vv/vvMainWindow.cxx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17 ======================================================================-====*/
  18
  19 #include <algorithm>
  20 #include <QMessageBox>
  21 #include <QInputDialog>
  22 #include <QTimer>
  23 #include "QTreePushButton.h"
  24
  25 // VV include
  26 #include "vvMainWindow.h"
  27 #include "vvHelpDialog.h"
  28 #include "vvDocumentation.h"
  29 #include "vvProgressDialog.h"
  30 #include "vvQDicomSeriesSelector.h"
  31 #include "vvSlicerManager.h"
  32 #include "clitkImageCommon.h"
  33 #include "vvSlicer.h"
  34 #include "vvInteractorStyleNavigator.h"
  35 #include "vvImageWriter.h"
  36 #include "vvResamplerDialog.h"
  37 #include "vvSegmentationDialog.h"
  38 #include "vvSurfaceViewerDialog.h"
  39 #include "vvDeformationDialog.h"
  40 #include "vvImageWarp.h"
  41 #include "vvUtils.h"
  42 #include "vvMaximumIntensityProjection.h"
  43 #include "vvMidPosition.h"
  44 #include "vvMesh.h"
  45 #include "vvStructSelector.h"
  46 #include "vvMeshReader.h"
  47 #include "vvConstants.h"
  48
  49 #ifdef CLITK_VV_USE_BDCM
  50 #include <bdcmDicomFilesSelectorDialog.h>
  51 #endif
  52
  53 // ITK include
  54 #include "itkImage.h"
  55 #include "itkImageFileReader.h"
  56 #include "itkByteSwapper.h"
  57 #include "itkCommand.h"
  58 #include "itkNumericSeriesFileNames.h"
  59
  60 // VTK include
  61 #include "vtkImageData.h"
  62 #include "vtkImageActor.h"
  63 #include "vtkCornerAnnotation.h"
  64 #include "vtkRenderWindow.h"
  65 #include "vtkRenderWindowInteractor.h"
  66 #include "vtkRenderer.h"
  67 #include "vtkRendererCollection.h"
  68 #include "vtkWindowToImageFilter.h"
  69 #include "vtkBMPWriter.h"
  70 #include "vtkTIFFWriter.h"
  71 #include "vtkPNMWriter.h"
  72 #include "vtkPNGWriter.h"
  73 #include "vtkJPEGWriter.h"
  74
  75 // Standard includes
  76 #include <iostream>
  77
  78 #define COLUMN_TREE 0
  79 #define COLUMN_UL_VIEW 1
  80 #define COLUMN_UR_VIEW 2
  81 #define COLUMN_DL_VIEW 3
  82 #define COLUMN_DR_VIEW 4
  83 #define COLUMN_CLOSE_IMAGE 5
  84 #define COLUMN_RELOAD_IMAGE 6
  85 #define COLUMN_IMAGE_NAME 7
  86
  87 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.hdr *.vox *.his *.xdr)"
  88
  89 /*Data Tree values
  90   0,Qt::UserRole full filename
  91   1,Qt::CheckStateRole checkbutton UL View
  92   1,Qt::UserRole overlay, fusion or vector
  93   2,Qt::CheckStateRole checkbutton UR View
  94   3,Qt::CheckStateRole checkbutton DL View
  95   4,Qt::CheckStateRole checkbutton DR View
  96   5,0  short filename
  97   5,Qt::UserRole mSlicerManager id*/
  98
  99 //------------------------------------------------------------------------------
 100 vvMainWindow::vvMainWindow():vvMainWindowBase() {
 101   setupUi(this); // this sets up the GUI
 102
 103   mInputPathName = "";
 104   mMenuTools = menuTools;
 105   mContextMenu = &contextMenu;
 106   mMenuExperimentalTools = menuExperimental;
 107   mMainWidget = this;
 108
 109   //Init the contextMenu
 110   this->setContextMenuPolicy(Qt::CustomContextMenu);
 111   contextActions.resize(0);
 112   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 113                                                         tr("O&pen new Image"));
 114   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 115   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 116   contextActions.push_back(actionOpen_new_image);
 117   contextMenu.addSeparator();
 118
 119   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 120                                                      tr("Close Current Image"));
 121   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 122   contextActions.push_back(actionClose_Image);
 123
 124   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 125                                                       tr("Reload Current Image"));
 126   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 127   contextActions.push_back(actionReload_image);
 128
 129   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 130                                                     tr("Save Current Image"));
 131   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 132   contextActions.push_back(actionSave_image);
 133
 134   contextMenu.addSeparator();
 135
 136   // QAction* actionCrop_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/crop.png")),
 137   //                                                   tr("Crop Current Image"));
 138   // connect(actionCrop_image,SIGNAL(triggered()),this,SLOT(CropImage()));
 139   // contextActions.push_back(actionCrop_image);
 140
 141   QAction* actionSplit_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/cut.png")),
 142                                                      tr("Split Current Image"));
 143   connect(actionSplit_image,SIGNAL(triggered()),this,SLOT(SplitImage()));
 144   contextActions.push_back(actionSplit_image);
 145
 146   contextMenu.addSeparator();
 147
 148   contextMenu.addAction(actionAdd_VF_to_current_Image);
 149   contextActions.push_back(actionAdd_VF_to_current_Image);
 150
 151   QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 152                                                                        tr("Add overlay image to current image"));
 153   contextMenu.addAction(actionAdd_Overlay_to_current_Image);
 154   contextActions.push_back(actionAdd_Overlay_to_current_Image);
 155
 156   connect(actionAdd_Overlay_to_current_Image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 157
 158   contextMenu.addAction(actionAdd_fusion_image);
 159   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 160   contextActions.push_back(actionAdd_fusion_image);
 161
 162   // TRIAL DS
 163   /*
 164   QMenu * m = new QMenu(menubar);
 165   m->setTitle("TOTO");
 166   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 167   contextMenu.addMenu(m);
 168   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 169                      tr("BIDON"));
 170   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 171                      tr("BIDON2"));
 172   m->addAction(a);
 173   m->addAction(b);
 174   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 175   */
 176
 177   //init the DataTree
 178   mSlicerManagers.resize(0);
 179
 180   QStringList header;
 181   header.append("");
 182   header.append("TL");
 183   header.append("TR");
 184   header.append("BL");
 185   header.append("BR");
 186   header.append("");
 187   header.append("");
 188   header.append("Name");
 189
 190   DataTree->setHeaderLabels(header);
 191   DataTree->resizeColumnToContents(COLUMN_TREE);
 192   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 193   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 194   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 195   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 196   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 197   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 198   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 199
 200   viewMode = 1;
 201   documentation = new vvDocumentation();
 202   help_dialog = new vvHelpDialog();
 203   dicomSeriesSelector = new vvDicomSeriesSelector();
 204
 205   inverseButton->setEnabled(0);
 206   actionAdd_Overlay_to_current_Image->setEnabled(0);
 207   actionSave_As->setEnabled(0);
 208   actionAdd_VF_to_current_Image->setEnabled(0);
 209   actionAdd_fusion_image->setEnabled(0);
 210
 211   //init the sliders
 212   verticalSliders.push_back(NOVerticalSlider);
 213   verticalSliders.push_back(NEVerticalSlider);
 214   verticalSliders.push_back(SOVerticalSlider);
 215   verticalSliders.push_back(SEVerticalSlider);
 216
 217   for (int i =0; i < 4; i++)
 218     verticalSliders[i]->hide();
 219
 220   horizontalSliders.push_back(NOHorizontalSlider);
 221   horizontalSliders.push_back(NEHorizontalSlider);
 222   horizontalSliders.push_back(SOHorizontalSlider);
 223   horizontalSliders.push_back(SEHorizontalSlider);
 224
 225   for (int i =0; i < 4; i++)
 226     horizontalSliders[i]->hide();
 227
 228
 229   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 230   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 231   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 232   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 233
 234   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 235   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 236   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 237   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 238
 239   //connect everything
 240   connect(actionMaximum_Intensity_Projection,SIGNAL(triggered()),this,SLOT(ComputeMIP()));
 241   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 242   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 243   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 244   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 245   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 246   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 247   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 248   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 249   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 250   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 251   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 252   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 253   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 254   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 255   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 256
 257   ///////////////////////////////////////////////
 258   contextMenu.addAction(actionResampler);
 259   connect(actionResampler,SIGNAL(triggered()),this,SLOT(ResampleCurrentImage()));
 260   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 261   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 262   ///////////////////////////////////////////////
 263
 264   actionNorth_East_Window->setEnabled(0);
 265   actionNorth_West_Window->setEnabled(0);
 266   actionSouth_East_Window->setEnabled(0);
 267   actionSouth_West_Window->setEnabled(0);
 268
 269   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 270   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 271   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 272   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 273
 274   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 275   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 276           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 277
 278   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 279   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 280   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 281   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 282   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 283   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 284
 285
 286   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 287
 288   connect(linkPanel,SIGNAL(addLink(QString,QString)),this,SLOT(AddLink(QString,QString)));
 289   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 290   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int)),this,SLOT(SetVFProperty(int,int,int)));
 291   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int)),this,SLOT(SetOverlayProperty(int)));
 292   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,double,double)),
 293           this,SLOT(SetFusionProperty(int,int,double,double)));
 294   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 295
 296   playMode = 0;//pause
 297   mFrameRate = 10;
 298   playButton->setEnabled(0);
 299   frameRateLabel->setEnabled(0);
 300   frameRateSpinBox->setEnabled(0);
 301   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 302   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 303
 304   goToCursorPushButton->setEnabled(0);
 305   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 306
 307   NOViewWidget->hide();
 308   NEViewWidget->hide();
 309   SOViewWidget->hide();
 310   SEViewWidget->hide();
 311
 312   //Recently opened files
 313   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 314   if ( !recent_files.empty() )
 315     {
 316       QMenu * rmenu = new QMenu("Recently opened files...");
 317       rmenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 318       menuFile->insertMenu(actionOpen_Image_With_Time,rmenu);
 319       for (std::list<std::string>::iterator i = recent_files.begin();i!=recent_files.end();i++)
 320         {
 321           QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")),
 322                                        (*i).c_str(),this);
 323           rmenu->addAction(current);
 324           connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 325         }
 326     }
 327
 328   // Adding all new tools (insertion in the menu)
 329   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 330
 331   if (!CLITK_EXPERIMENTAL)
 332       menuExperimental->menuAction()->setVisible(false);
 333 }
 334 //------------------------------------------------------------------------------
 335
 336
 337 //------------------------------------------------------------------------------
 338 void vvMainWindow::ComputeMIP()
 339 {
 340   vvMaximumIntensityProjection mip;
 341   vvSlicerManager* selected_slicer = mSlicerManagers[GetSlicerIndexFromItem(DataTree->selectedItems()[0])];
 342   QFileInfo info(selected_slicer->GetFileName().c_str());
 343   mip.Compute(selected_slicer);
 344   AddImage(mip.GetOutput(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_mip.mhd");
 345 }
 346 //------------------------------------------------------------------------------
 347
 348
 349 //------------------------------------------------------------------------------
 350 void vvMainWindow::ComputeMidPosition()
 351 {
 352   bool ok;
 353   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 354   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 355                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 356   if (ok)
 357     {
 358       vvMidPosition midp;
 359       midp.slicer_manager = mSlicerManagers[index];
 360       midp.reference_image_index = ref;
 361       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 362       midp.Update();
 363       if (midp.error)
 364         QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 365       else
 366         {
 367           QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 368           AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 369         }
 370       QApplication::restoreOverrideCursor();
 371     }
 372 }
 373 //------------------------------------------------------------------------------
 374
 375
 376 //------------------------------------------------------------------------------
