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(UpdateLinkedNavigation(std::string,vvSlicerManager*)),
 853               this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*)));
 854       connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 855               this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 856       connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 857       InitSlicers();
 858       numberofsuccesulreads++;
 859     }
 860   }
 861   if (numberofsuccesulreads) {
 862     NOViewWidget->show();
 863     NEViewWidget->show();
 864     SOViewWidget->show();
 865     SEViewWidget->show();
 866     UpdateTree();
 867     InitDisplay();
 868     ShowLastImage();
 869
 870     // Try to guess default WindowLevel
 871     double range[2];
 872     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 873     // DD(range[0]);
 874     //   DD(range[1]);
 875     if ((range[0] == 0) && (range[1] == 1)) {
 876       presetComboBox->setCurrentIndex(5);// binary
 877     } else {
 878       // TODO
 879     }
 880   }
 881   QApplication::restoreOverrideCursor();
 882 }
 883 //------------------------------------------------------------------------------
 884
 885 //------------------------------------------------------------------------------
 886 void vvMainWindow::UpdateTree()
 887 {
 888   DataTree->resizeColumnToContents(COLUMN_TREE);
 889   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 890   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 891   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 892   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 893   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 894   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 895   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 896 }
 897 //------------------------------------------------------------------------------
 898
 899 //------------------------------------------------------------------------------
 900 void vvMainWindow::CurrentImageChanged(std::string id)
 901 {
 902   //  DD("CurrentImageChanged");
 903   int selected = 0;
 904   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 905     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 906       selected = i;
 907     } else {
 908       DataTree->topLevelItem(i)->setSelected(0);
 909     }
 910     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 911       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 912
 913   }
 914   DataTree->topLevelItem(selected)->setSelected(1);
 915   //  DD(mSlicerManagers[selected]->GetFileName());
 916   emit SelectedImageHasChanged(mSlicerManagers[selected]);
 917 }
 918 //------------------------------------------------------------------------------
 919
 920 //------------------------------------------------------------------------------
 921 void vvMainWindow::ImageInfoChanged()
 922 {
 923   contextActions[7]->setEnabled(1);
 924   contextActions[6]->setEnabled(1);
 925   actionSave_As->setEnabled(1);
 926   actionAdd_VF_to_current_Image->setEnabled(1);
 927   actionAdd_fusion_image->setEnabled(1);
 928   actionNorth_East_Window->setEnabled(1);
 929   actionNorth_West_Window->setEnabled(1);
 930   actionSouth_East_Window->setEnabled(1);
 931   actionSouth_West_Window->setEnabled(1);
 932   inverseButton->setEnabled(1);
 933
 934   goToCursorPushButton->setEnabled(1);
 935
 936   if (DataTree->selectedItems().size()) {
 937     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 938
 939     colorMapComboBox->setEnabled(1);
 940     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
 941       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
 942           DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion") {
 943         colorMapComboBox->setEnabled(0);
 944         break;
 945       }
 946     }
 947
 948     std::vector<double> origin;
 949     std::vector<double> inputSpacing;
 950     std::vector<int> inputSize;
 951     std::vector<double> sizeMM;
 952     int dimension=0;
 953     QString pixelType;
 954     QString inputSizeInBytes;
 955     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
 956
 957     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1) {
 958       playButton->setEnabled(1);
 959       frameRateLabel->setEnabled(1);
 960       frameRateSpinBox->setEnabled(1);
 961     } else {
 962       playButton->setEnabled(0);
 963       frameRateLabel->setEnabled(0);
 964       frameRateSpinBox->setEnabled(0);
 965     }
 966
 967     //read image header
 968     int NPixel = 1;
 969
 970     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
 971       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
 972       dimension = imageSelected->GetNumberOfDimensions();
 973       origin.resize(dimension);
 974       inputSpacing.resize(dimension);
 975       inputSize.resize(dimension);
 976       sizeMM.resize(dimension);
 977       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
 978       for (int i = 0; i < dimension; i++) {
 979         origin[i] = imageSelected->GetOrigin()[i];
 980         inputSpacing[i] = imageSelected->GetSpacing()[i];
 981         inputSize[i] = imageSelected->GetSize()[i];
 982         sizeMM[i] = inputSize[i]*inputSpacing[i];
 983         NPixel *= inputSize[i];
 984       }
 985       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
 986     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
 987       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
 988       dimension = imageSelected->GetNumberOfDimensions();
 989       origin.resize(dimension);
 990       inputSpacing.resize(dimension);
 991       inputSize.resize(dimension);
 992       sizeMM.resize(dimension);
 993       pixelType = mSlicerManagers[index]->GetVF()->GetScalarTypeAsString().c_str();
 994       for (int i = 0; i < dimension; i++) {
 995         origin[i] = imageSelected->GetOrigin()[i];
 996         inputSpacing[i] = imageSelected->GetSpacing()[i];
 997         inputSize[i] = imageSelected->GetSize()[i];
 998         sizeMM[i] = inputSize[i]*inputSpacing[i];
 999         NPixel *= inputSize[i];
1000       }
1001       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1002     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1003       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1004       dimension = imageSelected->GetNumberOfDimensions();
1005       origin.resize(dimension);
1006       inputSpacing.resize(dimension);
1007       inputSize.resize(dimension);
1008       sizeMM.resize(dimension);
1009       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
1010       for (int i = 0; i < dimension; i++) {
1011         origin[i] = imageSelected->GetOrigin()[i];
1012         inputSpacing[i] = imageSelected->GetSpacing()[i];
1013         inputSize[i] = imageSelected->GetSize()[i];
1014         sizeMM[i] = inputSize[i]*inputSpacing[i];
1015         NPixel *= inputSize[i];
1016       }
1017       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1018     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1019       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1020       dimension = imageSelected->GetNumberOfDimensions();
1021       origin.resize(dimension);
1022       inputSpacing.resize(dimension);
1023       inputSize.resize(dimension);
1024       sizeMM.resize(dimension);
1025       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
1026       for (int i = 0; i < dimension; i++) {
1027         origin[i] = imageSelected->GetOrigin()[i];
1028         inputSpacing[i] = imageSelected->GetSpacing()[i];
1029         inputSize[i] = imageSelected->GetSize()[i];
1030         sizeMM[i] = inputSize[i]*inputSpacing[i];
1031         NPixel *= inputSize[i];
1032       }
1033       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1034     }
1035
1036     QString dim = QString::number(dimension) + " (";
1037     dim += pixelType + ")";
1038
1039     infoPanel->setFileName(image);
1040     infoPanel->setDimension(dim);
1041     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1042     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1043     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1044     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1045     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1046
1047     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1048                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1049     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1050     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1051
1052     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1053     for (int i = 0; i < 4; i++) {
1054       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1055         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1056         break;
1057       }
1058     }
1059     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1060     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1061     // DD(mSlicerManagers[index]->GetColorMap());
1062     // DD(mSlicerManagers[index]->GetPreset());
1063     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1064     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1065
1066     infoPanel->setFileName(image);
1067     infoPanel->setDimension(dim);
1068     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1069     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1070     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1071     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1072     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1073
1074     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1075                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1076     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1077     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1078
1079     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1080     for (int i = 0; i < 4; i++) {
1081       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1082         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1083         break;
1084       }
1085     }
1086     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1087     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1088     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1089     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1090
1091     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1092       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1093       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1094                                   mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1095                                   mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1096     } else {
1097       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1098       overlayPanel->getVFProperty(-1,-1,-1);
1099     }
