vv/vvMainWindow.cxx

   1 #include <algorithm>
   2 #include <QMessageBox>
   3 #include <QInputDialog>
   4 #include <QTimer>
   5 #include "QTreePushButton.h"
   6
   7 // VV include
   8 #include "vvMainWindow.h"
   9 #include "vvHelpDialog.h"
  10 #include "vvDocumentation.h"
  11 #include "vvProgressDialog.h"
  12 #include "vvQDicomSeriesSelector.h"
  13 #include "vvSlicerManager.h"
  14 #include "clitkImageCommon.h"
  15 #include "vvSlicer.h"
  16 #include "vvInteractorStyleNavigator.h"
  17 #include "vvImageWriter.h"
  18 #include "vvResamplerDialog.h"
  19 #include "vvSegmentationDialog.h"
  20 #include "vvSurfaceViewerDialog.h"
  21 #include "vvDeformationDialog.h"
  22 #include "vvImageWarp.h"
  23 #include "vvUtils.h"
  24 #include "vvMaximumIntensityProjection.h"
  25 #include "vvMidPosition.h"
  26 #include "vvMesh.h"
  27 #include "vvStructSelector.h"
  28 #include "vvMeshReader.h"
  29 #include "vvConstants.h"
  30
  31 #ifdef CLITK_VV_USE_BDCM
  32 #include <bdcmDicomFilesSelectorDialog.h>
  33 #endif
  34
  35 // ITK include
  36 #include "itkImage.h"
  37 #include "itkImageFileReader.h"
  38 #include "itkByteSwapper.h"
  39 #include "itkCommand.h"
  40 #include "itkNumericSeriesFileNames.h"
  41
  42 // VTK include
  43 #include "vtkImageData.h"
  44 #include "vtkImageActor.h"
  45 #include "vtkCornerAnnotation.h"
  46 #include "vtkRenderWindow.h"
  47 #include "vtkRenderWindowInteractor.h"
  48 #include "vtkRenderer.h"
  49 #include "vtkRendererCollection.h"
  50 #include "vtkWindowToImageFilter.h"
  51 #include "vtkBMPWriter.h"
  52 #include "vtkTIFFWriter.h"
  53 #include "vtkPNMWriter.h"
  54 #include "vtkPNGWriter.h"
  55 #include "vtkJPEGWriter.h"
  56
  57 // Standard includes
  58 #include <iostream>
  59
  60 #define COLUMN_TREE 0
  61 #define COLUMN_UL_VIEW 1
  62 #define COLUMN_UR_VIEW 2
  63 #define COLUMN_DL_VIEW 3
  64 #define COLUMN_DR_VIEW 4
  65 #define COLUMN_CLOSE_IMAGE 5
  66 #define COLUMN_RELOAD_IMAGE 6
  67 #define COLUMN_IMAGE_NAME 7
  68
  69 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.hdr *.vox *.his *.xdr)"
  70
  71 /*Data Tree values
  72   0,Qt::UserRole full filename
  73   1,Qt::CheckStateRole checkbutton UL View
  74   1,Qt::UserRole overlay, fusion or vector
  75   2,Qt::CheckStateRole checkbutton UR View
  76   3,Qt::CheckStateRole checkbutton DL View
  77   4,Qt::CheckStateRole checkbutton DR View
  78   5,0  short filename
  79   5,Qt::UserRole mSlicerManager id*/
  80
  81 //------------------------------------------------------------------------------
  82 vvMainWindow::vvMainWindow():vvMainWindowBase() {
  83   setupUi(this); // this sets up the GUI
  84
  85   mInputPathName = "";
  86   mMenuTools = menuTools;
  87   mMenuExperimentalTools = menuExperimental;
  88   mMainWidget = this;
  89
  90   //Init the contextMenu
  91   this->setContextMenuPolicy(Qt::CustomContextMenu);
  92   contextActions.resize(0);
  93   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/fileopen.png")),
  94                                                         tr("O&pen new Image"));
  95   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
  96   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
  97   contextActions.push_back(actionOpen_new_image);
  98   contextMenu.addSeparator();
  99
 100   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")),
 101                                                      tr("Close Current Image"));
 102   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 103   contextActions.push_back(actionClose_Image);
 104
 105   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")),
 106                                                       tr("Reload Current Image"));
 107   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 108   contextActions.push_back(actionReload_image);
 109
 110   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/filesave.png")),
 111                                                     tr("Save Current Image"));
 112   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 113   contextActions.push_back(actionSave_image);
 114
 115   contextMenu.addSeparator();
 116
 117   // QAction* actionCrop_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/crop.png")),
 118   //                                                   tr("Crop Current Image"));
 119   // connect(actionCrop_image,SIGNAL(triggered()),this,SLOT(CropImage()));
 120   // contextActions.push_back(actionCrop_image);
 121
 122   QAction* actionSplit_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/cut.png")),
 123                                                      tr("Split Current Image"));
 124   connect(actionSplit_image,SIGNAL(triggered()),this,SLOT(SplitImage()));
 125   contextActions.push_back(actionSplit_image);
 126
 127   contextMenu.addSeparator();
 128
 129   contextMenu.addAction(actionAdd_VF_to_current_Image);
 130   contextActions.push_back(actionAdd_VF_to_current_Image);
 131
 132   QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/GPSup.png")),
 133                                                                        tr("Add overlay image to current image"));
 134   contextMenu.addAction(actionAdd_Overlay_to_current_Image);
 135   contextActions.push_back(actionAdd_Overlay_to_current_Image);
 136
 137   connect(actionAdd_Overlay_to_current_Image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 138
 139   contextMenu.addAction(actionAdd_fusion_image);
 140   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 141   contextActions.push_back(actionAdd_fusion_image);
 142
 143   //init the DataTree
 144   mSlicerManagers.resize(0);
 145
 146   QStringList header;
 147   header.append("");
 148   header.append("TL");
 149   header.append("TR");
 150   header.append("BL");
 151   header.append("BR");
 152   header.append("");
 153   header.append("");
 154   header.append("Name");
 155
 156   DataTree->setHeaderLabels(header);
 157   DataTree->resizeColumnToContents(COLUMN_TREE);
 158   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 159   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 160   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 161   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 162   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 163   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 164   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 165
 166   viewMode = 1;
 167   documentation = new vvDocumentation();
 168   help_dialog = new vvHelpDialog();
 169   dicomSeriesSelector = new vvDicomSeriesSelector();
 170
 171   inverseButton->setEnabled(0);
 172   actionAdd_Overlay_to_current_Image->setEnabled(0);
 173   actionSave_As->setEnabled(0);
 174   actionAdd_VF_to_current_Image->setEnabled(0);
 175   actionAdd_fusion_image->setEnabled(0);
 176
 177   //init the sliders
 178   verticalSliders.push_back(NOVerticalSlider);
 179   verticalSliders.push_back(NEVerticalSlider);
 180   verticalSliders.push_back(SOVerticalSlider);
 181   verticalSliders.push_back(SEVerticalSlider);
 182
 183   for (int i =0; i < 4; i++)
 184     verticalSliders[i]->hide();
 185
 186   horizontalSliders.push_back(NOHorizontalSlider);
 187   horizontalSliders.push_back(NEHorizontalSlider);
 188   horizontalSliders.push_back(SOHorizontalSlider);
 189   horizontalSliders.push_back(SEHorizontalSlider);
 190
 191   for (int i =0; i < 4; i++)
 192     horizontalSliders[i]->hide();
 193
 194
 195   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 196   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 197   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 198   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 199
 200   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 201   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 202   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 203   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 204
 205   //connect everything
 206   connect(actionMaximum_Intensity_Projection,SIGNAL(triggered()),this,SLOT(ComputeMIP()));
 207   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 208   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 209   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 210   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 211   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 212   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 213   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 214   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 215   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 216   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 217   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 218   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 219   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 220   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 221   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 222
 223   ///////////////////////////////////////////////
 224   contextMenu.addAction(actionResampler);
 225   connect(actionResampler,SIGNAL(triggered()),this,SLOT(ResampleCurrentImage()));
 226   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 227   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 228   ///////////////////////////////////////////////
 229
 230   actionNorth_East_Window->setEnabled(0);
 231   actionNorth_West_Window->setEnabled(0);
 232   actionSouth_East_Window->setEnabled(0);
 233   actionSouth_West_Window->setEnabled(0);
 234
 235   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 236   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 237   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 238   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 239
 240   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 241   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 242           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 243
 244   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 245   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 246   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 247   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 248   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 249   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 250
 251
 252   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 253
 254   connect(linkPanel,SIGNAL(addLink(QString,QString)),this,SLOT(AddLink(QString,QString)));
 255   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 256   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int)),this,SLOT(SetVFProperty(int,int,int)));
 257   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int)),this,SLOT(SetOverlayProperty(int)));
 258   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,double,double)),
 259           this,SLOT(SetFusionProperty(int,int,double,double)));
 260   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 261
 262   playMode = 0;//pause
 263   mFrameRate = 10;
 264   playButton->setEnabled(0);
 265   frameRateLabel->setEnabled(0);
 266   frameRateSpinBox->setEnabled(0);
 267   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 268   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 269
 270   goToCursorPushButton->setEnabled(0);
 271   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 272
 273   NOViewWidget->hide();
 274   NEViewWidget->hide();
 275   SOViewWidget->hide();
 276   SEViewWidget->hide();
 277
 278   //Recently opened files
 279   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 280   if ( !recent_files.empty() )
 281     {
 282       QMenu * rmenu = new QMenu("Recently opened files...");
 283       rmenu->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/open.png")));
 284       menuFile->insertMenu(actionOpen_Image_With_Time,rmenu);
 285       for (std::list<std::string>::iterator i = recent_files.begin();i!=recent_files.end();i++)
 286         {
 287           QAction* current=new QAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/open.png")),
 288                                        (*i).c_str(),this);
 289           rmenu->addAction(current);
 290           connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 291         }
 292     }
 293
 294   // Adding all new tools (insertion in the menu)
 295   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 296
 297   if (!CLITK_EXPERIMENTAL)
 298       menuExperimental->menuAction()->setVisible(false);
 299 }
 300 //------------------------------------------------------------------------------
 301
 302
 303 //------------------------------------------------------------------------------
 304 void vvMainWindow::ComputeMIP()
 305 {
 306   vvMaximumIntensityProjection mip;
 307   vvSlicerManager* selected_slicer = mSlicerManagers[GetSlicerIndexFromItem(DataTree->selectedItems()[0])];
 308   QFileInfo info(selected_slicer->GetFileName().c_str());
 309   mip.Compute(selected_slicer);
 310   AddImage(mip.GetOutput(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_mip.mhd");
 311 }
 312 //------------------------------------------------------------------------------
 313
 314
 315 //------------------------------------------------------------------------------
 316 void vvMainWindow::ComputeMidPosition()
 317 {
 318   bool ok;
 319   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 320   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 321                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 322   if (ok)
 323     {
 324       vvMidPosition midp;
 325       midp.slicer_manager = mSlicerManagers[index];
 326       midp.reference_image_index = ref;
 327       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 328       midp.Update();
 329       if (midp.error)
 330         QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 331       else
 332         {
 333           QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 334           AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 335         }
 336       QApplication::restoreOverrideCursor();
 337     }
 338 }
 339 //------------------------------------------------------------------------------
 340
 341
 342 //------------------------------------------------------------------------------
 343 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 344 {
 345   QTreeWidgetItem *item = new QTreeWidgetItem();
 346   item->setData(0,Qt::UserRole,"filename.vtk");
 347   item->setData(1,Qt::UserRole,tr("contour"));
 348   QBrush brush;
 349   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 350   brush.setStyle(Qt::SolidPattern);
 351   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 352   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 353
