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   if (!mip.error)
 345       AddImage(mip.GetOutput(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_mip.mhd");
 346 }
 347 //------------------------------------------------------------------------------
 348
 349
 350 //------------------------------------------------------------------------------
 351 void vvMainWindow::ComputeMidPosition()
 352 {
 353   bool ok;
 354   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 355   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 356                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 357   if (ok)
 358     {
 359       vvMidPosition midp;
 360       midp.slicer_manager = mSlicerManagers[index];
 361       midp.reference_image_index = ref;
 362       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 363       midp.Update();
 364       if (midp.error)
 365         QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 366       else
 367         {
 368           QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 369           AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 370         }
 371       QApplication::restoreOverrideCursor();
 372     }
 373 }
 374 //------------------------------------------------------------------------------
 375
 376
 377 //------------------------------------------------------------------------------
 378 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 379 {
 380   QTreeWidgetItem *item = new QTreeWidgetItem();
 381   item->setData(0,Qt::UserRole,"filename.vtk");
 382   item->setData(1,Qt::UserRole,tr("contour"));
 383   QBrush brush;
 384   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 385   brush.setStyle(Qt::SolidPattern);
 386   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 387   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 388
 389   for (int j = 1; j <= 4; j++)
 390     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 391
 392   QTreePushButton* cButton = new QTreePushButton;
 393   cButton->setItem(item);
 394   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 395   cButton->setToolTip(tr("close image"));
 396   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 397   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 398           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 399
 400   QTreePushButton* rButton = new QTreePushButton;
 401   rButton->setItem(item);
 402   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 403   rButton->setToolTip(tr("reload image"));
 404   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 405   rButton->setEnabled(false);
 406   //Not implemented
 407   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 408   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 409
 410   DataTree->topLevelItem(image_index)->setExpanded(1);
 411   DataTree->topLevelItem(image_index)->addChild(item);
 412   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 413   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 414   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 415   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 416
 417   UpdateTree();
 418   mSlicerManagers[image_index]->AddContour(contour,propagation);
 419   mSlicerManagers[image_index]->Render();
 420 }
 421 //------------------------------------------------------------------------------
 422
 423
 424 //------------------------------------------------------------------------------
 425 void vvMainWindow::OpenVTKContour()
 426 {
 427   if (mSlicerManagers.size() > 0)
 428     {
 429       QString Extensions = "Images ( *.vtk; *.obj)";
 430       Extensions += ";;All Files (*)";
 431       QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 432       if (file.isNull())
 433         return;
 434       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 435       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 436       vvMeshReader reader;
 437       reader.SetImage(mSlicerManagers[index]->GetImage());
 438       reader.SetModeToVTK();
 439       reader.SetFilename(file.toStdString());
 440       reader.Update();
 441       AddContour(index,reader.GetOutput()[0],false);
 442       QApplication::restoreOverrideCursor();
 443     }
 444 }
 445 //------------------------------------------------------------------------------
 446
 447
 448 //------------------------------------------------------------------------------
 449 void vvMainWindow::OpenDCStructContour()
 450 {
 451   if (mSlicerManagers.size() > 0)
 452     {
 453       QString Extensions = "Dicom Files ( *.dcm; RS*)";
 454       Extensions += ";;All Files (*)";
 455       QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 456       if (file.isNull())
 457         return;
 458       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 459       vvMeshReader reader;
 460       reader.SetFilename(file.toStdString());
 461       vvStructSelector selector;
 462       selector.SetStructures(reader.GetROINames());
 463       if (!mSlicerManagers[index]->GetVF().IsNull())
 464         selector.EnablePropagationCheckBox();
 465       if (selector.exec())
 466         {
 467           QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 468           reader.SetSelectedItems(selector.getSelectedItems());
 469           reader.SetImage(mSlicerManagers[index]->GetImage());
 470           if (selector.PropagationEnabled())
 471             reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 472           reader.Update();
 473           std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 474           for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 475                i!=contours.end();i++)
 476             AddContour(index,*i,selector.PropagationEnabled());
 477           QApplication::restoreOverrideCursor();
 478         }
 479     }
 480 }
 481 //------------------------------------------------------------------------------
 482
 483
 484 //------------------------------------------------------------------------------
 485 void vvMainWindow::ComputeDeformableRegistration()
 486 {
 487   if (mSlicerManagers.size() > 0)
 488     {
 489       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 490       vvDeformationDialog dialog(index,mSlicerManagers);
 491       if (dialog.exec())
 492         {
 493           std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 494           AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 495           WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 496         }
 497       else
 498         std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 499     }
 500   else QMessageBox::information(this, "Need to open image","You must open an image first.");
 501 }
 502 //------------------------------------------------------------------------------
 503
 504
 505 //------------------------------------------------------------------------------
 506 void vvMainWindow::WarpImage()
 507 {
 508   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 509   if (!mSlicerManagers[index]->GetVF().IsNull())
 510     {
 511       bool ok;
 512       int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 513                                          mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 514       if (ok)
 515         {
 516           WarpImage(mSlicerManagers[index],ref);
 517         }
 518     }
 519   else
 520     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 521 }
 522 //------------------------------------------------------------------------------
 523
 524
 525 //------------------------------------------------------------------------------
 526 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 527 {
 528   if (!selected_slicer->GetVF().IsNull())
 529     {
 530       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 531       QFileInfo info(selected_slicer->GetFileName().c_str());
 532       vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 533                        reference_phase,this);
 534       if (warp.ComputeWarpedImage())
 535         {
 536           AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 537           AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 538           AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 539           QApplication::restoreOverrideCursor();
 540         }
 541       else
 542         {
 543           QApplication::restoreOverrideCursor();
 544           QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 545         }
 546     }
 547   else
 548     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 549 }
 550 //------------------------------------------------------------------------------
 551
 552
 553 //------------------------------------------------------------------------------
 554 vvMainWindow::~vvMainWindow() {
 555   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
 556     {
 557       if (mSlicerManagers[i] != NULL)
 558         delete mSlicerManagers[i];
 559     }
 560 }
 561 //------------------------------------------------------------------------------
 562
 563
 564 //------------------------------------------------------------------------------
 565 void vvMainWindow::MergeImages() {
 566   QString Extensions = EXTENSIONS;
 567   Extensions += ";;All Files (*)";
 568   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 569   if (files.isEmpty())
 570     return;
 571   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 572   std::vector<std::string> vector;
 573
 574   unsigned int currentDim = 0;
 575   std::vector<double> currentSpacing;
 576   std::vector<int> currentSize;
 577   std::vector<double> currentOrigin;
 578
 579   for (int i = 0; i < files.size(); i++)
 580     {
 581       itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 582               files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 583       reader->SetFileName(files[i].toStdString().c_str());
 584       reader->ReadImageInformation();
 585       if (reader)        {
 586           //NOViewWidget->hide();
 587           //NEViewWidget->hide();
 588           //SOViewWidget->hide();
 589           //SEViewWidget->hide();
 590           if (i == 0)
 591               currentDim = reader->GetNumberOfDimensions();
 592           bool IsOk = true;
 593           for (unsigned int j = 0;j < currentDim; j++)
 594           {
 595               if (i == 0)
 596               {
 597                   if (j == 0)
 598                   {
 599                       currentSpacing.resize(currentDim);
 600                       currentSize.resize(currentDim);
 601                       currentOrigin.resize(currentDim);
 602                   }
 603                   currentOrigin[j] = reader->GetOrigin(j);
 604                   currentSpacing[j] = reader->GetSpacing(j);
 605                   currentSize[j] = reader->GetDimensions(j);
 606               }
 607               else if (currentDim != reader->GetNumberOfDimensions()
 608                       || currentSpacing[j] != reader->GetSpacing(j)
 609                       || currentSize[j] != (int)reader->GetDimensions(j)
 610                       || currentOrigin[j] != reader->GetOrigin(j))
 611               {
 612                   QString error = "Cannot read file (too different from others ";
 613                   error += files[i].toStdString().c_str();
 614                   QMessageBox::information(this,tr("Reading problem"),error);
 615                   IsOk = false;
 616                   break;
 617               }
 618           }
 619           if (IsOk)
 620               vector.push_back(files[i].toStdString());
 621       }
 622     }
 623   if (vector.size() > 0)
 624     LoadImages(vector, MERGED);
 625 }
 626 //------------------------------------------------------------------------------
 627
 628
 629 //------------------------------------------------------------------------------
 630 void vvMainWindow::MergeImagesWithTime() {
 631   QString Extensions = EXTENSIONS;
 632   Extensions += ";;All Files (*)";
 633   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 634   if (files.isEmpty())
 635     return;
 636   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 637   std::vector<std::string> vector;
 638
 639   unsigned int currentDim = 0;
 640   std::vector<double> currentSpacing;
 641   std::vector<int> currentSize;
 642   std::vector<double> currentOrigin;
 643
 644   for (int i = 0; i < files.size(); i++)
 645     {
 646       itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 647                                                                             files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 648       if (reader)
 649         {
 650           reader->SetFileName(files[i].toStdString().c_str());
 651           reader->ReadImageInformation();
 652           if (i == 0)
 653             currentDim = reader->GetNumberOfDimensions();
 654           bool IsOk = true;
 655           for (unsigned int j = 0;j < currentDim; j++)
 656             {
 657               if (i == 0)
 658                 {
 659                   if (j == 0)
 660                     {
 661                       currentSpacing.resize(currentDim);
 662                       currentSize.resize(currentDim);
 663                       currentOrigin.resize(currentDim);
 664                     }
 665                   currentOrigin[j] = reader->GetOrigin(j);
 666                   currentSpacing[j] = reader->GetSpacing(j);
