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 #ifdef CLITK_VV_USE_BDCM
  49 #include <bdcmDicomFilesSelectorDialog.h>
  50 #endif
  51
  52 // ITK include
  53 #include "itkImage.h"
  54 #include "itkImageFileReader.h"
  55 #include "itkByteSwapper.h"
  56 #include "itkCommand.h"
  57 #include "itkNumericSeriesFileNames.h"
  58
  59 // VTK include
  60 #include "vtkImageData.h"
  61 #include "vtkImageActor.h"
  62 #include "vtkCornerAnnotation.h"
  63 #include "vtkRenderWindow.h"
  64 #include "vtkRenderWindowInteractor.h"
  65 #include "vtkRenderer.h"
  66 #include "vtkRendererCollection.h"
  67 #include "vtkWindowToImageFilter.h"
  68 #include "vtkBMPWriter.h"
  69 #include "vtkTIFFWriter.h"
  70 #include "vtkPNMWriter.h"
  71 #include "vtkPNGWriter.h"
  72 #include "vtkJPEGWriter.h"
  73
  74 // Standard includes
  75 #include <iostream>
  76
  77 #define COLUMN_TREE 0
  78 #define COLUMN_UL_VIEW 1
  79 #define COLUMN_UR_VIEW 2
  80 #define COLUMN_DL_VIEW 3
  81 #define COLUMN_DR_VIEW 4
  82 #define COLUMN_CLOSE_IMAGE 5
  83 #define COLUMN_RELOAD_IMAGE 6
  84 #define COLUMN_IMAGE_NAME 7
  85
  86 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.hdr *.vox *.his *.xdr)"
  87
  88 /*Data Tree values
  89   0,Qt::UserRole full filename
  90   1,Qt::CheckStateRole checkbutton UL View
  91   1,Qt::UserRole overlay, fusion or vector
  92   2,Qt::CheckStateRole checkbutton UR View
  93   3,Qt::CheckStateRole checkbutton DL View
  94   4,Qt::CheckStateRole checkbutton DR View
  95   5,0  short filename
  96   5,Qt::UserRole mSlicerManager id*/
  97
  98 //------------------------------------------------------------------------------
  99 vvMainWindow::vvMainWindow():vvMainWindowBase() {
 100   setupUi(this); // this sets up the GUI
 101
 102   mInputPathName = "";
 103   mMenuTools = menuTools;
 104   mContextMenu = &contextMenu;
 105   mMenuExperimentalTools = menuExperimental;
 106   mMainWidget = this;
 107   mCurrentTime = -1;
 108
 109   //Init the contextMenu
 110   this->setContextMenuPolicy(Qt::CustomContextMenu);
 111   contextActions.resize(0);
 112   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 113                                                         tr("O&pen new Image"));
 114   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 115   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 116   contextActions.push_back(actionOpen_new_image);
 117   contextMenu.addSeparator();
 118
 119   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 120                                                      tr("Close Current Image"));
 121   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 122   contextActions.push_back(actionClose_Image);
 123
 124   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 125                                                       tr("Reload Current Image"));
 126   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 127   contextActions.push_back(actionReload_image);
 128
 129   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 130                                                     tr("Save Current Image"));
 131   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 132   contextActions.push_back(actionSave_image);
 133
 134   contextMenu.addSeparator();
 135
 136   // QAction* actionCrop_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/crop.png")),
 137   //                                                   tr("Crop Current Image"));
 138   // connect(actionCrop_image,SIGNAL(triggered()),this,SLOT(CropImage()));
 139   // contextActions.push_back(actionCrop_image);
 140
 141   QAction* actionSplit_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/cut.png")),
 142                                                      tr("Split Current Image"));
 143   connect(actionSplit_image,SIGNAL(triggered()),this,SLOT(SplitImage()));
 144   contextActions.push_back(actionSplit_image);
 145
 146   contextMenu.addSeparator();
 147
 148   contextMenu.addAction(actionAdd_VF_to_current_Image);
 149   contextActions.push_back(actionAdd_VF_to_current_Image);
 150
 151   QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 152                                                                        tr("Add overlay image to current image"));
 153   contextMenu.addAction(actionAdd_Overlay_to_current_Image);
 154   contextActions.push_back(actionAdd_Overlay_to_current_Image);
 155
 156   connect(actionAdd_Overlay_to_current_Image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 157
 158   contextMenu.addAction(actionAdd_fusion_image);
 159   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 160   contextActions.push_back(actionAdd_fusion_image);
 161
 162   // TRIAL DS
 163   /*
 164   QMenu * m = new QMenu(menubar);
 165   m->setTitle("TOTO");
 166   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 167   contextMenu.addMenu(m);
 168   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 169                      tr("BIDON"));
 170   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 171                      tr("BIDON2"));
 172   m->addAction(a);
 173   m->addAction(b);
 174   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 175   */
 176
 177   //init the DataTree
 178   mSlicerManagers.resize(0);
 179
 180   QStringList header;
 181   header.append("");
 182   header.append("TL");
 183   header.append("TR");
 184   header.append("BL");