1100     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1101       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1102       overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1103     } else {
1104       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1105       overlayPanel->getOverlayProperty(-1);
1106     }
1107     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1108       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1109       overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1110                                       mSlicerManagers[index]->GetFusionColorMap(),
1111                                       mSlicerManagers[index]->GetFusionWindow(),
1112                                       mSlicerManagers[index]->GetFusionLevel());
1113     } else {
1114       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1115       overlayPanel->getFusionProperty(-1, -1,-1,-1);
1116     }
1117   }
1118 }
1119 //------------------------------------------------------------------------------
1120
1121 //------------------------------------------------------------------------------
1122 void vvMainWindow::ShowDocumentation()
1123 {
1124   documentation->show();
1125 }
1126 //------------------------------------------------------------------------------
1127 void vvMainWindow::ShowHelpDialog()
1128 {
1129   help_dialog->show();
1130 }
1131 //------------------------------------------------------------------------------
1132
1133 //------------------------------------------------------------------------------
1134 void vvMainWindow::ChangeViewMode()
1135 {
1136   QListIterator<int> it0(splitter_3->sizes());
1137   QListIterator<int> it1(splitter_3->sizes());
1138   int max0 = 0;
1139   int max1 = 1;
1140   while (it0.hasNext()) {
1141     max0 += it0.next();
1142   }
1143   while (it1.hasNext()) {
1144     max1 += it1.next();
1145   }
1146   QList<int> size0;
1147   QList<int> size1;
1148   if (viewMode == 1) {
1149     viewMode = 0;
1150     size0.push_back(max0);
1151     size0.push_back(0);
1152     size1.push_back(max1);
1153     size1.push_back(0);
1154     splitter_3->setSizes(size0);
1155     OSplitter->setSizes(size1);
1156     DataTree->setColumnHidden(2,1);
1157     DataTree->setColumnHidden(3,1);
1158     DataTree->setColumnHidden(4,1);
1159   } else {
1160     viewMode = 1;
1161     size0.push_back(int(max0/2));
1162     size0.push_back(int(max0/2));
1163     size1.push_back(int(max1/2));
1164     size1.push_back(int(max1/2));
1165     splitter_3->setSizes(size0);
1166     OSplitter->setSizes(size1);
1167     DataTree->setColumnHidden(2,0);
1168     DataTree->setColumnHidden(3,0);
1169     DataTree->setColumnHidden(4,0);
1170   }
1171 }
1172 //------------------------------------------------------------------------------
1173
1174 //------------------------------------------------------------------------------
1175 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1176 {
1177   QString result = "";// QString::number(size);
1178   //result += " bytes (";
1179   if (size > 1000000000) {
1180     size /= 1000000000;
1181     result += QString::number(size);
1182     result += "Gb";//)";
1183   } else if (size > 1000000) {
1184     size /= 1000000;
1185     result += QString::number(size);
1186     result += "Mb";//)";
1187   } else if (size > 1000) {
1188     size /= 1000;
1189     result += QString::number(size);
1190     result += "kb";//)";
1191   }
1192   return result;
1193 }
1194 //------------------------------------------------------------------------------
1195
1196 //------------------------------------------------------------------------------
1197 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1198 {
1199   QString result;
1200   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1201     if (i != 0)
1202       result += " ";
1203     result += QString::number(vectorDouble[i]);
1204   }
1205   return result;
1206 }
1207 //------------------------------------------------------------------------------
1208
1209 //------------------------------------------------------------------------------
1210 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1211 {
1212   QString result;
1213   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1214     if (i != 0)
1215       result += " ";
1216     result += QString::number(vectorInt[i]);
1217   }
1218   return result;
1219 }
1220 //------------------------------------------------------------------------------
1221
1222 //------------------------------------------------------------------------------
1223 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1224 {
1225   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1226   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1227     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1228       return i;
1229   }
1230   return -1;
1231 }
1232 //------------------------------------------------------------------------------
1233
1234 //------------------------------------------------------------------------------
1235 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1236 {
1237   QString id = sm->GetId().c_str();
1238   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1239     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1240       return DataTree->topLevelItem(i);
1241   }
1242   return NULL;
1243 }
1244 //------------------------------------------------------------------------------
1245
1246 //------------------------------------------------------------------------------
1247 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clicked_item, int column)
1248 {
1249   int index = GetSlicerIndexFromItem(clicked_item);
1250   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1251     return;
1252   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1253     //Trick to avoid redoing twice the job for a key (sr)
1254     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()-> GetInteractor()->SetKeySym("Crap");
1255
1256     QTreeWidgetItem* current_row=DataTree->topLevelItem(i);
1257     if (DataTree->topLevelItem(index) == current_row) {
1258       vvSlicer* clicked_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1259       if (current_row == clicked_item) {
1260         //If we just activated a slicer
1261         if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1262           mSlicerManagers[i]->UpdateSlicer(column-1,clicked_item->data(column,Qt::CheckStateRole).toInt());
1263           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1264           DisplaySliders(i,column-1);
1265           std::map<std::string,int> overlay_counts;
1266           for (int child = 0; child < current_row->childCount(); child++) {
1267             std::string overlay_type =
1268               current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1269             overlay_counts[overlay_type]++;
1270             current_row->child(child)->setData(column,Qt::CheckStateRole,
1271                                                current_row->data(column,Qt::CheckStateRole));
1272             clicked_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,true);
1273           }
1274         } else { //We don't allow simply desactivating a slicer
1275           clicked_item->setData(column,Qt::CheckStateRole,2);
1276           return;
1277         }
1278       }
1279       //if we clicked on the vector(or overlay) and not the image
1280       else {
1281         if (clicked_item->data(column,Qt::CheckStateRole).toInt()) {
1282           current_row->setData(column,Qt::CheckStateRole,2);
1283           mSlicerManagers[i]->UpdateSlicer(column-1,2);
1284           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1285           DisplaySliders(i,column-1);
1286         }
1287         int vis = clicked_item->data(column,Qt::CheckStateRole).toInt();
1288         std::string overlay_type = clicked_item->data(1,Qt::UserRole).toString().toStdString();
1289         int overlay_index=0;
1290         for (int child = 0; child < current_row->childCount(); child++) {
1291           if (current_row->child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1292             overlay_index++;
1293           if (current_row->child(child) == clicked_item) break;
1294         }
1295         clicked_slicer->SetActorVisibility(
1296           clicked_item->data(1,Qt::UserRole).toString().toStdString(), overlay_index-1,vis);
1297       }
1298     } else if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1299       current_row->setData(column,Qt::CheckStateRole,0);
1300       mSlicerManagers[i]->UpdateSlicer(column-1,0);
1301       std::map<std::string,int> overlay_counts;
1302       for (int child = 0; child < current_row->childCount(); child++) {
1303         std::string overlay_type =
1304           current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1305         overlay_counts[overlay_type]++;
1306         current_row->child(child)->setData(column,Qt::CheckStateRole,0);
1307         vvSlicer * current_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1308         current_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,false);
1309       }
1310     }
1311     //mSlicerManagers[i]->SetColorMap(-1);
1312     mSlicerManagers[i]->SetColorMap();
1313   }
1314   mSlicerManagers[index]->GetSlicer(column-1)->Render();
1315 }
1316 //------------------------------------------------------------------------------
1317
1318 void vvMainWindow::InitSlicers()
1319 {
1320   if (mSlicerManagers.size()) {
1321     mSlicerManagers.back()->GenerateDefaultLookupTable();
1322
1323     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1324     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1325     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1326     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1327   }
1328 }
1329
1330 //------------------------------------------------------------------------------
1331 void vvMainWindow::InitDisplay()
1332 {
1333   if (mSlicerManagers.size()) {
1334     //BE CAREFUL : this is absolutely necessary to set the interactor style
1335     //in order to have the same style instanciation for all SlicerManagers in
1336     // a same window
1337     for (int j = 0; j < 4; j++) {
1338       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1339       style->SetAutoAdjustCameraClippingRange(1);
1340       bool AlreadySelected = false;
1341       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1342         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1343
1344         //select the image only if previous are not selected
1345         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1346           mSlicerManagers[i]->UpdateSlicer(j,1);
1347           AlreadySelected = true;
1348         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1349           if (DataTree->selectedItems().size() == 0)
1350             DataTree->topLevelItem(i)->setSelected(1);