 667                   currentSize[j] = reader->GetDimensions(j);
 668                 }
 669               else if (currentDim != reader->GetNumberOfDimensions()
 670                        || currentSpacing[j] != reader->GetSpacing(j)
 671                        || currentSize[j] != (int)reader->GetDimensions(j)
 672                        || currentOrigin[j] != reader->GetOrigin(j))
 673                 {
 674                   QString error = "Cannot read file (too different from others ";
 675                   error += files[i].toStdString().c_str();
 676                   QMessageBox::information(this,tr("Reading problem"),error);
 677                   IsOk = false;
 678                   break;
 679                 }
 680             }
 681           if (IsOk)
 682             vector.push_back(files[i].toStdString());
 683         }
 684       else
 685         {
 686           QString error = "Cannot read file info for ";
 687           error += files[i].toStdString().c_str();
 688           error += "\n";
 689           error += "Maybe you're trying to open an image in an unsupported format?\n";
 690           QMessageBox::information(this,tr("Reading problem"),error);
 691         }
 692     }
 693   sort(vector.begin(),vector.end());
 694   if (vector.size() > 1)
 695     LoadImages(vector, MERGEDWITHTIME);
 696   else
 697     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.");
 698 }
 699 //------------------------------------------------------------------------------
 700
 701
 702 //------------------------------------------------------------------------------
 703 void vvMainWindow::OpenDicom() {
 704   std::vector<std::string> files;
 705
 706 #ifdef CLITK_VV_USE_BDCM
 707   bool r = bdcm::OpenDicomFilesSelectorDialog(files,
 708                                               "DicomFilesSelectorDialog test",
 709                                               0,0,800,800,1);
 710
 711   if (r) {
 712     std::cout << "$$$$ main : user clicked 'OK' $$$$"<<std::endl;
 713     std::cout << "$$$$ selected files : "<<std::endl;
 714     std::vector<std::string>::iterator i;
 715     for (i=files.begin();i!=files.end();++i) {
 716       std::cout << *i << std::endl;
 717     }
 718     std::cout << "$$$$ "<<std::endl;
 719
 720     LoadImages(files,DICOM);
 721   }
 722   else {
 723     std::cout << "$$$$ main : user clicked 'CANCEL' $$$$"<<std::endl;
 724   }
 725 #else
 726   std::cout << "dicomSeriesSelector " << std::endl;
 727   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 728     files = *(dicomSeriesSelector->GetFilenames());
 729     LoadImages(files,DICOM);
 730   }
 731 #endif
 732
 733 }
 734 //------------------------------------------------------------------------------
 735
 736 //------------------------------------------------------------------------------
 737 void vvMainWindow::OpenImages() {
 738   QString Extensions = EXTENSIONS;
 739   Extensions += ";;All Files (*)";
 740
 741   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 742   if (files.isEmpty())
 743     return;
 744   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 745   std::vector<std::string> vector;
 746   for (int i = 0; i < files.size(); i++)
 747     vector.push_back(files[i].toStdString());
 748   LoadImages(vector, IMAGE);
 749 }
 750 //------------------------------------------------------------------------------
 751 void vvMainWindow::OpenRecentImage()
 752 {
 753   QAction * caller = qobject_cast<QAction*>(sender());
 754   std::vector<std::string> images;
 755   images.push_back(caller->text().toStdString());
 756   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 757   LoadImages(images,IMAGE);
 758 }
 759 //------------------------------------------------------------------------------
 760
 761
 762 //------------------------------------------------------------------------------
 763 void vvMainWindow::OpenImageWithTime() {
 764   QString Extensions = EXTENSIONS;
 765   Extensions += ";;All Files (*)";
 766
 767   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 768   if (files.isEmpty())
 769     return;
 770   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 771   std::vector<std::string> vector;
 772   for (int i = 0; i < files.size(); i++)
 773     {
 774       vector.push_back(files[i].toStdString());
 775     }
 776   LoadImages(vector, IMAGEWITHTIME);
 777 }
 778 //------------------------------------------------------------------------------
 779
 780
 781 //------------------------------------------------------------------------------
 782 void vvMainWindow::LoadImages(std::vector<std::string> files, LoadedImageType filetype) {
 783   //Separate the way to open images and dicoms
 784   int fileSize;
 785   if (filetype == IMAGE || filetype == IMAGEWITHTIME)
 786     fileSize = files.size();
 787   else
 788     fileSize = 1;
 789
 790   //Only add to the list of recently opened files when a single file is opened,
 791   //to avoid polluting the list of recently opened files
 792   if (files.size() == 1)
 793     {
 794       QFileInfo finfo=tr(files[0].c_str());
 795       AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 796     }
 797   //init the progress events
 798   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 799   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 800   qApp->processEvents();
 801
 802   int numberofsuccesulreads=0;
 803   //open images as 1 or multiples
 804   for (int i = 0; i < fileSize; i++) {
 805
 806     progress.Update("Opening " + files[i]);
 807     progress.SetProgress(i,fileSize);
 808     qApp->processEvents();
 809
 810     //read the image and put it in mSlicerManagers
 811     vvSlicerManager* imageManager = new vvSlicerManager(4);
 812     qApp->processEvents();
 813
 814     bool SetImageSucceed=false;
 815
 816     // Change filename if an image with the same already exist
 817     //    DD(files[i]);
 818     int number=0;
 819     for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
 820       vvSlicerManager * v = mSlicerManagers[l];
 821       //      DD(v->GetBaseFileName());
 822       // DD(v->GetFileName());
 823       if (v->GetBaseFileName() ==
 824           vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(files[i]))) {
 825         number = std::max(number, v->GetBaseFileNameNumber()+1);
 826       }
 827     }
 828
 829
 830     if (filetype == IMAGE || filetype == IMAGEWITHTIME)
 831       SetImageSucceed = imageManager->SetImage(files[i],filetype, number);
 832     else
 833       {
 834         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 835       }
 836     if (SetImageSucceed == false)
 837       {
 838         QApplication::restoreOverrideCursor();
 839         QString error = "Cannot open file \n";
 840         error += imageManager->GetLastError().c_str();
 841         QMessageBox::information(this,tr("Reading problem"),error);
 842         delete imageManager;
 843       }
 844     else
 845       {
 846         mSlicerManagers.push_back(imageManager);
 847
 848         //create an item in the tree with good settings
 849         QTreeWidgetItem *item = new QTreeWidgetItem();
 850         item->setData(0,Qt::UserRole,files[i].c_str());
 851         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 852         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 853         qApp->processEvents();
 854
 855         //Create the buttons for reload and close
 856         qApp->processEvents();
 857         QTreePushButton* cButton = new QTreePushButton;
 858         cButton->setItem(item);
 859         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 860         cButton->setToolTip(tr("close image"));
 861         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 862         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 863                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 864
 865         QTreePushButton* rButton = new QTreePushButton;
 866         rButton->setItem(item);
 867         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 868         rButton->setToolTip(tr("reload image"));
 869         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 870         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 871                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 872
 873         DataTree->addTopLevelItem(item);
 874         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 875         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 876
 877         //set the id of the image
 878         QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 879         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 880         mSlicerManagers.back()->SetId(id.toStdString());
 881
 882         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 883
 884         connect(mSlicerManagers.back(),SIGNAL(currentImageChanged(std::string)),
 885                 this,SLOT(CurrentImageChanged(std::string)));
 886         connect(mSlicerManagers.back(),SIGNAL(
 887                                               UpdatePosition(int, double, double, double, double, double, double, double)),this,
 888                 SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 889         connect(mSlicerManagers.back(),SIGNAL(UpdateVector(int, double, double, double, double)),
 890                 this, SLOT(VectorChanged(int,double,double,double, double)));
 891         connect(mSlicerManagers.back(),SIGNAL(UpdateOverlay(int, double, double)),
 892                 this, SLOT(OverlayChanged(int,double,double)));
 893         connect(mSlicerManagers.back(),SIGNAL(UpdateFusion(int, double)),
 894                 this, SLOT(FusionChanged(int,double)));
 895         connect(mSlicerManagers.back(),SIGNAL(UpdateWindows(int, int, int)),
 896                 this,SLOT(WindowsChanged(int, int, int)));
 897         connect(mSlicerManagers.back(),SIGNAL(WindowLevelChanged(double, double,int, int)),
 898                 this,SLOT(WindowLevelChanged(double, double, int, int)));
 899         connect(mSlicerManagers.back(),SIGNAL(UpdateSlice(int,int)),
 900                 this,SLOT(UpdateSlice(int,int)));
 901         connect(mSlicerManagers.back(),SIGNAL(UpdateTSlice(int, int)),
 902                 this,SLOT(UpdateTSlice(int, int)));
 903         connect(mSlicerManagers.back(),SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 904                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 905         connect(mSlicerManagers.back(),SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 906                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 907         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 908         InitSlicers();
 909         numberofsuccesulreads++;
 910       }
 911   }
 912   if (numberofsuccesulreads)
 913     {
 914       NOViewWidget->show();
 915       NEViewWidget->show();
 916       SOViewWidget->show();
 917       SEViewWidget->show();
 918       UpdateTree();
 919       InitDisplay();
 920       ShowLastImage();
 921     }
 922   QApplication::restoreOverrideCursor();
 923
 924 }
 925 //------------------------------------------------------------------------------
 926
 927 //------------------------------------------------------------------------------
 928 void vvMainWindow::UpdateTree() {
 929   DataTree->resizeColumnToContents(COLUMN_TREE);
 930   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 931   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 932   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 933   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 934   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 935   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 936   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 937 }
 938 //------------------------------------------------------------------------------
 939
 940 //------------------------------------------------------------------------------
 941 void vvMainWindow::CurrentImageChanged(std::string id) {
 942   int selected = 0;
 943   for (int i = 0; i < DataTree->topLevelItemCount(); i++)
 944     {
 945       if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id)
 946         {
 947           selected = i;
 948         }
 949       else
 950         {
 951           DataTree->topLevelItem(i)->setSelected(0);
 952         }
 953       for (int child = 0; child < DataTree->topLevelItem(i)->childCount();child++)
 954         DataTree->topLevelItem(i)->child(child)->setSelected(0);
 955
 956     }
 957   DataTree->topLevelItem(selected)->setSelected(1);
 958 }
 959 //------------------------------------------------------------------------------
 960
 961 //------------------------------------------------------------------------------
 962 void vvMainWindow::ImageInfoChanged() {
 963   contextActions[7]->setEnabled(1);
 964   contextActions[6]->setEnabled(1);
 965   actionSave_As->setEnabled(1);
 966   actionAdd_VF_to_current_Image->setEnabled(1);
 967   actionAdd_fusion_image->setEnabled(1);
 968   actionNorth_East_Window->setEnabled(1);
 969   actionNorth_West_Window->setEnabled(1);
 970   actionSouth_East_Window->setEnabled(1);
 971   actionSouth_West_Window->setEnabled(1);
 972   inverseButton->setEnabled(1);
 973
 974   goToCursorPushButton->setEnabled(1);
 975
 976   if (DataTree->selectedItems().size()) {
 977     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 978
 979     colorMapComboBox->setEnabled(1);
 980     for (int i = 0; i < DataTree->topLevelItem(index)->childCount();i++)
