor();
2316           if (writer->GetLastError().size())
2317             {
2318               QString error = "Saving did not succeed\n";
2319               error += writer->GetLastError().c_str();
2320               QMessageBox::information(this,tr("Saving Problem"),error);
2321               SaveAs();
2322             }
2323         }
2324       else
2325         {
2326           QString error = fileformat.c_str();
2327           if (error.isEmpty())
2328             error += "no file format specified !";
2329           else
2330             error += " format unknown !!!\n";
2331           QMessageBox::information(this,tr("Saving Problem"),error);
2332           SaveAs();
2333         }
2334     }
2335 }
2336 //------------------------------------------------------------------------------
2337
2338 //------------------------------------------------------------------------------
2339 void vvMainWindow::AddLink(QString image1,QString image2) {
2340   for (unsigned int i = 0; i < mSlicerManagers.size();i++)
2341     {
2342       if (image1.toStdString() == mSlicerManagers[i]->GetId())
2343         {
2344           mSlicerManagers[i]->AddLink(image2.toStdString());
2345         }
2346       if (image2.toStdString() == mSlicerManagers[i]->GetId())
2347         {
2348           mSlicerManagers[i]->AddLink(image1.toStdString());
2349         }
2350     }
2351 }
2352 //------------------------------------------------------------------------------
2353
2354 //------------------------------------------------------------------------------
2355 void vvMainWindow::RemoveLink(QString image1,QString image2) {
2356   for (unsigned int i = 0; i < mSlicerManagers.size();i++)
2357     {
2358       if (image1.toStdString() == mSlicerManagers[i]->GetId())
2359         {
2360           mSlicerManagers[i]->RemoveLink(image2.toStdString());
2361         }
2362       if (image2.toStdString() == mSlicerManagers[i]->GetId())
2363         {
2364           mSlicerManagers[i]->RemoveLink(image1.toStdString());
2365         }
2366     }
2367 }
2368 //------------------------------------------------------------------------------
2369
2370 //------------------------------------------------------------------------------
2371 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2372 {
2373     int index = 0;
2374     while(sm != mSlicerManagers[index])
2375         index++;
2376     index = (index+offset) % mSlicerManagers.size();
2377
2378     QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2379     //CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2380     item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2381     DisplayChanged(item,slicer+1);
2382 }
2383 //------------------------------------------------------------------------------
2384
2385 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2386 {
2387   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2388     {
2389       if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1)
2390         {
2391           for (int j = 0; j < 4; j++)
2392             {
2393               mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2394               //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2395               //UpdateTSlice(j,value);
2396             }
2397           mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2398           break;
2399         }
2400     }
2401 }
2402 //------------------------------------------------------------------------------
2403
2404
2405 //------------------------------------------------------------------------------
2406 void vvMainWindow::NOHorizontalSliderMoved() {
2407   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2408   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2409  //  mCurrentTime = NOHorizontalSlider->value();
2410 }
2411 //------------------------------------------------------------------------------
2412
2413
2414 //------------------------------------------------------------------------------
2415 void vvMainWindow::NEHorizontalSliderMoved() {
2416   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2417   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2418  //  mCurrentTime = NEHorizontalSlider->value();
2419 }
2420 //------------------------------------------------------------------------------
2421
2422
2423 //------------------------------------------------------------------------------
2424 void vvMainWindow::SOHorizontalSliderMoved() {
2425   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2426   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2427   // mCurrentTime = SOHorizontalSlider->value();
2428 }
2429 //------------------------------------------------------------------------------
2430
2431
2432 //------------------------------------------------------------------------------
2433 void vvMainWindow::SEHorizontalSliderMoved() {
2434   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2435   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2436   // mCurrentTime = SEHorizontalSlider->value();
2437 }
2438 //------------------------------------------------------------------------------
2439
2440 //------------------------------------------------------------------------------
2441 void vvMainWindow::NOVerticalSliderChanged() {
2442   int value = NOVerticalSlider->value();
2443   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2444     {
2445       if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
2446         {
2447           mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2448           mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2449           // mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES.