 354   for (int j = 1; j <= 4; j++)
 355     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 356
 357   QTreePushButton* cButton = new QTreePushButton;
 358   cButton->setItem(item);
 359   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 360   cButton->setToolTip(tr("close image"));
 361   cButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")));
 362   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 363           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 364
 365   QTreePushButton* rButton = new QTreePushButton;
 366   rButton->setItem(item);
 367   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 368   rButton->setToolTip(tr("reload image"));
 369   rButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")));
 370   rButton->setEnabled(false);
 371   //Not implemented
 372   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 373   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 374
 375   DataTree->topLevelItem(image_index)->setExpanded(1);
 376   DataTree->topLevelItem(image_index)->addChild(item);
 377   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 378   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 379   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 380   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 381
 382   UpdateTree();
 383   mSlicerManagers[image_index]->AddContour(contour,propagation);
 384   mSlicerManagers[image_index]->Render();
 385 }
 386 //------------------------------------------------------------------------------
 387
 388
 389 //------------------------------------------------------------------------------
 390 void vvMainWindow::OpenVTKContour()
 391 {
 392   if (mSlicerManagers.size() > 0)
 393     {
 394       QString Extensions = "Images ( *.vtk; *.obj)";
 395       Extensions += ";;All Files (*)";
 396       QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 397       if (file.isNull())
 398         return;
 399       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 400       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 401       vvMeshReader reader;
 402       reader.SetImage(mSlicerManagers[index]->GetImage());
 403       reader.SetModeToVTK();
 404       reader.SetFilename(file.toStdString());
 405       reader.Update();
 406       AddContour(index,reader.GetOutput()[0],false);
 407       QApplication::restoreOverrideCursor();
 408     }
 409 }
 410 //------------------------------------------------------------------------------
 411
 412
 413 //------------------------------------------------------------------------------
 414 void vvMainWindow::OpenDCStructContour()
 415 {
 416   if (mSlicerManagers.size() > 0)
 417     {
 418       QString Extensions = "Dicom Files ( *.dcm; RS*)";
 419       Extensions += ";;All Files (*)";
 420       QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 421       if (file.isNull())
 422         return;
 423       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 424       vvMeshReader reader;
 425       reader.SetFilename(file.toStdString());
 426       vvStructSelector selector;
 427       selector.SetStructures(reader.GetROINames());
 428       if (!mSlicerManagers[index]->GetVF().IsNull())
 429         selector.EnablePropagationCheckBox();
 430       if (selector.exec())
 431         {
 432           QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 433           reader.SetSelectedItems(selector.getSelectedItems());
 434           reader.SetImage(mSlicerManagers[index]->GetImage());
 435           if (selector.PropagationEnabled())
 436             reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 437           reader.Update();
 438           std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 439           for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 440                i!=contours.end();i++)
 441             AddContour(index,*i,selector.PropagationEnabled());
 442           QApplication::restoreOverrideCursor();
 443         }
 444     }
 445 }
 446 //------------------------------------------------------------------------------
 447
 448
 449 //------------------------------------------------------------------------------
 450 void vvMainWindow::ComputeDeformableRegistration()
 451 {
 452   if (mSlicerManagers.size() > 0)
 453     {
 454       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 455       vvDeformationDialog dialog(index,mSlicerManagers);
 456       if (dialog.exec())
 457         {
 458           std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 459           AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 460           WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 461         }
 462       else
 463         std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 464     }
 465   else QMessageBox::information(this, "Need to open image","You must open an image first.");
 466 }
 467 //------------------------------------------------------------------------------
 468
 469
 470 //------------------------------------------------------------------------------
 471 void vvMainWindow::WarpImage()
 472 {
 473   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 474   if (!mSlicerManagers[index]->GetVF().IsNull())
 475     {
 476       bool ok;
 477       int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 478                                          mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 479       if (ok)
 480         {
 481           WarpImage(mSlicerManagers[index],ref);
 482         }
 483     }
 484   else
 485     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 486 }
 487 //------------------------------------------------------------------------------
 488
 489
 490 //------------------------------------------------------------------------------
 491 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 492 {
 493   if (!selected_slicer->GetVF().IsNull())
 494     {
 495       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 496       QFileInfo info(selected_slicer->GetFileName().c_str());
 497       vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 498                        reference_phase,this);
 499       if (warp.ComputeWarpedImage())
 500         {
 501           AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 502           AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 503           AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 504           QApplication::restoreOverrideCursor();
 505         }
 506       else
 507         {
 508           QApplication::restoreOverrideCursor();
 509           QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 510         }
 511     }
 512   else
 513     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 514 }
 515 //------------------------------------------------------------------------------
 516
 517
 518 //------------------------------------------------------------------------------
 519 vvMainWindow::~vvMainWindow() {
 520   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
 521     {
 522       if (mSlicerManagers[i] != NULL)
 523         delete mSlicerManagers[i];
 524     }
 525 }
 526 //------------------------------------------------------------------------------
 527
 528
 529 //------------------------------------------------------------------------------
 530 void vvMainWindow::MergeImages() {
 531   QString Extensions = EXTENSIONS;
 532   Extensions += ";;All Files (*)";
 533   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 534   if (files.isEmpty())
 535     return;
 536   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 537   std::vector<std::string> vector;
 538
 539   unsigned int currentDim = 0;
 540   std::vector<double> currentSpacing;
 541   std::vector<int> currentSize;
 542   std::vector<double> currentOrigin;
 543
 544   for (int i = 0; i < files.size(); i++)
 545     {
 546       itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 547               files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 548       reader->SetFileName(files[i].toStdString().c_str());
 549       reader->ReadImageInformation();
 550       if (reader)        {
 551           //NOViewWidget->hide();
 552           //NEViewWidget->hide();
 553           //SOViewWidget->hide();
 554           //SEViewWidget->hide();
 555           if (i == 0)
 556               currentDim = reader->GetNumberOfDimensions();
 557           bool IsOk = true;
 558           for (unsigned int j = 0;j < currentDim; j++)
 559           {
 560               if (i == 0)
 561               {
 562                   if (j == 0)
 563                   {
 564                       currentSpacing.resize(currentDim);
 565                       currentSize.resize(currentDim);
 566                       currentOrigin.resize(currentDim);
 567                   }
 568                   currentOrigin[j] = reader->GetOrigin(j);
 569                   currentSpacing[j] = reader->GetSpacing(j);
 570                   currentSize[j] = reader->GetDimensions(j);
 571               }
 572               else if (currentDim != reader->GetNumberOfDimensions()
 573                       || currentSpacing[j] != reader->GetSpacing(j)
 574                       || currentSize[j] != (int)reader->GetDimensions(j)
 575                       || currentOrigin[j] != reader->GetOrigin(j))
 576               {
 577                   QString error = "Cannot read file (too different from others ";
 578                   error += files[i].toStdString().c_str();
 579                   QMessageBox::information(this,tr("Reading problem"),error);
 580                   IsOk = false;
 581                   break;
 582               }
 583           }
 584           if (IsOk)
 585               vector.push_back(files[i].toStdString());
 586       }
 587     }
 588   if (vector.size() > 0)
 589     LoadImages(vector, MERGED);
 590 }
 591 //------------------------------------------------------------------------------
 592
 593
 594 //------------------------------------------------------------------------------
 595 void vvMainWindow::MergeImagesWithTime() {
 596   QString Extensions = EXTENSIONS;
 597   Extensions += ";;All Files (*)";
 598   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 599   if (files.isEmpty())
 600     return;
 601   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 602   std::vector<std::string> vector;
 603
 604   unsigned int currentDim = 0;
 605   std::vector<double> currentSpacing;
 606   std::vector<int> currentSize;
 607   std::vector<double> currentOrigin;
 608
 609   for (int i = 0; i < files.size(); i++)
 610     {
 611       itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 612                                                                             files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 613       if (reader)
 614         {
 615           reader->SetFileName(files[i].toStdString().c_str());
 616           reader->ReadImageInformation();
 617           if (i == 0)
 618             currentDim = reader->GetNumberOfDimensions();
 619           bool IsOk = true;
 620           for (unsigned int j = 0;j < currentDim; j++)
 621             {
 622               if (i == 0)
 623                 {
 624                   if (j == 0)
 625                     {
 626                       currentSpacing.resize(currentDim);
 627                       currentSize.resize(currentDim);
 628                       currentOrigin.resize(currentDim);
 629                     }
 630                   currentOrigin[j] = reader->GetOrigin(j);
 631                   currentSpacing[j] = reader->GetSpacing(j);
 632                   currentSize[j] = reader->GetDimensions(j);
 633                 }
 634               else if (currentDim != reader->GetNumberOfDimensions()
 635                        || currentSpacing[j] != reader->GetSpacing(j)
 636                        || currentSize[j] != (int)reader->GetDimensions(j)
 637                        || currentOrigin[j] != reader->GetOrigin(j))
 638                 {
 639                   QString error = "Cannot read file (too different from others ";
 640                   error += files[i].toStdString().c_str();
 641                   QMessageBox::information(this,tr("Reading problem"),error);
 642                   IsOk = false;
 643                   break;
 644                 }
 645             }
 646           if (IsOk)
 647             vector.push_back(files[i].toStdString());
 648         }
 649       else
 650         {
 651           QString error = "Cannot read file info for ";
 652           error += files[i].toStdString().c_str();
 653           error += "\n";
 654           error += "Maybe you're trying to open an image in an unsupported format?\n";
 655           QMessageBox::information(this,tr("Reading problem"),error);
 656         }
 657     }
 658   sort(vector.begin(),vector.end());
 659   if (vector.size() > 1)
 660     LoadImages(vector, MERGEDWITHTIME);
 661   else
 662     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.");
 663 }
 664 //------------------------------------------------------------------------------
 665
 666
 667 //------------------------------------------------------------------------------
 668 void vvMainWindow::OpenDicom() {
 669   std::vector<std::string> files;
 670
 671 #ifdef CLITK_VV_USE_BDCM
 672   bool r = bdcm::OpenDicomFilesSelectorDialog(files,
 673                                               "DicomFilesSelectorDialog test",
 674                                               0,0,800,800,1);
 675
 676   if (r) {
 677     std::cout << "$$$$ main : user clicked 'OK' $$$$"<<std::endl;
 678     std::cout << "$$$$ selected files : "<<std::endl;
 679     std::vector<std::string>::iterator i;
 680     for (i=files.begin();i!=files.end();++i) {
 681       std::cout << *i << std::endl;
 682     }
 683     std::cout << "$$$$ "<<std::endl;
 684
 685     LoadImages(files,DICOM);
 686   }
 687   else {
 688     std::cout << "$$$$ main : user clicked 'CANCEL' $$$$"<<std::endl;
 689   }
 690 #else
 691   std::cout << "dicomSeriesSelector " << std::endl;
 692   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 693     files = *(dicomSeriesSelector->GetFilenames());
 694     LoadImages(files,DICOM);
 695   }
 696 #endif
 697
 698 }
 699 //------------------------------------------------------------------------------
 700
 701 //------------------------------------------------------------------------------
 702 void vvMainWindow::OpenImages() {
 703   QString Extensions = EXTENSIONS;
 704   Extensions += ";;All Files (*)";
 705