1351           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1352           mSlicerManagers[i]->UpdateSlicer(j,1);
1353           DisplaySliders(i,j);
1354         } else {
1355           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1356           mSlicerManagers[i]->UpdateSlicer(j,0);
1357         }
1358       }
1359       style->Delete();
1360     }
1361   }
1362 }
1363 //------------------------------------------------------------------------------
1364
1365 //------------------------------------------------------------------------------
1366 void vvMainWindow::DisplaySliders(int slicer, int window)
1367 {
1368   int range[2];
1369   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1370   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1371
1372   int tRange[2];
1373   tRange[0] = 0;
1374   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1375   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1376   bool showHorizontal = false;
1377   bool showVertical = false;
1378   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1379       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1380           && mSlicerManagers[slicer]->GetType() != IMAGEWITHTIME
1381           && mSlicerManagers[slicer]->GetType() != MERGEDWITHTIME))
1382     showVertical = true;
1383   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1384       || mSlicerManagers[slicer]->GetType() == IMAGEWITHTIME
1385       || mSlicerManagers[slicer]->GetType() == MERGEDWITHTIME)
1386     showHorizontal = true;
1387
1388   if (showVertical)
1389     verticalSliders[window]->show();
1390   else
1391     verticalSliders[window]->hide();
1392   verticalSliders[window]->setRange(range[0],range[1]);
1393   verticalSliders[window]->setValue(position);
1394
1395   if (showHorizontal)
1396     horizontalSliders[window]->show();
1397   else
1398     horizontalSliders[window]->hide();
1399   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1400   horizontalSliders[window]->setValue(tPosition);
1401 }
1402 //------------------------------------------------------------------------------
1403
1404 //------------------------------------------------------------------------------
1405 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1406 {
1407   int index = GetSlicerIndexFromItem(item);
1408
1409   if (DataTree->topLevelItem(index) != item) {
1410     QString warning = "Do you really want to close the overlay : ";
1411     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1412     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1413                        warning, 0, this);
1414     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1415     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1416     if (msgBox.exec() == QMessageBox::AcceptRole) {
1417       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1418       int overlay_index=0;
1419       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1420         if (DataTree->topLevelItem(index)->\
1421             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1422           overlay_index++;
1423         if (DataTree->topLevelItem(index)->child(child) == item) break;
1424       }
1425       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1426       mSlicerManagers[index]->SetColorMap(0);
1427       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1428       mSlicerManagers[index]->Render();
1429     }
1430   } else if (DataTree->topLevelItemCount() <= 1) {
1431     QString warning = "Do you really want to close the image : ";
1432     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1433     warning += "\nThis is the last image, you're about to close vv !!!";
1434     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1435                        warning, 0, this);
1436     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1437     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1438     if (msgBox.exec() == QMessageBox::AcceptRole) {
1439       this->close();
1440     }
1441   } else {
1442     QString warning = "Do you really want to close the image : ";
1443     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1444     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1445                        warning, 0, this);
1446     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1447     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1448     if (msgBox.exec() == QMessageBox::AcceptRole) {
1449
1450       // Tell tools that we close an image
1451       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1452
1453       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1454       DataTree->takeTopLevelItem(index);
1455       for (int i = 0; i < index; i++) {
1456         Manageriter++;
1457       }
1458       linkPanel->removeImage(index);
1459       mSlicerManagers[index]->RemoveActors();
1460       delete mSlicerManagers[index];
1461       mSlicerManagers.erase(Manageriter);
1462
1463       //
1464       InitDisplay();
1465     }
1466   }
1467 }
1468 //------------------------------------------------------------------------------
1469
1470 //------------------------------------------------------------------------------
1471 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1472 {
1473   // int index = GetSlicerIndexFromItem(item);
1474   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1475   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1476   //     mSlicerManagers[index]->ReloadVF();
1477   //   else
1478   //     mSlicerManagers[index]->Reload();
1479
1480   //   QApplication::restoreOverrideCursor();
1481   int index = GetSlicerIndexFromItem(item);
1482   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1483   QString role=item->data(1,Qt::UserRole).toString();
1484   if ( role == "vector")
1485     mSlicerManagers[index]->ReloadVF();
1486   else if (role == "overlay")
1487     mSlicerManagers[index]->ReloadOverlay();
1488   else if (role == "fusion")
1489     mSlicerManagers[index]->ReloadFusion();
1490   else
1491     mSlicerManagers[index]->Reload();
1492
1493   // Update view and info
1494   ImageInfoChanged();
1495   mSlicerManagers[index]->Render();
1496   QApplication::restoreOverrideCursor();
1497 }
1498 //------------------------------------------------------------------------------
1499
1500 // void vvMainWindow::CropImage()
1501 // {
1502 //   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1503 //   vvCropDialog crop(mSlicerManagers,index);
1504 //   if(crop.exec())
1505 //     AddImage(crop.GetOutput(),"cropped.mhd");
1506 // }
1507
1508 //------------------------------------------------------------------------------
1509 void vvMainWindow::SplitImage()
1510 {
1511   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1512   int dim = mSlicerManagers[index]->GetDimension();
1513   QString warning = "Do you really want to split the ";
1514   warning += QString::number(dim) + "D image ";
1515   warning += DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString() + " into ";
1516   warning += QString::number(mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetSize()[dim-1]) + " ";
1517   warning += QString::number(dim-1) + "D images.";
1518   QMessageBox msgBox(QMessageBox::Warning, tr("Split Image"),
1519                      warning, 0, this);
1520   msgBox.addButton(tr("Split"), QMessageBox::AcceptRole);
1521   msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1522   if (msgBox.exec() == QMessageBox::AcceptRole) {
1523     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1524     if (dim > 2) {
1525       std::string filename = DataTree->selectedItems()[0]->data(0,Qt::UserRole).toString().toStdString();
1526       int numberOfSlice = mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetSize()[dim-1];
1527       std::string path = itksys::SystemTools::GetFilenamePath(
1528                            filename);
1529       path += "/";
1530       path += DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString().toStdString();
1531       path += "%03d";
1532       path += itksys::SystemTools::GetFilenameLastExtension(
1533                 filename).c_str();
1534
1535       typedef itk::NumericSeriesFileNames NameGeneratorType;
1536       NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
1537       nameGenerator->SetSeriesFormat(path.c_str());
1538       nameGenerator->SetStartIndex(0);
1539       nameGenerator->SetEndIndex(numberOfSlice-1);
1540       nameGenerator->SetIncrementIndex(1);
1541
1542       for (int i = 0; i < numberOfSlice; i++) {
1543         vvSlicerManager* imageManager = new vvSlicerManager(4);
1544         imageManager->SetExtractedImage(nameGenerator->GetFileNames()[i],
1545                                         mSlicerManagers[index]->GetSlicer(0)->GetImage(), i);
1546         mSlicerManagers.push_back(imageManager);
1547
1548         //create an item in the tree with good settings
1549         QTreeWidgetItem *item = new QTreeWidgetItem();
1550         item->setData(0,Qt::UserRole,nameGenerator->GetFileNames()[i].c_str());
1551         std::string fileI = itksys::SystemTools::GetFilenameWithoutLastExtension(
1552                               nameGenerator->GetFileNames()[i]).c_str();
1553         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileI.c_str());
1554         for (int j = 1; j <= 4; j++) {
1555           for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1556             DataTree->topLevelItem(i)->setData(j,Qt::CheckStateRole,0);
1557           }
1558           item->setData(j,Qt::CheckStateRole,2);
1559         }
1560
1561         //Create the buttons for reload and close
1562         QTreePushButton* cButton = new QTreePushButton;
1563         cButton->setItem(item);
1564         cButton->setColumn(COLUMN_CLOSE_IMAGE);
1565         cButton->setToolTip(tr("close image"));
1566         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1567         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1568                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1569
1570         QTreePushButton* rButton = new QTreePushButton;
1571         rButton->setItem(item);
1572         rButton->setColumn(COLUMN_RELOAD_IMAGE);
1573         rButton->setToolTip(tr("reload image"));
1574         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1575         rButton->setEnabled(false);
1576         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1577                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1578
1579         DataTree->addTopLevelItem(item);
1580         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1581         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1582
1583         //set the id of the image
1584         QString id = nameGenerator->GetFileNames()[i].c_str() + QString::number(mSlicerManagers.size()-1);
1585         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1586         mSlicerManagers.back()->SetId(id.toStdString());