 981       {
 982         if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
 983             DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion")
 984           {
 985             colorMapComboBox->setEnabled(0);
 986             break;
 987           }
 988       }
 989
 990     std::vector<double> origin;
 991     std::vector<double> inputSpacing;
 992     std::vector<int> inputSize;
 993     std::vector<double> sizeMM;
 994     int dimension=0;
 995     QString pixelType;
 996     QString inputSizeInBytes;
 997     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
 998
 999     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1)
1000       {
1001         playButton->setEnabled(1);
1002         frameRateLabel->setEnabled(1);
1003         frameRateSpinBox->setEnabled(1);
1004       }
1005     else
1006       {
1007         playButton->setEnabled(0);
1008         frameRateLabel->setEnabled(0);
1009         frameRateSpinBox->setEnabled(0);
1010       }
1011
1012     //read image header
1013     int NPixel = 1;
1014
1015     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0])
1016       {
1017         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1018         dimension = imageSelected->GetNumberOfDimensions();
1019         origin.resize(dimension);
1020         inputSpacing.resize(dimension);
1021         inputSize.resize(dimension);
1022         sizeMM.resize(dimension);
1023         pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
1024         for (int i = 0;i < dimension;i++)
1025           {
1026             origin[i] = imageSelected->GetOrigin()[i];
1027             inputSpacing[i] = imageSelected->GetSpacing()[i];
1028             inputSize[i] = imageSelected->GetSize()[i];
1029             sizeMM[i] = inputSize[i]*inputSpacing[i];
1030             NPixel *= inputSize[i];
1031           }
1032         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1033       }
1034     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector")
1035       {
1036         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1037         dimension = imageSelected->GetNumberOfDimensions();
1038         origin.resize(dimension);
1039         inputSpacing.resize(dimension);
1040         inputSize.resize(dimension);
1041         sizeMM.resize(dimension);
1042         pixelType = mSlicerManagers[index]->GetVF()->GetScalarTypeAsString().c_str();
1043         for (int i = 0;i < dimension;i++)
1044           {
1045             origin[i] = imageSelected->GetOrigin()[i];
1046             inputSpacing[i] = imageSelected->GetSpacing()[i];
1047             inputSize[i] = imageSelected->GetSize()[i];
1048             sizeMM[i] = inputSize[i]*inputSpacing[i];
1049             NPixel *= inputSize[i];
1050           }
1051         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1052       }
1053     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay")
1054       {
1055         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1056         dimension = imageSelected->GetNumberOfDimensions();
1057         origin.resize(dimension);
1058         inputSpacing.resize(dimension);
1059         inputSize.resize(dimension);
1060         sizeMM.resize(dimension);
1061         pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
1062         for (int i = 0;i < dimension;i++)
1063           {
1064             origin[i] = imageSelected->GetOrigin()[i];
1065             inputSpacing[i] = imageSelected->GetSpacing()[i];
1066             inputSize[i] = imageSelected->GetSize()[i];
1067             sizeMM[i] = inputSize[i]*inputSpacing[i];
1068             NPixel *= inputSize[i];
1069           }
1070         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1071       }
1072     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion")
1073       {
1074         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1075         dimension = imageSelected->GetNumberOfDimensions();
1076         origin.resize(dimension);
1077         inputSpacing.resize(dimension);
1078         inputSize.resize(dimension);
1079         sizeMM.resize(dimension);
1080         pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
1081         for (int i = 0;i < dimension;i++)
1082           {
1083             origin[i] = imageSelected->GetOrigin()[i];
1084             inputSpacing[i] = imageSelected->GetSpacing()[i];
1085             inputSize[i] = imageSelected->GetSize()[i];
1086             sizeMM[i] = inputSize[i]*inputSpacing[i];
1087             NPixel *= inputSize[i];
1088           }
1089         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1090       }
1091
1092     QString dim = QString::number(dimension) + " (";
1093     dim += pixelType + ")";
1094
1095     infoPanel->setFileName(image);
1096     infoPanel->setDimension(dim);
1097     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1098     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1099     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1100     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1101     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1102
1103     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1104                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1105     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1106     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1107
1108     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1109     for (int i = 0; i < 4;i++)
1110       {
1111         if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3)
1112           {
1113             mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1114             break;
1115           }
1116       }
1117     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1118     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1119     // DD(mSlicerManagers[index]->GetColorMap());
1120     // DD(mSlicerManagers[index]->GetPreset());
1121     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1122     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1123
1124     infoPanel->setFileName(image);
1125     infoPanel->setDimension(dim);
1126     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1127     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1128     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1129     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1130     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1131
1132     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1133                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1134     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1135     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1136
1137     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1138     for (int i = 0; i < 4;i++)
1139       {
1140         if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3)
1141           {
1142             mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1143             break;
1144           }
1145       }
1146     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1147     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1148     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1149     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1150
1151     if (mSlicerManagers[index]->GetSlicer(0)->GetVF())
1152       {
1153         overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1154         overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1155                                     mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1156                                     mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1157       }
1158     else
1159       {
1160         overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1161         overlayPanel->getVFProperty(-1,-1,-1);
1162       }
1163     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1164       {
1165         overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1166         overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1167       }
1168     else
1169       {
1170         overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1171         overlayPanel->getOverlayProperty(-1);
1172       }
1173     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion())
1174       {
1175         overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1176         overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1177                                         mSlicerManagers[index]->GetFusionColorMap(),
1178                                         mSlicerManagers[index]->GetFusionWindow(),
1179                                         mSlicerManagers[index]->GetFusionLevel());
1180       }
1181     else
1182       {
1183         overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1184         overlayPanel->getFusionProperty(-1, -1,-1,-1);
1185       }
1186   }
1187 }
1188 //------------------------------------------------------------------------------
1189
1190 //------------------------------------------------------------------------------
1191 void vvMainWindow::ShowDocumentation() {
1192   documentation->show();
1193 }
1194 //------------------------------------------------------------------------------
1195 void vvMainWindow::ShowHelpDialog() {
1196   help_dialog->show();
1197 }
1198 //------------------------------------------------------------------------------
1199
1200 //------------------------------------------------------------------------------
1201 void vvMainWindow::ChangeViewMode() {
1202   QListIterator<int> it0(splitter_3->sizes());
1203   QListIterator<int> it1(splitter_3->sizes());
1204   int max0 = 0;
1205   int max1 = 1;
1206   while (it0.hasNext())
1207     {
1208       max0 += it0.next();
1209     }
1210   while (it1.hasNext())
1211     {
1212       max1 += it1.next();
1213     }
1214   QList<int> size0;
1215   QList<int> size1;
1216   if (viewMode == 1)
1217     {
1218       viewMode = 0;
1219       size0.push_back(max0);
1220       size0.push_back(0);
1221       size1.push_back(max1);
1222       size1.push_back(0);
1223       splitter_3->setSizes(size0);
1224       OSplitter->setSizes(size1);
1225       DataTree->setColumnHidden(2,1);
1226       DataTree->setColumnHidden(3,1);
1227       DataTree->setColumnHidden(4,1);
1228     }
1229   else
1230     {
1231       viewMode = 1;
1232       size0.push_back(int(max0/2));
1233       size0.push_back(int(max0/2));
1234       size1.push_back(int(max1/2));
1235       size1.push_back(int(max1/2));
1236       splitter_3->setSizes(size0);
1237       OSplitter->setSizes(size1);
1238       DataTree->setColumnHidden(2,0);
1239       DataTree->setColumnHidden(3,0);
1240       DataTree->setColumnHidden(4,0);
1241     }
1242 }
1243 //------------------------------------------------------------------------------
1244
1245 //------------------------------------------------------------------------------
1246 QString vvMainWindow::GetSizeInBytes(unsigned long size) {
1247   QString result = "";// QString::number(size);
1248   //result += " bytes (";
1249   if (size > 1000000000)
1250     {
1251       size /= 1000000000;
1252       result += QString::number(size);
1253       result += "Gb";//)";
1254     }
1255   else if (size > 1000000)
1256     {
1257       size /= 1000000;
1258       result += QString::number(size);
1259       result += "Mb";//)";
1260     }
1261   else if (size > 1000)
1262     {
1263       size /= 1000;
1264       result += QString::number(size);
1265       result += "kb";//)";
1266     }
1267   return result;
1268 }
1269 //------------------------------------------------------------------------------
1270
1271 //------------------------------------------------------------------------------
1272 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble) {
1273   QString result;
1274   for (unsigned int i= 0; i < vectorDouble.size(); i++)
1275     {
1276       if (i != 0)
1277         result += " ";
1278       result += QString::number(vectorDouble[i]);
1279     }
1280   return result;
1281 }
1282 //------------------------------------------------------------------------------
1283
1284 //------------------------------------------------------------------------------
1285 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt) {
1286   QString result;
1287   for (unsigned int i= 0; i < vectorInt.size(); i++)
1288     {
1289       if (i != 0)
1290         result += " ";
1291       result += QString::number(vectorInt[i]);
1292     }
1293   return result;
1294 }
1295 //------------------------------------------------------------------------------
1296
1297 //------------------------------------------------------------------------------
1298 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item) {
1299   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1300   for (int i = 0; i < DataTree->topLevelItemCount(); i++)
1301     {
1302       if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1303         return i;
1304     }
1305   return -1;
1306 }
1307 //------------------------------------------------------------------------------
1308
1309 //------------------------------------------------------------------------------
1310 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clicked_item, int column) {
1311   int index = GetSlicerIndexFromItem(clicked_item);
1312   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1313     return;
1314   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