 377 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 378 {
 379   QTreeWidgetItem *item = new QTreeWidgetItem();
 380   item->setData(0,Qt::UserRole,"filename.vtk");
 381   item->setData(1,Qt::UserRole,tr("contour"));
 382   QBrush brush;
 383   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 384   brush.setStyle(Qt::SolidPattern);
 385   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 386   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 387
 388   for (int j = 1; j <= 4; j++)
 389     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 390
 391   QTreePushButton* cButton = new QTreePushButton;
 392   cButton->setItem(item);
 393   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 394   cButton->setToolTip(tr("close image"));
 395   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 396   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 397           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 398
 399   QTreePushButton* rButton = new QTreePushButton;
 400   rButton->setItem(item);
 401   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 402   rButton->setToolTip(tr("reload image"));
 403   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 404   rButton->setEnabled(false);
 405   //Not implemented
 406   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 407   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 408
 409   DataTree->topLevelItem(image_index)->setExpanded(1);
 410   DataTree->topLevelItem(image_index)->addChild(item);
 411   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 412   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 413   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 414   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 415
 416   UpdateTree();
 417   mSlicerManagers[image_index]->AddContour(contour,propagation);
 418   mSlicerManagers[image_index]->Render();
 419 }
 420 //------------------------------------------------------------------------------
 421
 422
 423 //------------------------------------------------------------------------------
 424 void vvMainWindow::OpenVTKContour()
 425 {
 426   if (mSlicerManagers.size() > 0)
 427     {
 428       QString Extensions = "Images ( *.vtk; *.obj)";
 429       Extensions += ";;All Files (*)";
 430       QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 431       if (file.isNull())
 432         return;
 433       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 434       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 435       vvMeshReader reader;
 436       reader.SetImage(mSlicerManagers[index]->GetImage());
 437       reader.SetModeToVTK();
 438       reader.SetFilename(file.toStdString());
 439       reader.Update();
 440       AddContour(index,reader.GetOutput()[0],false);
 441       QApplication::restoreOverrideCursor();
 442     }
 443 }
 444 //------------------------------------------------------------------------------
 445
 446
 447 //------------------------------------------------------------------------------
 448 void vvMainWindow::OpenDCStructContour()
 449 {
 450   if (mSlicerManagers.size() > 0)
 451     {
 452       QString Extensions = "Dicom Files ( *.dcm; RS*)";
 453       Extensions += ";;All Files (*)";
 454       QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 455       if (file.isNull())
 456         return;
 457       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 458       vvMeshReader reader;
 459       reader.SetFilename(file.toStdString());
 460       vvStructSelector selector;
 461       selector.SetStructures(reader.GetROINames());
 462       if (!mSlicerManagers[index]->GetVF().IsNull())
 463         selector.EnablePropagationCheckBox();
 464       if (selector.exec())
 465         {
 466           QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 467           reader.SetSelectedItems(selector.getSelectedItems());
 468           reader.SetImage(mSlicerManagers[index]->GetImage());
 469           if (selector.PropagationEnabled())
 470             reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 471           reader.Update();
 472           std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 473           for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 474                i!=contours.end();i++)
 475             AddContour(index,*i,selector.PropagationEnabled());
 476           QApplication::restoreOverrideCursor();
 477         }
 478     }
 479 }
 480 //------------------------------------------------------------------------------
 481
 482
 483 //------------------------------------------------------------------------------
 484 void vvMainWindow::ComputeDeformableRegistration()
 485 {
 486   if (mSlicerManagers.size() > 0)
 487     {
 488       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 489       vvDeformationDialog dialog(index,mSlicerManagers);
 490       if (dialog.exec())
 491         {
 492           std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 493           AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 494           WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 495         }
 496       else
 497         std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 498     }
 499   else QMessageBox::information(this, "Need to open image","You must open an image first.");
 500 }
 501 //------------------------------------------------------------------------------
 502
 503
 504 //------------------------------------------------------------------------------
 505 void vvMainWindow::WarpImage()
 506 {
 507   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 508   if (!mSlicerManagers[index]->GetVF().IsNull())
 509     {
 510       bool ok;
 511       int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 512                                          mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 513       if (ok)
 514         {
 515           WarpImage(mSlicerManagers[index],ref);
 516         }
 517     }
 518   else
 519     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 520 }
 521 //------------------------------------------------------------------------------
 522
 523
 524 //------------------------------------------------------------------------------
 525 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 526 {
 527   if (!selected_slicer->GetVF().IsNull())
 528     {
 529       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 530       QFileInfo info(selected_slicer->GetFileName().c_str());
 531       vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 532                        reference_phase,this);
 533       if (warp.ComputeWarpedImage())
 534         {
 535           AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 536           AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 537           AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 538           QApplication::restoreOverrideCursor();
 539         }
 540       else
 541         {
 542           QApplication::restoreOverrideCursor();
 543           QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 544         }
 545     }
 546   else
 547     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 548 }
 549 //------------------------------------------------------------------------------
 550
 551
 552 //------------------------------------------------------------------------------
 553 vvMainWindow::~vvMainWindow() {
 554   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
 555     {
 556       if (mSlicerManagers[i] != NULL)
 557         delete mSlicerManagers[i];
 558     }
 559 }
 560 //------------------------------------------------------------------------------
 561
 562
 563 //------------------------------------------------------------------------------
 564 void vvMainWindow::MergeImages() {
 565   QString Extensions = EXTENSIONS;
 566   Extensions += ";;All Files (*)";
 567   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 568   if (files.isEmpty())
 569     return;
 570   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 571   std::vector<std::string> vector;
 572
 573   unsigned int currentDim = 0;
 574   std::vector<double> currentSpacing;
 575   std::vector<int> currentSize;
 576   std::vector<double> currentOrigin;
 577
 578   for (int i = 0; i < files.size(); i++)
 579     {
 580       itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 581               files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 582       reader->SetFileName(files[i].toStdString().c_str());
 583       reader->ReadImageInformation();
 584       if (reader)        {
 585           //NOViewWidget->hide();
 586           //NEViewWidget->hide();
 587           //SOViewWidget->hide();
 588           //SEViewWidget->hide();
 589           if (i == 0)
 590               currentDim = reader->GetNumberOfDimensions();
 591           bool IsOk = true;
 592           for (unsigned int j = 0;j < currentDim; j++)
 593           {
 594               if (i == 0)
 595               {
 596                   if (j == 0)
 597                   {
 598                       currentSpacing.resize(currentDim);
 599                       currentSize.resize(currentDim);
 600                       currentOrigin.resize(currentDim);
 601                   }
 602                   currentOrigin[j] = reader->GetOrigin(j);
 603                   currentSpacing[j] = reader->GetSpacing(j);
 604                   currentSize[j] = reader->GetDimensions(j);
 605               }
 606               else if (currentDim != reader->GetNumberOfDimensions()
 607                       || currentSpacing[j] != reader->GetSpacing(j)
 608                       || currentSize[j] != (int)reader->GetDimensions(j)
 609                       || currentOrigin[j] != reader->GetOrigin(j))
 610               {
 611                   QString error = "Cannot read file (too different from others ";
 612                   error += files[i].toStdString().c_str();
 613                   QMessageBox::information(this,tr("Reading problem"),error);
 614                   IsOk = false;
 615                   break;
 616               }
 617           }
 618           if (IsOk)
 619               vector.push_back(files[i].toStdString());
 620       }
 621     }
 622   if (vector.size() > 0)
 623     LoadImages(vector, MERGED);
 624 }
 625 //------------------------------------------------------------------------------
 626
 627
 628 //------------------------------------------------------------------------------
 629 void vvMainWindow::MergeImagesWithTime() {
 630   QString Extensions = EXTENSIONS;
 631   Extensions += ";;All Files (*)";
 632   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 633   if (files.isEmpty())
 634     return;
 635   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 636   std::vector<std::string> vector;
 637
 638   unsigned int currentDim = 0;
 639   std::vector<double> currentSpacing;
 640   std::vector<int> currentSize;
 641   std::vector<double> currentOrigin;
 642
 643   for (int i = 0; i < files.size(); i++)
 644     {
 645       itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 646                                                                             files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 647       if (reader)
 648         {
 649           reader->SetFileName(files[i].toStdString().c_str());
 650           reader->ReadImageInformation();
 651           if (i == 0)
 652             currentDim = reader->GetNumberOfDimensions();
 653           bool IsOk = true;
 654           for (unsigned int j = 0;j < currentDim; j++)
 655             {
 656               if (i == 0)
 657                 {
 658                   if (j == 0)
 659                     {
 660                       currentSpacing.resize(currentDim);
 661                       currentSize.resize(currentDim);
 662                       currentOrigin.resize(currentDim);
 663                     }
 664                   currentOrigin[j] = reader->GetOrigin(j);
 665                   currentSpacing[j] = reader->GetSpacing(j);
 666                   currentSize[j] = reader->GetDimensions(j);
 667                 }
 668               else if (currentDim != reader->GetNumberOfDimensions()
 669                        || currentSpacing[j] != reader->GetSpacing(j)
 670                        || currentSize[j] != (int)reader->GetDimensions(j)
 671                        || currentOrigin[j] != reader->GetOrigin(j))
 672                 {
 673                   QString error = "Cannot read file (too different from others ";
 674                   error += files[i].toStdString().c_str();
 675                   QMessageBox::information(this,tr("Reading problem"),error);
 676                   IsOk = false;
 677                   break;
 678                 }
 679             }
 680           if (IsOk)
 681             vector.push_back(files[i].toStdString());
 682         }
 683       else
 684         {
 685           QString error = "Cannot read file info for ";
 686           error += files[i].toStdString().c_str();
 687           error += "\n";
 688           error += "Maybe you're trying to open an image in an unsupported format?\n";
 689           QMessageBox::information(this,tr("Reading problem"),error);
 690         }
 691     }
 692   sort(vector.begin(),vector.end());
 693   if (vector.size() > 1)
 694     LoadImages(vector, MERGEDWITHTIME);
 695   else
 696     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.");
 697 }
 698 //------------------------------------------------------------------------------
 699
 700
 701 //------------------------------------------------------------------------------
 702 void vvMainWindow::OpenDicom() {
 703   std::vector<std::string> files;
 704
 705 #ifdef CLITK_VV_USE_BDCM
 706   bool r = bdcm::OpenDicomFilesSelectorDialog(files,
 707                                               "DicomFilesSelectorDialog test",
 708                                               0,0,800,800,1);
 709
 710   if (r) {
 711     std::cout << "$$$$ main : user clicked 'OK' $$$$"<<std::endl;
 712     std::cout << "$$$$ selected files : "<<std::endl;
 713     std::vector<std::string>::iterator i;
 714     for (i=files.begin();i!=files.end();++i) {
 715       std::cout << *i << std::endl;
 716     }
 717     std::cout << "$$$$ "<<std::endl;
 718
 719     LoadImages(files,DICOM);
 720   }
 721   else {
 722     std::cout << "$$$$ main : user clicked 'CANCEL' $$$$"<<std::endl;
 723   }
 724 #else
 725   std::cout << "dicomSeriesSelector " << std::endl;
 726   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 727     files = *(dicomSeriesSelector->GetFilenames());
 728     LoadImages(files,DICOM);
 729   }
 730 #endif
 731
 732 }
 733 //------------------------------------------------------------------------------