1587         linkPanel->addImage(fileI, id.toStdString());
1588         connect(mSlicerManagers.back(),SIGNAL(currentImageChanged(std::string)),
1589                 this,SLOT(CurrentImageChanged(std::string)));
1590         connect(mSlicerManagers.back(),SIGNAL(
1591                   UpdatePosition(int, double, double, double, double, double, double, double)),this,
1592                 SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
1593         connect(mSlicerManagers.back(),SIGNAL(UpdateVector(int, double, double, double, double)),
1594                 this, SLOT(VectorChanged(int,double,double,double, double)));
1595         connect(mSlicerManagers.back(),SIGNAL(UpdateOverlay(int, double, double)),
1596                 this, SLOT(OverlayChanged(int,double,double)));
1597         connect(mSlicerManagers.back(),SIGNAL(UpdateFusion(int, double)),
1598                 this, SLOT(FusionChanged(int,double)));
1599         connect(mSlicerManagers.back(),SIGNAL(UpdateWindows(int, int, int)),
1600                 this,SLOT(WindowsChanged(int, int, int)));
1601         connect(mSlicerManagers.back(),SIGNAL(WindowLevelChanged(double, double,int, int)),
1602                 this,SLOT(WindowLevelChanged(double, double, int, int)));
1603         connect(mSlicerManagers.back(),SIGNAL(UpdateSlice(int,int)),
1604                 this,SLOT(UpdateSlice(int,int)));
1605         connect(mSlicerManagers.back(),SIGNAL(UpdateTSlice(int, int)),
1606                 this,SLOT(UpdateTSlice(int, int)));
1607         connect(mSlicerManagers.back(),SIGNAL(UpdateSliceRange(int,int,int,int,int)),
1608                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
1609         connect(mSlicerManagers.back(),SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
1610                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
1611         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*)),
1612                 this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*)));
1613         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
1614         UpdateTree();
1615         qApp->processEvents();
1616         InitSlicers();
1617         InitDisplay();
1618         qApp->processEvents();
1619       }
1620       QApplication::restoreOverrideCursor();
1621     } else {
1622       QApplication::restoreOverrideCursor();
1623       QString error = "Cannot split file (dimensions must be greater than 2) ";
1624       QMessageBox::information(this,tr("Splitting problem"),error);
1625     }
1626   }
1627 }
1628 //------------------------------------------------------------------------------
1629
1630 //------------------------------------------------------------------------------
1631 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1632 {
1633   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1634 }
1635 //------------------------------------------------------------------------------
1636
1637 //------------------------------------------------------------------------------
1638 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1639 {
1640   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1641 }
1642 //------------------------------------------------------------------------------
1643
1644 //------------------------------------------------------------------------------
1645 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1646 {
1647   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1648 }
1649 //------------------------------------------------------------------------------
1650
1651 //------------------------------------------------------------------------------
1652 void vvMainWindow::FusionChanged(int visibility, double value)
1653 {
1654   overlayPanel->getCurrentFusionInfo(visibility,value);
1655 }
1656 //------------------------------------------------------------------------------
1657
1658 //------------------------------------------------------------------------------
1659 void vvMainWindow::WindowsChanged(int window, int view, int slice)
1660 {
1661   infoPanel->setViews(window, view, slice);
1662 }
1663 //------------------------------------------------------------------------------
1664
1665 //------------------------------------------------------------------------------
1666 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap)
1667 {
1668   windowSpinBox->setValue(window);
1669   levelSpinBox->setValue(level);
1670   colorMapComboBox->setCurrentIndex(colormap);
1671   presetComboBox->setCurrentIndex(preset);
1672 }
1673 //------------------------------------------------------------------------------
1674
1675 //------------------------------------------------------------------------------
1676 void vvMainWindow::WindowLevelEdited()
1677 {
1678   presetComboBox->setCurrentIndex(6);
1679   UpdateWindowLevel();
1680 }
1681 //------------------------------------------------------------------------------
1682
1683 //------------------------------------------------------------------------------
1684 void vvMainWindow::UpdateWindowLevel()
1685 {
1686   if (DataTree->selectedItems().size()) {
1687     if (presetComboBox->currentIndex() == 7) //For ventilation
1688       colorMapComboBox->setCurrentIndex(5);
1689     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1690     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1691     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1692     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1693     mSlicerManagers[index]->Render();
1694   }
1695 }
1696 //------------------------------------------------------------------------------
1697
1698 //------------------------------------------------------------------------------
1699 void vvMainWindow::UpdateColorMap()
1700 {
1701   if (DataTree->selectedItems().size()) {
1702     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1703     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1704     mSlicerManagers[index]->Render();
1705   }
1706 }
1707 //------------------------------------------------------------------------------
1708 void vvMainWindow::SwitchWindowLevel()
1709 {
1710   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1711   int window = mSlicerManagers[index]->GetColorWindow();
1712   presetComboBox->setCurrentIndex(6);
1713   windowSpinBox->setValue(-window);
1714   UpdateWindowLevel();
1715 }
1716 //------------------------------------------------------------------------------
1717
1718 //------------------------------------------------------------------------------
1719 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1720 {
1721   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1722     if (mSlicerManagers[i]->GetId() == id) {
1723       //mSlicerManagers[i]->SetTSlice(temps);
1724       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1725       mSlicerManagers[i]->UpdateViews(0,slicer);
1726       break;
1727     }
1728   }
1729 }
1730 //------------------------------------------------------------------------------
1731
1732 //------------------------------------------------------------------------------
1733 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm)
1734 {
1735   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1736     if (id == mSlicerManagers[i]->GetId()) {
1737       mSlicerManagers[i]->UpdateLinkedNavigation(sm->GetSlicer(0));
1738     }
1739   }
1740 }
1741 //------------------------------------------------------------------------------
1742
1743 //------------------------------------------------------------------------------
1744 void vvMainWindow::ShowContextMenu(QPoint point)
1745 {
1746   if (!DataTree->selectedItems().size()) {
1747     contextActions[1]->setEnabled(0);
1748     contextActions[2]->setEnabled(0);
1749     contextActions[3]->setEnabled(0);
1750     contextActions[4]->setEnabled(0);
1751     contextActions[5]->setEnabled(0);
1752     contextActions[6]->setEnabled(0);
1753     contextActions[7]->setEnabled(0);
1754   } else {
1755     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1756     contextActions[1]->setEnabled(1);
1757     contextActions[2]->setEnabled(
1758       DataTree->itemWidget(DataTree->selectedItems()[0],
1759                            COLUMN_RELOAD_IMAGE)->isEnabled());
1760     contextActions[3]->setEnabled(1);
1761     contextActions[5]->setEnabled(1);
1762     contextActions[6]->setEnabled(1);
1763     contextActions[7]->setEnabled(1);
1764
1765     if (mSlicerManagers[index]->GetDimension() < 3)
1766       contextActions[4]->setEnabled(0);
1767     else
1768       contextActions[4]->setEnabled(1);
1769   }
1770   contextMenu.exec(QCursor::pos());
1771 }
1772 //------------------------------------------------------------------------------
1773
1774 //------------------------------------------------------------------------------
1775 void vvMainWindow::CloseImage()
1776 {
1777   CloseImage(DataTree->selectedItems()[0],0);
1778 }
1779 //------------------------------------------------------------------------------
1780
1781 //------------------------------------------------------------------------------
1782 void vvMainWindow::ReloadImage()
1783 {
1784   ReloadImage(DataTree->selectedItems()[0],0);
1785 }
1786 //------------------------------------------------------------------------------
1787
1788 //------------------------------------------------------------------------------
1789 void vvMainWindow::SelectOverlayImage()
1790 {
1791   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1792
1793   //check if one overlay image is added
1794   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1795     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1796       QString error = "Cannot add more than one compared image\n";
1797       error += "Please remove first ";
1798       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1799       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1800       return;
1801     }
1802
1803   QString Extensions = EXTENSIONS;
1804   Extensions += ";;All Files (*)";
1805   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1806   if (!file.isEmpty())
1807     AddOverlayImage(index,file);
1808 }
1809 //------------------------------------------------------------------------------
1810
1811 //------------------------------------------------------------------------------
1812 void vvMainWindow::AddOverlayImage(int index, QString file)
1813 {
1814
1815   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1816   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1817                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1818   reader->SetFileName(file.toStdString().c_str());
1819   reader->ReadImageInformation();
1820   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1821   int dimension = reader->GetNumberOfDimensions();
1822   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1823   vvProgressDialog progress("Opening " + file.toStdString());