 706   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 707   if (files.isEmpty())
 708     return;
 709   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 710   std::vector<std::string> vector;
 711   for (int i = 0; i < files.size(); i++)
 712     vector.push_back(files[i].toStdString());
 713   LoadImages(vector, IMAGE);
 714 }
 715 //------------------------------------------------------------------------------
 716 void vvMainWindow::OpenRecentImage()
 717 {
 718   QAction * caller = qobject_cast<QAction*>(sender());
 719   std::vector<std::string> images;
 720   images.push_back(caller->text().toStdString());
 721   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 722   LoadImages(images,IMAGE);
 723 }
 724
 725 //------------------------------------------------------------------------------
 726 void vvMainWindow::OpenImageWithTime() {
 727   QString Extensions = EXTENSIONS;
 728   Extensions += ";;All Files (*)";
 729
 730   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 731   if (files.isEmpty())
 732     return;
 733   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 734   std::vector<std::string> vector;
 735   for (int i = 0; i < files.size(); i++)
 736     {
 737       vector.push_back(files[i].toStdString());
 738     }
 739   LoadImages(vector, IMAGEWITHTIME);
 740 }
 741 //------------------------------------------------------------------------------
 742
 743 //------------------------------------------------------------------------------
 744 void vvMainWindow::LoadImages(std::vector<std::string> files, LoadedImageType filetype) {
 745   //Separate the way to open images and dicoms
 746   int fileSize;
 747   if (filetype == IMAGE || filetype == IMAGEWITHTIME)
 748     fileSize = files.size();
 749   else
 750     fileSize = 1;
 751
 752   //Only add to the list of recently opened files when a single file is opened,
 753   //to avoid polluting the list of recently opened files
 754   if (files.size() == 1)
 755     {
 756       QFileInfo finfo=tr(files[0].c_str());
 757       AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 758     }
 759   //init the progress events
 760   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 761   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 762   qApp->processEvents();
 763
 764   int numberofsuccesulreads=0;
 765   //open images as 1 or multiples
 766   for (int i = 0; i < fileSize; i++) {
 767
 768     progress.Update("Opening " + files[i]);
 769     progress.SetProgress(i,fileSize);
 770     qApp->processEvents();
 771
 772     //read the image and put it in mSlicerManagers
 773     vvSlicerManager* imageManager = new vvSlicerManager(4);
 774     qApp->processEvents();
 775
 776     bool SetImageSucceed=false;
 777
 778     if (filetype == IMAGE || filetype == IMAGEWITHTIME)
 779       SetImageSucceed = imageManager->SetImage(files[i],filetype);
 780     else
 781       {
 782         SetImageSucceed = imageManager->SetImages(files,filetype);
 783       }
 784     if (SetImageSucceed == false)
 785       {
 786         QApplication::restoreOverrideCursor();
 787         QString error = "Cannot open file \n";
 788         error += imageManager->GetLastError().c_str();
 789         QMessageBox::information(this,tr("Reading problem"),error);
 790         delete imageManager;
 791       }
 792     else
 793       {
 794         mSlicerManagers.push_back(imageManager);
 795
 796         //create an item in the tree with good settings
 797         QTreeWidgetItem *item = new QTreeWidgetItem();
 798         item->setData(0,Qt::UserRole,files[i].c_str());
 799         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 800         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 801         qApp->processEvents();
 802
 803         //Create the buttons for reload and close
 804         qApp->processEvents();
 805         QTreePushButton* cButton = new QTreePushButton;
 806         cButton->setItem(item);
 807         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 808         cButton->setToolTip(tr("close image"));
 809         cButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")));
 810         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 811                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 812
 813         QTreePushButton* rButton = new QTreePushButton;
 814         rButton->setItem(item);
 815         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 816         rButton->setToolTip(tr("reload image"));
 817         rButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")));
 818         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 819                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 820
 821         DataTree->addTopLevelItem(item);
 822         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 823         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 824
 825         //set the id of the image
 826         QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 827         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 828         mSlicerManagers.back()->SetId(id.toStdString());
 829
 830         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 831
 832         connect(mSlicerManagers.back(),SIGNAL(currentImageChanged(std::string)),
 833                 this,SLOT(CurrentImageChanged(std::string)));
 834         connect(mSlicerManagers.back(),SIGNAL(
 835                                               UpdatePosition(int, double, double, double, double, double, double, double)),this,
 836                 SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 837         connect(mSlicerManagers.back(),SIGNAL(UpdateVector(int, double, double, double, double)),
 838                 this, SLOT(VectorChanged(int,double,double,double, double)));
 839         connect(mSlicerManagers.back(),SIGNAL(UpdateOverlay(int, double, double)),
 840                 this, SLOT(OverlayChanged(int,double,double)));
 841         connect(mSlicerManagers.back(),SIGNAL(UpdateFusion(int, double)),
 842                 this, SLOT(FusionChanged(int,double)));
 843         connect(mSlicerManagers.back(),SIGNAL(UpdateWindows(int, int, int)),
 844                 this,SLOT(WindowsChanged(int, int, int)));
 845         connect(mSlicerManagers.back(),SIGNAL(WindowLevelChanged(double, double,int, int)),
 846                 this,SLOT(WindowLevelChanged(double, double, int, int)));
 847         connect(mSlicerManagers.back(),SIGNAL(UpdateSlice(int,int)),
 848                 this,SLOT(UpdateSlice(int,int)));
 849         connect(mSlicerManagers.back(),SIGNAL(UpdateTSlice(int, int)),
 850                 this,SLOT(UpdateTSlice(int, int)));
 851         connect(mSlicerManagers.back(),SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 852                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 853         connect(mSlicerManagers.back(),SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 854                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 855         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 856         InitSlicers();
 857         numberofsuccesulreads++;
 858       }
 859   }
 860   if (numberofsuccesulreads)
 861     {
 862       NOViewWidget->show();
 863       NEViewWidget->show();
 864       SOViewWidget->show();
 865       SEViewWidget->show();
 866       UpdateTree();
 867       InitDisplay();
 868       ShowLastImage();
 869     }
 870   QApplication::restoreOverrideCursor();
 871
 872 }
 873 //------------------------------------------------------------------------------
 874
 875 //------------------------------------------------------------------------------
 876 void vvMainWindow::UpdateTree() {
 877   DataTree->resizeColumnToContents(COLUMN_TREE);
 878   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 879   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 880   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 881   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 882   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 883   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 884   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 885 }
 886 //------------------------------------------------------------------------------
 887
 888 //------------------------------------------------------------------------------
 889 void vvMainWindow::CurrentImageChanged(std::string id) {
 890   int selected = 0;
 891   for (int i = 0; i < DataTree->topLevelItemCount(); i++)
 892     {
 893       if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id)
 894         {
 895           selected = i;
 896         }
 897       else
 898         {
 899           DataTree->topLevelItem(i)->setSelected(0);
 900         }
 901       for (int child = 0; child < DataTree->topLevelItem(i)->childCount();child++)
 902         DataTree->topLevelItem(i)->child(child)->setSelected(0);
 903
 904     }
 905   DataTree->topLevelItem(selected)->setSelected(1);
 906 }
 907 //------------------------------------------------------------------------------
 908
 909 //------------------------------------------------------------------------------
 910 void vvMainWindow::ImageInfoChanged() {
 911   contextActions[7]->setEnabled(1);
 912   contextActions[6]->setEnabled(1);
 913   actionSave_As->setEnabled(1);
 914   actionAdd_VF_to_current_Image->setEnabled(1);
 915   actionAdd_fusion_image->setEnabled(1);
 916   actionNorth_East_Window->setEnabled(1);
 917   actionNorth_West_Window->setEnabled(1);
 918   actionSouth_East_Window->setEnabled(1);
 919   actionSouth_West_Window->setEnabled(1);
 920   inverseButton->setEnabled(1);
 921
 922   goToCursorPushButton->setEnabled(1);
 923
 924   if (DataTree->selectedItems().size()) {
 925     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 926
 927     colorMapComboBox->setEnabled(1);
 928     for (int i = 0; i < DataTree->topLevelItem(index)->childCount();i++)
 929       {
 930         if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
 931             DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion")
 932           {
 933             colorMapComboBox->setEnabled(0);
 934             break;
 935           }
 936       }
 937
 938     std::vector<double> origin;
 939     std::vector<double> inputSpacing;
 940     std::vector<int> inputSize;
 941     std::vector<double> sizeMM;
 942     int dimension=0;
 943     QString pixelType;
 944     QString inputSizeInBytes;
 945     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
 946
 947     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1)
 948       {
 949         playButton->setEnabled(1);
 950         frameRateLabel->setEnabled(1);
 951         frameRateSpinBox->setEnabled(1);
 952       }
 953     else
 954       {
 955         playButton->setEnabled(0);
 956         frameRateLabel->setEnabled(0);
 957         frameRateSpinBox->setEnabled(0);
 958       }
 959
 960     //read image header
 961     int NPixel = 1;
 962
 963     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0])
 964       {
 965         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
 966         dimension = imageSelected->GetNumberOfDimensions();
 967         origin.resize(dimension);
 968         inputSpacing.resize(dimension);
 969         inputSize.resize(dimension);
 970         sizeMM.resize(dimension);
 971         pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
 972         for (int i = 0;i < dimension;i++)
 973           {
 974             origin[i] = imageSelected->GetOrigin()[i];
 975             inputSpacing[i] = imageSelected->GetSpacing()[i];
 976             inputSize[i] = imageSelected->GetSize()[i];
 977             sizeMM[i] = inputSize[i]*inputSpacing[i];
 978             NPixel *= inputSize[i];
 979           }
 980         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
 981       }
 982     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector")
 983       {
 984         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
 985         dimension = imageSelected->GetNumberOfDimensions();
 986         origin.resize(dimension);
 987         inputSpacing.resize(dimension);
 988         inputSize.resize(dimension);
 989         sizeMM.resize(dimension);
 990         pixelType = mSlicerManagers[index]->GetVF()->GetScalarTypeAsString().c_str();
 991         for (int i = 0;i < dimension;i++)
 992           {
 993             origin[i] = imageSelected->GetOrigin()[i];
 994             inputSpacing[i] = imageSelected->GetSpacing()[i];
 995             inputSize[i] = imageSelected->GetSize()[i];
 996             sizeMM[i] = inputSize[i]*inputSpacing[i];
 997             NPixel *= inputSize[i];
 998           }
 999         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1000       }
1001     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay")
1002       {
1003         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1004         dimension = imageSelected->GetNumberOfDimensions();
1005         origin.resize(dimension);
1006         inputSpacing.resize(dimension);
1007         inputSize.resize(dimension);
1008         sizeMM.resize(dimension);
1009         pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
1010         for (int i = 0;i < dimension;i++)
1011           {
1012             origin[i] = imageSelected->GetOrigin()[i];
1013             inputSpacing[i] = imageSelected->GetSpacing()[i];
1014             inputSize[i] = imageSelected->GetSize()[i];
1015             sizeMM[i] = inputSize[i]*inputSpacing[i];
1016             NPixel *= inputSize[i];
1017           }
1018         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1019       }
1020     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion")
1021       {
1022         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1023         dimension = imageSelected->GetNumberOfDimensions();
1024         origin.resize(dimension);
1025         inputSpacing.resize(dimension);
1026         inputSize.resize(dimension);
1027         sizeMM.resize(dimension);
1028         pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
1029         for (int i = 0;i < dimension;i++)
1030           {
1031             origin[i] = imageSelected->GetOrigin()[i];
1032             inputSpacing[i] = imageSelected->GetSpacing()[i];
1033             inputSize[i] = imageSelected->GetSize()[i];
1034             sizeMM[i] = inputSize[i]*inputSpacing[i];
1035             NPixel *= inputSize[i];
1036           }
1037         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1038       }
1039
1040     QString dim = QString::number(dimension) + " (";
1041     dim += pixelType + ")";
1042