 185   header.append("BR");
 186   header.append("");
 187   header.append("");
 188   header.append("Name");
 189
 190   DataTree->setHeaderLabels(header);
 191   DataTree->resizeColumnToContents(COLUMN_TREE);
 192   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 193   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 194   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 195   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 196   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 197   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 198   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 199
 200   viewMode = 1;
 201   documentation = new vvDocumentation();
 202   help_dialog = new vvHelpDialog();
 203   dicomSeriesSelector = new vvDicomSeriesSelector();
 204
 205   inverseButton->setEnabled(0);
 206   actionAdd_Overlay_to_current_Image->setEnabled(0);
 207   actionSave_As->setEnabled(0);
 208   actionAdd_VF_to_current_Image->setEnabled(0);
 209   actionAdd_fusion_image->setEnabled(0);
 210
 211   //init the sliders
 212   verticalSliders.push_back(NOVerticalSlider);
 213   verticalSliders.push_back(NEVerticalSlider);
 214   verticalSliders.push_back(SOVerticalSlider);
 215   verticalSliders.push_back(SEVerticalSlider);
 216
 217   for (int i =0; i < 4; i++)
 218     verticalSliders[i]->hide();
 219
 220   horizontalSliders.push_back(NOHorizontalSlider);
 221   horizontalSliders.push_back(NEHorizontalSlider);
 222   horizontalSliders.push_back(SOHorizontalSlider);
 223   horizontalSliders.push_back(SEHorizontalSlider);
 224
 225   for (int i =0; i < 4; i++)
 226     horizontalSliders[i]->hide();
 227
 228
 229   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 230   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 231   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 232   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 233
 234   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 235   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 236   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 237   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 238
 239   //connect everything
 240   connect(actionMaximum_Intensity_Projection,SIGNAL(triggered()),this,SLOT(ComputeMIP()));
 241   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 242   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 243   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 244   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 245   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 246   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 247   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 248   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 249   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 250   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 251   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 252   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 253   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 254   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 255   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 256
 257   ///////////////////////////////////////////////
 258   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 259   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 260   ///////////////////////////////////////////////
 261
 262   actionNorth_East_Window->setEnabled(0);
 263   actionNorth_West_Window->setEnabled(0);
 264   actionSouth_East_Window->setEnabled(0);
 265   actionSouth_West_Window->setEnabled(0);
 266
 267   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 268   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 269   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 270   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 271
 272   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 273   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 274           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 275
 276   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 277   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 278   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 279   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 280   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 281   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 282
 283
 284   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 285
 286   connect(linkPanel,SIGNAL(addLink(QString,QString)),this,SLOT(AddLink(QString,QString)));
 287   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 288   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int)),this,SLOT(SetVFProperty(int,int,int,int)));
 289   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int)),this,SLOT(SetOverlayProperty(int)));
 290   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,double,double)),
 291           this,SLOT(SetFusionProperty(int,int,double,double)));
 292   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 293
 294   playMode = 0;//pause
 295   mFrameRate = 10;
 296   playButton->setEnabled(0);
 297   frameRateLabel->setEnabled(0);
 298   frameRateSpinBox->setEnabled(0);
 299   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 300   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 301
 302   goToCursorPushButton->setEnabled(0);