1824   qApp->processEvents();
1825
1826   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1827   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component)) {
1828     //create an item in the tree with good settings
1829     QTreeWidgetItem *item = new QTreeWidgetItem();
1830     item->setData(0,Qt::UserRole,file.toStdString().c_str());
1831     item->setData(1,Qt::UserRole,tr("overlay"));
1832     item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
1833     qApp->processEvents();
1834
1835     for (int j = 1; j <= 4; j++) {
1836       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1837       mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("overlay",0,
1838           DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1839     }
1840
1841     //Create the buttons for reload and close
1842     qApp->processEvents();
1843     QTreePushButton* cButton = new QTreePushButton;
1844     cButton->setItem(item);
1845     cButton->setColumn(COLUMN_CLOSE_IMAGE);
1846     cButton->setToolTip(tr("close image"));
1847     cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1848     connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1849             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1850
1851     QTreePushButton* rButton = new QTreePushButton;
1852     rButton->setItem(item);
1853     rButton->setColumn(COLUMN_RELOAD_IMAGE);
1854     rButton->setToolTip(tr("reload image"));
1855     rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1856     connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1857             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1858
1859     DataTree->topLevelItem(index)->setExpanded(1);
1860     DataTree->topLevelItem(index)->addChild(item);
1861     DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1862     DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1863
1864     //set the id of the image
1865     QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1866     item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1867     UpdateTree();
1868     qApp->processEvents();
1869     ImageInfoChanged();
1870     QApplication::restoreOverrideCursor();
1871   } else {
1872     QApplication::restoreOverrideCursor();
1873     QString error = "Cannot import the new image.\n";
1874     error += mSlicerManagers[index]->GetLastError().c_str();
1875     QMessageBox::information(this,tr("Problem reading image !"),error);
1876   }
1877 }
1878
1879 void vvMainWindow::AddFusionImage()
1880 {
1881   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1882
1883   //check if one fusion image is added
1884   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1885     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
1886       QString error = "Cannot add more than one fusion image\n";
1887       error += "Please remove first ";
1888       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1889       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1890       return;
1891     }
1892
1893   QString Extensions = EXTENSIONS;
1894   Extensions += ";;All Files (*)";
1895   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1896   if (!file.isEmpty()) {
1897     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1898     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1899                                          file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1900     reader->SetFileName(file.toStdString().c_str());
1901     reader->ReadImageInformation();
1902     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1903     if (reader) {
1904       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1905       vvProgressDialog progress("Opening fusion");
1906       qApp->processEvents();
1907
1908       std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1909       if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1910                                             reader->GetNumberOfDimensions(), component)) {
1911         //create an item in the tree with good settings
1912         QTreeWidgetItem *item = new QTreeWidgetItem();
1913         item->setData(0,Qt::UserRole,file.toStdString().c_str());
1914         item->setData(1,Qt::UserRole,tr("fusion"));
1915         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
1916         qApp->processEvents();
1917
1918         for (int j = 1; j <= 4; j++) {
1919           item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1920           mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("fusion",0,
1921               DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1922         }
1923
1924         //Create the buttons for reload and close
1925         qApp->processEvents();
1926         QTreePushButton* cButton = new QTreePushButton;
1927         cButton->setItem(item);
1928         cButton->setColumn(COLUMN_CLOSE_IMAGE);
1929         cButton->setToolTip(tr("close image"));
1930         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1931         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1932                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1933
1934         QTreePushButton* rButton = new QTreePushButton;
1935         rButton->setItem(item);
1936         rButton->setColumn(COLUMN_RELOAD_IMAGE);
1937         rButton->setToolTip(tr("reload image"));
1938         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1939         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1940                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1941
1942         DataTree->topLevelItem(index)->setExpanded(1);
1943         DataTree->topLevelItem(index)->addChild(item);
1944         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1945         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1946
1947         //set the id of the image
1948         QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1949         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1950         UpdateTree();
1951         qApp->processEvents();
1952         ImageInfoChanged();
1953         QApplication::restoreOverrideCursor();
1954       } else {
1955         QApplication::restoreOverrideCursor();
1956         QString error = "Cannot import the new image.\n";
1957         error += mSlicerManagers[index]->GetLastError().c_str();
1958         QMessageBox::information(this,tr("Problem reading image !"),error);
1959       }
1960     } else {
1961       QString error = "Cannot import the new image.\n";
1962       QMessageBox::information(this,tr("Problem reading image !"),error);
1963     }
1964   }
1965 }
1966 //------------------------------------------------------------------------------
1967
1968
1969 //------------------------------------------------------------------------------
1970 void vvMainWindow::OpenField()
1971 {
1972   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1973   //check if a vector field has already been added
1974   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1975     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
1976       QString error = "Cannot add more than one vector field\n";
1977       error += "Please remove first ";
1978       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1979       QMessageBox::information(this,tr("Problem adding vector field!"),error);
1980       return;
1981     }
1982
1983   QString Extensions = "Images ( *.mhd)";
1984   Extensions += ";;Images ( *.vf)";
1985   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
1986   if (!file.isEmpty())
1987     AddField(file,index);
1988 }
1989 //------------------------------------------------------------------------------
1990
1991
1992 //------------------------------------------------------------------------------
1993 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
1994 {
1995   //create an item in the tree with good settings
1996   QTreeWidgetItem *item = new QTreeWidgetItem();
1997   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
1998   item->setData(1,Qt::UserRole,tr("vector"));
1999   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename);
2000   qApp->processEvents();
2001
2002   for (int j = 1; j <= 4; j++) {
2003     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2004     mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("vector",0,
2005         DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
2006   }
2007
2008   //Create the buttons for reload and close
2009   qApp->processEvents();
2010   QTreePushButton* cButton = new QTreePushButton;
2011   cButton->setItem(item);
2012   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2013   cButton->setToolTip(tr("close vector field"));
2014   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2015   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2016           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2017
2018   QTreePushButton* rButton = new QTreePushButton;
2019   rButton->setItem(item);
2020   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2021   rButton->setToolTip(tr("reload vector field"));
2022   rButton->setEnabled(from_disk);
2023   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2024   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2025           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2026
2027   DataTree->topLevelItem(index)->setExpanded(1);
2028   DataTree->topLevelItem(index)->addChild(item);
2029   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2030   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2031
2032   //set the id of the image
2033   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2034   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2035   UpdateTree();
2036   qApp->processEvents();
2037   ImageInfoChanged();
2038   QApplication::restoreOverrideCursor();
2039 }
2040 //------------------------------------------------------------------------------
2041
2042
2043 //------------------------------------------------------------------------------
2044 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2045 {
2046   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2047   vvSlicerManager* imageManager = mSlicerManagers[index];
2048   if (imageManager->SetVF(vf,file.toStdString())) {
2049     AddFieldEntry(file,index,false);
2050   } else {
2051     QString error = "Cannot import the vector field for this image.\n";
2052     error += imageManager->GetLastError().c_str();
2053     QMessageBox::information(this,tr("Problem reading VF !"),error);
2054   }
2055   QApplication::restoreOverrideCursor();
2056 }
2057 //------------------------------------------------------------------------------
2058
2059
2060 //------------------------------------------------------------------------------
2061 void vvMainWindow::AddField(QString file,int index)
2062 {
2063   if (QFile::exists(file)) {
2064     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2065