1315     {
1316       QTreeWidgetItem* current_row=DataTree->topLevelItem(i);
1317       if (DataTree->topLevelItem(index) == current_row)
1318         {
1319           vvSlicer* clicked_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1320           if (current_row == clicked_item)
1321             {
1322               //If we just activated a slicer
1323               if (current_row->data(column,Qt::CheckStateRole).toInt() > 0)
1324                 {
1325                   mSlicerManagers[i]->UpdateSlicer(column-1,clicked_item->data(column,Qt::CheckStateRole).toInt());
1326                   mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1327                   DisplaySliders(i,column-1);
1328                   std::map<std::string,int> overlay_counts;
1329                   for (int child = 0; child < current_row->childCount(); child++)
1330                     {
1331                       std::string overlay_type =
1332                         current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1333                       overlay_counts[overlay_type]++;
1334                       current_row->child(child)->setData(column,Qt::CheckStateRole,
1335                                                          current_row->data(column,Qt::CheckStateRole));
1336                       clicked_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,true);
1337                     }
1338                 }
1339               else //We don't allow simply desactivating a slicer
1340                 {
1341                   clicked_item->setData(column,Qt::CheckStateRole,2);
1342                   return;
1343                 }
1344             }
1345           //if we clicked on the vector(or overlay) and not the image
1346           else
1347             {
1348               if (clicked_item->data(column,Qt::CheckStateRole).toInt())
1349                 {
1350                   current_row->setData(column,Qt::CheckStateRole,2);
1351                   mSlicerManagers[i]->UpdateSlicer(column-1,2);
1352                   mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1353                   DisplaySliders(i,column-1);
1354                 }
1355               int vis = clicked_item->data(column,Qt::CheckStateRole).toInt();
1356               std::string overlay_type = clicked_item->data(1,Qt::UserRole).toString().toStdString();
1357               int overlay_index=0;
1358               for (int child = 0; child < current_row->childCount(); child++)
1359                 {
1360                   if (current_row->child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1361                     overlay_index++;
1362                   if (current_row->child(child) == clicked_item) break;
1363                 }
1364               clicked_slicer->SetActorVisibility(
1365                                                  clicked_item->data(1,Qt::UserRole).toString().toStdString(), overlay_index-1,vis);
1366             }
1367         }
1368       else if (current_row->data(column,Qt::CheckStateRole).toInt() > 0)
1369         {
1370           current_row->setData(column,Qt::CheckStateRole,0);
1371           mSlicerManagers[i]->UpdateSlicer(column-1,0);
1372           std::map<std::string,int> overlay_counts;
1373           for (int child = 0; child < current_row->childCount(); child++)
1374             {
1375               std::string overlay_type =
1376                 current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1377               overlay_counts[overlay_type]++;
1378               current_row->child(child)->setData(column,Qt::CheckStateRole,0);
1379               vvSlicer * current_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1380               current_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,false);
1381             }
1382         }
1383       //mSlicerManagers[i]->SetColorMap(-1);
1384       mSlicerManagers[i]->SetColorMap();
1385     }
1386   mSlicerManagers[index]->GetSlicer(column-1)->Render();
1387 }
1388 //------------------------------------------------------------------------------
1389
1390 void vvMainWindow::InitSlicers()
1391 {
1392   if (mSlicerManagers.size())
1393     {
1394       mSlicerManagers.back()->GenerateDefaultLookupTable();
1395
1396       mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1397       mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1398       mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1399       mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1400     }
1401 }
1402
1403 //------------------------------------------------------------------------------
1404 void vvMainWindow::InitDisplay() {
1405   if (mSlicerManagers.size())
1406     {
1407       //BE CAREFUL : this is absolutely necessary to set the interactor style
1408       //in order to have the same style instanciation for all SlicerManagers in
1409       // a same window
1410       for (int j = 0; j < 4; j++)
1411         {
1412           vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1413           style->SetAutoAdjustCameraClippingRange(1);
1414           bool AlreadySelected = false;
1415           for (int i = 0; i < DataTree->topLevelItemCount(); i++)
1416             {
1417               mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1418
1419               //select the image only if previous are not selected
1420               if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1)
1421                 {
1422                   mSlicerManagers[i]->UpdateSlicer(j,1);
1423                   AlreadySelected = true;
1424                 }
1425               else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected)
1426                 {
1427                   if (DataTree->selectedItems().size() == 0)
1428                     DataTree->topLevelItem(i)->setSelected(1);
1429                   DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1430                   mSlicerManagers[i]->UpdateSlicer(j,1);
1431                   DisplaySliders(i,j);
1432                 }
1433               else
1434                 {
1435                   DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1436                   mSlicerManagers[i]->UpdateSlicer(j,0);
1437                 }
1438             }
1439           style->Delete();
1440         }
1441     }
1442 }
1443 //------------------------------------------------------------------------------
1444
1445 //------------------------------------------------------------------------------
1446 void vvMainWindow::DisplaySliders(int slicer, int window) {
1447   int range[2];
1448   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1449   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1450
1451   int tRange[2];
1452   tRange[0] = 0;
1453   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1454   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1455   bool showHorizontal = false;
1456   bool showVertical = false;
1457   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1458       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1459           && mSlicerManagers[slicer]->GetType() != IMAGEWITHTIME
1460           && mSlicerManagers[slicer]->GetType() != MERGEDWITHTIME))
1461     showVertical = true;
1462   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1463       || mSlicerManagers[slicer]->GetType() == IMAGEWITHTIME
1464       || mSlicerManagers[slicer]->GetType() == MERGEDWITHTIME)
1465     showHorizontal = true;
1466
1467   if (showVertical)
1468     verticalSliders[window]->show();
1469   else
1470     verticalSliders[window]->hide();
1471   verticalSliders[window]->setRange(range[0],range[1]);
1472   verticalSliders[window]->setValue(position);
1473
1474   if (showHorizontal)
1475     horizontalSliders[window]->show();
1476   else
1477     horizontalSliders[window]->hide();
1478   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1479   horizontalSliders[window]->setValue(tPosition);
1480 }
1481 //------------------------------------------------------------------------------
1482
1483 //------------------------------------------------------------------------------
1484 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column) {
1485   int index = GetSlicerIndexFromItem(item);
1486
1487   if (DataTree->topLevelItem(index) != item)
1488     {
1489       QString warning = "Do you really want to close the overlay : ";
1490       warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1491       QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1492                          warning, 0, this);
1493       msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1494       msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1495       if (msgBox.exec() == QMessageBox::AcceptRole)
1496         {
1497           std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1498           int overlay_index=0;
1499           for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1500             {
1501               if (DataTree->topLevelItem(index)->\
1502                   child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1503                 overlay_index++;
1504               if (DataTree->topLevelItem(index)->child(child) == item) break;
1505             }
1506           mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1507           mSlicerManagers[index]->SetColorMap(0);
1508           DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1509           mSlicerManagers[index]->Render();
1510         }
1511     }
1512   else if (DataTree->topLevelItemCount() <= 1)
1513     {
1514       QString warning = "Do you really want to close the image : ";
1515       warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1516       warning += "\nThis is the last image, you're about to close vv !!!";
1517       QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1518                          warning, 0, this);
1519       msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1520       msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1521       if (msgBox.exec() == QMessageBox::AcceptRole)
1522         {
1523           this->close();
1524         }
1525     }
1526   else
1527     {
1528       QString warning = "Do you really want to close the image : ";
1529       warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1530       QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1531                          warning, 0, this);
1532       msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1533       msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1534       if (msgBox.exec() == QMessageBox::AcceptRole)
1535         {
1536
1537           // Tell tools that we close an image
1538           emit AnImageIsBeingClosed(mSlicerManagers[index]);
1539
1540           std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1541           DataTree->takeTopLevelItem(index);
1542           for (int i = 0; i < index; i++)
1543             {
1544               Manageriter++;
1545             }
1546           linkPanel->removeImage(index);
1547           mSlicerManagers[index]->RemoveActors();
1548           delete mSlicerManagers[index];
1549           mSlicerManagers.erase(Manageriter);
1550
1551           //
1552           InitDisplay();
1553         }
1554     }
1555 }
1556 //------------------------------------------------------------------------------
1557
1558 //------------------------------------------------------------------------------
1559 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column) {
1560   // int index = GetSlicerIndexFromItem(item);
1561   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1562   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1563   //     mSlicerManagers[index]->ReloadVF();
1564   //   else
1565   //     mSlicerManagers[index]->Reload();
1566
1567   //   QApplication::restoreOverrideCursor();
1568   int index = GetSlicerIndexFromItem(item);
1569   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1570   QString role=item->data(1,Qt::UserRole).toString();
1571   if ( role == "vector")
1572     mSlicerManagers[index]->ReloadVF();
1573   else if (role == "overlay")
1574     mSlicerManagers[index]->ReloadOverlay();
1575   else if (role == "fusion")
1576     mSlicerManagers[index]->ReloadFusion();
1577   else
1578     mSlicerManagers[index]->Reload();
1579   QApplication::restoreOverrideCursor();
1580 }
1581 //------------------------------------------------------------------------------
1582
1583 // void vvMainWindow::CropImage()
1584 // {
1585 //   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1586 //   vvCropDialog crop(mSlicerManagers,index);
1587 //   if(crop.exec())
1588 //     AddImage(crop.GetOutput(),"cropped.mhd");
1589 // }
1590
1591 //------------------------------------------------------------------------------
1592 void vvMainWindow::SplitImage() {
1593   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1594   int dim = mSlicerManagers[index]->GetDimension();
1595   QString warning = "Do you really want to split the ";
1596   warning += QString::number(dim) + "D image ";
1597   warning += DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString() + " into ";
1598   warning += QString::number(mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetSize()[dim-1]) + " ";
1599   warning += QString::number(dim-1) + "D images.";
1600   QMessageBox msgBox(QMessageBox::Warning, tr("Split Image"),
1601                      warning, 0, this);