2450           mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2451           break;
2452         }
2453     }
2454 }
2455 //------------------------------------------------------------------------------
2456
2457
2458 //------------------------------------------------------------------------------
2459 void vvMainWindow::NEVerticalSliderChanged() {
2460   int value = NEVerticalSlider->value();
2461   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2462     {
2463       if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1)
2464         {
2465           mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2466           mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2467           mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2468           break;
2469         }
2470     }
2471 }
2472 //------------------------------------------------------------------------------
2473
2474
2475 //------------------------------------------------------------------------------
2476 void vvMainWindow::SOVerticalSliderChanged() {
2477   int value = SOVerticalSlider->value();
2478   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2479     {
2480       if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
2481         {
2482           mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2483           mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2484           mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2485           break;
2486         }
2487     }
2488 }
2489 //------------------------------------------------------------------------------
2490
2491
2492 //------------------------------------------------------------------------------
2493 void vvMainWindow::SEVerticalSliderChanged() {
2494   int value = SEVerticalSlider->value();
2495   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2496     {
2497       if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1)
2498         {
2499           mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2500           mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2501           mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2502           break;
2503         }
2504     }
2505 }
2506 //------------------------------------------------------------------------------
2507
2508
2509 //------------------------------------------------------------------------------
2510 void vvMainWindow::UpdateSlice(int slicer, int slice) {
2511   if (slicer == 0) {
2512     if (slice != NOVerticalSlider->value())
2513       NOVerticalSlider->setValue(slice);
2514   }
2515   else if (slicer == 1)
2516     NEVerticalSlider->setValue(slice);
2517   else if (slicer == 2)
2518     SOVerticalSlider->setValue(slice);
2519   else if (slicer == 3)
2520     SEVerticalSlider->setValue(slice);
2521 }
2522 //------------------------------------------------------------------------------
2523
2524
2525 //------------------------------------------------------------------------------
2526 void vvMainWindow::UpdateTSlice(int slicer, int slice) {
2527   switch (slicer)
2528     {
2529     case 0:
2530       NOHorizontalSlider->setValue(slice);
2531       break;
2532     case 1:
2533       NEHorizontalSlider->setValue(slice);
2534       break;
2535     case 2:
2536       SOHorizontalSlider->setValue(slice);
2537       break;
2538     case 3:
2539       SEHorizontalSlider->setValue(slice);
2540       break;
2541     }
2542 }
2543 //------------------------------------------------------------------------------
2544
2545
2546 //------------------------------------------------------------------------------
2547 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax) {
2548   int position = int((min+max)/2);
2549   int tPosition = int((tmin+tmax)/2);
2550   if (slicer == 0)
2551     {
2552       NOVerticalSlider->setValue(position);
2553       NOVerticalSlider->setRange(min,max);
2554       NOHorizontalSlider->setRange(tmin,tmax);
2555       NOHorizontalSlider->setValue(tPosition);
2556     }
2557   else if (slicer == 1)
2558     {
2559       NEVerticalSlider->setValue(position);
2560       NEVerticalSlider->setRange(min,max);
2561       NEHorizontalSlider->setRange(tmin,tmax);
2562       NEHorizontalSlider->setValue(tPosition);
2563     }
2564   else if (slicer == 2)
2565     {
2566       SOVerticalSlider->setValue(position);
2567       SOVerticalSlider->setRange(min,max);
2568       SOHorizontalSlider->setRange(tmin,tmax);
2569       SOHorizontalSlider->setValue(tPosition);
2570     }
2571   else if (slicer == 3)
2572     {
2573       SEVerticalSlider->setValue(position);
2574       SEVerticalSlider->setRange(min,max);
2575       SEHorizontalSlider->setRange(tmin,tmax);
2576       SEHorizontalSlider->setValue(tPosition);
2577     }
2578 }
2579 //------------------------------------------------------------------------------
2580
2581
2582 //------------------------------------------------------------------------------
2583 void vvMainWindow::SaveNOScreenshot() {
2584   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2585   w2i->SetInput(NOViewWidget->GetRenderWindow());
2586   w2i->Update();
2587   SaveScreenshot(w2i->GetOutput());
2588   w2i->Delete();
2589 }
2590 //------------------------------------------------------------------------------
2591
2592
2593 //------------------------------------------------------------------------------
2594 void vvMainWindow::SaveNEScreenshot() {
2595   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2596   w2i->SetInput(NEViewWidget->GetRenderWindow());
2597   w2i->Update();
2598   SaveScreenshot(w2i->GetOutput());
2599   w2i->Delete();
2600 }
2601 //------------------------------------------------------------------------------
2602
2603
2604 //------------------------------------------------------------------------------