2066     //init the progress events
2067     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2068     vvProgressDialog progress("Opening " + file.toStdString());
2069     qApp->processEvents();
2070
2071     //read the vector and put it in the current mSlicerManager
2072     vvSlicerManager* imageManager = mSlicerManagers[index];
2073     qApp->processEvents();
2074
2075     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2076     if (imageManager->SetVF(file.toStdString())) {
2077       imageManager->Render();
2078       AddFieldEntry(file,index,true);
2079     } else {
2080       QApplication::restoreOverrideCursor();
2081       QString error = "Cannot import the vector field for this image.\n";
2082       error += imageManager->GetLastError().c_str();
2083       QMessageBox::information(this,tr("Problem reading VF !"),error);
2084     }
2085   } else
2086     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2087
2088 }
2089 //------------------------------------------------------------------------------
2090
2091
2092 //------------------------------------------------------------------------------
2093 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width)
2094 {
2095   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2096   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2097     for (int i = 0; i < 4; i++) {
2098       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2099       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2100       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2101       if (log > 0)
2102         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2103       else
2104         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2105     }
2106   }
2107 }
2108 //------------------------------------------------------------------------------
2109
2110
2111 //------------------------------------------------------------------------------
2112 void vvMainWindow::SetOverlayProperty(int color)
2113 {
2114   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2115   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2116     mSlicerManagers[index]->SetOverlayColor(color);
2117     mSlicerManagers[index]->SetColorMap(0);
2118     mSlicerManagers[index]->Render();
2119   }
2120 }
2121 //------------------------------------------------------------------------------
2122
2123 //------------------------------------------------------------------------------
2124 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level)
2125 {
2126   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2127   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2128     mSlicerManagers[index]->SetFusionOpacity(opacity);
2129     mSlicerManagers[index]->SetFusionColorMap(colormap);
2130     mSlicerManagers[index]->SetFusionWindow(window);
2131     mSlicerManagers[index]->SetFusionLevel(level);
2132     mSlicerManagers[index]->SetColorMap(0);
2133     mSlicerManagers[index]->Render();
2134   }
2135 }
2136 //------------------------------------------------------------------------------
2137
2138 //------------------------------------------------------------------------------
2139 void vvMainWindow::SaveAs()
2140 {
2141   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2142     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2143     return;
2144   }
2145
2146   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2147   int dimension = mSlicerManagers[index]->GetDimension();
2148   QStringList OutputListeFormat;
2149   OutputListeFormat.clear();
2150   if (dimension == 1) {
2151     OutputListeFormat.push_back(".mhd");
2152   }
2153   if (dimension == 2) {
2154     OutputListeFormat.push_back(".bmp");
2155     OutputListeFormat.push_back(".png");
2156     OutputListeFormat.push_back(".jpeg");
2157     OutputListeFormat.push_back(".tif");
2158     OutputListeFormat.push_back(".mhd");
2159     OutputListeFormat.push_back(".hdr");
2160     OutputListeFormat.push_back(".vox");
2161   } else if (dimension == 3) {
2162     OutputListeFormat.push_back(".mhd");
2163     OutputListeFormat.push_back(".hdr");
2164     OutputListeFormat.push_back(".vox");
2165   } else if (dimension == 4) {
2166     OutputListeFormat.push_back(".mhd");
2167   }
2168   QString Extensions = "AllFiles(*.*)";
2169   for (int i = 0; i < OutputListeFormat.count(); i++) {
2170     Extensions += ";;Images ( *";
2171     Extensions += OutputListeFormat[i];
2172     Extensions += ")";
2173   }
2174   QString fileName = QFileDialog::getSaveFileName(this,
2175                      tr("Save As"),
2176                      mSlicerManagers[index]->GetFileName().c_str(),
2177                      Extensions);
2178   if (!fileName.isEmpty()) {
2179     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2180     if (OutputListeFormat.contains(
2181           fileformat.c_str())) {
2182       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2183       std::string action = "Saving";
2184       vvProgressDialog progress("Saving "+fileName.toStdString());
2185       qApp->processEvents();
2186       vvImageWriter *writer = new vvImageWriter;
2187       writer->SetOutputFileName(fileName.toStdString());
2188       writer->SetInput(mSlicerManagers[index]->GetImage());
2189       writer->Update();
2190       QApplication::restoreOverrideCursor();
2191       if (writer->GetLastError().size()) {
2192         QString error = "Saving did not succeed\n";
2193         error += writer->GetLastError().c_str();
2194         QMessageBox::information(this,tr("Saving Problem"),error);
2195         SaveAs();
2196       }
2197     } else {
2198       QString error = fileformat.c_str();
2199       if (error.isEmpty())
2200         error += "no file format specified !";
2201       else
2202         error += " format unknown !!!\n";
2203       QMessageBox::information(this,tr("Saving Problem"),error);
2204       SaveAs();
2205     }
2206   }
2207 }
2208 //------------------------------------------------------------------------------
2209
2210
2211 //------------------------------------------------------------------------------
2212 void vvMainWindow::AddLink(QString image1,QString image2)
2213 {
2214   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2215     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2216       mSlicerManagers[i]->AddLink(image2.toStdString());
2217     }
2218     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2219       mSlicerManagers[i]->AddLink(image1.toStdString());
2220     }
2221   }
2222 }
2223 //------------------------------------------------------------------------------
2224
2225
2226 //------------------------------------------------------------------------------
2227 void vvMainWindow::RemoveLink(QString image1,QString image2)
2228 {
2229   // DD("vvMainWindow:RemoveLink");
2230   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2231     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2232       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2233     }
2234     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2235       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2236     }
2237   }
2238 }
2239 //------------------------------------------------------------------------------
2240
2241 //------------------------------------------------------------------------------
2242 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2243 {
2244   int index = 0;
2245   while(sm != mSlicerManagers[index])
2246     index++;
2247   index = (index+offset) % mSlicerManagers.size();
2248
2249   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2250   //CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2251   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2252   DisplayChanged(item,slicer+1);
2253 }
2254 //------------------------------------------------------------------------------
2255
2256 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2257 {
2258   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2259     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2260       for (int j = 0; j < 4; j++) {
2261         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2262         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2263         //UpdateTSlice(j,value);
2264       }
2265       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2266       break;
2267     }
2268   }
2269 }
2270 //------------------------------------------------------------------------------
2271
2272
2273 //------------------------------------------------------------------------------
2274 void vvMainWindow::NOHorizontalSliderMoved()
2275 {
2276   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2277   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2278 //  mCurrentTime = NOHorizontalSlider->value();
2279 }
2280 //------------------------------------------------------------------------------
2281
2282
2283 //------------------------------------------------------------------------------
2284 void vvMainWindow::NEHorizontalSliderMoved()
2285 {
2286   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2287   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2288 //  mCurrentTime = NEHorizontalSlider->value();
2289 }
2290 //------------------------------------------------------------------------------
2291
2292
2293 //------------------------------------------------------------------------------
2294 void vvMainWindow::SOHorizontalSliderMoved()
2295 {
2296   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2297   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2298   // mCurrentTime = SOHorizontalSlider->value();
2299 }
2300 //------------------------------------------------------------------------------
2301
2302
2303 //------------------------------------------------------------------------------
2304 void vvMainWindow::SEHorizontalSliderMoved()
2305 {
2306   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2307   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2308   // mCurrentTime = SEHorizontalSlider->value();
2309 }
2310 //------------------------------------------------------------------------------
2311
2312 //------------------------------------------------------------------------------
2313 void vvMainWindow::NOVerticalSliderChanged()
2314 {
2315   static int value=-1;
2316   if (value == NOVerticalSlider->value()) return;
2317   else value = NOVerticalSlider->value();
2318   //  int value = NOVerticalSlider->value();
2319   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2320     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2321       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2322         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2323         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2324
2325         // If nor Update/Render -> slider not work
2326         // only render = ok navigation, but for contour Update needed but slower ?