 734
 735 //------------------------------------------------------------------------------
 736 void vvMainWindow::OpenImages() {
 737   QString Extensions = EXTENSIONS;
 738   Extensions += ";;All Files (*)";
 739
 740   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 741   if (files.isEmpty())
 742     return;
 743   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 744   std::vector<std::string> vector;
 745   for (int i = 0; i < files.size(); i++)
 746     vector.push_back(files[i].toStdString());
 747   LoadImages(vector, IMAGE);
 748 }
 749 //------------------------------------------------------------------------------
 750 void vvMainWindow::OpenRecentImage()
 751 {
 752   QAction * caller = qobject_cast<QAction*>(sender());
 753   std::vector<std::string> images;
 754   images.push_back(caller->text().toStdString());
 755   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 756   LoadImages(images,IMAGE);
 757 }
 758 //------------------------------------------------------------------------------
 759
 760
 761 //------------------------------------------------------------------------------
 762 void vvMainWindow::OpenImageWithTime() {
 763   QString Extensions = EXTENSIONS;
 764   Extensions += ";;All Files (*)";
 765
 766   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 767   if (files.isEmpty())
 768     return;
 769   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 770   std::vector<std::string> vector;
 771   for (int i = 0; i < files.size(); i++)
 772     {
 773       vector.push_back(files[i].toStdString());
 774     }
 775   LoadImages(vector, IMAGEWITHTIME);
 776 }
 777 //------------------------------------------------------------------------------
 778
 779
 780 //------------------------------------------------------------------------------
 781 void vvMainWindow::LoadImages(std::vector<std::string> files, LoadedImageType filetype) {
 782   //Separate the way to open images and dicoms
 783   int fileSize;
 784   if (filetype == IMAGE || filetype == IMAGEWITHTIME)
 785     fileSize = files.size();
 786   else
 787     fileSize = 1;
 788
 789   //Only add to the list of recently opened files when a single file is opened,
 790   //to avoid polluting the list of recently opened files
 791   if (files.size() == 1)
 792     {
 793       QFileInfo finfo=tr(files[0].c_str());
 794       AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 795     }
 796   //init the progress events
 797   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 798   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 799   qApp->processEvents();
 800
 801   int numberofsuccesulreads=0;
 802   //open images as 1 or multiples
 803   for (int i = 0; i < fileSize; i++) {
 804
 805     progress.Update("Opening " + files[i]);
 806     progress.SetProgress(i,fileSize);
 807     qApp->processEvents();
 808
 809     //read the image and put it in mSlicerManagers
 810     vvSlicerManager* imageManager = new vvSlicerManager(4);
 811     qApp->processEvents();
 812
 813     bool SetImageSucceed=false;
 814
 815     // Change filename if an image with the same already exist
 816     //    DD(files[i]);
 817     int number=0;
 818     for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
 819       vvSlicerManager * v = mSlicerManagers[l];
 820       //      DD(v->GetBaseFileName());
 821       // DD(v->GetFileName());
 822       if (v->GetBaseFileName() ==
 823           vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(files[i]))) {
 824         number = std::max(number, v->GetBaseFileNameNumber()+1);
 825       }
 826     }
 827
 828
 829     if (filetype == IMAGE || filetype == IMAGEWITHTIME)
 830       SetImageSucceed = imageManager->SetImage(files[i],filetype, number);
 831     else
 832       {
 833         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 834       }
 835     if (SetImageSucceed == false)
 836       {
 837         QApplication::restoreOverrideCursor();
 838         QString error = "Cannot open file \n";
 839         error += imageManager->GetLastError().c_str();
 840         QMessageBox::information(this,tr("Reading problem"),error);
 841         delete imageManager;
 842       }
 843     else
 844       {
 845         mSlicerManagers.push_back(imageManager);
 846
 847         //create an item in the tree with good settings
 848         QTreeWidgetItem *item = new QTreeWidgetItem();
 849         item->setData(0,Qt::UserRole,files[i].c_str());
 850         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 851         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 852         qApp->processEvents();
 853
 854         //Create the buttons for reload and close
 855         qApp->processEvents();
 856         QTreePushButton* cButton = new QTreePushButton;
 857         cButton->setItem(item);
 858         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 859         cButton->setToolTip(tr("close image"));
 860         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 861         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 862                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 863
 864         QTreePushButton* rButton = new QTreePushButton;
 865         rButton->setItem(item);
 866         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 867         rButton->setToolTip(tr("reload image"));
 868         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 869         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 870                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 871
 872         DataTree->addTopLevelItem(item);
 873         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 874         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 875
 876         //set the id of the image
 877         QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 878         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 879         mSlicerManagers.back()->SetId(id.toStdString());
 880
 881         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 882
 883         connect(mSlicerManagers.back(),SIGNAL(currentImageChanged(std::string)),
 884                 this,SLOT(CurrentImageChanged(std::string)));
 885         connect(mSlicerManagers.back(),SIGNAL(
 886                                               UpdatePosition(int, double, double, double, double, double, double, double)),this,
 887                 SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 888         connect(mSlicerManagers.back(),SIGNAL(UpdateVector(int, double, double, double, double)),
 889                 this, SLOT(VectorChanged(int,double,double,double, double)));
 890         connect(mSlicerManagers.back(),SIGNAL(UpdateOverlay(int, double, double)),
 891                 this, SLOT(OverlayChanged(int,double,double)));
 892         connect(mSlicerManagers.back(),SIGNAL(UpdateFusion(int, double)),
 893                 this, SLOT(FusionChanged(int,double)));
 894         connect(mSlicerManagers.back(),SIGNAL(UpdateWindows(int, int, int)),
 895                 this,SLOT(WindowsChanged(int, int, int)));
 896         connect(mSlicerManagers.back(),SIGNAL(WindowLevelChanged(double, double,int, int)),
 897                 this,SLOT(WindowLevelChanged(double, double, int, int)));
 898         connect(mSlicerManagers.back(),SIGNAL(UpdateSlice(int,int)),
 899                 this,SLOT(UpdateSlice(int,int)));
 900         connect(mSlicerManagers.back(),SIGNAL(UpdateTSlice(int, int)),
 901                 this,SLOT(UpdateTSlice(int, int)));
 902         connect(mSlicerManagers.back(),SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 903                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 904         connect(mSlicerManagers.back(),SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 905                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 906         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 907         InitSlicers();
 908         numberofsuccesulreads++;
 909       }
 910   }
 911   if (numberofsuccesulreads)
 912     {
 913       NOViewWidget->show();
 914       NEViewWidget->show();
 915       SOViewWidget->show();
 916       SEViewWidget->show();
 917       UpdateTree();
 918       InitDisplay();
 919       ShowLastImage();
 920     }
 921   QApplication::restoreOverrideCursor();
 922
 923 }
 924 //------------------------------------------------------------------------------
 925
 926 //------------------------------------------------------------------------------
 927 void vvMainWindow::UpdateTree() {
 928   DataTree->resizeColumnToContents(COLUMN_TREE);
 929   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 930   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 931   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 932   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 933   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 934   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 935   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 936 }
 937 //------------------------------------------------------------------------------
 938
 939 //------------------------------------------------------------------------------
 940 void vvMainWindow::CurrentImageChanged(std::string id) {
 941   int selected = 0;
 942   for (int i = 0; i < DataTree->topLevelItemCount(); i++)
 943     {
 944       if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id)
 945         {
 946           selected = i;
 947         }
 948       else
 949         {
 950           DataTree->topLevelItem(i)->setSelected(0);
 951         }
 952       for (int child = 0; child < DataTree->topLevelItem(i)->childCount();child++)
 953         DataTree->topLevelItem(i)->child(child)->setSelected(0);
 954
 955     }
 956   DataTree->topLevelItem(selected)->setSelected(1);
 957 }
 958 //------------------------------------------------------------------------------
 959
 960 //------------------------------------------------------------------------------
 961 void vvMainWindow::ImageInfoChanged() {
 962   contextActions[7]->setEnabled(1);
 963   contextActions[6]->setEnabled(1);
 964   actionSave_As->setEnabled(1);
 965   actionAdd_VF_to_current_Image->setEnabled(1);
 966   actionAdd_fusion_image->setEnabled(1);
 967   actionNorth_East_Window->setEnabled(1);
 968   actionNorth_West_Window->setEnabled(1);
 969   actionSouth_East_Window->setEnabled(1);
 970   actionSouth_West_Window->setEnabled(1);
 971   inverseButton->setEnabled(1);
 972
 973   goToCursorPushButton->setEnabled(1);
 974
 975   if (DataTree->selectedItems().size()) {
 976     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 977
 978     colorMapComboBox->setEnabled(1);
 979     for (int i = 0; i < DataTree->topLevelItem(index)->childCount();i++)
 980       {
 981         if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
 982             DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion")
 983           {
 984             colorMapComboBox->setEnabled(0);
 985             break;
 986           }
 987       }
 988
 989     std::vector<double> origin;
 990     std::vector<double> inputSpacing;
 991     std::vector<int> inputSize;
 992     std::vector<double> sizeMM;
 993     int dimension=0;
 994     QString pixelType;
 995     QString inputSizeInBytes;
 996     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
 997
 998     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1)
 999       {
1000         playButton->setEnabled(1);
1001         frameRateLabel->setEnabled(1);
1002         frameRateSpinBox->setEnabled(1);
1003       }
1004     else
1005       {
1006         playButton->setEnabled(0);
1007         frameRateLabel->setEnabled(0);
1008         frameRateSpinBox->setEnabled(0);
1009       }
1010
1011     //read image header
1012     int NPixel = 1;
1013
1014     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0])
1015       {
1016         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1017         dimension = imageSelected->GetNumberOfDimensions();
1018         origin.resize(dimension);
1019         inputSpacing.resize(dimension);
1020         inputSize.resize(dimension);
1021         sizeMM.resize(dimension);
1022         pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
1023         for (int i = 0;i < dimension;i++)
1024           {
1025             origin[i] = imageSelected->GetOrigin()[i];
1026             inputSpacing[i] = imageSelected->GetSpacing()[i];
1027             inputSize[i] = imageSelected->GetSize()[i];
1028             sizeMM[i] = inputSize[i]*inputSpacing[i];
1029             NPixel *= inputSize[i];
1030           }
1031         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1032       }
1033     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector")
1034       {
1035         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1036         dimension = imageSelected->GetNumberOfDimensions();
1037         origin.resize(dimension);
1038         inputSpacing.resize(dimension);
1039         inputSize.resize(dimension);
1040         sizeMM.resize(dimension);
1041         pixelType = mSlicerManagers[index]->GetVF()->GetScalarTypeAsString().c_str();
1042         for (int i = 0;i < dimension;i++)
1043           {
1044             origin[i] = imageSelected->GetOrigin()[i];
1045             inputSpacing[i] = imageSelected->GetSpacing()[i];
1046             inputSize[i] = imageSelected->GetSize()[i];
1047             sizeMM[i] = inputSize[i]*inputSpacing[i];
1048             NPixel *= inputSize[i];
1049           }
1050         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1051       }
1052     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay")
1053       {
1054         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1055         dimension = imageSelected->GetNumberOfDimensions();
1056         origin.resize(dimension);
1057         inputSpacing.resize(dimension);
1058         inputSize.resize(dimension);
1059         sizeMM.resize(dimension);
1060         pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
1061         for (int i = 0;i < dimension;i++)
1062           {
1063             origin[i] = imageSelected->GetOrigin()[i];
1064             inputSpacing[i] = imageSelected->GetSpacing()[i];
1065             inputSize[i] = imageSelected->GetSize()[i];
1066             sizeMM[i] = inputSize[i]*inputSpacing[i];
1067             NPixel *= inputSize[i];
1068           }
1069         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1070       }
1071     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion")
1072       {
1073         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1074         dimension = imageSelected->GetNumberOfDimensions();
1075         origin.resize(dimension);
1076         inputSpacing.resize(dimension);
