vv/vvMainWindow.cxx

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