 303   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 304
 305   NOViewWidget->hide();
 306   NEViewWidget->hide();
 307   SOViewWidget->hide();
 308   SEViewWidget->hide();
 309
 310   //Recently opened files
 311   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 312   if ( !recent_files.empty() )
 313     {
 314       QMenu * rmenu = new QMenu("Recently opened files...");
 315       rmenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 316       menuFile->insertMenu(actionOpen_Image_With_Time,rmenu);
 317       for (std::list<std::string>::iterator i = recent_files.begin();i!=recent_files.end();i++)
 318         {
 319           QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")),
 320                                        (*i).c_str(),this);
 321           rmenu->addAction(current);
 322           connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 323         }
 324     }
 325
 326   // Adding all new tools (insertion in the menu)
 327   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 328
 329   if (!CLITK_EXPERIMENTAL)
 330       menuExperimental->menuAction()->setVisible(false);
 331 }
 332 //------------------------------------------------------------------------------
 333
 334
 335 //------------------------------------------------------------------------------
 336 void vvMainWindow::ComputeMIP()
 337 {
 338   vvMaximumIntensityProjection mip;
 339   vvSlicerManager* selected_slicer = mSlicerManagers[GetSlicerIndexFromItem(DataTree->selectedItems()[0])];
 340   QFileInfo info(selected_slicer->GetFileName().c_str());
 341   mip.Compute(selected_slicer);
 342   if (!mip.error)
 343       AddImage(mip.GetOutput(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_mip.mhd");
 344 }
 345 //------------------------------------------------------------------------------
 346
 347
 348 //------------------------------------------------------------------------------
 349 void vvMainWindow::ComputeMidPosition()
 350 {
 351   bool ok;
 352   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 353   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 354                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 355   if (ok)
 356     {
 357       vvMidPosition midp;
 358       midp.slicer_manager = mSlicerManagers[index];
 359       midp.reference_image_index = ref;
 360       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 361       midp.Update();
 362       if (midp.error)
 363         QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 364       else
 365         {
 366           QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 367           AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 368         }
 369       QApplication::restoreOverrideCursor();
 370     }
 371 }
 372 //------------------------------------------------------------------------------
 373
 374
 375 //------------------------------------------------------------------------------
 376 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 377 {
 378   QTreeWidgetItem *item = new QTreeWidgetItem();
 379   item->setData(0,Qt::UserRole,"filename.vtk");
 380   item->setData(1,Qt::UserRole,tr("contour"));
 381   QBrush brush;
 382   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 383   brush.setStyle(Qt::SolidPattern);
 384   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 385   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 386
 387   for (int j = 1; j <= 4; j++)
 388     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 389
 390   QTreePushButton* cButton = new QTreePushButton;
 391   cButton->setItem(item);
 392   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 393   cButton->setToolTip(tr("close image"));
 394   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 395   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 396           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 397
 398   QTreePushButton* rButton = new QTreePushButton;
 399   rButton->setItem(item);
 400   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 401   rButton->setToolTip(tr("reload image"));
 402   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 403   rButton->setEnabled(false);
 404   //Not implemented
 405   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 406   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 407
 408   DataTree->topLevelItem(image_index)->setExpanded(1);
 409   DataTree->topLevelItem(image_index)->addChild(item);
 410   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 411   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 412   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 413   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 414
 415   UpdateTree();
 416   mSlicerManagers[image_index]->AddContour(contour,propagation);
 417   mSlicerManagers[image_index]->Render();
 418 }
 419 //------------------------------------------------------------------------------
 420
 421
 422 //------------------------------------------------------------------------------
 423 void vvMainWindow::OpenVTKContour()
 424 {
 425   if (mSlicerManagers.size() > 0)
 426     {
 427       QString Extensions = "Images ( *.vtk *.obj)";
 428       Extensions += ";;All Files (*)";
 429       QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 430       if (file.isNull())
 431         return;