1043     infoPanel->setFileName(image);
1044     infoPanel->setDimension(dim);
1045     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1046     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1047     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1048     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1049     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1050
1051     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1052                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1053     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1054     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1055
1056     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1057     for (int i = 0; i < 4;i++)
1058       {
1059         if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3)
1060           {
1061             mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1062             break;
1063           }
1064       }
1065     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1066     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1067     // DD(mSlicerManagers[index]->GetColorMap());
1068     // DD(mSlicerManagers[index]->GetPreset());
1069     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1070     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1071
1072     infoPanel->setFileName(image);
1073     infoPanel->setDimension(dim);
1074     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1075     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1076     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1077     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1078     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1079
1080     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1081                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1082     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1083     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1084
1085     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1086     for (int i = 0; i < 4;i++)
1087       {
1088         if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3)
1089           {
1090             mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1091             break;
1092           }
1093       }
1094     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1095     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1096     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1097     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1098
1099     if (mSlicerManagers[index]->GetSlicer(0)->GetVF())
1100       {
1101         overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1102         overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1103                                     mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1104                                     mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1105       }
1106     else
1107       {
1108         overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1109         overlayPanel->getVFProperty(-1,-1,-1);
1110       }
1111     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1112       {
1113         overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1114         overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1115       }
1116     else
1117       {
1118         overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1119         overlayPanel->getOverlayProperty(-1);
1120       }
1121     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion())
1122       {
1123         overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1124         overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1125                                         mSlicerManagers[index]->GetFusionColorMap(),
1126                                         mSlicerManagers[index]->GetFusionWindow(),
1127                                         mSlicerManagers[index]->GetFusionLevel());
1128       }
1129     else
1130       {
1131         overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1132         overlayPanel->getFusionProperty(-1, -1,-1,-1);
1133       }
1134   }
1135 }
1136 //------------------------------------------------------------------------------
1137
1138 //------------------------------------------------------------------------------
1139 void vvMainWindow::ShowDocumentation() {
1140   documentation->show();
1141 }
1142 //------------------------------------------------------------------------------
1143 void vvMainWindow::ShowHelpDialog() {
1144   help_dialog->show();
1145 }
1146 //------------------------------------------------------------------------------
1147
1148 //------------------------------------------------------------------------------
1149 void vvMainWindow::ChangeViewMode() {
1150   QListIterator<int> it0(splitter_3->sizes());
1151   QListIterator<int> it1(splitter_3->sizes());
1152   int max0 = 0;
1153   int max1 = 1;
1154   while (it0.hasNext())
1155     {
1156       max0 += it0.next();
1157     }
1158   while (it1.hasNext())
1159     {
1160       max1 += it1.next();
1161     }
1162   QList<int> size0;
1163   QList<int> size1;
1164   if (viewMode == 1)
1165     {
1166       viewMode = 0;
1167       size0.push_back(max0);
1168       size0.push_back(0);
1169       size1.push_back(max1);
1170       size1.push_back(0);
1171       splitter_3->setSizes(size0);
1172       OSplitter->setSizes(size1);
1173       DataTree->setColumnHidden(2,1);
1174       DataTree->setColumnHidden(3,1);
1175       DataTree->setColumnHidden(4,1);
1176     }
1177   else
1178     {
1179       viewMode = 1;
1180       size0.push_back(int(max0/2));
1181       size0.push_back(int(max0/2));
1182       size1.push_back(int(max1/2));
1183       size1.push_back(int(max1/2));
1184       splitter_3->setSizes(size0);
1185       OSplitter->setSizes(size1);
1186       DataTree->setColumnHidden(2,0);
1187       DataTree->setColumnHidden(3,0);
1188       DataTree->setColumnHidden(4,0);
1189     }
1190 }
1191 //------------------------------------------------------------------------------
1192
1193 //------------------------------------------------------------------------------
1194 QString vvMainWindow::GetSizeInBytes(unsigned long size) {
1195   QString result = "";// QString::number(size);
1196   //result += " bytes (";
1197   if (size > 1000000000)
1198     {
1199       size /= 1000000000;
1200       result += QString::number(size);
1201       result += "Gb";//)";
1202     }
1203   else if (size > 1000000)
1204     {
1205       size /= 1000000;
1206       result += QString::number(size);
1207       result += "Mb";//)";
1208     }
1209   else if (size > 1000)
1210     {
1211       size /= 1000;
1212       result += QString::number(size);
1213       result += "kb";//)";
1214     }
1215   return result;
1216 }
1217 //------------------------------------------------------------------------------
1218
1219 //------------------------------------------------------------------------------
1220 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble) {
1221   QString result;
1222   for (unsigned int i= 0; i < vectorDouble.size(); i++)
1223     {
1224       if (i != 0)
1225         result += " ";
1226       result += QString::number(vectorDouble[i]);
1227     }
1228   return result;
1229 }
1230 //------------------------------------------------------------------------------
1231
1232 //------------------------------------------------------------------------------
1233 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt) {
1234   QString result;
1235   for (unsigned int i= 0; i < vectorInt.size(); i++)
1236     {
1237       if (i != 0)
1238         result += " ";
1239       result += QString::number(vectorInt[i]);
1240     }
1241   return result;
1242 }
1243 //------------------------------------------------------------------------------
1244
1245 //------------------------------------------------------------------------------
1246 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item) {
1247   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1248   for (int i = 0; i < DataTree->topLevelItemCount(); i++)
1249     {
1250       if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1251         return i;
1252     }
1253   return -1;
1254 }
1255 //------------------------------------------------------------------------------
1256
1257 //------------------------------------------------------------------------------
1258 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clicked_item, int column) {
1259   int index = GetSlicerIndexFromItem(clicked_item);
1260   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1261     return;
1262   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
1263     {
1264       QTreeWidgetItem* current_row=DataTree->topLevelItem(i);
1265       if (DataTree->topLevelItem(index) == current_row)
1266         {
1267           vvSlicer* clicked_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1268           if (current_row == clicked_item)
1269             {
1270               //If we just activated a slicer
1271               if (current_row->data(column,Qt::CheckStateRole).toInt() > 0)
1272                 {
1273                   mSlicerManagers[i]->UpdateSlicer(column-1,clicked_item->data(column,Qt::CheckStateRole).toInt());
1274                   mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1275                   DisplaySliders(i,column-1);
1276                   std::map<std::string,int> overlay_counts;
1277                   for (int child = 0; child < current_row->childCount(); child++)
1278                     {
1279                       std::string overlay_type =
1280                         current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1281                       overlay_counts[overlay_type]++;
1282                       current_row->child(child)->setData(column,Qt::CheckStateRole,
1283                                                          current_row->data(column,Qt::CheckStateRole));
1284                       clicked_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,true);
1285                     }
1286                 }
1287               else //We don't allow simply desactivating a slicer
1288                 {
1289                   clicked_item->setData(column,Qt::CheckStateRole,2);
1290                   return;
1291                 }
1292             }
1293           //if we clicked on the vector(or overlay) and not the image
1294           else
1295             {
1296               if (clicked_item->data(column,Qt::CheckStateRole).toInt())
1297                 {
1298                   current_row->setData(column,Qt::CheckStateRole,2);
1299                   mSlicerManagers[i]->UpdateSlicer(column-1,2);
1300                   mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1301                   DisplaySliders(i,column-1);
1302                 }
1303               int vis = clicked_item->data(column,Qt::CheckStateRole).toInt();
1304               std::string overlay_type = clicked_item->data(1,Qt::UserRole).toString().toStdString();
1305               int overlay_index=0;
1306               for (int child = 0; child < current_row->childCount(); child++)
1307                 {
1308                   if (current_row->child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1309                     overlay_index++;
1310                   if (current_row->child(child) == clicked_item) break;
1311                 }
1312               clicked_slicer->SetActorVisibility(
1313                                                  clicked_item->data(1,Qt::UserRole).toString().toStdString(), overlay_index-1,vis);
1314             }
1315         }
1316       else if (current_row->data(column,Qt::CheckStateRole).toInt() > 0)
1317         {
1318           current_row->setData(column,Qt::CheckStateRole,0);
1319           mSlicerManagers[i]->UpdateSlicer(column-1,0);
1320           std::map<std::string,int> overlay_counts;
1321           for (int child = 0; child < current_row->childCount(); child++)
1322             {
1323               std::string overlay_type =
1324                 current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1325               overlay_counts[overlay_type]++;
1326               current_row->child(child)->setData(column,Qt::CheckStateRole,0);
1327               vvSlicer * current_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1328               current_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,false);
1329             }
1330         }
1331       //mSlicerManagers[i]->SetColorMap(-1);
1332       mSlicerManagers[i]->SetColorMap();
1333     }
1334   mSlicerManagers[index]->GetSlicer(column-1)->Render();
1335 }
1336 //------------------------------------------------------------------------------
1337
1338 void vvMainWindow::InitSlicers()
1339 {
1340   if (mSlicerManagers.size())
1341     {
1342       mSlicerManagers.back()->GenerateDefaultLookupTable();
1343
1344       mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1345       mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1346       mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1347       mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1348     }
1349 }
1350
1351 //------------------------------------------------------------------------------
1352 void vvMainWindow::InitDisplay() {
1353   if (mSlicerManagers.size())
1354     {
1355       //BE CAREFUL : this is absolutely necessary to set the interactor style
1356       //in order to have the same style instanciation for all SlicerManagers in
1357       // a same window
1358       for (int j = 0; j < 4; j++)
1359         {
1360           vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1361           style->SetAutoAdjustCameraClippingRange(1);
1362           bool AlreadySelected = false;
1363           for (int i = 0; i < DataTree->topLevelItemCount(); i++)
1364             {
1365               mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1366
1367               //select the image only if previous are not selected
1368               if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1)
1369                 {
1370                   mSlicerManagers[i]->UpdateSlicer(j,1);
1371                   AlreadySelected = true;
1372                 }
1373               else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected)
1374                 {
1375                   if (DataTree->selectedItems().size() == 0)
1376                     DataTree->topLevelItem(i)->setSelected(1);