2605 void vvMainWindow::SaveSOScreenshot() {
2606   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2607   w2i->SetInput(SOViewWidget->GetRenderWindow());
2608   w2i->Update();
2609   SaveScreenshot(w2i->GetOutput());
2610   w2i->Delete();
2611 }
2612 //------------------------------------------------------------------------------
2613
2614
2615 //------------------------------------------------------------------------------
2616 void vvMainWindow::SaveSEScreenshot() {
2617   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2618   w2i->SetInput(SEViewWidget->GetRenderWindow());
2619   w2i->Update();
2620   SaveScreenshot(w2i->GetOutput());
2621   w2i->Delete();
2622 }
2623 //------------------------------------------------------------------------------
2624
2625
2626 //------------------------------------------------------------------------------
2627 void vvMainWindow::SaveScreenshot(vtkImageData* image) {
2628   QString Extensions = "Images( *.png);;";
2629   Extensions += "Images( *.jpg);;";
2630   Extensions += "Images( *.bmp);;";
2631   Extensions += "Images( *.tif);;";
2632   Extensions += "Images( *.ppm)";
2633   QString fileName = QFileDialog::getSaveFileName(this,
2634                                                   tr("Save As"),
2635                                                   itksys::SystemTools::GetFilenamePath(
2636                                                                                        mSlicerManagers[0]->GetFileName()).c_str(),
2637                                                   Extensions);
2638   if (!fileName.isEmpty())
2639     {
2640       const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2641       if (!strcmp(ext, ".bmp"))
2642         {
2643           vtkBMPWriter *bmp = vtkBMPWriter::New();
2644           bmp->SetInput(image);
2645           bmp->SetFileName(fileName.toStdString().c_str());
2646           bmp->Write();
2647           bmp->Delete();
2648         }
2649       else if (!strcmp(ext, ".tif"))
2650         {
2651           vtkTIFFWriter *tif = vtkTIFFWriter::New();
2652           tif->SetInput(image);
2653           tif->SetFileName(fileName.toStdString().c_str());
2654           tif->Write();
2655           tif->Delete();
2656         }
2657       else if (!strcmp(ext, ".ppm"))
2658         {
2659           vtkPNMWriter *pnm = vtkPNMWriter::New();
2660           pnm->SetInput(image);
2661           pnm->SetFileName(fileName.toStdString().c_str());
2662           pnm->Write();
2663           pnm->Delete();
2664         }
2665       else if (!strcmp(ext, ".png"))
2666         {
2667           vtkPNGWriter *png = vtkPNGWriter::New();
2668           png->SetInput(image);
2669           png->SetFileName(fileName.toStdString().c_str());
2670           png->Write();
2671           png->Delete();
2672         }
2673       else if (!strcmp(ext, ".jpg"))
2674         {
2675           vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2676           jpg->SetInput(image);
2677           jpg->SetFileName(fileName.toStdString().c_str());
2678           jpg->Write();
2679           jpg->Delete();
2680         }
2681       else
2682         {
2683           QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2684         }
2685     }
2686
2687 }
2688 //------------------------------------------------------------------------------
2689
2690
2691 //------------------------------------------------------------------------------
2692 void vvMainWindow::GoToCursor() {
2693   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2694   for (int column = 1; column < 5; column++)
2695     {
2696       if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1)
2697         {
2698           double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2699           mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2700                                                                           cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2701           mSlicerManagers[index]->UpdateViews(1,column-1);
2702           mSlicerManagers[index]->UpdateLinked(column-1);
2703           break;
2704         }
2705     }
2706 }
2707 //------------------------------------------------------------------------------
2708
2709 //------------------------------------------------------------------------------
2710 void vvMainWindow::PlayPause() {
2711   if (playMode)
2712     {
2713       playMode = 0;
2714       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2715       ImageInfoChanged();
2716       return;
2717     }
2718   else
2719     {
2720       int image_number=DataTree->topLevelItemCount();
2721       bool has_temporal;
2722       for (int i=0;i<image_number;i++)
2723         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1)
2724           {
2725             has_temporal=true;
2726             break;
2727           }
2728       if (has_temporal)
2729         {
2730           playMode = 1;
2731           playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2732           QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2733         }
2734     }
2735 }
2736 //------------------------------------------------------------------------------
2737
2738 //------------------------------------------------------------------------------
2739 void vvMainWindow::PlayNext() {
2740   if (playMode && !this->isHidden())
2741     {
2742       int image_number=DataTree->topLevelItemCount();
2743       ///Only play one slicer per SM, and only if the SM is being displayed
2744       for (int i=0;i<image_number;i++)
2745         for (int j=0;j<4;j++)
2746           if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2747               DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0)
2748             {