 432       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 433       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 434       vvMeshReader reader;
 435       reader.SetImage(mSlicerManagers[index]->GetImage());
 436       reader.SetModeToVTK();
 437       reader.SetFilename(file.toStdString());
 438       reader.Update();
 439       AddContour(index,reader.GetOutput()[0],false);
 440       QApplication::restoreOverrideCursor();
 441     }
 442 }
 443 //------------------------------------------------------------------------------
 444
 445
 446 //------------------------------------------------------------------------------
 447 void vvMainWindow::OpenDCStructContour()
 448 {
 449   if (mSlicerManagers.size() > 0)
 450     {
 451       QString Extensions = "Dicom Files ( *.dcm; RS*)";
 452       Extensions += ";;All Files (*)";
 453       QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 454       if (file.isNull())
 455         return;
 456       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 457       vvMeshReader reader;
 458       reader.SetFilename(file.toStdString());
 459       vvStructSelector selector;
 460       selector.SetStructures(reader.GetROINames());
 461       if (!mSlicerManagers[index]->GetVF().IsNull())
 462         selector.EnablePropagationCheckBox();
 463       if (selector.exec())
 464         {
 465           QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 466           reader.SetSelectedItems(selector.getSelectedItems());
 467           reader.SetImage(mSlicerManagers[index]->GetImage());
 468           if (selector.PropagationEnabled())
 469             reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 470           reader.Update();
 471           std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 472           for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 473                i!=contours.end();i++)
 474             AddContour(index,*i,selector.PropagationEnabled());
 475           QApplication::restoreOverrideCursor();
 476         }
 477     }
 478 }
 479 //------------------------------------------------------------------------------
 480
 481
 482 //------------------------------------------------------------------------------
 483 void vvMainWindow::ComputeDeformableRegistration()
 484 {
 485   if (mSlicerManagers.size() > 0)
 486     {
 487       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 488       vvDeformationDialog dialog(index,mSlicerManagers);
 489       if (dialog.exec())
 490         {
 491           std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 492           AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 493           WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 494         }
 495       else
 496         std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 497     }
 498   else QMessageBox::information(this, "Need to open image","You must open an image first.");
 499 }
 500 //------------------------------------------------------------------------------
 501
 502
 503 //------------------------------------------------------------------------------
 504 void vvMainWindow::WarpImage()
 505 {
 506   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 507   if (!mSlicerManagers[index]->GetVF().IsNull())
 508     {
 509       bool ok;
 510       int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 511                                          mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 512       if (ok)
 513         {
 514           WarpImage(mSlicerManagers[index],ref);
 515         }
 516     }
 517   else
 518     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 519 }
 520 //------------------------------------------------------------------------------
 521
 522
 523 //------------------------------------------------------------------------------
 524 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 525 {
 526   if (!selected_slicer->GetVF().IsNull())
 527     {
 528       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 529       QFileInfo info(selected_slicer->GetFileName().c_str());
 530       vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 531                        reference_phase,this);
 532       if (warp.ComputeWarpedImage())
 533         {
 534           AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 535           AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 536           AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 537           QApplication::restoreOverrideCursor();
 538         }
 539       else
 540         {
 541           QApplication::restoreOverrideCursor();
 542           QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 543         }
 544     }
 545   else
 546     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 547 }
 548 //------------------------------------------------------------------------------
 549
 550
 551 //------------------------------------------------------------------------------
 552 vvMainWindow::~vvMainWindow() {
 553   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
 554     {
 555       if (mSlicerManagers[i] != NULL)
 556         delete mSlicerManagers[i];
 557     }
 558 }
 559 //------------------------------------------------------------------------------
 560
 561
 562 //------------------------------------------------------------------------------
 563 void vvMainWindow::MergeImages() {