1602   msgBox.addButton(tr("Split"), QMessageBox::AcceptRole);
1603   msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1604   if (msgBox.exec() == QMessageBox::AcceptRole)
1605     {
1606       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1607       if (dim > 2)
1608         {
1609           std::string filename = DataTree->selectedItems()[0]->data(0,Qt::UserRole).toString().toStdString();
1610           int numberOfSlice = mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetSize()[dim-1];
1611           std::string path = itksys::SystemTools::GetFilenamePath(
1612                                                                   filename);
1613           path += "/";
1614           path += DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString().toStdString();
1615           path += "%03d";
1616           path += itksys::SystemTools::GetFilenameLastExtension(
1617                                                                 filename).c_str();
1618
1619           typedef itk::NumericSeriesFileNames NameGeneratorType;
1620           NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
1621           nameGenerator->SetSeriesFormat(path.c_str());
1622           nameGenerator->SetStartIndex(0);
1623           nameGenerator->SetEndIndex(numberOfSlice-1);
1624           nameGenerator->SetIncrementIndex(1);
1625
1626           for (int i = 0; i < numberOfSlice; i++)
1627             {
1628               vvSlicerManager* imageManager = new vvSlicerManager(4);
1629               imageManager->SetExtractedImage(nameGenerator->GetFileNames()[i],
1630                                               mSlicerManagers[index]->GetSlicer(0)->GetImage(), i);
1631               mSlicerManagers.push_back(imageManager);
1632
1633               //create an item in the tree with good settings
1634               QTreeWidgetItem *item = new QTreeWidgetItem();
1635               item->setData(0,Qt::UserRole,nameGenerator->GetFileNames()[i].c_str());
1636               std::string fileI = itksys::SystemTools::GetFilenameWithoutLastExtension(
1637                                                                                        nameGenerator->GetFileNames()[i]).c_str();
1638               item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileI.c_str());
1639               for (int j = 1; j <= 4; j++)
1640                 {
1641                   for (int i = 0; i < DataTree->topLevelItemCount(); i++)
1642                     {
1643                       DataTree->topLevelItem(i)->setData(j,Qt::CheckStateRole,0);
1644                     }
1645                   item->setData(j,Qt::CheckStateRole,2);
1646                 }
1647
1648               //Create the buttons for reload and close
1649               QTreePushButton* cButton = new QTreePushButton;
1650               cButton->setItem(item);
1651               cButton->setColumn(COLUMN_CLOSE_IMAGE);
1652               cButton->setToolTip(tr("close image"));
1653               cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1654               connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1655                       this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1656
1657               QTreePushButton* rButton = new QTreePushButton;
1658               rButton->setItem(item);
1659               rButton->setColumn(COLUMN_RELOAD_IMAGE);
1660               rButton->setToolTip(tr("reload image"));
1661               rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1662               rButton->setEnabled(false);
1663               connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1664                       this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1665
1666               DataTree->addTopLevelItem(item);
1667               DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1668               DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1669
1670               //set the id of the image
1671               QString id = nameGenerator->GetFileNames()[i].c_str() + QString::number(mSlicerManagers.size()-1);
1672               item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1673               mSlicerManagers.back()->SetId(id.toStdString());
1674               linkPanel->addImage(fileI, id.toStdString());
1675               connect(mSlicerManagers.back(),SIGNAL(currentImageChanged(std::string)),
1676                       this,SLOT(CurrentImageChanged(std::string)));
1677               connect(mSlicerManagers.back(),SIGNAL(
1678                                                     UpdatePosition(int, double, double, double, double, double, double, double)),this,
1679                       SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
1680               connect(mSlicerManagers.back(),SIGNAL(UpdateVector(int, double, double, double, double)),
1681                       this, SLOT(VectorChanged(int,double,double,double, double)));
1682               connect(mSlicerManagers.back(),SIGNAL(UpdateOverlay(int, double, double)),
1683                       this, SLOT(OverlayChanged(int,double,double)));
1684               connect(mSlicerManagers.back(),SIGNAL(UpdateFusion(int, double)),
1685                       this, SLOT(FusionChanged(int,double)));
1686               connect(mSlicerManagers.back(),SIGNAL(UpdateWindows(int, int, int)),
1687                       this,SLOT(WindowsChanged(int, int, int)));
1688               connect(mSlicerManagers.back(),SIGNAL(WindowLevelChanged(double, double,int, int)),
1689                       this,SLOT(WindowLevelChanged(double, double, int, int)));
1690               connect(mSlicerManagers.back(),SIGNAL(UpdateSlice(int,int)),
1691                       this,SLOT(UpdateSlice(int,int)));
1692               connect(mSlicerManagers.back(),SIGNAL(UpdateTSlice(int, int)),
1693                       this,SLOT(UpdateTSlice(int, int)));
1694               connect(mSlicerManagers.back(),SIGNAL(UpdateSliceRange(int,int,int,int,int)),
1695                       this,SLOT(UpdateSliceRange(int,int,int,int,int)));
1696               connect(mSlicerManagers.back(),SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
1697                       this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
1698               connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
1699               UpdateTree();
1700               qApp->processEvents();
1701               InitSlicers();
1702               InitDisplay();
1703               qApp->processEvents();
1704             }
1705           QApplication::restoreOverrideCursor();
1706         }
1707       else
1708         {
1709           QApplication::restoreOverrideCursor();
1710           QString error = "Cannot split file (dimensions must be greater than 2) ";
1711           QMessageBox::information(this,tr("Splitting problem"),error);
1712         }
1713     }
1714 }
1715 //------------------------------------------------------------------------------
1716
1717 //------------------------------------------------------------------------------
1718 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value) {
1719   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1720 }
1721 //------------------------------------------------------------------------------
1722
1723 //------------------------------------------------------------------------------
1724 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value) {
1725   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1726 }
1727 //------------------------------------------------------------------------------
1728
1729 //------------------------------------------------------------------------------
1730 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef) {
1731   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1732 }
1733 //------------------------------------------------------------------------------
1734
1735 //------------------------------------------------------------------------------
1736 void vvMainWindow::FusionChanged(int visibility, double value) {
1737   overlayPanel->getCurrentFusionInfo(visibility,value);
1738 }
1739 //------------------------------------------------------------------------------
1740
1741 //------------------------------------------------------------------------------
1742 void vvMainWindow::WindowsChanged(int window, int view, int slice) {
1743   infoPanel->setViews(window, view, slice);
1744 }
1745 //------------------------------------------------------------------------------
1746
1747 //------------------------------------------------------------------------------
1748 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap) {
1749   windowSpinBox->setValue(window);
1750   levelSpinBox->setValue(level);
1751   colorMapComboBox->setCurrentIndex(colormap);
1752   presetComboBox->setCurrentIndex(preset);
1753 }
1754 //------------------------------------------------------------------------------
1755
1756 //------------------------------------------------------------------------------
1757 void vvMainWindow::WindowLevelEdited() {
1758   presetComboBox->setCurrentIndex(6);
1759   UpdateWindowLevel();
1760 }
1761 //------------------------------------------------------------------------------
1762
1763 //------------------------------------------------------------------------------
1764 void vvMainWindow::UpdateWindowLevel() {
1765   if (DataTree->selectedItems().size())
1766     {
1767       if (presetComboBox->currentIndex() == 7) //For ventilation
1768         colorMapComboBox->setCurrentIndex(5);
1769       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1770       mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1771       mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1772       mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1773       mSlicerManagers[index]->Render();
1774     }
1775 }
1776 //------------------------------------------------------------------------------
1777
1778 //------------------------------------------------------------------------------
1779 void vvMainWindow::UpdateColorMap() {
1780   if (DataTree->selectedItems().size())
1781     {
1782       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1783       mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1784       mSlicerManagers[index]->Render();
1785     }
1786 }
1787 //------------------------------------------------------------------------------
1788 void vvMainWindow::SwitchWindowLevel() {
1789   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1790   int window = mSlicerManagers[index]->GetColorWindow();
1791   presetComboBox->setCurrentIndex(6);
1792   windowSpinBox->setValue(-window);
1793   UpdateWindowLevel();
1794 }
1795 //------------------------------------------------------------------------------
1796
1797 //------------------------------------------------------------------------------
1798 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps) {
1799   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
1800     {
1801       if (mSlicerManagers[i]->GetId() == id)
1802         {
1803           //mSlicerManagers[i]->SetTSlice(temps);
1804           mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1805           mSlicerManagers[i]->UpdateViews(0,slicer);
1806           break;
1807         }
1808     }
1809 }
1810 //------------------------------------------------------------------------------
1811
1812 //------------------------------------------------------------------------------
1813 void vvMainWindow::ShowContextMenu(QPoint point) {
1814   if (!DataTree->selectedItems().size())
1815     {
1816       contextActions[1]->setEnabled(0);
1817       contextActions[2]->setEnabled(0);
1818       contextActions[3]->setEnabled(0);
1819       contextActions[4]->setEnabled(0);
1820       contextActions[5]->setEnabled(0);
1821       contextActions[6]->setEnabled(0);
1822       contextActions[7]->setEnabled(0);
1823     }
1824   else
1825     {
1826       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1827       contextActions[1]->setEnabled(1);
1828       contextActions[2]->setEnabled(
1829                                     DataTree->itemWidget(DataTree->selectedItems()[0],
1830                                                          COLUMN_RELOAD_IMAGE)->isEnabled());
1831       contextActions[3]->setEnabled(1);
1832       contextActions[5]->setEnabled(1);
1833       contextActions[6]->setEnabled(1);
1834       contextActions[7]->setEnabled(1);
1835
1836       if (mSlicerManagers[index]->GetDimension() < 3)
1837         contextActions[4]->setEnabled(0);
1838       else
1839         contextActions[4]->setEnabled(1);
1840     }
1841   contextMenu.exec(QCursor::pos());
1842 }
1843 //------------------------------------------------------------------------------
1844
1845 //------------------------------------------------------------------------------
1846 void vvMainWindow::CloseImage() {
1847   CloseImage(DataTree->selectedItems()[0],0);
1848 }
1849 //------------------------------------------------------------------------------
1850
1851 //------------------------------------------------------------------------------
1852 void vvMainWindow::ReloadImage() {
1853   ReloadImage(DataTree->selectedItems()[0],0);
1854 }
1855 //------------------------------------------------------------------------------
1856
1857 //------------------------------------------------------------------------------
1858 void vvMainWindow::SelectOverlayImage() {
1859   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1860