1377                   DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1378                   mSlicerManagers[i]->UpdateSlicer(j,1);
1379                   DisplaySliders(i,j);
1380                 }
1381               else
1382                 {
1383                   DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1384                   mSlicerManagers[i]->UpdateSlicer(j,0);
1385                 }
1386             }
1387           style->Delete();
1388         }
1389     }
1390 }
1391 //------------------------------------------------------------------------------
1392
1393 //------------------------------------------------------------------------------
1394 void vvMainWindow::DisplaySliders(int slicer, int window) {
1395   int range[2];
1396   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1397   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1398
1399   int tRange[2];
1400   tRange[0] = 0;
1401   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1402   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1403   bool showHorizontal = false;
1404   bool showVertical = false;
1405   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1406       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1407           && mSlicerManagers[slicer]->GetType() != IMAGEWITHTIME
1408           && mSlicerManagers[slicer]->GetType() != MERGEDWITHTIME))
1409     showVertical = true;
1410   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1411       || mSlicerManagers[slicer]->GetType() == IMAGEWITHTIME
1412       || mSlicerManagers[slicer]->GetType() == MERGEDWITHTIME)
1413     showHorizontal = true;
1414
1415   if (showVertical)
1416     verticalSliders[window]->show();
1417   else
1418     verticalSliders[window]->hide();
1419   verticalSliders[window]->setRange(range[0],range[1]);
1420   verticalSliders[window]->setValue(position);
1421
1422   if (showHorizontal)
1423     horizontalSliders[window]->show();
1424   else
1425     horizontalSliders[window]->hide();
1426   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1427   horizontalSliders[window]->setValue(tPosition);
1428 }
1429 //------------------------------------------------------------------------------
1430
1431 //------------------------------------------------------------------------------
1432 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column) {
1433   int index = GetSlicerIndexFromItem(item);
1434
1435   if (DataTree->topLevelItem(index) != item)
1436     {
1437       QString warning = "Do you really want to close the overlay : ";
1438       warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1439       QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1440                          warning, 0, this);
1441       msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1442       msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1443       if (msgBox.exec() == QMessageBox::AcceptRole)
1444         {
1445           std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1446           int overlay_index=0;
1447           for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1448             {
1449               if (DataTree->topLevelItem(index)->\
1450                   child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1451                 overlay_index++;
1452               if (DataTree->topLevelItem(index)->child(child) == item) break;
1453             }
1454           mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1455           mSlicerManagers[index]->SetColorMap(0);
1456           DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1457           mSlicerManagers[index]->Render();
1458         }
1459     }
1460   else if (DataTree->topLevelItemCount() <= 1)
1461     {
1462       QString warning = "Do you really want to close the image : ";
1463       warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1464       warning += "\nThis is the last image, you're about to close vv !!!";
1465       QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1466                          warning, 0, this);
1467       msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1468       msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1469       if (msgBox.exec() == QMessageBox::AcceptRole)
1470         {
1471           this->close();
1472         }
1473     }
1474   else
1475     {
1476       QString warning = "Do you really want to close the image : ";
1477       warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1478       QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1479                          warning, 0, this);
1480       msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1481       msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1482       if (msgBox.exec() == QMessageBox::AcceptRole)
1483         {
1484
1485           // Tell tools that we close an image
1486           emit AnImageIsBeingClosed(mSlicerManagers[index]);
1487
1488           std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1489           DataTree->takeTopLevelItem(index);
1490           for (int i = 0; i < index; i++)
1491             {
1492               Manageriter++;
1493             }
1494           linkPanel->removeImage(index);
1495           mSlicerManagers[index]->RemoveActors();
1496           delete mSlicerManagers[index];
1497           mSlicerManagers.erase(Manageriter);
1498
1499           //
1500           InitDisplay();
1501         }
1502     }
1503 }
1504 //------------------------------------------------------------------------------
1505
1506 //------------------------------------------------------------------------------
1507 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column) {
1508   // int index = GetSlicerIndexFromItem(item);
1509   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1510   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1511   //     mSlicerManagers[index]->ReloadVF();
1512   //   else
1513   //     mSlicerManagers[index]->Reload();
1514
1515   //   QApplication::restoreOverrideCursor();
1516   int index = GetSlicerIndexFromItem(item);
1517   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1518   QString role=item->data(1,Qt::UserRole).toString();
1519   if ( role == "vector")
1520     mSlicerManagers[index]->ReloadVF();
1521   else if (role == "overlay")
1522     mSlicerManagers[index]->ReloadOverlay();
1523   else if (role == "fusion")
1524     mSlicerManagers[index]->ReloadFusion();
1525   else
1526     mSlicerManagers[index]->Reload();
1527   QApplication::restoreOverrideCursor();
1528 }
1529 //------------------------------------------------------------------------------
1530
1531 // void vvMainWindow::CropImage()
1532 // {
1533 //   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1534 //   vvCropDialog crop(mSlicerManagers,index);
1535 //   if(crop.exec())
1536 //     AddImage(crop.GetOutput(),"cropped.mhd");
1537 // }
1538
1539 //------------------------------------------------------------------------------
1540 void vvMainWindow::SplitImage() {
1541   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1542   int dim = mSlicerManagers[index]->GetDimension();
1543   QString warning = "Do you really want to split the ";
1544   warning += QString::number(dim) + "D image ";
1545   warning += DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString() + " into ";
1546   warning += QString::number(mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetSize()[dim-1]) + " ";
1547   warning += QString::number(dim-1) + "D images.";
1548   QMessageBox msgBox(QMessageBox::Warning, tr("Split Image"),
1549                      warning, 0, this);
1550   msgBox.addButton(tr("Split"), QMessageBox::AcceptRole);
1551   msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1552   if (msgBox.exec() == QMessageBox::AcceptRole)
1553     {
1554       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1555       if (dim > 2)
1556         {
1557           std::string filename = DataTree->selectedItems()[0]->data(0,Qt::UserRole).toString().toStdString();
1558           int numberOfSlice = mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetSize()[dim-1];
1559           std::string path = itksys::SystemTools::GetFilenamePath(
1560                                                                   filename);
1561           path += "/";
1562           path += DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString().toStdString();
1563           path += "%03d";
1564           path += itksys::SystemTools::GetFilenameLastExtension(
1565                                                                 filename).c_str();
1566
1567           typedef itk::NumericSeriesFileNames NameGeneratorType;
1568           NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
1569           nameGenerator->SetSeriesFormat(path.c_str());
1570           nameGenerator->SetStartIndex(0);
1571           nameGenerator->SetEndIndex(numberOfSlice-1);
1572           nameGenerator->SetIncrementIndex(1);
1573
1574           for (int i = 0; i < numberOfSlice; i++)
1575             {
1576               vvSlicerManager* imageManager = new vvSlicerManager(4);
1577               imageManager->SetExtractedImage(nameGenerator->GetFileNames()[i],
1578                                               mSlicerManagers[index]->GetSlicer(0)->GetImage(), i);
1579               mSlicerManagers.push_back(imageManager);
1580
1581               //create an item in the tree with good settings
1582               QTreeWidgetItem *item = new QTreeWidgetItem();
1583               item->setData(0,Qt::UserRole,nameGenerator->GetFileNames()[i].c_str());
1584               std::string fileI = itksys::SystemTools::GetFilenameWithoutLastExtension(
1585                                                                                        nameGenerator->GetFileNames()[i]).c_str();
1586               item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileI.c_str());
1587               for (int j = 1; j <= 4; j++)
1588                 {
1589                   for (int i = 0; i < DataTree->topLevelItemCount(); i++)
1590                     {
1591                       DataTree->topLevelItem(i)->setData(j,Qt::CheckStateRole,0);
1592                     }
1593                   item->setData(j,Qt::CheckStateRole,2);
1594                 }
1595
1596               //Create the buttons for reload and close
1597               QTreePushButton* cButton = new QTreePushButton;
1598               cButton->setItem(item);
1599               cButton->setColumn(COLUMN_CLOSE_IMAGE);
1600               cButton->setToolTip(tr("close image"));
1601               cButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")));
1602               connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1603                       this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1604
1605               QTreePushButton* rButton = new QTreePushButton;
1606               rButton->setItem(item);
1607               rButton->setColumn(COLUMN_RELOAD_IMAGE);
1608               rButton->setToolTip(tr("reload image"));
1609               rButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")));
1610               rButton->setEnabled(false);
1611               connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1612                       this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1613
1614               DataTree->addTopLevelItem(item);
1615               DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1616               DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1617
1618               //set the id of the image
1619               QString id = nameGenerator->GetFileNames()[i].c_str() + QString::number(mSlicerManagers.size()-1);
1620               item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1621               mSlicerManagers.back()->SetId(id.toStdString());
1622               linkPanel->addImage(fileI, id.toStdString());
1623               connect(mSlicerManagers.back(),SIGNAL(currentImageChanged(std::string)),
1624                       this,SLOT(CurrentImageChanged(std::string)));
1625               connect(mSlicerManagers.back(),SIGNAL(
1626                                                     UpdatePosition(int, double, double, double, double, double, double, double)),this,
1627                       SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
1628               connect(mSlicerManagers.back(),SIGNAL(UpdateVector(int, double, double, double, double)),
1629                       this, SLOT(VectorChanged(int,double,double,double, double)));
1630               connect(mSlicerManagers.back(),SIGNAL(UpdateOverlay(int, double, double)),
1631                       this, SLOT(OverlayChanged(int,double,double)));
1632               connect(mSlicerManagers.back(),SIGNAL(UpdateFusion(int, double)),
1633                       this, SLOT(FusionChanged(int,double)));
1634               connect(mSlicerManagers.back(),SIGNAL(UpdateWindows(int, int, int)),
1635                       this,SLOT(WindowsChanged(int, int, int)));
1636               connect(mSlicerManagers.back(),SIGNAL(WindowLevelChanged(double, double,int, int)),
1637                       this,SLOT(WindowLevelChanged(double, double, int, int)));
1638               connect(mSlicerManagers.back(),SIGNAL(UpdateSlice(int,int)),
1639                       this,SLOT(UpdateSlice(int,int)));
1640               connect(mSlicerManagers.back(),SIGNAL(UpdateTSlice(int, int)),
1641                       this,SLOT(UpdateTSlice(int, int)));
1642               connect(mSlicerManagers.back(),SIGNAL(UpdateSliceRange(int,int,int,int,int)),
1643                       this,SLOT(UpdateSliceRange(int,int,int,int,int)));
1644               connect(mSlicerManagers.back(),SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
1645                       this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
1646               connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
1647               UpdateTree();
1648               qApp->processEvents();
1649               InitSlicers();
1650               InitDisplay();
1651               qApp->processEvents();
1652             }
1653           QApplication::restoreOverrideCursor();
1654         }
1655       else
1656         {
1657           QApplication::restoreOverrideCursor();
1658           QString error = "Cannot split file (dimensions must be greater than 2) ";
1659           QMessageBox::information(this,tr("Splitting problem"),error);
1660         }
1661     }
1662 }
1663 //------------------------------------------------------------------------------
1664
1665 //------------------------------------------------------------------------------
1666 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value) {