 564   QString Extensions = EXTENSIONS;
 565   Extensions += ";;All Files (*)";
 566   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 567   if (files.isEmpty())
 568     return;
 569   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 570   std::vector<std::string> vector;
 571
 572   unsigned int currentDim = 0;
 573   std::vector<double> currentSpacing;
 574   std::vector<int> currentSize;
 575   std::vector<double> currentOrigin;
 576
 577   for (int i = 0; i < files.size(); i++)
 578     {
 579       itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 580               files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 581       reader->SetFileName(files[i].toStdString().c_str());
 582       reader->ReadImageInformation();
 583       if (reader)        {
 584           //NOViewWidget->hide();
 585           //NEViewWidget->hide();
 586           //SOViewWidget->hide();
 587           //SEViewWidget->hide();
 588           if (i == 0)
 589               currentDim = reader->GetNumberOfDimensions();
 590           bool IsOk = true;
 591           for (unsigned int j = 0;j < currentDim; j++)
 592           {
 593               if (i == 0)
 594               {
 595                   if (j == 0)
 596                   {
 597                       currentSpacing.resize(currentDim);
 598                       currentSize.resize(currentDim);
 599                       currentOrigin.resize(currentDim);
 600                   }
 601                   currentOrigin[j] = reader->GetOrigin(j);
 602                   currentSpacing[j] = reader->GetSpacing(j);
 603                   currentSize[j] = reader->GetDimensions(j);
 604               }
 605               else if (currentDim != reader->GetNumberOfDimensions()
 606                       || currentSpacing[j] != reader->GetSpacing(j)
 607                       || currentSize[j] != (int)reader->GetDimensions(j)
 608                       || currentOrigin[j] != reader->GetOrigin(j))
 609               {
 610                   QString error = "Cannot read file (too different from others ";
 611                   error += files[i].toStdString().c_str();
 612                   QMessageBox::information(this,tr("Reading problem"),error);
 613                   IsOk = false;
 614                   break;
 615               }
 616           }
 617           if (IsOk)
 618               vector.push_back(files[i].toStdString());
 619       }
 620     }
 621   if (vector.size() > 0)
 622     LoadImages(vector, MERGED);
 623 }
 624 //------------------------------------------------------------------------------
 625
 626
 627 //------------------------------------------------------------------------------
 628 void vvMainWindow::MergeImagesWithTime() {
 629   QString Extensions = EXTENSIONS;
 630   Extensions += ";;All Files (*)";
 631   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 632   if (files.isEmpty())
 633     return;
 634   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 635   std::vector<std::string> vector;
 636
 637   unsigned int currentDim = 0;
 638   std::vector<double> currentSpacing;
 639   std::vector<int> currentSize;
 640   std::vector<double> currentOrigin;
 641
 642   for (int i = 0; i < files.size(); i++)
 643     {
 644       itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 645                                                                             files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 646       if (reader)
 647         {
 648           reader->SetFileName(files[i].toStdString().c_str());
 649           reader->ReadImageInformation();
 650           if (i == 0)
 651             currentDim = reader->GetNumberOfDimensions();
 652           bool IsOk = true;
 653           for (unsigned int j = 0;j < currentDim; j++)
 654             {
 655               if (i == 0)
 656                 {
 657                   if (j == 0)
 658                     {
 659                       currentSpacing.resize(currentDim);
 660                       currentSize.resize(currentDim);
 661                       currentOrigin.resize(currentDim);
 662                     }
 663                   currentOrigin[j] = reader->GetOrigin(j);
 664                   currentSpacing[j] = reader->GetSpacing(j);
 665                   currentSize[j] = reader->GetDimensions(j);
 666                 }
 667               else if (currentDim != reader->GetNumberOfDimensions()
 668                        || currentSpacing[j] != reader->GetSpacing(j)
 669                        || currentSize[j] != (int)reader->GetDimensions(j)
 670                        || currentOrigin[j] != reader->GetOrigin(j))
 671                 {
 672                   QString error = "Cannot read file (too different from others ";
 673                   error += files[i].toStdString().c_str();
 674                   QMessageBox::information(this,tr("Reading problem"),error);
 675                   IsOk = false;
 676                   break;
 677                 }
 678             }
 679           if (IsOk)
 680             vector.push_back(files[i].toStdString());
 681         }
 682       else
 683         {
 684           QString error = "Cannot read file info for ";
 685           error += files[i].toStdString().c_str();
 686           error += "\n";
 687           error += "Maybe you're trying to open an image in an unsupported format?\n";