1861   //check if one overlay image is added
1862   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1863     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay")
1864       {
1865         QString error = "Cannot add more than one compared image\n";
1866         error += "Please remove first ";
1867         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1868         QMessageBox::information(this,tr("Problem adding compared image !"),error);
1869         return;
1870       }
1871
1872   QString Extensions = EXTENSIONS;
1873   Extensions += ";;All Files (*)";
1874   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1875   if (!file.isEmpty())
1876     AddOverlayImage(index,file);
1877 }
1878 //------------------------------------------------------------------------------
1879
1880 //------------------------------------------------------------------------------
1881 void vvMainWindow::AddOverlayImage(int index, QString file) {
1882   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1883   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1884                                                                         file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1885   reader->SetFileName(file.toStdString().c_str());
1886   reader->ReadImageInformation();
1887   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1888   int dimension = reader->GetNumberOfDimensions();
1889   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1890   vvProgressDialog progress("Opening " + file.toStdString());
1891   qApp->processEvents();
1892
1893   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1894   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component))
1895     {
1896       //create an item in the tree with good settings
1897       QTreeWidgetItem *item = new QTreeWidgetItem();
1898       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1899       item->setData(1,Qt::UserRole,tr("overlay"));
1900       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
1901       qApp->processEvents();
1902
1903       for (int j = 1; j <= 4; j++)
1904         {
1905           item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1906           mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("overlay",0,
1907                                                                      DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1908         }
1909
1910       //Create the buttons for reload and close
1911       qApp->processEvents();
1912       QTreePushButton* cButton = new QTreePushButton;
1913       cButton->setItem(item);
1914       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1915       cButton->setToolTip(tr("close image"));
1916       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1917       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1918               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1919
1920       QTreePushButton* rButton = new QTreePushButton;
1921       rButton->setItem(item);
1922       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1923       rButton->setToolTip(tr("reload image"));
1924       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1925       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1926               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1927
1928       DataTree->topLevelItem(index)->setExpanded(1);
1929       DataTree->topLevelItem(index)->addChild(item);
1930       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1931       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1932
1933       //set the id of the image
1934       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1935       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1936       UpdateTree();
1937       qApp->processEvents();
1938       ImageInfoChanged();
1939       QApplication::restoreOverrideCursor();
1940     }
1941   else
1942     {
1943       QApplication::restoreOverrideCursor();
1944       QString error = "Cannot import the new image.\n";
1945       error += mSlicerManagers[index]->GetLastError().c_str();
1946       QMessageBox::information(this,tr("Problem reading image !"),error);
1947     }
1948 }
1949
1950 void vvMainWindow::AddFusionImage()
1951 {
1952   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1953
1954   //check if one fusion image is added
1955   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1956     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion")
1957       {
1958         QString error = "Cannot add more than one fusion image\n";
1959         error += "Please remove first ";
1960         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1961         QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1962         return;
1963       }
1964
1965   QString Extensions = EXTENSIONS;
1966   Extensions += ";;All Files (*)";
1967   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1968   if (!file.isEmpty())
1969     {
1970       mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1971       itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1972                                                                             file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1973       reader->SetFileName(file.toStdString().c_str());
1974       reader->ReadImageInformation();
1975       std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1976       if (reader)
1977         {
1978           QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1979           vvProgressDialog progress("Opening fusion");
1980           qApp->processEvents();
1981
1982           std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1983           if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1984                                                 reader->GetNumberOfDimensions(), component))
1985             {
1986               //create an item in the tree with good settings
1987               QTreeWidgetItem *item = new QTreeWidgetItem();
1988               item->setData(0,Qt::UserRole,file.toStdString().c_str());
1989               item->setData(1,Qt::UserRole,tr("fusion"));
1990               item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
1991               qApp->processEvents();
1992
1993               for (int j = 1; j <= 4; j++)
1994                 {
1995                   item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1996                   mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("fusion",0,
1997                                                                              DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1998                 }
1999
2000               //Create the buttons for reload and close
2001               qApp->processEvents();
2002               QTreePushButton* cButton = new QTreePushButton;
2003               cButton->setItem(item);
2004               cButton->setColumn(COLUMN_CLOSE_IMAGE);
2005               cButton->setToolTip(tr("close image"));
2006               cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2007               connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2008                       this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2009
2010               QTreePushButton* rButton = new QTreePushButton;
2011               rButton->setItem(item);
2012               rButton->setColumn(COLUMN_RELOAD_IMAGE);
2013               rButton->setToolTip(tr("reload image"));
2014               rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2015               connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2016                       this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2017
2018               DataTree->topLevelItem(index)->setExpanded(1);
2019               DataTree->topLevelItem(index)->addChild(item);
2020               DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2021               DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2022
2023               //set the id of the image
2024               QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2025               item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2026               UpdateTree();
2027               qApp->processEvents();
2028               ImageInfoChanged();
2029               QApplication::restoreOverrideCursor();
2030             }
2031           else
2032             {
2033               QApplication::restoreOverrideCursor();
2034               QString error = "Cannot import the new image.\n";
2035               error += mSlicerManagers[index]->GetLastError().c_str();
2036               QMessageBox::information(this,tr("Problem reading image !"),error);
2037             }
2038         }
2039       else
2040         {
2041           QString error = "Cannot import the new image.\n";
2042           QMessageBox::information(this,tr("Problem reading image !"),error);
2043         }
2044     }
2045 }
2046
2047
2048 void vvMainWindow::OpenField()
2049 {
2050   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2051   //check if a vector field has already been added
2052   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2053     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector")
2054       {
2055         QString error = "Cannot add more than one vector field\n";
2056         error += "Please remove first ";
2057         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2058         QMessageBox::information(this,tr("Problem adding vector field!"),error);
2059         return;
2060       }
2061
2062   QString Extensions = "Images ( *.mhd)";
2063   Extensions += ";;Images ( *.vf)";
2064   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2065   if (!file.isEmpty())
2066     AddField(file,index);
2067 }
2068
2069 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2070 {
2071   //create an item in the tree with good settings
2072   QTreeWidgetItem *item = new QTreeWidgetItem();
2073   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2074   item->setData(1,Qt::UserRole,tr("vector"));
2075   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename);
2076   qApp->processEvents();
2077
2078   for (int j = 1; j <= 4; j++)
2079     {
2080       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2081       mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("vector",0,
2082                                                                  DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
2083     }
2084
2085   //Create the buttons for reload and close
2086   qApp->processEvents();
2087   QTreePushButton* cButton = new QTreePushButton;
2088   cButton->setItem(item);
2089   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2090   cButton->setToolTip(tr("close vector field"));
2091   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2092   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2093           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2094
2095   QTreePushButton* rButton = new QTreePushButton;
2096   rButton->setItem(item);
2097   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2098   rButton->setToolTip(tr("reload vector field"));
2099   rButton->setEnabled(from_disk);
2100   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2101   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2102           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2103
2104   DataTree->topLevelItem(index)->setExpanded(1);
2105   DataTree->topLevelItem(index)->addChild(item);
2106   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2107   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2108
2109   //set the id of the image
2110   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2111   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2112   UpdateTree();
2113   qApp->processEvents();
2114   ImageInfoChanged();
2115   QApplication::restoreOverrideCursor();
2116 }
2117
2118 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2119 {
2120   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2121   vvSlicerManager* imageManager = mSlicerManagers[index];
2122   if (imageManager->SetVF(vf,file.toStdString()))
2123     {
2124       AddFieldEntry(file,index,false);
2125     }
2126   else
2127     {
2128       QString error = "Cannot import the vector field for this image.\n";
2129       error += imageManager->GetLastError().c_str();
2130       QMessageBox::information(this,tr("Problem reading VF !"),error);
2131     }
2132   QApplication::restoreOverrideCursor();
2133 }
2134
2135 void vvMainWindow::AddField(QString file,int index)
2136 {
2137   if (QFile::exists(file))
2138     {
2139       mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2140
2141       //init the progress events
2142       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2143       vvProgressDialog progress("Opening " + file.toStdString());
2144       qApp->processEvents();
2145
2146       //read the vector and put it in the current mSlicerManager
2147       vvSlicerManager* imageManager = mSlicerManagers[index];
2148       qApp->processEvents();
2149
2150       std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2151       if (imageManager->SetVF(file.toStdString()))
2152         {
2153           imageManager->Render();
2154           AddFieldEntry(file,index,true);
2155         }
2156       else
2157         {
2158           QApplication::restoreOverrideCursor();
2159           QString error = "Cannot import the vector field for this image.\n";
2160           error += imageManager->GetLastError().c_str();