1077         inputSize.resize(dimension);
1078         sizeMM.resize(dimension);
1079         pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
1080         for (int i = 0;i < dimension;i++)
1081           {
1082             origin[i] = imageSelected->GetOrigin()[i];
1083             inputSpacing[i] = imageSelected->GetSpacing()[i];
1084             inputSize[i] = imageSelected->GetSize()[i];
1085             sizeMM[i] = inputSize[i]*inputSpacing[i];
1086             NPixel *= inputSize[i];
1087           }
1088         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1089       }
1090
1091     QString dim = QString::number(dimension) + " (";
1092     dim += pixelType + ")";
1093
1094     infoPanel->setFileName(image);
1095     infoPanel->setDimension(dim);
1096     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1097     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1098     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1099     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1100     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1101
1102     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1103                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1104     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1105     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1106
1107     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1108     for (int i = 0; i < 4;i++)
1109       {
1110         if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3)
1111           {
1112             mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1113             break;
1114           }
1115       }
1116     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1117     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1118     // DD(mSlicerManagers[index]->GetColorMap());
1119     // DD(mSlicerManagers[index]->GetPreset());
1120     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1121     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1122
1123     infoPanel->setFileName(image);
1124     infoPanel->setDimension(dim);
1125     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1126     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1127     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1128     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1129     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1130
1131     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1132                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1133     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1134     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1135
1136     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1137     for (int i = 0; i < 4;i++)
1138       {
1139         if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3)
1140           {
1141             mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1142             break;
1143           }
1144       }
1145     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1146     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1147     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1148     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1149
1150     if (mSlicerManagers[index]->GetSlicer(0)->GetVF())
1151       {
1152         overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1153         overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1154                                     mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1155                                     mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1156       }
1157     else
1158       {
1159         overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1160         overlayPanel->getVFProperty(-1,-1,-1);
1161       }
1162     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1163       {
1164         overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1165         overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1166       }
1167     else
1168       {
1169         overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1170         overlayPanel->getOverlayProperty(-1);
1171       }
1172     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion())
1173       {
1174         overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1175         overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1176                                         mSlicerManagers[index]->GetFusionColorMap(),
1177                                         mSlicerManagers[index]->GetFusionWindow(),
1178                                         mSlicerManagers[index]->GetFusionLevel());
1179       }
1180     else
1181       {
1182         overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1183         overlayPanel->getFusionProperty(-1, -1,-1,-1);
1184       }
1185   }
1186 }
1187 //------------------------------------------------------------------------------
1188
1189 //------------------------------------------------------------------------------
1190 void vvMainWindow::ShowDocumentation() {
1191   documentation->show();
1192 }
1193 //------------------------------------------------------------------------------
1194 void vvMainWindow::ShowHelpDialog() {
1195   help_dialog->show();
1196 }
1197 //------------------------------------------------------------------------------
1198
1199 //------------------------------------------------------------------------------
1200 void vvMainWindow::ChangeViewMode() {
1201   QListIterator<int> it0(splitter_3->sizes());
1202   QListIterator<int> it1(splitter_3->sizes());
1203   int max0 = 0;
1204   int max1 = 1;
1205   while (it0.hasNext())
1206     {
1207       max0 += it0.next();
1208     }
1209   while (it1.hasNext())
1210     {
1211       max1 += it1.next();
1212     }
1213   QList<int> size0;
1214   QList<int> size1;
1215   if (viewMode == 1)
1216     {
1217       viewMode = 0;
1218       size0.push_back(max0);
1219       size0.push_back(0);
1220       size1.push_back(max1);
1221       size1.push_back(0);
1222       splitter_3->setSizes(size0);
1223       OSplitter->setSizes(size1);
1224       DataTree->setColumnHidden(2,1);
1225       DataTree->setColumnHidden(3,1);
1226       DataTree->setColumnHidden(4,1);
1227     }
1228   else
1229     {
1230       viewMode = 1;
1231       size0.push_back(int(max0/2));
1232       size0.push_back(int(max0/2));
1233       size1.push_back(int(max1/2));
1234       size1.push_back(int(max1/2));
1235       splitter_3->setSizes(size0);
1236       OSplitter->setSizes(size1);
1237       DataTree->setColumnHidden(2,0);
1238       DataTree->setColumnHidden(3,0);
1239       DataTree->setColumnHidden(4,0);
1240     }
1241 }
1242 //------------------------------------------------------------------------------
1243
1244 //------------------------------------------------------------------------------
1245 QString vvMainWindow::GetSizeInBytes(unsigned long size) {
1246   QString result = "";// QString::number(size);
1247   //result += " bytes (";
1248   if (size > 1000000000)
1249     {
1250       size /= 1000000000;
1251       result += QString::number(size);
1252       result += "Gb";//)";
1253     }
1254   else if (size > 1000000)
1255     {
1256       size /= 1000000;
1257       result += QString::number(size);
1258       result += "Mb";//)";
1259     }
1260   else if (size > 1000)
1261     {
1262       size /= 1000;
1263       result += QString::number(size);
1264       result += "kb";//)";
1265     }
1266   return result;
1267 }
1268 //------------------------------------------------------------------------------
1269
1270 //------------------------------------------------------------------------------
1271 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble) {
1272   QString result;
1273   for (unsigned int i= 0; i < vectorDouble.size(); i++)
1274     {
1275       if (i != 0)
1276         result += " ";
1277       result += QString::number(vectorDouble[i]);
1278     }
1279   return result;
1280 }
1281 //------------------------------------------------------------------------------
1282
1283 //------------------------------------------------------------------------------
1284 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt) {
1285   QString result;
1286   for (unsigned int i= 0; i < vectorInt.size(); i++)
1287     {
1288       if (i != 0)
1289         result += " ";
1290       result += QString::number(vectorInt[i]);
1291     }
1292   return result;
1293 }
1294 //------------------------------------------------------------------------------
1295
1296 //------------------------------------------------------------------------------
1297 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item) {
1298   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1299   for (int i = 0; i < DataTree->topLevelItemCount(); i++)
1300     {
1301       if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1302         return i;
1303     }
1304   return -1;
1305 }
1306 //------------------------------------------------------------------------------
1307
1308 //------------------------------------------------------------------------------
1309 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clicked_item, int column) {
1310   int index = GetSlicerIndexFromItem(clicked_item);
1311   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1312     return;
1313   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
1314     {
1315       QTreeWidgetItem* current_row=DataTree->topLevelItem(i);
1316       if (DataTree->topLevelItem(index) == current_row)
1317         {
1318           vvSlicer* clicked_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1319           if (current_row == clicked_item)
1320             {
1321               //If we just activated a slicer
1322               if (current_row->data(column,Qt::CheckStateRole).toInt() > 0)
1323                 {
1324                   mSlicerManagers[i]->UpdateSlicer(column-1,clicked_item->data(column,Qt::CheckStateRole).toInt());
1325                   mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1326                   DisplaySliders(i,column-1);
1327                   std::map<std::string,int> overlay_counts;
1328                   for (int child = 0; child < current_row->childCount(); child++)
1329                     {
1330                       std::string overlay_type =
1331                         current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1332                       overlay_counts[overlay_type]++;
1333                       current_row->child(child)->setData(column,Qt::CheckStateRole,
1334                                                          current_row->data(column,Qt::CheckStateRole));
1335                       clicked_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,true);
1336                     }
1337                 }
1338               else //We don't allow simply desactivating a slicer
1339                 {
1340                   clicked_item->setData(column,Qt::CheckStateRole,2);
1341                   return;
1342                 }
1343             }
1344           //if we clicked on the vector(or overlay) and not the image
1345           else
1346             {
1347               if (clicked_item->data(column,Qt::CheckStateRole).toInt())
1348                 {
1349                   current_row->setData(column,Qt::CheckStateRole,2);
1350                   mSlicerManagers[i]->UpdateSlicer(column-1,2);
1351                   mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1352                   DisplaySliders(i,column-1);
1353                 }
1354               int vis = clicked_item->data(column,Qt::CheckStateRole).toInt();
1355               std::string overlay_type = clicked_item->data(1,Qt::UserRole).toString().toStdString();
1356               int overlay_index=0;
1357               for (int child = 0; child < current_row->childCount(); child++)
1358                 {
1359                   if (current_row->child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1360                     overlay_index++;
1361                   if (current_row->child(child) == clicked_item) break;
1362                 }
1363               clicked_slicer->SetActorVisibility(
1364                                                  clicked_item->data(1,Qt::UserRole).toString().toStdString(), overlay_index-1,vis);
1365             }
1366         }
1367       else if (current_row->data(column,Qt::CheckStateRole).toInt() > 0)
1368         {
1369           current_row->setData(column,Qt::CheckStateRole,0);
1370           mSlicerManagers[i]->UpdateSlicer(column-1,0);
1371           std::map<std::string,int> overlay_counts;
1372           for (int child = 0; child < current_row->childCount(); child++)
1373             {
1374               std::string overlay_type =
1375                 current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1376               overlay_counts[overlay_type]++;
1377               current_row->child(child)->setData(column,Qt::CheckStateRole,0);
1378               vvSlicer * current_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1379               current_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,false);
1380             }
1381         }
1382       //mSlicerManagers[i]->SetColorMap(-1);
1383       mSlicerManagers[i]->SetColorMap();
1384     }
1385   mSlicerManagers[index]->GetSlicer(column-1)->Render();
1386 }
1387 //------------------------------------------------------------------------------
1388
1389 void vvMainWindow::InitSlicers()
1390 {
1391   if (mSlicerManagers.size())
1392     {
1393       mSlicerManagers.back()->GenerateDefaultLookupTable();
1394
1395       mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1396       mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1397       mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1398       mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1399     }
1400 }
1401
1402 //------------------------------------------------------------------------------
1403 void vvMainWindow::InitDisplay() {
1404   if (mSlicerManagers.size())
1405     {
1406       //BE CAREFUL : this is absolutely necessary to set the interactor style
1407       //in order to have the same style instanciation for all SlicerManagers in
1408       // a same window
1409       for (int j = 0; j < 4; j++)
1410         {
1411           vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1412           style->SetAutoAdjustCameraClippingRange(1);
1413           bool AlreadySelected = false;
1414           for (int i = 0; i < DataTree->topLevelItemCount(); i++)
1415             {
1416               mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1417
1418               //select the image only if previous are not selected