 688           QMessageBox::information(this,tr("Reading problem"),error);
 689         }
 690     }
 691   sort(vector.begin(),vector.end());
 692   if (vector.size() > 1)
 693     LoadImages(vector, MERGEDWITHTIME);
 694   else
 695     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.");
 696 }
 697 //------------------------------------------------------------------------------
 698
 699
 700 //------------------------------------------------------------------------------
 701 void vvMainWindow::OpenDicom() {
 702   std::vector<std::string> files;
 703
 704 #ifdef CLITK_VV_USE_BDCM
 705   bool r = bdcm::OpenDicomFilesSelectorDialog(files,
 706                                               "DicomFilesSelectorDialog test",
 707                                               0,0,800,800,1);
 708
 709   if (r) {
 710     std::cout << "$$$$ main : user clicked 'OK' $$$$"<<std::endl;
 711     std::cout << "$$$$ selected files : "<<std::endl;
 712     std::vector<std::string>::iterator i;
 713     for (i=files.begin();i!=files.end();++i) {
 714       std::cout << *i << std::endl;
 715     }
 716     std::cout << "$$$$ "<<std::endl;
 717
 718     LoadImages(files,DICOM);
 719   }
 720   else {
 721     std::cout << "$$$$ main : user clicked 'CANCEL' $$$$"<<std::endl;
 722   }
 723 #else
 724   std::cout << "dicomSeriesSelector " << std::endl;
 725   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 726     files = *(dicomSeriesSelector->GetFilenames());
 727     LoadImages(files,DICOM);
 728   }
 729 #endif
 730
 731 }
 732 //------------------------------------------------------------------------------
 733
 734 //------------------------------------------------------------------------------
 735 void vvMainWindow::OpenImages() {
 736   QString Extensions = EXTENSIONS;
 737   Extensions += ";;All Files (*)";
 738
 739   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 740   if (files.isEmpty())
 741     return;
 742   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 743   std::vector<std::string> vector;
 744   for (int i = 0; i < files.size(); i++)
 745     vector.push_back(files[i].toStdString());
 746   LoadImages(vector, IMAGE);
 747 }
 748 //------------------------------------------------------------------------------
 749 void vvMainWindow::OpenRecentImage()
 750 {
 751   QAction * caller = qobject_cast<QAction*>(sender());
 752   std::vector<std::string> images;
 753   images.push_back(caller->text().toStdString());
 754   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 755   LoadImages(images,IMAGE);
 756 }
 757 //------------------------------------------------------------------------------
 758
 759
 760 //------------------------------------------------------------------------------
 761 void vvMainWindow::OpenImageWithTime() {
 762   QString Extensions = EXTENSIONS;
 763   Extensions += ";;All Files (*)";
 764
 765   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 766   if (files.isEmpty())
 767     return;
 768   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 769   std::vector<std::string> vector;
 770   for (int i = 0; i < files.size(); i++)
 771     {
 772       vector.push_back(files[i].toStdString());
 773     }
 774   LoadImages(vector, IMAGEWITHTIME);
 775 }
 776 //------------------------------------------------------------------------------
 777
 778
 779 //------------------------------------------------------------------------------
 780 void vvMainWindow::LoadImages(std::vector<std::string> files, LoadedImageType filetype) {
 781   //Separate the way to open images and dicoms
 782   int fileSize;
 783   if (filetype == IMAGE || filetype == IMAGEWITHTIME)
 784     fileSize = files.size();
 785   else
 786     fileSize = 1;
 787
 788   //Only add to the list of recently opened files when a single file is opened,
 789   //to avoid polluting the list of recently opened files
 790   if (files.size() == 1)
 791     {
 792       QFileInfo finfo=tr(files[0].c_str());
 793       AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 794     }
 795   //init the progress events
 796   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 797   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 798   qApp->processEvents();
 799
 800   int numberofsuccesulreads=0;
 801   //open images as 1 or multiples
 802   for (int i = 0; i < fileSize; i++) {
 803
 804     progress.Update("Opening " + files[i]);
 805     progress.SetProgress(i,fileSize);
 806     qApp->processEvents();
 807
 808     //read the image and put it in mSlicerManagers
 809     vvSlicerManager* imageManager = new vvSlicerManager(4);
 810     qApp->processEvents();
 811
 812     bool SetImageSucceed=false;
 813
 814     // Change filename if an image with the same already exist
 815     //    DD(files[i]);
 816     int number=0;
 817     for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
 818       vvSlicerManager * v = mSlicerManagers[l];
 819       //      DD(v->GetBaseFileName());
 820       // DD(v->GetFileName());
 821       if (v->GetBaseFileName() ==
 822           vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(files[i]))) {
 823         number = std::max(number, v->GetBaseFileNameNumber()+1);
 824       }
 825     }
 826
 827
 828     if (filetype == IMAGE || filetype == IMAGEWITHTIME)
 829       SetImageSucceed = imageManager->SetImage(files[i],filetype, number);
 830     else