1667   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1668 }
1669 //------------------------------------------------------------------------------
1670
1671 //------------------------------------------------------------------------------
1672 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value) {
1673   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1674 }
1675 //------------------------------------------------------------------------------
1676
1677 //------------------------------------------------------------------------------
1678 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef) {
1679   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1680 }
1681 //------------------------------------------------------------------------------
1682
1683 //------------------------------------------------------------------------------
1684 void vvMainWindow::FusionChanged(int visibility, double value) {
1685   overlayPanel->getCurrentFusionInfo(visibility,value);
1686 }
1687 //------------------------------------------------------------------------------
1688
1689 //------------------------------------------------------------------------------
1690 void vvMainWindow::WindowsChanged(int window, int view, int slice) {
1691   infoPanel->setViews(window, view, slice);
1692 }
1693 //------------------------------------------------------------------------------
1694
1695 //------------------------------------------------------------------------------
1696 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap) {
1697   windowSpinBox->setValue(window);
1698   levelSpinBox->setValue(level);
1699   colorMapComboBox->setCurrentIndex(colormap);
1700   presetComboBox->setCurrentIndex(preset);
1701 }
1702 //------------------------------------------------------------------------------
1703
1704 //------------------------------------------------------------------------------
1705 void vvMainWindow::WindowLevelEdited() {
1706   presetComboBox->setCurrentIndex(6);
1707   UpdateWindowLevel();
1708 }
1709 //------------------------------------------------------------------------------
1710
1711 //------------------------------------------------------------------------------
1712 void vvMainWindow::UpdateWindowLevel() {
1713   if (DataTree->selectedItems().size())
1714     {
1715       if (presetComboBox->currentIndex() == 7) //For ventilation
1716         colorMapComboBox->setCurrentIndex(5);
1717       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1718       mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1719       mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1720       mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1721       mSlicerManagers[index]->Render();
1722     }
1723 }
1724 //------------------------------------------------------------------------------
1725
1726 //------------------------------------------------------------------------------
1727 void vvMainWindow::UpdateColorMap() {
1728   if (DataTree->selectedItems().size())
1729     {
1730       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1731       mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1732       mSlicerManagers[index]->Render();
1733     }
1734 }
1735 //------------------------------------------------------------------------------
1736 void vvMainWindow::SwitchWindowLevel() {
1737   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1738   int window = mSlicerManagers[index]->GetColorWindow();
1739   presetComboBox->setCurrentIndex(6);
1740   windowSpinBox->setValue(-window);
1741   UpdateWindowLevel();
1742 }
1743 //------------------------------------------------------------------------------
1744
1745 //------------------------------------------------------------------------------
1746 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps) {
1747   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
1748     {
1749       if (mSlicerManagers[i]->GetId() == id)
1750         {
1751           //mSlicerManagers[i]->SetTSlice(temps);
1752           mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1753           mSlicerManagers[i]->UpdateViews(0,slicer);
1754           break;
1755         }
1756     }
1757 }
1758 //------------------------------------------------------------------------------
1759
1760 //------------------------------------------------------------------------------
1761 void vvMainWindow::ShowContextMenu(QPoint point) {
1762   if (!DataTree->selectedItems().size())
1763     {
1764       contextActions[1]->setEnabled(0);
1765       contextActions[2]->setEnabled(0);
1766       contextActions[3]->setEnabled(0);
1767       contextActions[4]->setEnabled(0);
1768       contextActions[5]->setEnabled(0);
1769       contextActions[6]->setEnabled(0);
1770       contextActions[7]->setEnabled(0);
1771     }
1772   else
1773     {
1774       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1775       contextActions[1]->setEnabled(1);
1776       contextActions[2]->setEnabled(
1777                                     DataTree->itemWidget(DataTree->selectedItems()[0],
1778                                                          COLUMN_RELOAD_IMAGE)->isEnabled());
1779       contextActions[3]->setEnabled(1);
1780       contextActions[5]->setEnabled(1);
1781       contextActions[6]->setEnabled(1);
1782       contextActions[7]->setEnabled(1);
1783
1784       if (mSlicerManagers[index]->GetDimension() < 3)
1785         contextActions[4]->setEnabled(0);
1786       else
1787         contextActions[4]->setEnabled(1);
1788     }
1789   contextMenu.exec(QCursor::pos());
1790 }
1791 //------------------------------------------------------------------------------
1792
1793 //------------------------------------------------------------------------------
1794 void vvMainWindow::CloseImage() {
1795   CloseImage(DataTree->selectedItems()[0],0);
1796 }
1797 //------------------------------------------------------------------------------
1798
1799 //------------------------------------------------------------------------------
1800 void vvMainWindow::ReloadImage() {
1801   ReloadImage(DataTree->selectedItems()[0],0);
1802 }
1803 //------------------------------------------------------------------------------
1804
1805 //------------------------------------------------------------------------------
1806 void vvMainWindow::SelectOverlayImage() {
1807   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1808
1809   //check if one overlay image is added
1810   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1811     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay")
1812       {
1813         QString error = "Cannot add more than one compared image\n";
1814         error += "Please remove first ";
1815         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1816         QMessageBox::information(this,tr("Problem adding compared image !"),error);
1817         return;
1818       }
1819
1820   QString Extensions = EXTENSIONS;
1821   Extensions += ";;All Files (*)";
1822   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1823   if (!file.isEmpty())
1824     AddOverlayImage(index,file);
1825 }
1826 //------------------------------------------------------------------------------
1827
1828 //------------------------------------------------------------------------------
1829 void vvMainWindow::AddOverlayImage(int index, QString file) {
1830   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1831   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1832                                                                         file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1833   reader->SetFileName(file.toStdString().c_str());
1834   reader->ReadImageInformation();
1835   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1836   int dimension = reader->GetNumberOfDimensions();
1837   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1838   vvProgressDialog progress("Opening " + file.toStdString());
1839   qApp->processEvents();
1840
1841   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1842   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component))
1843     {
1844       //create an item in the tree with good settings
1845       QTreeWidgetItem *item = new QTreeWidgetItem();
1846       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1847       item->setData(1,Qt::UserRole,tr("overlay"));
1848       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
1849       qApp->processEvents();
1850
1851       for (int j = 1; j <= 4; j++)
1852         {
1853           item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1854           mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("overlay",0,
1855                                                                      DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1856         }
1857
1858       //Create the buttons for reload and close
1859       qApp->processEvents();
1860       QTreePushButton* cButton = new QTreePushButton;
1861       cButton->setItem(item);
1862       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1863       cButton->setToolTip(tr("close image"));
1864       cButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")));
1865       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1866               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1867
1868       QTreePushButton* rButton = new QTreePushButton;
1869       rButton->setItem(item);
1870       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1871       rButton->setToolTip(tr("reload image"));
1872       rButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")));
1873       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1874               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1875
1876       DataTree->topLevelItem(index)->setExpanded(1);
1877       DataTree->topLevelItem(index)->addChild(item);
1878       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1879       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1880
1881       //set the id of the image
1882       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1883       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1884       UpdateTree();
1885       qApp->processEvents();
1886       ImageInfoChanged();
1887       QApplication::restoreOverrideCursor();
1888     }
1889   else
1890     {
1891       QApplication::restoreOverrideCursor();
1892       QString error = "Cannot import the new image.\n";
1893       error += mSlicerManagers[index]->GetLastError().c_str();
1894       QMessageBox::information(this,tr("Problem reading image !"),error);
1895     }
1896 }
1897
1898 void vvMainWindow::AddFusionImage()
1899 {
1900   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1901
1902   //check if one fusion image is added
1903   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1904     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion")
1905       {
1906         QString error = "Cannot add more than one fusion image\n";
1907         error += "Please remove first ";
1908         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1909         QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1910         return;
1911       }
1912
1913   QString Extensions = EXTENSIONS;
1914   Extensions += ";;All Files (*)";
1915   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1916   if (!file.isEmpty())
1917     {
1918       mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1919       itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1920                                                                             file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1921       reader->SetFileName(file.toStdString().c_str());
1922       reader->ReadImageInformation();
1923       std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1924       if (reader)
1925         {
1926           QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1927           vvProgressDialog progress("Opening fusion");
1928           qApp->processEvents();
1929
1930           std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1931           if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1932                                                 reader->GetNumberOfDimensions(), component))
1933             {
1934               //create an item in the tree with good settings
1935               QTreeWidgetItem *item = new QTreeWidgetItem();
1936               item->setData(0,Qt::UserRole,file.toStdString().c_str());
1937               item->setData(1,Qt::UserRole,tr("fusion"));
1938               item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
1939               qApp->processEvents();
1940
1941               for (int j = 1; j <= 4; j++)
1942                 {
1943                   item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1944                   mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("fusion",0,
1945                                                                              DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1946                 }
1947
1948               //Create the buttons for reload and close
1949               qApp->processEvents();
1950               QTreePushButton* cButton = new QTreePushButton;
1951               cButton->setItem(item);
1952               cButton->setColumn(COLUMN_CLOSE_IMAGE);
1953               cButton->setToolTip(tr("close image"));
1954               cButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")));
1955               connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1956                       this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1957
1958               QTreePushButton* rButton = new QTreePushButton;
1959               rButton->setItem(item);
1960               rButton->setColumn(COLUMN_RELOAD_IMAGE);
1961               rButton->setToolTip(tr("reload image"));
1962               rButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")));
1963               connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1964                       this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1965
1966               DataTree->topLevelItem(index)->setExpanded(1);
1967               DataTree->topLevelItem(index)->addChild(item);
1968               DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1969               DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1970
1971               //set the id of the image
1972               QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1973               item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1974               UpdateTree();