1419               if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1)
1420                 {
1421                   mSlicerManagers[i]->UpdateSlicer(j,1);
1422                   AlreadySelected = true;
1423                 }
1424               else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected)
1425                 {
1426                   if (DataTree->selectedItems().size() == 0)
1427                     DataTree->topLevelItem(i)->setSelected(1);
1428                   DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1429                   mSlicerManagers[i]->UpdateSlicer(j,1);
1430                   DisplaySliders(i,j);
1431                 }
1432               else
1433                 {
1434                   DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1435                   mSlicerManagers[i]->UpdateSlicer(j,0);
1436                 }
1437             }
1438           style->Delete();
1439         }
1440     }
1441 }
1442 //------------------------------------------------------------------------------
1443
1444 //------------------------------------------------------------------------------
1445 void vvMainWindow::DisplaySliders(int slicer, int window) {
1446   int range[2];
1447   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1448   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1449
1450   int tRange[2];
1451   tRange[0] = 0;
1452   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1453   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1454   bool showHorizontal = false;
1455   bool showVertical = false;
1456   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1457       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1458           && mSlicerManagers[slicer]->GetType() != IMAGEWITHTIME
1459           && mSlicerManagers[slicer]->GetType() != MERGEDWITHTIME))
1460     showVertical = true;
1461   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1462       || mSlicerManagers[slicer]->GetType() == IMAGEWITHTIME
1463       || mSlicerManagers[slicer]->GetType() == MERGEDWITHTIME)
1464     showHorizontal = true;
1465
1466   if (showVertical)
1467     verticalSliders[window]->show();
1468   else
1469     verticalSliders[window]->hide();
1470   verticalSliders[window]->setRange(range[0],range[1]);
1471   verticalSliders[window]->setValue(position);
1472
1473   if (showHorizontal)
1474     horizontalSliders[window]->show();
1475   else
1476     horizontalSliders[window]->hide();
1477   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1478   horizontalSliders[window]->setValue(tPosition);
1479 }
1480 //------------------------------------------------------------------------------
1481
1482 //------------------------------------------------------------------------------
1483 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column) {
1484   int index = GetSlicerIndexFromItem(item);
1485
1486   if (DataTree->topLevelItem(index) != item)
1487     {
1488       QString warning = "Do you really want to close the overlay : ";
1489       warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1490       QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1491                          warning, 0, this);
1492       msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1493       msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1494       if (msgBox.exec() == QMessageBox::AcceptRole)
1495         {
1496           std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1497           int overlay_index=0;
1498           for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1499             {
1500               if (DataTree->topLevelItem(index)->\
1501                   child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1502                 overlay_index++;
1503               if (DataTree->topLevelItem(index)->child(child) == item) break;
1504             }
1505           mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1506           mSlicerManagers[index]->SetColorMap(0);
1507           DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1508           mSlicerManagers[index]->Render();
1509         }
1510     }
1511   else if (DataTree->topLevelItemCount() <= 1)
1512     {
1513       QString warning = "Do you really want to close the image : ";
1514       warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1515       warning += "\nThis is the last image, you're about to close vv !!!";
1516       QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1517                          warning, 0, this);
1518       msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1519       msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1520       if (msgBox.exec() == QMessageBox::AcceptRole)
1521         {
1522           this->close();
1523         }
1524     }
1525   else
1526     {
1527       QString warning = "Do you really want to close the image : ";
1528       warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1529       QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1530                          warning, 0, this);
1531       msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1532       msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1533       if (msgBox.exec() == QMessageBox::AcceptRole)
1534         {
1535
1536           // Tell tools that we close an image
1537           emit AnImageIsBeingClosed(mSlicerManagers[index]);
1538
1539           std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1540           DataTree->takeTopLevelItem(index);
1541           for (int i = 0; i < index; i++)
1542             {
1543               Manageriter++;
1544             }
1545           linkPanel->removeImage(index);
1546           mSlicerManagers[index]->RemoveActors();
1547           delete mSlicerManagers[index];
1548           mSlicerManagers.erase(Manageriter);
1549
1550           //
1551           InitDisplay();
1552         }
1553     }
1554 }
1555 //------------------------------------------------------------------------------
1556
1557 //------------------------------------------------------------------------------
1558 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column) {
1559   // int index = GetSlicerIndexFromItem(item);
1560   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1561   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1562   //     mSlicerManagers[index]->ReloadVF();
1563   //   else
1564   //     mSlicerManagers[index]->Reload();
1565
1566   //   QApplication::restoreOverrideCursor();
1567   int index = GetSlicerIndexFromItem(item);
1568   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1569   QString role=item->data(1,Qt::UserRole).toString();
1570   if ( role == "vector")
1571     mSlicerManagers[index]->ReloadVF();
1572   else if (role == "overlay")
1573     mSlicerManagers[index]->ReloadOverlay();
1574   else if (role == "fusion")
1575     mSlicerManagers[index]->ReloadFusion();
1576   else
1577     mSlicerManagers[index]->Reload();
1578   QApplication::restoreOverrideCursor();
1579 }
1580 //------------------------------------------------------------------------------
1581
1582 // void vvMainWindow::CropImage()
1583 // {
1584 //   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1585 //   vvCropDialog crop(mSlicerManagers,index);
1586 //   if(crop.exec())
1587 //     AddImage(crop.GetOutput(),"cropped.mhd");
1588 // }
1589
1590 //------------------------------------------------------------------------------
1591 void vvMainWindow::SplitImage() {
1592   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1593   int dim = mSlicerManagers[index]->GetDimension();
1594   QString warning = "Do you really want to split the ";
1595   warning += QString::number(dim) + "D image ";
1596   warning += DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString() + " into ";
1597   warning += QString::number(mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetSize()[dim-1]) + " ";
1598   warning += QString::number(dim-1) + "D images.";
1599   QMessageBox msgBox(QMessageBox::Warning, tr("Split Image"),
1600                      warning, 0, this);
1601   msgBox.addButton(tr("Split"), QMessageBox::AcceptRole);
1602   msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1603   if (msgBox.exec() == QMessageBox::AcceptRole)
1604     {
1605       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1606       if (dim > 2)
1607         {
1608           std::string filename = DataTree->selectedItems()[0]->data(0,Qt::UserRole).toString().toStdString();
1609           int numberOfSlice = mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetSize()[dim-1];
1610           std::string path = itksys::SystemTools::GetFilenamePath(
1611                                                                   filename);
1612           path += "/";
1613           path += DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString().toStdString();
1614           path += "%03d";
1615           path += itksys::SystemTools::GetFilenameLastExtension(
1616                                                                 filename).c_str();
1617
1618           typedef itk::NumericSeriesFileNames NameGeneratorType;
1619           NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
1620           nameGenerator->SetSeriesFormat(path.c_str());
1621           nameGenerator->SetStartIndex(0);
1622           nameGenerator->SetEndIndex(numberOfSlice-1);
1623           nameGenerator->SetIncrementIndex(1);
1624
1625           for (int i = 0; i < numberOfSlice; i++)
1626             {
1627               vvSlicerManager* imageManager = new vvSlicerManager(4);
1628               imageManager->SetExtractedImage(nameGenerator->GetFileNames()[i],
1629                                               mSlicerManagers[index]->GetSlicer(0)->GetImage(), i);
1630               mSlicerManagers.push_back(imageManager);
1631
1632               //create an item in the tree with good settings
1633               QTreeWidgetItem *item = new QTreeWidgetItem();
1634               item->setData(0,Qt::UserRole,nameGenerator->GetFileNames()[i].c_str());
1635               std::string fileI = itksys::SystemTools::GetFilenameWithoutLastExtension(
1636                                                                                        nameGenerator->GetFileNames()[i]).c_str();
1637               item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileI.c_str());
1638               for (int j = 1; j <= 4; j++)
1639                 {
1640                   for (int i = 0; i < DataTree->topLevelItemCount(); i++)
1641                     {
1642                       DataTree->topLevelItem(i)->setData(j,Qt::CheckStateRole,0);
1643                     }
1644                   item->setData(j,Qt::CheckStateRole,2);
1645                 }
1646
1647               //Create the buttons for reload and close
1648               QTreePushButton* cButton = new QTreePushButton;
1649               cButton->setItem(item);
1650               cButton->setColumn(COLUMN_CLOSE_IMAGE);
1651               cButton->setToolTip(tr("close image"));
1652               cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1653               connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1654                       this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1655
1656               QTreePushButton* rButton = new QTreePushButton;
1657               rButton->setItem(item);
1658               rButton->setColumn(COLUMN_RELOAD_IMAGE);
1659               rButton->setToolTip(tr("reload image"));
1660               rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1661               rButton->setEnabled(false);
1662               connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1663                       this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1664
1665               DataTree->addTopLevelItem(item);
1666               DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1667               DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1668
1669               //set the id of the image
1670               QString id = nameGenerator->GetFileNames()[i].c_str() + QString::number(mSlicerManagers.size()-1);
1671               item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1672               mSlicerManagers.back()->SetId(id.toStdString());
1673               linkPanel->addImage(fileI, id.toStdString());
1674               connect(mSlicerManagers.back(),SIGNAL(currentImageChanged(std::string)),
1675                       this,SLOT(CurrentImageChanged(std::string)));
1676               connect(mSlicerManagers.back(),SIGNAL(
1677                                                     UpdatePosition(int, double, double, double, double, double, double, double)),this,
1678                       SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
1679               connect(mSlicerManagers.back(),SIGNAL(UpdateVector(int, double, double, double, double)),
1680                       this, SLOT(VectorChanged(int,double,double,double, double)));
1681               connect(mSlicerManagers.back(),SIGNAL(UpdateOverlay(int, double, double)),
1682                       this, SLOT(OverlayChanged(int,double,double)));
1683               connect(mSlicerManagers.back(),SIGNAL(UpdateFusion(int, double)),
1684                       this, SLOT(FusionChanged(int,double)));
1685               connect(mSlicerManagers.back(),SIGNAL(UpdateWindows(int, int, int)),
1686                       this,SLOT(WindowsChanged(int, int, int)));
1687               connect(mSlicerManagers.back(),SIGNAL(WindowLevelChanged(double, double,int, int)),
1688                       this,SLOT(WindowLevelChanged(double, double, int, int)));
1689               connect(mSlicerManagers.back(),SIGNAL(UpdateSlice(int,int)),
1690                       this,SLOT(UpdateSlice(int,int)));
1691               connect(mSlicerManagers.back(),SIGNAL(UpdateTSlice(int, int)),
1692                       this,SLOT(UpdateTSlice(int, int)));
1693               connect(mSlicerManagers.back(),SIGNAL(UpdateSliceRange(int,int,int,int,int)),
1694                       this,SLOT(UpdateSliceRange(int,int,int,int,int)));
1695               connect(mSlicerManagers.back(),SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
1696                       this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
1697               connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
1698               UpdateTree();
1699               qApp->processEvents();
1700               InitSlicers();
1701               InitDisplay();
1702               qApp->processEvents();
1703             }
1704           QApplication::restoreOverrideCursor();
1705         }
1706       else
1707         {
1708           QApplication::restoreOverrideCursor();