2161           QMessageBox::information(this,tr("Problem reading VF !"),error);
2162         }
2163     }
2164   else
2165     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2166
2167 }
2168 //------------------------------------------------------------------------------
2169
2170 //------------------------------------------------------------------------------
2171 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log) {
2172   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2173   if (mSlicerManagers[index]->GetSlicer(0)->GetVF())
2174     {
2175       for (int i = 0; i < 4; i++)
2176         {
2177           mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2178           mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2179           if (log > 0)
2180             mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2181           else
2182             mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2183         }
2184     }
2185 }
2186 //------------------------------------------------------------------------------
2187
2188 //------------------------------------------------------------------------------
2189 void vvMainWindow::SetOverlayProperty(int color) {
2190   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2191   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
2192     {
2193       mSlicerManagers[index]->SetOverlayColor(color);
2194       mSlicerManagers[index]->SetColorMap(0);
2195       mSlicerManagers[index]->Render();
2196     }
2197 }
2198 //------------------------------------------------------------------------------
2199
2200 //------------------------------------------------------------------------------
2201 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level) {
2202   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2203   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion())
2204     {
2205       mSlicerManagers[index]->SetFusionOpacity(opacity);
2206       mSlicerManagers[index]->SetFusionColorMap(colormap);
2207       mSlicerManagers[index]->SetFusionWindow(window);
2208       mSlicerManagers[index]->SetFusionLevel(level);
2209       mSlicerManagers[index]->SetColorMap(0);
2210       mSlicerManagers[index]->Render();
2211     }
2212 }
2213 //------------------------------------------------------------------------------
2214
2215 //------------------------------------------------------------------------------
2216 void vvMainWindow::SaveAs() {
2217   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector")
2218     {
2219       QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2220       return;
2221     }
2222
2223   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2224   int dimension = mSlicerManagers[index]->GetDimension();
2225   QStringList OutputListeFormat;
2226   OutputListeFormat.clear();
2227   if (dimension == 1)
2228     {
2229       OutputListeFormat.push_back(".mhd");
2230     }
2231   if (dimension == 2)
2232     {
2233       OutputListeFormat.push_back(".bmp");
2234       OutputListeFormat.push_back(".png");
2235       OutputListeFormat.push_back(".jpeg");
2236       OutputListeFormat.push_back(".tif");
2237       OutputListeFormat.push_back(".mhd");
2238       OutputListeFormat.push_back(".hdr");
2239       OutputListeFormat.push_back(".vox");
2240     }
2241   else if (dimension == 3)
2242     {
2243       OutputListeFormat.push_back(".mhd");
2244       OutputListeFormat.push_back(".hdr");
2245       OutputListeFormat.push_back(".vox");
2246     }
2247   else if (dimension == 4)
2248     {
2249       OutputListeFormat.push_back(".mhd");
2250     }
2251   QString Extensions = "AllFiles(*.*)";
2252   for (int i = 0; i < OutputListeFormat.count(); i++)
2253     {
2254       Extensions += ";;Images ( *";
2255       Extensions += OutputListeFormat[i];
2256       Extensions += ")";
2257     }
2258   QString fileName = QFileDialog::getSaveFileName(this,
2259                                                   tr("Save As"),
2260                                                   mSlicerManagers[index]->GetFileName().c_str(),
2261                                                   Extensions);
2262   if (!fileName.isEmpty())
2263     {
2264       std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2265       if (OutputListeFormat.contains(
2266                                      fileformat.c_str()))
2267         {
2268           QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2269           std::string action = "Saving";
2270           vvProgressDialog progress("Saving "+fileName.toStdString());
2271           qApp->processEvents();
2272           vvImageWriter *writer = new vvImageWriter;
2273           writer->SetOutputFileName(fileName.toStdString());
2274           writer->SetInput(mSlicerManagers[index]->GetImage());
2275           writer->Update();
2276           QApplication::restoreOverrideCursor();
2277           if (writer->GetLastError().size())
2278             {
2279               QString error = "Saving did not succeed\n";
2280               error += writer->GetLastError().c_str();
2281               QMessageBox::information(this,tr("Saving Problem"),error);
2282               SaveAs();
2283             }
2284         }
2285       else
2286         {
2287           QString error = fileformat.c_str();
2288           if (error.isEmpty())
2289             error += "no file format specified !";
2290           else
2291             error += " format unknown !!!\n";
2292           QMessageBox::information(this,tr("Saving Problem"),error);
2293           SaveAs();
2294         }
2295     }
2296 }
2297 //------------------------------------------------------------------------------
2298
2299 //------------------------------------------------------------------------------
2300 void vvMainWindow::AddLink(QString image1,QString image2) {
2301   for (unsigned int i = 0; i < mSlicerManagers.size();i++)
2302     {
2303       if (image1.toStdString() == mSlicerManagers[i]->GetId())
2304         {
2305           mSlicerManagers[i]->AddLink(image2.toStdString());
2306         }
2307       if (image2.toStdString() == mSlicerManagers[i]->GetId())
2308         {
2309           mSlicerManagers[i]->AddLink(image1.toStdString());
2310         }
2311     }
2312 }
2313 //------------------------------------------------------------------------------
2314
2315 //------------------------------------------------------------------------------
2316 void vvMainWindow::RemoveLink(QString image1,QString image2) {
2317   for (unsigned int i = 0; i < mSlicerManagers.size();i++)
2318     {
2319       if (image1.toStdString() == mSlicerManagers[i]->GetId())
2320         {
2321           mSlicerManagers[i]->RemoveLink(image2.toStdString());
2322         }
2323       if (image2.toStdString() == mSlicerManagers[i]->GetId())
2324         {
2325           mSlicerManagers[i]->RemoveLink(image1.toStdString());
2326         }
2327     }
2328 }
2329 //------------------------------------------------------------------------------
2330
2331 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2332 {
2333   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2334     {
2335       if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1)
2336         {
2337           for (int j = 0; j < 4; j++)
2338             {
2339               mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2340               //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2341               //UpdateTSlice(j,value);
2342             }
2343           mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2344           break;
2345         }
2346     }
2347 }
2348
2349 //------------------------------------------------------------------------------
2350 void vvMainWindow::NOHorizontalSliderMoved() {
2351   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2352 }
2353 //------------------------------------------------------------------------------
2354
2355 //------------------------------------------------------------------------------
2356 void vvMainWindow::NEHorizontalSliderMoved() {
2357   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2358 }
2359 //------------------------------------------------------------------------------
2360
2361 //------------------------------------------------------------------------------
2362 void vvMainWindow::SOHorizontalSliderMoved() {
2363   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2364 }
2365 //------------------------------------------------------------------------------
2366
2367 //------------------------------------------------------------------------------
2368 void vvMainWindow::SEHorizontalSliderMoved() {
2369   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2370 }
2371 //------------------------------------------------------------------------------
2372
2373 //------------------------------------------------------------------------------
2374 void vvMainWindow::NOVerticalSliderChanged() {
2375   int value = NOVerticalSlider->value();
2376   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2377     {
2378       if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
2379         {
2380           mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2381           mSlicerManagers[i]->UpdateSlice(0); // <-- DS add this. Not too much update ?
2382           break;
2383         }
2384     }
2385 }
2386 //------------------------------------------------------------------------------
2387
2388 //------------------------------------------------------------------------------
2389 void vvMainWindow::NEVerticalSliderChanged() {
2390   int value = NEVerticalSlider->value();
2391   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2392     {
2393       if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1)
2394         {
2395           mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2396           break;
2397         }
2398     }
2399 }
2400 //------------------------------------------------------------------------------
2401
2402 //------------------------------------------------------------------------------
2403 void vvMainWindow::SOVerticalSliderChanged() {
2404   int value = SOVerticalSlider->value();
2405   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2406     {
2407       if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
2408         {
2409           mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2410           break;
2411         }
2412     }
2413 }
2414 //------------------------------------------------------------------------------
2415
2416 //------------------------------------------------------------------------------
2417 void vvMainWindow::SEVerticalSliderChanged() {
2418   int value = SEVerticalSlider->value();
2419   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2420     {
2421       if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1)
2422         {
2423           mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2424           break;
2425         }
2426     }
2427 }
2428 //------------------------------------------------------------------------------
2429
2430 //------------------------------------------------------------------------------
2431 void vvMainWindow::UpdateSlice(int slicer, int slice) {
2432   if (slicer == 0) {
2433     if (slice != NOVerticalSlider->value())
2434       NOVerticalSlider->setValue(slice);
2435   }
2436   else if (slicer == 1)
2437     NEVerticalSlider->setValue(slice);
2438   else if (slicer == 2)
2439     SOVerticalSlider->setValue(slice);
2440   else if (slicer == 3)
2441     SEVerticalSlider->setValue(slice);
2442 }
2443 //------------------------------------------------------------------------------
2444
2445 //------------------------------------------------------------------------------
2446 void vvMainWindow::UpdateTSlice(int slicer, int slice) {
2447   switch (slicer)
2448     {
2449     case 0:
2450       NOHorizontalSlider->setValue(slice);
2451       break;
2452     case 1:
2453       NEHorizontalSlider->setValue(slice);
2454       break;
2455     case 2:
2456       SOHorizontalSlider->setValue(slice);
2457       break;
2458     case 3:
2459       SEHorizontalSlider->setValue(slice);
2460       break;
2461     }
2462 }
2463 //------------------------------------------------------------------------------
2464
2465 //------------------------------------------------------------------------------
2466 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax) {
2467   int position = int((min+max)/2);
2468   int tPosition = int((tmin+tmax)/2);
2469   if (slicer == 0)
2470     {
2471       NOVerticalSlider->setValue(position);
2472       NOVerticalSlider->setRange(min,max);
2473       NOHorizontalSlider->setRange(tmin,tmax);
2474       NOHorizontalSlider->setValue(tPosition);
2475     }
2476   else if (slicer == 1)
2477     {
2478       NEVerticalSlider->setValue(position);
2479       NEVerticalSlider->setRange(min,max);
2480       NEHorizontalSlider->setRange(tmin,tmax);
2481       NEHorizontalSlider->setValue(tPosition);
2482     }
2483   else if (slicer == 2)
2484     {
2485       SOVerticalSlider->setValue(position);
2486       SOVerticalSlider->setRange(min,max);
2487       SOHorizontalSlider->setRange(tmin,tmax);
2488       SOHorizontalSlider->setValue(tPosition);
2489     }
2490   else if (slicer == 3)
2491     {
2492       SEVerticalSlider->setValue(position);
2493       SEVerticalSlider->setRange(min,max);
2494       SEHorizontalSlider->setRange(tmin,tmax);