 831       {
 832         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 833       }
 834     if (SetImageSucceed == false)
 835       {
 836         QApplication::restoreOverrideCursor();
 837         QString error = "Cannot open file \n";
 838         error += imageManager->GetLastError().c_str();
 839         QMessageBox::information(this,tr("Reading problem"),error);
 840         delete imageManager;
 841       }
 842     else
 843       {
 844         mSlicerManagers.push_back(imageManager);
 845
 846         //create an item in the tree with good settings
 847         QTreeWidgetItem *item = new QTreeWidgetItem();
 848         item->setData(0,Qt::UserRole,files[i].c_str());
 849         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 850         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 851         qApp->processEvents();
 852
 853         //Create the buttons for reload and close
 854         qApp->processEvents();
 855         QTreePushButton* cButton = new QTreePushButton;
 856         cButton->setItem(item);
 857         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 858         cButton->setToolTip(tr("close image"));
 859         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 860         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 861                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 862
 863         QTreePushButton* rButton = new QTreePushButton;
 864         rButton->setItem(item);
 865         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 866         rButton->setToolTip(tr("reload image"));
 867         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 868         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 869                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 870
 871         DataTree->addTopLevelItem(item);
 872         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 873         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 874
 875         //set the id of the image
 876         QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 877         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 878         mSlicerManagers.back()->SetId(id.toStdString());
 879
 880         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 881
 882         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 883                 this,SLOT(CurrentImageChanged(std::string)));
 884         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 885              this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 886         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 887                 this, SLOT(VectorChanged(int,double,double,double, double)));
 888         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 889                 this, SLOT(OverlayChanged(int,double,double)));
 890         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 891                 this, SLOT(FusionChanged(int,double)));
 892         connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
 893                 this,SLOT(WindowsChanged(int, int, int)));
 894         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
 895                 this,SLOT(WindowLevelChanged(double, double, int, int)));
 896         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 897                 this,SLOT(UpdateSlice(int,int)));
 898         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 899                 this,SLOT(UpdateTSlice(int, int)));
 900         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 901                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 902         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 903                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 904         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 905                 this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 906         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 907         InitSlicers();
 908         numberofsuccesulreads++;
 909       }
 910   }
 911   if (numberofsuccesulreads)
 912     {
 913       NOViewWidget->show();
 914       NEViewWidget->show();
 915       SOViewWidget->show();
 916       SEViewWidget->show();
 917       UpdateTree();
 918       InitDisplay();
 919       ShowLastImage();
 920     }
 921   QApplication::restoreOverrideCursor();
 922
 923   // Try to guess default WindowLevel
 924   double range[2];
 925   mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 926   // DD(range[0]);
 927   //   DD(range[1]);
 928   if ((range[0] == 0) && (range[1] == 1)) {
 929     presetComboBox->setCurrentIndex(5);// binary
 930   }
 931   else {
 932     // TODO
 933   }
 934 }
 935 //------------------------------------------------------------------------------
 936
 937 //------------------------------------------------------------------------------
 938 void vvMainWindow::UpdateTree() {
 939   DataTree->resizeColumnToContents(COLUMN_TREE);
 940   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 941   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 942   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 943   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 944   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 945   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 946   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 947 }