2327
2328         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2329         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2330       }
2331       break;
2332     }
2333   }
2334 }
2335 //------------------------------------------------------------------------------
2336
2337
2338 //------------------------------------------------------------------------------
2339 void vvMainWindow::NEVerticalSliderChanged()
2340 {
2341   static int value=-1;
2342   if (value == NEVerticalSlider->value()) return;
2343   else value = NEVerticalSlider->value();
2344   //  int value = NEVerticalSlider->value();
2345   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2346     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2347       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2348         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2349         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2350         mSlicerManagers[i]->UpdateSlice(1);
2351         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2352       }
2353       break;
2354     }
2355   }
2356 }
2357 //------------------------------------------------------------------------------
2358
2359
2360 //------------------------------------------------------------------------------
2361 void vvMainWindow::SOVerticalSliderChanged()
2362 {
2363   // DD("SOVerticalSliderChanged");
2364   static int value=-1;
2365   // DD(value);
2366 //   DD(SOVerticalSlider->value());
2367   if (value == SOVerticalSlider->value()) return;
2368   else value = SOVerticalSlider->value();
2369   //int value = SOVerticalSlider->value();
2370   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2371     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2372       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2373         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2374         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2375         mSlicerManagers[i]->UpdateSlice(2);
2376         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2377       }
2378       // else { DD("avoid SOVerticalSlider slicer update"); }
2379       break;
2380     }
2381   }
2382 }
2383 //------------------------------------------------------------------------------
2384
2385
2386 //------------------------------------------------------------------------------
2387 void vvMainWindow::SEVerticalSliderChanged()
2388 {
2389   static int value=-1;
2390   if (value == SEVerticalSlider->value()) return;
2391   else value = SEVerticalSlider->value();
2392   // int value = SEVerticalSlider->value();
2393   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2394     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2395       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2396         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2397         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2398         mSlicerManagers[i]->UpdateSlice(3);
2399         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2400       }
2401       break;
2402     }
2403   }
2404 }
2405 //------------------------------------------------------------------------------
2406
2407
2408 //------------------------------------------------------------------------------
2409 void vvMainWindow::UpdateSlice(int slicer, int slice)
2410 {
2411   // DD("vvMainWindow::UpdateSlice");
2412 //   DD(slicer);
2413 //   DD(slice);
2414   if (slicer == 0) {
2415     //    if (slice != NOVerticalSlider->value())
2416     NOVerticalSlider->setValue(slice);
2417   } else {
2418     if (slicer == 1)
2419       NEVerticalSlider->setValue(slice);
2420     else {
2421       if (slicer == 2)
2422         SOVerticalSlider->setValue(slice);
2423       else {
2424         if (slicer == 3)
2425           SEVerticalSlider->setValue(slice);
2426       }
2427     }
2428   }
2429   // DD("vvMainWindow:UpdateSlice END");
2430 }
2431 //------------------------------------------------------------------------------
2432
2433
2434 //------------------------------------------------------------------------------
2435 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2436 {
2437   switch (slicer) {
2438   case 0:
2439     NOHorizontalSlider->setValue(slice);
2440     break;
2441   case 1:
2442     NEHorizontalSlider->setValue(slice);
2443     break;
2444   case 2:
2445     SOHorizontalSlider->setValue(slice);
2446     break;
2447   case 3:
2448     SEHorizontalSlider->setValue(slice);
2449     break;
2450   }
2451 }
2452 //------------------------------------------------------------------------------
2453
2454
2455 //------------------------------------------------------------------------------
2456 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2457 {
2458   int position = int((min+max)/2);
2459   int tPosition = int((tmin+tmax)/2);
2460   if (slicer == 0) {
2461     NOVerticalSlider->setValue(position);
2462     NOVerticalSlider->setRange(min,max);
2463     NOHorizontalSlider->setRange(tmin,tmax);
2464     NOHorizontalSlider->setValue(tPosition);
2465   } else if (slicer == 1) {
2466     NEVerticalSlider->setValue(position);
2467     NEVerticalSlider->setRange(min,max);
2468     NEHorizontalSlider->setRange(tmin,tmax);
2469     NEHorizontalSlider->setValue(tPosition);
2470   } else if (slicer == 2) {
2471     SOVerticalSlider->setValue(position);
2472     SOVerticalSlider->setRange(min,max);
2473     SOHorizontalSlider->setRange(tmin,tmax);
2474     SOHorizontalSlider->setValue(tPosition);
2475   } else if (slicer == 3) {
2476     SEVerticalSlider->setValue(position);
2477     SEVerticalSlider->setRange(min,max);
2478     SEHorizontalSlider->setRange(tmin,tmax);
2479     SEHorizontalSlider->setValue(tPosition);
2480   }
2481 }
2482 //------------------------------------------------------------------------------
2483
2484
2485 //------------------------------------------------------------------------------
2486 void vvMainWindow::SaveNOScreenshot()
2487 {
2488   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2489   w2i->SetInput(NOViewWidget->GetRenderWindow());
2490   w2i->Update();
2491   SaveScreenshot(w2i->GetOutput());
2492   w2i->Delete();
2493 }
2494 //------------------------------------------------------------------------------
2495
2496
2497 //------------------------------------------------------------------------------
2498 void vvMainWindow::SaveNEScreenshot()
2499 {
2500   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2501   w2i->SetInput(NEViewWidget->GetRenderWindow());
2502   w2i->Update();
2503   SaveScreenshot(w2i->GetOutput());
2504   w2i->Delete();
2505 }
2506 //------------------------------------------------------------------------------
2507
2508
2509 //------------------------------------------------------------------------------
2510 void vvMainWindow::SaveSOScreenshot()
2511 {
2512   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2513   w2i->SetInput(SOViewWidget->GetRenderWindow());
2514   w2i->Update();
2515   SaveScreenshot(w2i->GetOutput());
2516   w2i->Delete();
2517 }
2518 //------------------------------------------------------------------------------
2519
2520
2521 //------------------------------------------------------------------------------
2522 void vvMainWindow::SaveSEScreenshot()
2523 {
2524   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2525   w2i->SetInput(SEViewWidget->GetRenderWindow());
2526   w2i->Update();
2527   SaveScreenshot(w2i->GetOutput());
2528   w2i->Delete();
2529 }
2530 //------------------------------------------------------------------------------
2531
2532
2533 //------------------------------------------------------------------------------
2534 void vvMainWindow::SaveScreenshot(vtkImageData* image)
2535 {
2536   QString Extensions = "Images( *.png);;";
2537   Extensions += "Images( *.jpg);;";
2538   Extensions += "Images( *.bmp);;";
2539   Extensions += "Images( *.tif);;";
2540   Extensions += "Images( *.ppm)";
2541   QString fileName = QFileDialog::getSaveFileName(this,
2542                      tr("Save As"),
2543                      itksys::SystemTools::GetFilenamePath(
2544                        mSlicerManagers[0]->GetFileName()).c_str(),
2545                      Extensions);
2546   if (!fileName.isEmpty()) {
2547     const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2548     if (!strcmp(ext, ".bmp")) {
2549       vtkBMPWriter *bmp = vtkBMPWriter::New();
2550       bmp->SetInput(image);
2551       bmp->SetFileName(fileName.toStdString().c_str());
2552       bmp->Write();
2553       bmp->Delete();
2554     } else if (!strcmp(ext, ".tif")) {
2555       vtkTIFFWriter *tif = vtkTIFFWriter::New();
2556       tif->SetInput(image);
2557       tif->SetFileName(fileName.toStdString().c_str());
2558       tif->Write();
2559       tif->Delete();
2560     } else if (!strcmp(ext, ".ppm")) {
2561       vtkPNMWriter *pnm = vtkPNMWriter::New();