2749               mSlicerManagers[i]->SetNextTSlice(j);
2750               break;
2751             }
2752       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2753     }
2754 }
2755 //------------------------------------------------------------------------------
2756
2757 void vvMainWindow::ShowLastImage()
2758 {
2759   if (mSlicerManagers.size() > 1)
2760     {
2761       QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2762       CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2763       item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2764       DisplayChanged(item,1);
2765     }
2766 }
2767
2768 //------------------------------------------------------------------------------
2769 void vvMainWindow::UpdateRenderWindows() {
2770   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2771   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2772   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2773   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2774 }
2775 //------------------------------------------------------------------------------
2776
2777 //------------------------------------------------------------------------------
2778 void vvMainWindow::SegmentationOnCurrentImage() {
2779   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2780
2781   vvSegmentationDialog segmentation;
2782   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2783   segmentation.exec();
2784 }
2785 //------------------------------------------------------------------------------
2786
2787 void vvMainWindow::SurfaceViewerLaunch()
2788 {
2789   vvSurfaceViewerDialog surfaceViewer;
2790   surfaceViewer.exec();
2791 }
2792
2793 //------------------------------------------------------------------------------
2794 void vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2795 {
2796   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
2797   slicer_manager->SetImage(image);
2798   slicer_manager->SetFilename(filename);
2799   mSlicerManagers.push_back(slicer_manager);
2800
2801   //create an item in the tree with good settings
2802   QTreeWidgetItem *item = new QTreeWidgetItem();
2803   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2804   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
2805   qApp->processEvents();
2806
2807   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2808
2809   //Create the buttons for reload and close
2810   qApp->processEvents();
2811   QTreePushButton* cButton = new QTreePushButton;
2812   cButton->setItem(item);
2813   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2814   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2815   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2816           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2817
2818   QTreePushButton* rButton = new QTreePushButton;
2819   rButton->setItem(item);
2820   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2821   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2822   rButton->setEnabled(0);
2823   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2824           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2825
2826   DataTree->addTopLevelItem(item);
2827   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2828   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2829
2830   //set the id of the image
2831   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2832   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2833   mSlicerManagers.back()->SetId(id.toStdString());
2834
2835   linkPanel->addImage(filename, id.toStdString());
2836
2837   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
2838           this, SLOT(CurrentImageChanged(std::string)));
2839   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
2840           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2841   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
2842           this, SLOT(VectorChanged(int,double,double,double, double)));
2843   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
2844           this, SLOT(OverlayChanged(int,double,double)));
2845   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
2846           this, SLOT(FusionChanged(int,double)));
2847   connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
2848           this,SLOT(WindowsChanged(int, int, int)));
2849   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
2850           this,SLOT(WindowLevelChanged(double, double, int, int)));
2851   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
2852           this,SLOT(UpdateSlice(int,int)));
2853   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
2854           this,SLOT(UpdateTSlice(int, int)));
2855   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2856           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2857   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2858           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2859   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
2860           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
2861   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2862   UpdateTree();
2863   qApp->processEvents();
2864   InitSlicers();
2865   ShowLastImage();
2866   InitDisplay();
2867   qApp->processEvents();
2868 }
2869 //------------------------------------------------------------------------------
2870
2871
2872 //------------------------------------------------------------------------------
2873 void vvMainWindow::UpdateCurrentSlicer() {
2874   int index = -1;
2875   if (DataTree->selectedItems().size() > 0) {
2876     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2877   }
2878   mSlicerManagerCurrentIndex = index;
2879 }
2880 //------------------------------------------------------------------------------
2881