1975               qApp->processEvents();
1976               ImageInfoChanged();
1977               QApplication::restoreOverrideCursor();
1978             }
1979           else
1980             {
1981               QApplication::restoreOverrideCursor();
1982               QString error = "Cannot import the new image.\n";
1983               error += mSlicerManagers[index]->GetLastError().c_str();
1984               QMessageBox::information(this,tr("Problem reading image !"),error);
1985             }
1986         }
1987       else
1988         {
1989           QString error = "Cannot import the new image.\n";
1990           QMessageBox::information(this,tr("Problem reading image !"),error);
1991         }
1992     }
1993 }
1994
1995
1996 void vvMainWindow::OpenField()
1997 {
1998   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1999   //check if a vector field has already been added
2000   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2001     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector")
2002       {
2003         QString error = "Cannot add more than one vector field\n";
2004         error += "Please remove first ";
2005         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2006         QMessageBox::information(this,tr("Problem adding vector field!"),error);
2007         return;
2008       }
2009
2010   QString Extensions = "Images ( *.mhd)";
2011   Extensions += ";;Images ( *.vf)";
2012   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2013   if (!file.isEmpty())
2014     AddField(file,index);
2015 }
2016
2017 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2018 {
2019   //create an item in the tree with good settings
2020   QTreeWidgetItem *item = new QTreeWidgetItem();
2021   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2022   item->setData(1,Qt::UserRole,tr("vector"));
2023   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename);
2024   qApp->processEvents();
2025
2026   for (int j = 1; j <= 4; j++)
2027     {
2028       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2029       mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("vector",0,
2030                                                                  DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
2031     }
2032
2033   //Create the buttons for reload and close
2034   qApp->processEvents();
2035   QTreePushButton* cButton = new QTreePushButton;
2036   cButton->setItem(item);
2037   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2038   cButton->setToolTip(tr("close vector field"));
2039   cButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")));
2040   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2041           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2042
2043   QTreePushButton* rButton = new QTreePushButton;
2044   rButton->setItem(item);
2045   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2046   rButton->setToolTip(tr("reload vector field"));
2047   rButton->setEnabled(from_disk);
2048   rButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")));
2049   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2050           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2051
2052   DataTree->topLevelItem(index)->setExpanded(1);
2053   DataTree->topLevelItem(index)->addChild(item);
2054   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2055   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2056
2057   //set the id of the image
2058   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2059   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2060   UpdateTree();
2061   qApp->processEvents();
2062   ImageInfoChanged();
2063   QApplication::restoreOverrideCursor();
2064 }
2065
2066 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2067 {
2068   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2069   vvSlicerManager* imageManager = mSlicerManagers[index];
2070   if (imageManager->SetVF(vf,file.toStdString()))
2071     {
2072       AddFieldEntry(file,index,false);
2073     }
2074   else
2075     {
2076       QString error = "Cannot import the vector field for this image.\n";
2077       error += imageManager->GetLastError().c_str();
2078       QMessageBox::information(this,tr("Problem reading VF !"),error);
2079     }
2080   QApplication::restoreOverrideCursor();
2081 }
2082
2083 void vvMainWindow::AddField(QString file,int index)
2084 {
2085   if (QFile::exists(file))
2086     {
2087       mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2088
2089       //init the progress events
2090       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2091       vvProgressDialog progress("Opening " + file.toStdString());
2092       qApp->processEvents();
2093
2094       //read the vector and put it in the current mSlicerManager
2095       vvSlicerManager* imageManager = mSlicerManagers[index];
2096       qApp->processEvents();
2097
2098       std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2099       if (imageManager->SetVF(file.toStdString()))
2100         {
2101           imageManager->Render();
2102           AddFieldEntry(file,index,true);
2103         }
2104       else
2105         {
2106           QApplication::restoreOverrideCursor();
2107           QString error = "Cannot import the vector field for this image.\n";
2108           error += imageManager->GetLastError().c_str();
2109           QMessageBox::information(this,tr("Problem reading VF !"),error);
2110         }
2111     }
2112   else
2113     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2114
2115 }
2116 //------------------------------------------------------------------------------
2117
2118 //------------------------------------------------------------------------------
2119 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log) {
2120   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2121   if (mSlicerManagers[index]->GetSlicer(0)->GetVF())
2122     {
2123       for (int i = 0; i < 4; i++)
2124         {
2125           mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2126           mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2127           if (log > 0)
2128             mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2129           else
2130             mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2131         }
2132     }
2133 }
2134 //------------------------------------------------------------------------------
2135
2136 //------------------------------------------------------------------------------
2137 void vvMainWindow::SetOverlayProperty(int color) {
2138   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2139   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
2140     {
2141       mSlicerManagers[index]->SetOverlayColor(color);
2142       mSlicerManagers[index]->SetColorMap(0);
2143       mSlicerManagers[index]->Render();
2144     }
2145 }
2146 //------------------------------------------------------------------------------
2147
2148 //------------------------------------------------------------------------------
2149 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level) {
2150   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2151   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion())
2152     {
2153       mSlicerManagers[index]->SetFusionOpacity(opacity);
2154       mSlicerManagers[index]->SetFusionColorMap(colormap);
2155       mSlicerManagers[index]->SetFusionWindow(window);
2156       mSlicerManagers[index]->SetFusionLevel(level);
2157       mSlicerManagers[index]->SetColorMap(0);
2158       mSlicerManagers[index]->Render();
2159     }
2160 }
2161 //------------------------------------------------------------------------------
2162
2163 //------------------------------------------------------------------------------
2164 void vvMainWindow::SaveAs() {
2165   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector")
2166     {
2167       QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2168       return;
2169     }
2170
2171   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2172   int dimension = mSlicerManagers[index]->GetDimension();
2173   QStringList OutputListeFormat;
2174   OutputListeFormat.clear();
2175   if (dimension == 1)
2176     {
2177       OutputListeFormat.push_back(".mhd");
2178     }
2179   if (dimension == 2)
2180     {
2181       OutputListeFormat.push_back(".bmp");
2182       OutputListeFormat.push_back(".png");
2183       OutputListeFormat.push_back(".jpeg");
2184       OutputListeFormat.push_back(".tif");
2185       OutputListeFormat.push_back(".mhd");
2186       OutputListeFormat.push_back(".hdr");
2187       OutputListeFormat.push_back(".vox");
2188     }
2189   else if (dimension == 3)
2190     {
2191       OutputListeFormat.push_back(".mhd");
2192       OutputListeFormat.push_back(".hdr");
2193       OutputListeFormat.push_back(".vox");
2194     }
2195   else if (dimension == 4)
2196     {
2197       OutputListeFormat.push_back(".mhd");
2198     }
2199   QString Extensions = "AllFiles(*.*)";
2200   for (int i = 0; i < OutputListeFormat.count(); i++)
2201     {
2202       Extensions += ";;Images ( *";
2203       Extensions += OutputListeFormat[i];
2204       Extensions += ")";
2205     }
2206   QString fileName = QFileDialog::getSaveFileName(this,
2207                                                   tr("Save As"),
2208                                                   mSlicerManagers[index]->GetFileName().c_str(),
2209                                                   Extensions);
2210   if (!fileName.isEmpty())
2211     {
2212       std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2213       if (OutputListeFormat.contains(
2214                                      fileformat.c_str()))
2215         {
2216           QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2217           std::string action = "Saving";
2218           vvProgressDialog progress("Saving "+fileName.toStdString());
2219           qApp->processEvents();
2220           vvImageWriter *writer = new vvImageWriter;
2221           writer->SetOutputFileName(fileName.toStdString());
2222           writer->SetInput(mSlicerManagers[index]->GetImage());
2223           writer->Update();
2224           QApplication::restoreOverrideCursor();
2225           if (writer->GetLastError().size())
2226             {
2227               QString error = "Saving did not succeed\n";
2228               error += writer->GetLastError().c_str();
2229               QMessageBox::information(this,tr("Saving Problem"),error);
2230               SaveAs();
2231             }
2232         }
2233       else
2234         {
2235           QString error = fileformat.c_str();
2236           if (error.isEmpty())
2237             error += "no file format specified !";
2238           else
2239             error += " format unknown !!!\n";
2240           QMessageBox::information(this,tr("Saving Problem"),error);
2241           SaveAs();
2242         }
2243     }
2244 }
2245 //------------------------------------------------------------------------------
2246
2247 //------------------------------------------------------------------------------
2248 void vvMainWindow::AddLink(QString image1,QString image2) {
2249   for (unsigned int i = 0; i < mSlicerManagers.size();i++)
2250     {
2251       if (image1.toStdString() == mSlicerManagers[i]->GetId())
2252         {
2253           mSlicerManagers[i]->AddLink(image2.toStdString());
2254         }
2255       if (image2.toStdString() == mSlicerManagers[i]->GetId())
2256         {
2257           mSlicerManagers[i]->AddLink(image1.toStdString());
2258         }
2259     }
2260 }
2261 //------------------------------------------------------------------------------
2262
2263 //------------------------------------------------------------------------------
2264 void vvMainWindow::RemoveLink(QString image1,QString image2) {
2265   for (unsigned int i = 0; i < mSlicerManagers.size();i++)
2266     {
2267       if (image1.toStdString() == mSlicerManagers[i]->GetId())
2268         {
2269           mSlicerManagers[i]->RemoveLink(image2.toStdString());
2270         }
2271       if (image2.toStdString() == mSlicerManagers[i]->GetId())
2272         {
2273           mSlicerManagers[i]->RemoveLink(image1.toStdString());
2274         }
2275     }
2276 }
2277 //------------------------------------------------------------------------------
2278
2279 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2280 {
2281   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2282     {
2283       if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1)
2284         {
2285           for (int j = 0; j < 4; j++)
2286             {
2287               mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2288               //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2289               //UpdateTSlice(j,value);
2290             }
2291           mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2292           break;
2293         }
2294     }
2295 }
2296
2297 //------------------------------------------------------------------------------
2298 void vvMainWindow::NOHorizontalSliderMoved() {
2299   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2300 }
2301 //------------------------------------------------------------------------------
2302
2303 //------------------------------------------------------------------------------
2304 void vvMainWindow::NEHorizontalSliderMoved() {
2305   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2306 }
2307 //------------------------------------------------------------------------------
2308
2309 //------------------------------------------------------------------------------
2310 void vvMainWindow::SOHorizontalSliderMoved() {
2311   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2312 }
2313 //------------------------------------------------------------------------------
2314
2315 //------------------------------------------------------------------------------
2316 void vvMainWindow::SEHorizontalSliderMoved() {
2317   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2318 }
2319 //------------------------------------------------------------------------------
2320
2321 //------------------------------------------------------------------------------
2322 void vvMainWindow::NOVerticalSliderChanged() {
2323   int value = NOVerticalSlider->value();
2324   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2325     {
2326       if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
2327         {
2328           mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2329           mSlicerManagers[i]->UpdateSlice(0); // <-- DS add this. Not too much update ?