2562       pnm->SetInput(image);
2563       pnm->SetFileName(fileName.toStdString().c_str());
2564       pnm->Write();
2565       pnm->Delete();
2566     } else if (!strcmp(ext, ".png")) {
2567       vtkPNGWriter *png = vtkPNGWriter::New();
2568       png->SetInput(image);
2569       png->SetFileName(fileName.toStdString().c_str());
2570       png->Write();
2571       png->Delete();
2572     } else if (!strcmp(ext, ".jpg")) {
2573       vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2574       jpg->SetInput(image);
2575       jpg->SetFileName(fileName.toStdString().c_str());
2576       jpg->Write();
2577       jpg->Delete();
2578     } else {
2579       QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2580     }
2581   }
2582
2583 }
2584 //------------------------------------------------------------------------------
2585
2586
2587 //------------------------------------------------------------------------------
2588 void vvMainWindow::GoToCursor()
2589 {
2590   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2591   for (int column = 1; column < 5; column++) {
2592     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
2593       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2594       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2595         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2596       mSlicerManagers[index]->UpdateViews(1,column-1);
2597       mSlicerManagers[index]->UpdateLinked(column-1);
2598       break;
2599     }
2600   }
2601 }
2602 //------------------------------------------------------------------------------
2603
2604 //------------------------------------------------------------------------------
2605 void vvMainWindow::PlayPause()
2606 {
2607   if (playMode) {
2608     playMode = 0;
2609     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2610     ImageInfoChanged();
2611     return;
2612   } else {
2613     int image_number=DataTree->topLevelItemCount();
2614     bool has_temporal;
2615     for (int i=0; i<image_number; i++)
2616       if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1) {
2617         has_temporal=true;
2618         break;
2619       }
2620     if (has_temporal) {
2621       playMode = 1;
2622       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2623       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2624     }
2625   }
2626 }
2627 //------------------------------------------------------------------------------
2628
2629 //------------------------------------------------------------------------------
2630 void vvMainWindow::PlayNext()
2631 {
2632   if (playMode && !this->isHidden()) {
2633     int image_number=DataTree->topLevelItemCount();
2634     ///Only play one slicer per SM, and only if the SM is being displayed
2635     for (int i=0; i<image_number; i++)
2636       for (int j=0; j<4; j++)
2637         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2638             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
2639           mSlicerManagers[i]->SetNextTSlice(j);
2640           break;
2641         }
2642     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2643   }
2644 }
2645 //------------------------------------------------------------------------------
2646
2647 void vvMainWindow::ShowLastImage()
2648 {
2649   if (mSlicerManagers.size() > 1) {
2650     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2651     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2652     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2653     DisplayChanged(item,1);
2654   }
2655 }
2656
2657 //------------------------------------------------------------------------------
2658 void vvMainWindow::UpdateRenderWindows()
2659 {
2660   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2661   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2662   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2663   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2664 }
2665 //------------------------------------------------------------------------------
2666
2667 //------------------------------------------------------------------------------
2668 void vvMainWindow::SegmentationOnCurrentImage()
2669 {
2670   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2671
2672   vvSegmentationDialog segmentation;
2673   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2674   segmentation.exec();
2675 }
2676 //------------------------------------------------------------------------------
2677
2678 void vvMainWindow::SurfaceViewerLaunch()
2679 {
2680   vvSurfaceViewerDialog surfaceViewer;
2681   surfaceViewer.exec();
2682 }
2683
2684 //------------------------------------------------------------------------------
2685 void vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2686 {
2687   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
2688   slicer_manager->SetImage(image);
2689   slicer_manager->SetFilename(filename);
2690   mSlicerManagers.push_back(slicer_manager);
2691
2692   //create an item in the tree with good settings
2693   QTreeWidgetItem *item = new QTreeWidgetItem();
2694   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2695   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
2696   qApp->processEvents();
2697
2698   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2699
2700   //Create the buttons for reload and close
2701   qApp->processEvents();
2702   QTreePushButton* cButton = new QTreePushButton;
2703   cButton->setItem(item);
2704   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2705   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2706   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2707           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2708
2709   QTreePushButton* rButton = new QTreePushButton;
2710   rButton->setItem(item);
2711   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2712   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2713   rButton->setEnabled(0);
2714   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2715           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2716
2717   DataTree->addTopLevelItem(item);
2718   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2719   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2720
2721   //set the id of the image
2722   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2723   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2724   mSlicerManagers.back()->SetId(id.toStdString());
2725
2726   linkPanel->addImage(filename, id.toStdString());
2727
2728   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
2729           this, SLOT(CurrentImageChanged(std::string)));
2730   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
2731           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2732   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
2733           this, SLOT(VectorChanged(int,double,double,double, double)));
2734   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
2735           this, SLOT(OverlayChanged(int,double,double)));
2736   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
2737           this, SLOT(FusionChanged(int,double)));
2738   connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
2739           this,SLOT(WindowsChanged(int, int, int)));
2740   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
2741           this,SLOT(WindowLevelChanged(double, double, int, int)));
2742   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
2743           this,SLOT(UpdateSlice(int,int)));
2744   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
2745           this,SLOT(UpdateTSlice(int, int)));
2746   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2747           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2748   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2749           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2750   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*)),
2751           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*)));
2752   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
2753           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
2754   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2755   UpdateTree();
2756   qApp->processEvents();
2757   InitSlicers();
2758   ShowLastImage();
2759   InitDisplay();
2760   qApp->processEvents();
2761 }
2762 //------------------------------------------------------------------------------
2763
2764
2765 //------------------------------------------------------------------------------
2766 void vvMainWindow::UpdateCurrentSlicer()
2767 {
2768   int index = -1;
2769   if (DataTree->selectedItems().size() > 0) {
2770     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2771   }
2772   mSlicerManagerCurrentIndex = index;
2773 }
2774 //------------------------------------------------------------------------------
2775