1709           QString error = "Cannot split file (dimensions must be greater than 2) ";
1710           QMessageBox::information(this,tr("Splitting problem"),error);
1711         }
1712     }
1713 }
1714 //------------------------------------------------------------------------------
1715
1716 //------------------------------------------------------------------------------
1717 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value) {
1718   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1719 }
1720 //------------------------------------------------------------------------------
1721
1722 //------------------------------------------------------------------------------
1723 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value) {
1724   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1725 }
1726 //------------------------------------------------------------------------------
1727
1728 //------------------------------------------------------------------------------
1729 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef) {
1730   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1731 }
1732 //------------------------------------------------------------------------------
1733
1734 //------------------------------------------------------------------------------
1735 void vvMainWindow::FusionChanged(int visibility, double value) {
1736   overlayPanel->getCurrentFusionInfo(visibility,value);
1737 }
1738 //------------------------------------------------------------------------------
1739
1740 //------------------------------------------------------------------------------
1741 void vvMainWindow::WindowsChanged(int window, int view, int slice) {
1742   infoPanel->setViews(window, view, slice);
1743 }
1744 //------------------------------------------------------------------------------
1745
1746 //------------------------------------------------------------------------------
1747 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap) {
1748   windowSpinBox->setValue(window);
1749   levelSpinBox->setValue(level);
1750   colorMapComboBox->setCurrentIndex(colormap);
1751   presetComboBox->setCurrentIndex(preset);
1752 }
1753 //------------------------------------------------------------------------------
1754
1755 //------------------------------------------------------------------------------
1756 void vvMainWindow::WindowLevelEdited() {
1757   presetComboBox->setCurrentIndex(6);
1758   UpdateWindowLevel();
1759 }
1760 //------------------------------------------------------------------------------
1761
1762 //------------------------------------------------------------------------------
1763 void vvMainWindow::UpdateWindowLevel() {
1764   if (DataTree->selectedItems().size())
1765     {
1766       if (presetComboBox->currentIndex() == 7) //For ventilation
1767         colorMapComboBox->setCurrentIndex(5);
1768       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1769       mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1770       mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1771       mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1772       mSlicerManagers[index]->Render();
1773     }
1774 }
1775 //------------------------------------------------------------------------------
1776
1777 //------------------------------------------------------------------------------
1778 void vvMainWindow::UpdateColorMap() {
1779   if (DataTree->selectedItems().size())
1780     {
1781       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1782       mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1783       mSlicerManagers[index]->Render();
1784     }
1785 }
1786 //------------------------------------------------------------------------------
1787 void vvMainWindow::SwitchWindowLevel() {
1788   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1789   int window = mSlicerManagers[index]->GetColorWindow();
1790   presetComboBox->setCurrentIndex(6);
1791   windowSpinBox->setValue(-window);
1792   UpdateWindowLevel();
1793 }
1794 //------------------------------------------------------------------------------
1795
1796 //------------------------------------------------------------------------------
1797 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps) {
1798   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
1799     {
1800       if (mSlicerManagers[i]->GetId() == id)
1801         {
1802           //mSlicerManagers[i]->SetTSlice(temps);
1803           mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1804           mSlicerManagers[i]->UpdateViews(0,slicer);
1805           break;
1806         }
1807     }
1808 }
1809 //------------------------------------------------------------------------------
1810
1811 //------------------------------------------------------------------------------
1812 void vvMainWindow::ShowContextMenu(QPoint point) {
1813   if (!DataTree->selectedItems().size())
1814     {
1815       contextActions[1]->setEnabled(0);
1816       contextActions[2]->setEnabled(0);
1817       contextActions[3]->setEnabled(0);
1818       contextActions[4]->setEnabled(0);
1819       contextActions[5]->setEnabled(0);
1820       contextActions[6]->setEnabled(0);
1821       contextActions[7]->setEnabled(0);
1822     }
1823   else
1824     {
1825       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1826       contextActions[1]->setEnabled(1);
1827       contextActions[2]->setEnabled(
1828                                     DataTree->itemWidget(DataTree->selectedItems()[0],
1829                                                          COLUMN_RELOAD_IMAGE)->isEnabled());
1830       contextActions[3]->setEnabled(1);
1831       contextActions[5]->setEnabled(1);
1832       contextActions[6]->setEnabled(1);
1833       contextActions[7]->setEnabled(1);
1834
1835       if (mSlicerManagers[index]->GetDimension() < 3)
1836         contextActions[4]->setEnabled(0);
1837       else
1838         contextActions[4]->setEnabled(1);
1839     }
1840   contextMenu.exec(QCursor::pos());
1841 }
1842 //------------------------------------------------------------------------------
1843
1844 //------------------------------------------------------------------------------
1845 void vvMainWindow::CloseImage() {
1846   CloseImage(DataTree->selectedItems()[0],0);
1847 }
1848 //------------------------------------------------------------------------------
1849
1850 //------------------------------------------------------------------------------
1851 void vvMainWindow::ReloadImage() {
1852   ReloadImage(DataTree->selectedItems()[0],0);
1853 }
1854 //------------------------------------------------------------------------------
1855
1856 //------------------------------------------------------------------------------
1857 void vvMainWindow::SelectOverlayImage() {
1858   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1859
1860   //check if one overlay image is added
1861   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1862     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay")
1863       {
1864         QString error = "Cannot add more than one compared image\n";
1865         error += "Please remove first ";
1866         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1867         QMessageBox::information(this,tr("Problem adding compared image !"),error);
1868         return;
1869       }
1870
1871   QString Extensions = EXTENSIONS;
1872   Extensions += ";;All Files (*)";
1873   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1874   if (!file.isEmpty())
1875     AddOverlayImage(index,file);
1876 }
1877 //------------------------------------------------------------------------------
1878
1879 //------------------------------------------------------------------------------
1880 void vvMainWindow::AddOverlayImage(int index, QString file) {
1881   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1882   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1883                                                                         file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1884   reader->SetFileName(file.toStdString().c_str());
1885   reader->ReadImageInformation();
1886   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1887   int dimension = reader->GetNumberOfDimensions();
1888   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1889   vvProgressDialog progress("Opening " + file.toStdString());
1890   qApp->processEvents();
1891
1892   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1893   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component))
1894     {
1895       //create an item in the tree with good settings
1896       QTreeWidgetItem *item = new QTreeWidgetItem();
1897       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1898       item->setData(1,Qt::UserRole,tr("overlay"));
1899       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
1900       qApp->processEvents();
1901
1902       for (int j = 1; j <= 4; j++)
1903         {
1904           item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1905           mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("overlay",0,
1906                                                                      DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1907         }
1908
1909       //Create the buttons for reload and close
1910       qApp->processEvents();
1911       QTreePushButton* cButton = new QTreePushButton;
1912       cButton->setItem(item);
1913       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1914       cButton->setToolTip(tr("close image"));
1915       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1916       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1917               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1918
1919       QTreePushButton* rButton = new QTreePushButton;
1920       rButton->setItem(item);
1921       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1922       rButton->setToolTip(tr("reload image"));
1923       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1924       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1925               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1926
1927       DataTree->topLevelItem(index)->setExpanded(1);
1928       DataTree->topLevelItem(index)->addChild(item);
1929       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1930       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1931
1932       //set the id of the image
1933       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1934       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1935       UpdateTree();
1936       qApp->processEvents();
1937       ImageInfoChanged();
1938       QApplication::restoreOverrideCursor();
1939     }
1940   else
1941     {
1942       QApplication::restoreOverrideCursor();
1943       QString error = "Cannot import the new image.\n";
1944       error += mSlicerManagers[index]->GetLastError().c_str();
1945       QMessageBox::information(this,tr("Problem reading image !"),error);
1946     }
1947 }
1948
1949 void vvMainWindow::AddFusionImage()
1950 {
1951   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1952
1953   //check if one fusion image is added
1954   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1955     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion")
1956       {
1957         QString error = "Cannot add more than one fusion image\n";
1958         error += "Please remove first ";
1959         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1960         QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1961         return;
1962       }
1963
1964   QString Extensions = EXTENSIONS;
1965   Extensions += ";;All Files (*)";
1966   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1967   if (!file.isEmpty())
1968     {
1969       mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1970       itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1971                                                                             file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1972       reader->SetFileName(file.toStdString().c_str());
1973       reader->ReadImageInformation();
1974       std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1975       if (reader)
1976         {
1977           QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1978           vvProgressDialog progress("Opening fusion");
1979           qApp->processEvents();
1980
1981           std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1982           if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1983                                                 reader->GetNumberOfDimensions(), component))
1984             {
1985               //create an item in the tree with good settings
1986               QTreeWidgetItem *item = new QTreeWidgetItem();
1987               item->setData(0,Qt::UserRole,file.toStdString().c_str());
1988               item->setData(1,Qt::UserRole,tr("fusion"));
1989               item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
1990               qApp->processEvents();
1991
1992               for (int j = 1; j <= 4; j++)
1993                 {
1994                   item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1995                   mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("fusion",0,
1996                                                                              DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1997                 }
1998
1999               //Create the buttons for reload and close
2000               qApp->processEvents();
2001               QTreePushButton* cButton = new QTreePushButton;
2002               cButton->setItem(item);
2003               cButton->setColumn(COLUMN_CLOSE_IMAGE);
2004               cButton->setToolTip(tr("close image"));
2005               cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2006               connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2007                       this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2008
2009               QTreePushButton* rButton = new QTreePushButton;
2010               rButton->setItem(item);
2011               rButton->setColumn(COLUMN_RELOAD_IMAGE);
2012               rButton->setToolTip(tr("reload image"));
2013               rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2014               connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2015                       this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2016
2017               DataTree->topLevelItem(index)->setExpanded(1);
2018               DataTree->topLevelItem(index)->addChild(item);
2019               DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2020               DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2021
2022               //set the id of the image