2330           break;
2331         }
2332     }
2333 }
2334 //------------------------------------------------------------------------------
2335
2336 //------------------------------------------------------------------------------
2337 void vvMainWindow::NEVerticalSliderChanged() {
2338   int value = NEVerticalSlider->value();
2339   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2340     {
2341       if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1)
2342         {
2343           mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2344           break;
2345         }
2346     }
2347 }
2348 //------------------------------------------------------------------------------
2349
2350 //------------------------------------------------------------------------------
2351 void vvMainWindow::SOVerticalSliderChanged() {
2352   int value = SOVerticalSlider->value();
2353   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2354     {
2355       if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
2356         {
2357           mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2358           break;
2359         }
2360     }
2361 }
2362 //------------------------------------------------------------------------------
2363
2364 //------------------------------------------------------------------------------
2365 void vvMainWindow::SEVerticalSliderChanged() {
2366   int value = SEVerticalSlider->value();
2367   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2368     {
2369       if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1)
2370         {
2371           mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2372           break;
2373         }
2374     }
2375 }
2376 //------------------------------------------------------------------------------
2377
2378 //------------------------------------------------------------------------------
2379 void vvMainWindow::UpdateSlice(int slicer, int slice) {
2380   if (slicer == 0) {
2381     if (slice != NOVerticalSlider->value())
2382       NOVerticalSlider->setValue(slice);
2383   }
2384   else if (slicer == 1)
2385     NEVerticalSlider->setValue(slice);
2386   else if (slicer == 2)
2387     SOVerticalSlider->setValue(slice);
2388   else if (slicer == 3)
2389     SEVerticalSlider->setValue(slice);
2390 }
2391 //------------------------------------------------------------------------------
2392
2393 //------------------------------------------------------------------------------
2394 void vvMainWindow::UpdateTSlice(int slicer, int slice) {
2395   switch (slicer)
2396     {
2397     case 0:
2398       NOHorizontalSlider->setValue(slice);
2399       break;
2400     case 1:
2401       NEHorizontalSlider->setValue(slice);
2402       break;
2403     case 2:
2404       SOHorizontalSlider->setValue(slice);
2405       break;
2406     case 3:
2407       SEHorizontalSlider->setValue(slice);
2408       break;
2409     }
2410 }
2411 //------------------------------------------------------------------------------
2412
2413 //------------------------------------------------------------------------------
2414 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax) {
2415   int position = int((min+max)/2);
2416   int tPosition = int((tmin+tmax)/2);
2417   if (slicer == 0)
2418     {
2419       NOVerticalSlider->setValue(position);
2420       NOVerticalSlider->setRange(min,max);
2421       NOHorizontalSlider->setRange(tmin,tmax);
2422       NOHorizontalSlider->setValue(tPosition);
2423     }
2424   else if (slicer == 1)
2425     {
2426       NEVerticalSlider->setValue(position);
2427       NEVerticalSlider->setRange(min,max);
2428       NEHorizontalSlider->setRange(tmin,tmax);
2429       NEHorizontalSlider->setValue(tPosition);
2430     }
2431   else if (slicer == 2)
2432     {
2433       SOVerticalSlider->setValue(position);
2434       SOVerticalSlider->setRange(min,max);
2435       SOHorizontalSlider->setRange(tmin,tmax);
2436       SOHorizontalSlider->setValue(tPosition);
2437     }
2438   else if (slicer == 3)
2439     {
2440       SEVerticalSlider->setValue(position);
2441       SEVerticalSlider->setRange(min,max);
2442       SEHorizontalSlider->setRange(tmin,tmax);
2443       SEHorizontalSlider->setValue(tPosition);
2444     }
2445 }
2446 //------------------------------------------------------------------------------
2447
2448 //------------------------------------------------------------------------------
2449 void vvMainWindow::SaveNOScreenshot() {
2450   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2451   w2i->SetInput(NOViewWidget->GetRenderWindow());
2452   w2i->Update();
2453   SaveScreenshot(w2i->GetOutput());
2454   w2i->Delete();
2455 }
2456 //------------------------------------------------------------------------------
2457
2458 //------------------------------------------------------------------------------
2459 void vvMainWindow::SaveNEScreenshot() {
2460   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2461   w2i->SetInput(NEViewWidget->GetRenderWindow());
2462   w2i->Update();
2463   SaveScreenshot(w2i->GetOutput());
2464   w2i->Delete();
2465 }
2466 //------------------------------------------------------------------------------
2467
2468 //------------------------------------------------------------------------------
2469 void vvMainWindow::SaveSOScreenshot() {
2470   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2471   w2i->SetInput(SOViewWidget->GetRenderWindow());
2472   w2i->Update();
2473   SaveScreenshot(w2i->GetOutput());
2474   w2i->Delete();
2475 }
2476 //------------------------------------------------------------------------------
2477
2478 //------------------------------------------------------------------------------
2479 void vvMainWindow::SaveSEScreenshot() {
2480   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2481   w2i->SetInput(SEViewWidget->GetRenderWindow());
2482   w2i->Update();
2483   SaveScreenshot(w2i->GetOutput());
2484   w2i->Delete();
2485 }
2486 //------------------------------------------------------------------------------
2487
2488 //------------------------------------------------------------------------------
2489 void vvMainWindow::SaveScreenshot(vtkImageData* image) {
2490   QString Extensions = "Images( *.png);;";
2491   Extensions += "Images( *.jpg);;";
2492   Extensions += "Images( *.bmp);;";
2493   Extensions += "Images( *.tif);;";
2494   Extensions += "Images( *.ppm)";
2495   QString fileName = QFileDialog::getSaveFileName(this,
2496                                                   tr("Save As"),
2497                                                   itksys::SystemTools::GetFilenamePath(
2498                                                                                        mSlicerManagers[0]->GetFileName()).c_str(),
2499                                                   Extensions);
2500   if (!fileName.isEmpty())
2501     {
2502       const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2503       if (!strcmp(ext, ".bmp"))
2504         {
2505           vtkBMPWriter *bmp = vtkBMPWriter::New();
2506           bmp->SetInput(image);
2507           bmp->SetFileName(fileName.toStdString().c_str());
2508           bmp->Write();
2509           bmp->Delete();
2510         }
2511       else if (!strcmp(ext, ".tif"))
2512         {
2513           vtkTIFFWriter *tif = vtkTIFFWriter::New();
2514           tif->SetInput(image);
2515           tif->SetFileName(fileName.toStdString().c_str());
2516           tif->Write();
2517           tif->Delete();
2518         }
2519       else if (!strcmp(ext, ".ppm"))
2520         {
2521           vtkPNMWriter *pnm = vtkPNMWriter::New();
2522           pnm->SetInput(image);
2523           pnm->SetFileName(fileName.toStdString().c_str());
2524           pnm->Write();
2525           pnm->Delete();
2526         }
2527       else if (!strcmp(ext, ".png"))
2528         {
2529           vtkPNGWriter *png = vtkPNGWriter::New();
2530           png->SetInput(image);
2531           png->SetFileName(fileName.toStdString().c_str());
2532           png->Write();
2533           png->Delete();
2534         }
2535       else if (!strcmp(ext, ".jpg"))
2536         {
2537           vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2538           jpg->SetInput(image);
2539           jpg->SetFileName(fileName.toStdString().c_str());
2540           jpg->Write();
2541           jpg->Delete();
2542         }
2543       else
2544         {
2545           QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2546         }
2547     }
2548
2549 }
2550 //------------------------------------------------------------------------------
2551
2552 //------------------------------------------------------------------------------
2553 void vvMainWindow::GoToCursor() {
2554   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2555   for (int column = 1; column < 5; column++)
2556     {
2557       if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1)
2558         {
2559           double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2560           mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2561                                                                           cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2562           mSlicerManagers[index]->UpdateViews(1,column-1);
2563           mSlicerManagers[index]->UpdateLinked(column-1);
2564           break;
2565         }
2566     }
2567 }
2568 //------------------------------------------------------------------------------
2569
2570 //------------------------------------------------------------------------------
2571 void vvMainWindow::PlayPause() {
2572   if (playMode)
2573     {
2574       playMode = 0;
2575       playButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/player_play.png")));
2576       ImageInfoChanged();
2577       return;
2578     }
2579   else
2580     {
2581       int image_number=DataTree->topLevelItemCount();
2582       bool has_temporal;
2583       for (int i=0;i<image_number;i++)
2584         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1)
2585           {
2586             has_temporal=true;
2587             break;
2588           }
2589       if (has_temporal)
2590         {
2591           playMode = 1;
2592           playButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/player_pause.png")));
2593           QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2594         }
2595     }
2596 }
2597 //------------------------------------------------------------------------------
2598
2599 //------------------------------------------------------------------------------
2600 void vvMainWindow::PlayNext() {
2601   if (playMode && !this->isHidden())
2602     {
2603       int image_number=DataTree->topLevelItemCount();
2604       ///Only play one slicer per SM, and only if the SM is being displayed
2605       for (int i=0;i<image_number;i++)
2606         for (int j=0;j<4;j++)
2607           if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2608               DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0)
2609             {
2610               mSlicerManagers[i]->SetNextTSlice(j);
2611               break;
2612             }
2613       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2614     }
2615 }
2616 //------------------------------------------------------------------------------
2617
2618 void vvMainWindow::ShowLastImage()
2619 {
2620   if (mSlicerManagers.size() > 1)
2621     {
2622       QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2623       CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2624       item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2625       DisplayChanged(item,1);
2626     }
2627 }
2628
2629 //------------------------------------------------------------------------------
2630 void vvMainWindow::UpdateRenderWindows() {
2631   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2632   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2633   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2634   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2635 }
2636 //------------------------------------------------------------------------------
2637
2638 //------------------------------------------------------------------------------
2639 void vvMainWindow::ResampleCurrentImage() {
2640   vvResamplerDialog resampler;
2641   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2642   resampler.SetSlicerManagers(mSlicerManagers,index);
2643   if (resampler.exec())
2644     AddImage(resampler.GetOutput(),resampler.GetOutputFileName());
2645 }
2646 //------------------------------------------------------------------------------
2647
2648 //------------------------------------------------------------------------------
2649 void vvMainWindow::SegmentationOnCurrentImage() {
2650   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2651
2652   vvSegmentationDialog segmentation;
2653   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2654   segmentation.exec();
2655 }
2656 //------------------------------------------------------------------------------
2657
2658 void vvMainWindow::SurfaceViewerLaunch()
2659 {
2660   vvSurfaceViewerDialog surfaceViewer;
2661   surfaceViewer.exec();
2662 }
2663
2664 //------------------------------------------------------------------------------
2665 void vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2666 {
2667   vvSlicerManager* m = new vvSlicerManager(4);
2668   m->SetImage(image);
2669   m->SetFilename(filename);
2670   AddImage(m);
2671 }
2672
2673 //------------------------------------------------------------------------------
2674 void vvMainWindow::AddImage(vvSlicerManager * slicer_manager) {
2675   mSlicerManagers.push_back(slicer_manager);
2676
2677   std::string filename = slicer_manager->GetFileName();
2678
2679   //create an item in the tree with good settings
2680   QTreeWidgetItem *item = new QTreeWidgetItem();
2681   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2682   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
2683   qApp->processEvents();
2684
2685   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2686
2687   //Create the buttons for reload and close
2688   qApp->processEvents();
2689   QTreePushButton* cButton = new QTreePushButton;
2690   cButton->setItem(item);
2691   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2692   cButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")));
2693   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2694           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2695
2696   QTreePushButton* rButton = new QTreePushButton;
2697   rButton->setItem(item);
2698   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2699   rButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")));
2700   rButton->setEnabled(0);
2701   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2702           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2703
2704   DataTree->addTopLevelItem(item);
2705   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2706   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2707
2708   //set the id of the image
2709   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2710   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2711   mSlicerManagers.back()->SetId(id.toStdString());
2712
2713   linkPanel->addImage(filename, id.toStdString());
2714
2715   connect(mSlicerManagers.back(),SIGNAL(currentImageChanged(std::string)),
2716           this,SLOT(CurrentImageChanged(std::string)));
2717   connect(mSlicerManagers.back(),SIGNAL(
2718                                         UpdatePosition(int, double, double, double, double, double, double, double)),this,
2719           SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2720   connect(mSlicerManagers.back(),SIGNAL(UpdateVector(int, double, double, double, double)),
2721           this, SLOT(VectorChanged(int,double,double,double, double)));
2722   connect(mSlicerManagers.back(),SIGNAL(UpdateOverlay(int, double, double)),
2723           this, SLOT(OverlayChanged(int,double,double)));
2724   connect(mSlicerManagers.back(),SIGNAL(UpdateFusion(int, double)),
2725           this, SLOT(FusionChanged(int,double)));
2726   connect(mSlicerManagers.back(),SIGNAL(UpdateWindows(int, int, int)),
2727           this,SLOT(WindowsChanged(int, int, int)));
2728   connect(mSlicerManagers.back(),SIGNAL(WindowLevelChanged(double, double,int, int)),
2729           this,SLOT(WindowLevelChanged(double, double, int, int)));
2730   connect(mSlicerManagers.back(),SIGNAL(UpdateSlice(int,int)),
2731           this,SLOT(UpdateSlice(int,int)));
2732   connect(mSlicerManagers.back(),SIGNAL(UpdateTSlice(int, int)),
2733           this,SLOT(UpdateTSlice(int, int)));
2734   connect(mSlicerManagers.back(),SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2735           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2736   connect(mSlicerManagers.back(),SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2737           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2738   connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2739   UpdateTree();
2740   qApp->processEvents();
2741   InitSlicers();
2742   ShowLastImage();
2743   InitDisplay();
2744   qApp->processEvents();
2745 }
2746 //------------------------------------------------------------------------------
2747
2748
2749 //------------------------------------------------------------------------------
2750 void vvMainWindow::UpdateCurrentSlicer() {
2751   int index = -1;
2752   if (DataTree->selectedItems().size() > 0) {
2753     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2754   }
2755   mSlicerManagerCurrentIndex = index;
2756 }
2757 //------------------------------------------------------------------------------
2758