2495       SEHorizontalSlider->setValue(tPosition);
2496     }
2497 }
2498 //------------------------------------------------------------------------------
2499
2500 //------------------------------------------------------------------------------
2501 void vvMainWindow::SaveNOScreenshot() {
2502   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2503   w2i->SetInput(NOViewWidget->GetRenderWindow());
2504   w2i->Update();
2505   SaveScreenshot(w2i->GetOutput());
2506   w2i->Delete();
2507 }
2508 //------------------------------------------------------------------------------
2509
2510 //------------------------------------------------------------------------------
2511 void vvMainWindow::SaveNEScreenshot() {
2512   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2513   w2i->SetInput(NEViewWidget->GetRenderWindow());
2514   w2i->Update();
2515   SaveScreenshot(w2i->GetOutput());
2516   w2i->Delete();
2517 }
2518 //------------------------------------------------------------------------------
2519
2520 //------------------------------------------------------------------------------
2521 void vvMainWindow::SaveSOScreenshot() {
2522   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2523   w2i->SetInput(SOViewWidget->GetRenderWindow());
2524   w2i->Update();
2525   SaveScreenshot(w2i->GetOutput());
2526   w2i->Delete();
2527 }
2528 //------------------------------------------------------------------------------
2529
2530 //------------------------------------------------------------------------------
2531 void vvMainWindow::SaveSEScreenshot() {
2532   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2533   w2i->SetInput(SEViewWidget->GetRenderWindow());
2534   w2i->Update();
2535   SaveScreenshot(w2i->GetOutput());
2536   w2i->Delete();
2537 }
2538 //------------------------------------------------------------------------------
2539
2540 //------------------------------------------------------------------------------
2541 void vvMainWindow::SaveScreenshot(vtkImageData* image) {
2542   QString Extensions = "Images( *.png);;";
2543   Extensions += "Images( *.jpg);;";
2544   Extensions += "Images( *.bmp);;";
2545   Extensions += "Images( *.tif);;";
2546   Extensions += "Images( *.ppm)";
2547   QString fileName = QFileDialog::getSaveFileName(this,
2548                                                   tr("Save As"),
2549                                                   itksys::SystemTools::GetFilenamePath(
2550                                                                                        mSlicerManagers[0]->GetFileName()).c_str(),
2551                                                   Extensions);
2552   if (!fileName.isEmpty())
2553     {
2554       const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2555       if (!strcmp(ext, ".bmp"))
2556         {
2557           vtkBMPWriter *bmp = vtkBMPWriter::New();
2558           bmp->SetInput(image);
2559           bmp->SetFileName(fileName.toStdString().c_str());
2560           bmp->Write();
2561           bmp->Delete();
2562         }
2563       else if (!strcmp(ext, ".tif"))
2564         {
2565           vtkTIFFWriter *tif = vtkTIFFWriter::New();
2566           tif->SetInput(image);
2567           tif->SetFileName(fileName.toStdString().c_str());
2568           tif->Write();
2569           tif->Delete();
2570         }
2571       else if (!strcmp(ext, ".ppm"))
2572         {
2573           vtkPNMWriter *pnm = vtkPNMWriter::New();
2574           pnm->SetInput(image);
2575           pnm->SetFileName(fileName.toStdString().c_str());
2576           pnm->Write();
2577           pnm->Delete();
2578         }
2579       else if (!strcmp(ext, ".png"))
2580         {
2581           vtkPNGWriter *png = vtkPNGWriter::New();
2582           png->SetInput(image);
2583           png->SetFileName(fileName.toStdString().c_str());
2584           png->Write();
2585           png->Delete();
2586         }
2587       else if (!strcmp(ext, ".jpg"))
2588         {
2589           vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2590           jpg->SetInput(image);
2591           jpg->SetFileName(fileName.toStdString().c_str());
2592           jpg->Write();
2593           jpg->Delete();
2594         }
2595       else
2596         {
2597           QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2598         }
2599     }
2600
2601 }
2602 //------------------------------------------------------------------------------
2603
2604 //------------------------------------------------------------------------------
2605 void vvMainWindow::GoToCursor() {
2606   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2607   for (int column = 1; column < 5; column++)
2608     {
2609       if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1)
2610         {
2611           double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2612           mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2613                                                                           cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2614           mSlicerManagers[index]->UpdateViews(1,column-1);
2615           mSlicerManagers[index]->UpdateLinked(column-1);
2616           break;
2617         }
2618     }
2619 }
2620 //------------------------------------------------------------------------------
2621
2622 //------------------------------------------------------------------------------
2623 void vvMainWindow::PlayPause() {
2624   if (playMode)
2625     {
2626       playMode = 0;
2627       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2628       ImageInfoChanged();
2629       return;
2630     }
2631   else
2632     {
2633       int image_number=DataTree->topLevelItemCount();
2634       bool has_temporal;
2635       for (int i=0;i<image_number;i++)
2636         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1)
2637           {
2638             has_temporal=true;
2639             break;
2640           }
2641       if (has_temporal)
2642         {
2643           playMode = 1;
2644           playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2645           QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2646         }
2647     }
2648 }
2649 //------------------------------------------------------------------------------
2650
2651 //------------------------------------------------------------------------------
2652 void vvMainWindow::PlayNext() {
2653   if (playMode && !this->isHidden())
2654     {
2655       int image_number=DataTree->topLevelItemCount();
2656       ///Only play one slicer per SM, and only if the SM is being displayed
2657       for (int i=0;i<image_number;i++)
2658         for (int j=0;j<4;j++)
2659           if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2660               DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0)
2661             {
2662               mSlicerManagers[i]->SetNextTSlice(j);
2663               break;
2664             }
2665       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2666     }
2667 }
2668 //------------------------------------------------------------------------------
2669
2670 void vvMainWindow::ShowLastImage()
2671 {
2672   if (mSlicerManagers.size() > 1)
2673     {
2674       QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2675       CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2676       item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2677       DisplayChanged(item,1);
2678     }
2679 }
2680
2681 //------------------------------------------------------------------------------
2682 void vvMainWindow::UpdateRenderWindows() {
2683   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2684   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2685   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2686   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2687 }
2688 //------------------------------------------------------------------------------
2689
2690 //------------------------------------------------------------------------------
2691 void vvMainWindow::ResampleCurrentImage() {
2692   vvResamplerDialog resampler;
2693   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2694   resampler.SetSlicerManagers(mSlicerManagers,index);
2695   if (resampler.exec())
2696     AddImage(resampler.GetOutput(),resampler.GetOutputFileName());
2697 }
2698 //------------------------------------------------------------------------------
2699
2700 //------------------------------------------------------------------------------
2701 void vvMainWindow::SegmentationOnCurrentImage() {
2702   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2703
2704   vvSegmentationDialog segmentation;
2705   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2706   segmentation.exec();
2707 }
2708 //------------------------------------------------------------------------------
2709
2710 void vvMainWindow::SurfaceViewerLaunch()
2711 {
2712   vvSurfaceViewerDialog surfaceViewer;
2713   surfaceViewer.exec();
2714 }
2715
2716 //------------------------------------------------------------------------------
2717 void vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2718 {
2719   vvSlicerManager* m = new vvSlicerManager(4);
2720   m->SetImage(image);
2721   m->SetFilename(filename);
2722   AddImage(m);
2723 }
2724
2725 //------------------------------------------------------------------------------
2726 void vvMainWindow::AddImage(vvSlicerManager * slicer_manager) {
2727   mSlicerManagers.push_back(slicer_manager);
2728
2729   std::string filename = slicer_manager->GetFileName();
2730
2731   //create an item in the tree with good settings
2732   QTreeWidgetItem *item = new QTreeWidgetItem();
2733   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2734   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
2735   qApp->processEvents();
2736
2737   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2738
2739   //Create the buttons for reload and close
2740   qApp->processEvents();
2741   QTreePushButton* cButton = new QTreePushButton;
2742   cButton->setItem(item);
2743   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2744   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2745   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2746           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2747
2748   QTreePushButton* rButton = new QTreePushButton;
2749   rButton->setItem(item);
2750   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2751   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2752   rButton->setEnabled(0);
2753   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2754           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2755
2756   DataTree->addTopLevelItem(item);
2757   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2758   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2759
2760   //set the id of the image
2761   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2762   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2763   mSlicerManagers.back()->SetId(id.toStdString());
2764
2765   linkPanel->addImage(filename, id.toStdString());
2766
2767   connect(mSlicerManagers.back(),SIGNAL(currentImageChanged(std::string)),
2768           this,SLOT(CurrentImageChanged(std::string)));
2769   connect(mSlicerManagers.back(),SIGNAL(
2770                                         UpdatePosition(int, double, double, double, double, double, double, double)),this,
2771           SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2772   connect(mSlicerManagers.back(),SIGNAL(UpdateVector(int, double, double, double, double)),
2773           this, SLOT(VectorChanged(int,double,double,double, double)));
2774   connect(mSlicerManagers.back(),SIGNAL(UpdateOverlay(int, double, double)),
2775           this, SLOT(OverlayChanged(int,double,double)));
2776   connect(mSlicerManagers.back(),SIGNAL(UpdateFusion(int, double)),
2777           this, SLOT(FusionChanged(int,double)));
2778   connect(mSlicerManagers.back(),SIGNAL(UpdateWindows(int, int, int)),
2779           this,SLOT(WindowsChanged(int, int, int)));
2780   connect(mSlicerManagers.back(),SIGNAL(WindowLevelChanged(double, double,int, int)),
2781           this,SLOT(WindowLevelChanged(double, double, int, int)));
2782   connect(mSlicerManagers.back(),SIGNAL(UpdateSlice(int,int)),
2783           this,SLOT(UpdateSlice(int,int)));
2784   connect(mSlicerManagers.back(),SIGNAL(UpdateTSlice(int, int)),
2785           this,SLOT(UpdateTSlice(int, int)));
2786   connect(mSlicerManagers.back(),SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2787           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2788   connect(mSlicerManagers.back(),SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2789           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2790   connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2791   UpdateTree();
2792   qApp->processEvents();
2793   InitSlicers();
2794   ShowLastImage();
2795   InitDisplay();
2796   qApp->processEvents();
2797 }
2798 //------------------------------------------------------------------------------
2799
2800
2801 //------------------------------------------------------------------------------
2802 void vvMainWindow::UpdateCurrentSlicer() {
2803   int index = -1;
2804   if (DataTree->selectedItems().size() > 0) {
2805     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2806   }
2807   mSlicerManagerCurrentIndex = index;
2808 }
2809 //------------------------------------------------------------------------------
2810