2023               QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2024               item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2025               UpdateTree();
2026               qApp->processEvents();
2027               ImageInfoChanged();
2028               QApplication::restoreOverrideCursor();
2029             }
2030           else
2031             {
2032               QApplication::restoreOverrideCursor();
2033               QString error = "Cannot import the new image.\n";
2034               error += mSlicerManagers[index]->GetLastError().c_str();
2035               QMessageBox::information(this,tr("Problem reading image !"),error);
2036             }
2037         }
2038       else
2039         {
2040           QString error = "Cannot import the new image.\n";
2041           QMessageBox::information(this,tr("Problem reading image !"),error);
2042         }
2043     }
2044 }
2045
2046
2047 void vvMainWindow::OpenField()
2048 {
2049   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2050   //check if a vector field has already been added
2051   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2052     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector")
2053       {
2054         QString error = "Cannot add more than one vector field\n";
2055         error += "Please remove first ";
2056         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2057         QMessageBox::information(this,tr("Problem adding vector field!"),error);
2058         return;
2059       }
2060
2061   QString Extensions = "Images ( *.mhd)";
2062   Extensions += ";;Images ( *.vf)";
2063   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2064   if (!file.isEmpty())
2065     AddField(file,index);
2066 }
2067
2068 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2069 {
2070   //create an item in the tree with good settings
2071   QTreeWidgetItem *item = new QTreeWidgetItem();
2072   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2073   item->setData(1,Qt::UserRole,tr("vector"));
2074   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename);
2075   qApp->processEvents();
2076
2077   for (int j = 1; j <= 4; j++)
2078     {
2079       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2080       mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("vector",0,
2081                                                                  DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
2082     }
2083
2084   //Create the buttons for reload and close
2085   qApp->processEvents();
2086   QTreePushButton* cButton = new QTreePushButton;
2087   cButton->setItem(item);
2088   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2089   cButton->setToolTip(tr("close vector field"));
2090   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2091   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2092           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2093
2094   QTreePushButton* rButton = new QTreePushButton;
2095   rButton->setItem(item);
2096   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2097   rButton->setToolTip(tr("reload vector field"));
2098   rButton->setEnabled(from_disk);
2099   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2100   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2101           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2102
2103   DataTree->topLevelItem(index)->setExpanded(1);
2104   DataTree->topLevelItem(index)->addChild(item);
2105   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2106   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2107
2108   //set the id of the image
2109   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2110   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2111   UpdateTree();
2112   qApp->processEvents();
2113   ImageInfoChanged();
2114   QApplication::restoreOverrideCursor();
2115 }
2116
2117 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2118 {
2119   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2120   vvSlicerManager* imageManager = mSlicerManagers[index];
2121   if (imageManager->SetVF(vf,file.toStdString()))
2122     {
2123       AddFieldEntry(file,index,false);
2124     }
2125   else
2126     {
2127       QString error = "Cannot import the vector field for this image.\n";
2128       error += imageManager->GetLastError().c_str();
2129       QMessageBox::information(this,tr("Problem reading VF !"),error);
2130     }
2131   QApplication::restoreOverrideCursor();
2132 }
2133
2134 void vvMainWindow::AddField(QString file,int index)
2135 {
2136   if (QFile::exists(file))
2137     {
2138       mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2139
2140       //init the progress events
2141       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2142       vvProgressDialog progress("Opening " + file.toStdString());
2143       qApp->processEvents();
2144
2145       //read the vector and put it in the current mSlicerManager
2146       vvSlicerManager* imageManager = mSlicerManagers[index];
2147       qApp->processEvents();
2148
2149       std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2150       if (imageManager->SetVF(file.toStdString()))
2151         {
2152           imageManager->Render();
2153           AddFieldEntry(file,index,true);
2154         }
2155       else
2156         {
2157           QApplication::restoreOverrideCursor();
2158           QString error = "Cannot import the vector field for this image.\n";
2159           error += imageManager->GetLastError().c_str();
2160           QMessageBox::information(this,tr("Problem reading VF !"),error);
2161         }
2162     }
2163   else
2164     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2165
2166 }
2167 //------------------------------------------------------------------------------
2168
2169 //------------------------------------------------------------------------------
2170 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log) {
2171   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2172   if (mSlicerManagers[index]->GetSlicer(0)->GetVF())
2173     {
2174       for (int i = 0; i < 4; i++)
2175         {
2176           mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2177           mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2178           if (log > 0)
2179             mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2180           else
2181             mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2182         }
2183     }
2184 }
2185 //------------------------------------------------------------------------------
2186
2187 //------------------------------------------------------------------------------
2188 void vvMainWindow::SetOverlayProperty(int color) {
2189   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2190   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
2191     {
2192       mSlicerManagers[index]->SetOverlayColor(color);
2193       mSlicerManagers[index]->SetColorMap(0);
2194       mSlicerManagers[index]->Render();
2195     }
2196 }
2197 //------------------------------------------------------------------------------
2198
2199 //------------------------------------------------------------------------------
2200 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level) {
2201   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2202   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion())
2203     {
2204       mSlicerManagers[index]->SetFusionOpacity(opacity);
2205       mSlicerManagers[index]->SetFusionColorMap(colormap);
2206       mSlicerManagers[index]->SetFusionWindow(window);
2207       mSlicerManagers[index]->SetFusionLevel(level);
2208       mSlicerManagers[index]->SetColorMap(0);
2209       mSlicerManagers[index]->Render();
2210     }
2211 }
2212 //------------------------------------------------------------------------------
2213
2214 //------------------------------------------------------------------------------
2215 void vvMainWindow::SaveAs() {
2216   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector")
2217     {
2218       QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2219       return;
2220     }
2221
2222   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2223   int dimension = mSlicerManagers[index]->GetDimension();
2224   QStringList OutputListeFormat;
2225   OutputListeFormat.clear();
2226   if (dimension == 1)
2227     {
2228       OutputListeFormat.push_back(".mhd");
2229     }
2230   if (dimension == 2)
2231     {
2232       OutputListeFormat.push_back(".bmp");
2233       OutputListeFormat.push_back(".png");
2234       OutputListeFormat.push_back(".jpeg");
2235       OutputListeFormat.push_back(".tif");
2236       OutputListeFormat.push_back(".mhd");
2237       OutputListeFormat.push_back(".hdr");
2238       OutputListeFormat.push_back(".vox");
2239     }
2240   else if (dimension == 3)
2241     {
2242       OutputListeFormat.push_back(".mhd");
2243       OutputListeFormat.push_back(".hdr");
2244       OutputListeFormat.push_back(".vox");
2245     }
2246   else if (dimension == 4)
2247     {
2248       OutputListeFormat.push_back(".mhd");
2249     }
2250   QString Extensions = "AllFiles(*.*)";
2251   for (int i = 0; i < OutputListeFormat.count(); i++)
2252     {
2253       Extensions += ";;Images ( *";
2254       Extensions += OutputListeFormat[i];
2255       Extensions += ")";
2256     }
2257   QString fileName = QFileDialog::getSaveFileName(this,
2258                                                   tr("Save As"),
2259                                                   mSlicerManagers[index]->GetFileName().c_str(),
2260                                                   Extensions);
2261   if (!fileName.isEmpty())
2262     {
2263       std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2264       if (OutputListeFormat.contains(
2265                                      fileformat.c_str()))
2266         {
2267           QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2268           std::string action = "Saving";
2269           vvProgressDialog progress("Saving "+fileName.toStdString());
2270           qApp->processEvents();
2271           vvImageWriter *writer = new vvImageWriter;
2272           writer->SetOutputFileName(fileName.toStdString());
2273           writer->SetInput(mSlicerManagers[index]->GetImage());
2274           writer->Update();
2275           QApplication::restoreOverrideCursor();
2276           if (writer->GetLastError().size())
2277             {
2278               QString error = "Saving did not succeed\n";
2279               error += writer->GetLastError().c_str();
2280               QMessageBox::information(this,tr("Saving Problem"),error);
2281               SaveAs();
2282             }
2283         }
2284       else
2285         {
2286           QString error = fileformat.c_str();
2287           if (error.isEmpty())
2288             error += "no file format specified !";
2289           else
2290             error += " format unknown !!!\n";
2291           QMessageBox::information(this,tr("Saving Problem"),error);
2292           SaveAs();
2293         }
2294     }
2295 }
2296 //------------------------------------------------------------------------------
2297
2298 //------------------------------------------------------------------------------
2299 void vvMainWindow::AddLink(QString image1,QString image2) {
2300   for (unsigned int i = 0; i < mSlicerManagers.size();i++)
2301     {
2302       if (image1.toStdString() == mSlicerManagers[i]->GetId())
2303         {
2304           mSlicerManagers[i]->AddLink(image2.toStdString());
2305         }
2306       if (image2.toStdString() == mSlicerManagers[i]->GetId())
2307         {
2308           mSlicerManagers[i]->AddLink(image1.toStdString());
2309         }
2310     }
2311 }
2312 //------------------------------------------------------------------------------
2313
2314 //------------------------------------------------------------------------------
2315 void vvMainWindow::RemoveLink(QString image1,QString image2) {
2316   for (unsigned int i = 0; i < mSlicerManagers.size();i++)
2317     {
2318       if (image1.toStdString() == mSlicerManagers[i]->GetId())
2319         {
2320           mSlicerManagers[i]->RemoveLink(image2.toStdString());
2321         }
2322       if (image2.toStdString() == mSlicerManagers[i]->GetId())
2323         {
2324           mSlicerManagers[i]->RemoveLink(image1.toStdString());
2325         }
2326     }
2327 }
2328 //------------------------------------------------------------------------------
2329
2330 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2331 {
2332   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2333     {
2334       if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1)
2335         {
2336           for (int j = 0; j < 4; j++)
2337             {
2338               mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2339               //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2340               //UpdateTSlice(j,value);
2341             }
2342           mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2343           break;
2344         }
2345     }
2346 }
2347
2348 //------------------------------------------------------------------------------
2349 void vvMainWindow::NOHorizontalSliderMoved() {
2350   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2351 }
2352 //------------------------------------------------------------------------------
2353
2354 //------------------------------------------------------------------------------
2355 void vvMainWindow::NEHorizontalSliderMoved() {
2356   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2357 }
2358 //------------------------------------------------------------------------------
2359
2360 //------------------------------------------------------------------------------
2361 void vvMainWindow::SOHorizontalSliderMoved() {
2362   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2363 }
2364 //------------------------------------------------------------------------------
2365
2366 //------------------------------------------------------------------------------
2367 void vvMainWindow::SEHorizontalSliderMoved() {
2368   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2369 }
2370 //------------------------------------------------------------------------------
2371
2372 //------------------------------------------------------------------------------
2373 void vvMainWindow::NOVerticalSliderChanged() {
2374   int value = NOVerticalSlider->value();
2375   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2376     {
2377       if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
2378         {
2379           mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2380           mSlicerManagers[i]->UpdateSlice(0); // <-- DS add this. Not too much update ?
2381           break;
2382         }
2383     }
2384 }
2385 //------------------------------------------------------------------------------
2386
2387 //------------------------------------------------------------------------------
2388 void vvMainWindow::NEVerticalSliderChanged() {
2389   int value = NEVerticalSlider->value();
2390   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2391     {
2392       if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1)
2393         {
2394           mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2395           break;
2396         }
2397     }
2398 }
2399 //------------------------------------------------------------------------------
2400
2401 //------------------------------------------------------------------------------
2402 void vvMainWindow::SOVerticalSliderChanged() {
2403   int value = SOVerticalSlider->value();
2404   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2405     {
2406       if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
2407         {
2408           mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2409           break;
2410         }
2411     }
2412 }
2413 //------------------------------------------------------------------------------
2414
2415 //------------------------------------------------------------------------------
2416 void vvMainWindow::SEVerticalSliderChanged() {
2417   int value = SEVerticalSlider->value();
2418   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2419     {
2420       if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1)
2421         {
2422           mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2423           break;
2424         }
2425     }
2426 }
2427 //------------------------------------------------------------------------------
2428
2429 //------------------------------------------------------------------------------
2430 void vvMainWindow::UpdateSlice(int slicer, int slice) {
2431   if (slicer == 0) {
2432     if (slice != NOVerticalSlider->value())
2433       NOVerticalSlider->setValue(slice);
2434   }
2435   else if (slicer == 1)
2436     NEVerticalSlider->setValue(slice);
2437   else if (slicer == 2)
2438     SOVerticalSlider->setValue(slice);
2439   else if (slicer == 3)
2440     SEVerticalSlider->setValue(slice);
2441 }
2442 //------------------------------------------------------------------------------
2443
2444 //------------------------------------------------------------------------------
2445 void vvMainWindow::UpdateTSlice(int slicer, int slice) {
2446   switch (slicer)
2447     {
2448     case 0:
2449       NOHorizontalSlider->setValue(slice);
2450       break;
2451     case 1:
2452       NEHorizontalSlider->setValue(slice);
2453       break;
2454     case 2:
2455       SOHorizontalSlider->setValue(slice);
2456       break;
2457     case 3:
2458       SEHorizontalSlider->setValue(slice);
2459       break;
2460     }
2461 }
2462 //------------------------------------------------------------------------------
2463
2464 //------------------------------------------------------------------------------
2465 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax) {
2466   int position = int((min+max)/2);
2467   int tPosition = int((tmin+tmax)/2);
2468   if (slicer == 0)
2469     {
2470       NOVerticalSlider->setValue(position);
2471       NOVerticalSlider->setRange(min,max);
2472       NOHorizontalSlider->setRange(tmin,tmax);
2473       NOHorizontalSlider->setValue(tPosition);
2474     }
2475   else if (slicer == 1)
2476     {
2477       NEVerticalSlider->setValue(position);
2478       NEVerticalSlider->setRange(min,max);
2479       NEHorizontalSlider->setRange(tmin,tmax);
2480       NEHorizontalSlider->setValue(tPosition);
2481     }
2482   else if (slicer == 2)
2483     {
2484       SOVerticalSlider->setValue(position);
2485       SOVerticalSlider->setRange(min,max);
2486       SOHorizontalSlider->setRange(tmin,tmax);
2487       SOHorizontalSlider->setValue(tPosition);
2488     }
2489   else if (slicer == 3)
2490     {
2491       SEVerticalSlider->setValue(position);
2492       SEVerticalSlider->setRange(min,max);
2493       SEHorizontalSlider->setRange(tmin,tmax);
2494       SEHorizontalSlider->setValue(tPosition);
2495     }
2496 }
2497 //------------------------------------------------------------------------------
2498
2499 //------------------------------------------------------------------------------
2500 void vvMainWindow::SaveNOScreenshot() {
2501   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2502   w2i->SetInput(NOViewWidget->GetRenderWindow());
2503   w2i->Update();
2504   SaveScreenshot(w2i->GetOutput());
2505   w2i->Delete();
2506 }
2507 //------------------------------------------------------------------------------
2508
2509 //------------------------------------------------------------------------------
2510 void vvMainWindow::SaveNEScreenshot() {
2511   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2512   w2i->SetInput(NEViewWidget->GetRenderWindow());
2513   w2i->Update();
2514   SaveScreenshot(w2i->GetOutput());
2515   w2i->Delete();
2516 }
2517 //------------------------------------------------------------------------------
2518
2519 //------------------------------------------------------------------------------
2520 void vvMainWindow::SaveSOScreenshot() {
2521   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2522   w2i->SetInput(SOViewWidget->GetRenderWindow());
2523   w2i->Update();
2524   SaveScreenshot(w2i->GetOutput());
2525   w2i->Delete();
2526 }
2527 //------------------------------------------------------------------------------
2528
2529 //------------------------------------------------------------------------------
2530 void vvMainWindow::SaveSEScreenshot() {
2531   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2532   w2i->SetInput(SEViewWidget->GetRenderWindow());
2533   w2i->Update();
2534   SaveScreenshot(w2i->GetOutput());
2535   w2i->Delete();
2536 }
2537 //------------------------------------------------------------------------------
2538
2539 //------------------------------------------------------------------------------
2540 void vvMainWindow::SaveScreenshot(vtkImageData* image) {
2541   QString Extensions = "Images( *.png);;";
2542   Extensions += "Images( *.jpg);;";
2543   Extensions += "Images( *.bmp);;";
2544   Extensions += "Images( *.tif);;";
2545   Extensions += "Images( *.ppm)";
2546   QString fileName = QFileDialog::getSaveFileName(this,
2547                                                   tr("Save As"),
2548                                                   itksys::SystemTools::GetFilenamePath(
2549                                                                                        mSlicerManagers[0]->GetFileName()).c_str(),
2550                                                   Extensions);
2551   if (!fileName.isEmpty())
2552     {
2553       const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2554       if (!strcmp(ext, ".bmp"))
2555         {
2556           vtkBMPWriter *bmp = vtkBMPWriter::New();
2557           bmp->SetInput(image);
2558           bmp->SetFileName(fileName.toStdString().c_str());
2559           bmp->Write();
2560           bmp->Delete();
2561         }
2562       else if (!strcmp(ext, ".tif"))
2563         {
2564           vtkTIFFWriter *tif = vtkTIFFWriter::New();
2565           tif->SetInput(image);
2566           tif->SetFileName(fileName.toStdString().c_str());
2567           tif->Write();
2568           tif->Delete();
2569         }
2570       else if (!strcmp(ext, ".ppm"))
2571         {
2572           vtkPNMWriter *pnm = vtkPNMWriter::New();
2573           pnm->SetInput(image);
2574           pnm->SetFileName(fileName.toStdString().c_str());
2575           pnm->Write();
2576           pnm->Delete();
2577         }
2578       else if (!strcmp(ext, ".png"))
2579         {
2580           vtkPNGWriter *png = vtkPNGWriter::New();
2581           png->SetInput(image);
2582           png->SetFileName(fileName.toStdString().c_str());
2583           png->Write();
2584           png->Delete();
2585         }
2586       else if (!strcmp(ext, ".jpg"))
2587         {
2588           vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2589           jpg->SetInput(image);
2590           jpg->SetFileName(fileName.toStdString().c_str());
2591           jpg->Write();
2592           jpg->Delete();
2593         }
2594       else
2595         {
2596           QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2597         }
2598     }
2599
2600 }
2601 //------------------------------------------------------------------------------
2602
2603 //------------------------------------------------------------------------------
2604 void vvMainWindow::GoToCursor() {
2605   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2606   for (int column = 1; column < 5; column++)
2607     {
2608       if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1)
2609         {
2610           double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2611           mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2612                                                                           cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2613           mSlicerManagers[index]->UpdateViews(1,column-1);
2614           mSlicerManagers[index]->UpdateLinked(column-1);
2615           break;
2616         }
2617     }
2618 }
2619 //------------------------------------------------------------------------------
2620
2621 //------------------------------------------------------------------------------
2622 void vvMainWindow::PlayPause() {
2623   if (playMode)
2624     {
2625       playMode = 0;
2626       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2627       ImageInfoChanged();
2628       return;
2629     }
2630   else
2631     {
2632       int image_number=DataTree->topLevelItemCount();
2633       bool has_temporal;
2634       for (int i=0;i<image_number;i++)
2635         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1)
2636           {
2637             has_temporal=true;
2638             break;
2639           }
2640       if (has_temporal)
2641         {
2642           playMode = 1;
2643           playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2644           QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2645         }
2646     }
2647 }
2648 //------------------------------------------------------------------------------
2649
2650 //------------------------------------------------------------------------------
2651 void vvMainWindow::PlayNext() {
2652   if (playMode && !this->isHidden())
2653     {
2654       int image_number=DataTree->topLevelItemCount();
2655       ///Only play one slicer per SM, and only if the SM is being displayed
2656       for (int i=0;i<image_number;i++)
2657         for (int j=0;j<4;j++)
2658           if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2659               DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0)
2660             {
2661               mSlicerManagers[i]->SetNextTSlice(j);
2662               break;
2663             }
2664       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2665     }
2666 }
2667 //------------------------------------------------------------------------------
2668
2669 void vvMainWindow::ShowLastImage()
2670 {
2671   if (mSlicerManagers.size() > 1)
2672     {
2673       QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2674       CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2675       item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2676       DisplayChanged(item,1);
2677     }
2678 }
2679
2680 //------------------------------------------------------------------------------
2681 void vvMainWindow::UpdateRenderWindows() {
2682   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2683   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2684   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2685   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2686 }
2687 //------------------------------------------------------------------------------
2688
2689 //------------------------------------------------------------------------------
2690 void vvMainWindow::ResampleCurrentImage() {
2691   vvResamplerDialog resampler;
2692   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2693   resampler.SetSlicerManagers(mSlicerManagers,index);
2694   if (resampler.exec())
2695     AddImage(resampler.GetOutput(),resampler.GetOutputFileName());
2696 }
2697 //------------------------------------------------------------------------------
2698
2699 //------------------------------------------------------------------------------
2700 void vvMainWindow::SegmentationOnCurrentImage() {
2701   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2702
2703   vvSegmentationDialog segmentation;
2704   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2705   segmentation.exec();
2706 }
2707 //------------------------------------------------------------------------------
2708
2709 void vvMainWindow::SurfaceViewerLaunch()
2710 {
2711   vvSurfaceViewerDialog surfaceViewer;
2712   surfaceViewer.exec();
2713 }
2714
2715 //------------------------------------------------------------------------------
2716 void vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2717 {
2718   vvSlicerManager* m = new vvSlicerManager(4);
2719   m->SetImage(image);
2720   m->SetFilename(filename);
2721   AddImage(m);
2722 }
2723
2724 //------------------------------------------------------------------------------
2725 void vvMainWindow::AddImage(vvSlicerManager * slicer_manager) {
2726   mSlicerManagers.push_back(slicer_manager);
2727
2728   std::string filename = slicer_manager->GetFileName();
2729
2730   //create an item in the tree with good settings
2731   QTreeWidgetItem *item = new QTreeWidgetItem();
2732   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2733   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
2734   qApp->processEvents();
2735
2736   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2737
2738   //Create the buttons for reload and close
2739   qApp->processEvents();
2740   QTreePushButton* cButton = new QTreePushButton;
2741   cButton->setItem(item);
2742   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2743   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2744   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2745           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2746
2747   QTreePushButton* rButton = new QTreePushButton;
2748   rButton->setItem(item);
2749   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2750   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2751   rButton->setEnabled(0);
2752   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2753           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2754
2755   DataTree->addTopLevelItem(item);
2756   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2757   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2758
2759   //set the id of the image
2760   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2761   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2762   mSlicerManagers.back()->SetId(id.toStdString());
2763
2764   linkPanel->addImage(filename, id.toStdString());
2765
2766   connect(mSlicerManagers.back(),SIGNAL(currentImageChanged(std::string)),
2767           this,SLOT(CurrentImageChanged(std::string)));
2768   connect(mSlicerManagers.back(),SIGNAL(
2769                                         UpdatePosition(int, double, double, double, double, double, double, double)),this,
2770           SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2771   connect(mSlicerManagers.back(),SIGNAL(UpdateVector(int, double, double, double, double)),
2772           this, SLOT(VectorChanged(int,double,double,double, double)));
2773   connect(mSlicerManagers.back(),SIGNAL(UpdateOverlay(int, double, double)),
2774           this, SLOT(OverlayChanged(int,double,double)));
2775   connect(mSlicerManagers.back(),SIGNAL(UpdateFusion(int, double)),
2776           this, SLOT(FusionChanged(int,double)));
2777   connect(mSlicerManagers.back(),SIGNAL(UpdateWindows(int, int, int)),
2778           this,SLOT(WindowsChanged(int, int, int)));
2779   connect(mSlicerManagers.back(),SIGNAL(WindowLevelChanged(double, double,int, int)),
2780           this,SLOT(WindowLevelChanged(double, double, int, int)));
2781   connect(mSlicerManagers.back(),SIGNAL(UpdateSlice(int,int)),
2782           this,SLOT(UpdateSlice(int,int)));
2783   connect(mSlicerManagers.back(),SIGNAL(UpdateTSlice(int, int)),
2784           this,SLOT(UpdateTSlice(int, int)));
2785   connect(mSlicerManagers.back(),SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2786           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2787   connect(mSlicerManagers.back(),SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2788           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2789   connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2790   UpdateTree();
2791   qApp->processEvents();
2792   InitSlicers();
2793   ShowLastImage();
2794   InitDisplay();
2795   qApp->processEvents();
2796 }
2797 //------------------------------------------------------------------------------
2798
2799
2800 //------------------------------------------------------------------------------
2801 void vvMainWindow::UpdateCurrentSlicer() {
2802   int index = -1;
2803   if (DataTree->selectedItems().size() > 0) {
2804     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2805   }
2806   mSlicerManagerCurrentIndex = index;
2807 }
2808 //------------------------------------------------------------------------------
2809