 948 //------------------------------------------------------------------------------
 949
 950 //------------------------------------------------------------------------------
 951 void vvMainWindow::CurrentImageChanged(std::string id) {
 952   int selected = 0;
 953   for (int i = 0; i < DataTree->topLevelItemCount(); i++)
 954     {
 955       if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id)
 956         {
 957           selected = i;
 958         }
 959       else
 960         {
 961           DataTree->topLevelItem(i)->setSelected(0);
 962         }
 963       for (int child = 0; child < DataTree->topLevelItem(i)->childCount();child++)
 964         DataTree->topLevelItem(i)->child(child)->setSelected(0);
 965
 966     }
 967   DataTree->topLevelItem(selected)->setSelected(1);
 968 }
 969 //------------------------------------------------------------------------------
 970
 971 //------------------------------------------------------------------------------
 972 void vvMainWindow::ImageInfoChanged() {
 973   contextActions[7]->setEnabled(1);
 974   contextActions[6]->setEnabled(1);
 975   actionSave_As->setEnabled(1);
 976   actionAdd_VF_to_current_Image->setEnabled(1);
 977   actionAdd_fusion_image->setEnabled(1);
 978   actionNorth_East_Window->setEnabled(1);
 979   actionNorth_West_Window->setEnabled(1);
 980   actionSouth_East_Window->setEnabled(1);
 981   actionSouth_West_Window->setEnabled(1);
 982   inverseButton->setEnabled(1);
 983
 984   goToCursorPushButton->setEnabled(1);
 985
 986   if (DataTree->selectedItems().size()) {
 987     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 988
 989     colorMapComboBox->setEnabled(1);
 990     for (int i = 0; i < DataTree->topLevelItem(index)->childCount();i++)
 991       {
 992         if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
 993             DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion")
 994           {
 995             colorMapComboBox->setEnabled(0);
 996             break;
 997           }
 998       }
 999
1000     std::vector<double> origin;
1001     std::vector<double> inputSpacing;
1002     std::vector<int> inputSize;
1003     std::vector<double> sizeMM;
1004     int dimension=0;
1005     QString pixelType;
1006     QString inputSizeInBytes;
1007     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1008
1009     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1)
1010       {
1011         playButton->setEnabled(1);
1012         frameRateLabel->setEnabled(1);
1013         frameRateSpinBox->setEnabled(1);
1014       }
1015     else
1016       {
1017         playButton->setEnabled(0);
1018         frameRateLabel->setEnabled(0);
1019         frameRateSpinBox->setEnabled(0);
1020       }
1021
1022     //read image header
1023     int NPixel = 1;
1024
1025     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0])
1026       {
1027         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1028         dimension = imageSelected->GetNumberOfDimensions();
1029         origin.resize(dimension);
1030         inputSpacing.resize(dimension);
1031         inputSize.resize(dimension);
1032         sizeMM.resize(dimension);
1033         pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
1034         for (int i = 0;i < dimension;i++)
1035           {
1036             origin[i] = imageSelected->GetOrigin()[i];
1037             inputSpacing[i] = imageSelected->GetSpacing()[i];
1038             inputSize[i] = imageSelected->GetSize()[i];
1039             sizeMM[i] = inputSize[i]*inputSpacing[i];
1040             NPixel *= inputSize[i];
1041           }
1042         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1043       }
1044     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector")
1045       {
1046         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1047         dimension = imageSelected->GetNumberOfDimensions();
1048         origin.resize(dimension);
1049         inputSpacing.resize(dimension);
1050         inputSize.resize(dimension);
1051         sizeMM.resize(dimension);
1052         pixelType = mSlicerManagers[index]->GetVF()->GetScalarTypeAsString().c_str();
1053         for (int i = 0;i < dimension;i++)
1054           {
1055             origin[i] = imageSelected->GetOrigin()[i];
1056             inputSpacing[i] = imageSelected->GetSpacing()[i];
1057             inputSize[i] = imageSelected->GetSize()[i];
1058             sizeMM[i] = inputSize[i]*inputSpacing[i];
1059             NPixel *= inputSize[i];
1060           }
1061         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1062       }
1063     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay")
1064       {
1065         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1066         dimension = imageSelected->GetNumberOfDimensions();
1067         origin.resize(dimension);
1068         inputSpacing.resize(dimension);
1069         inputSize.resize(dimension);
1070         sizeMM.resize(dimension);
1071         pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
1072         for (int i = 0;i < dimension;i++)
1073           {
1074             origin[i] = imageSelected->GetOrigin()[i];
1075             inputSpacing[i] = imageSelected->GetSpacing()[i];
1076             inputSize[i] = imageSelected->GetSize()[i];
1077             sizeMM[i] = inputSize[i]*inputSpacing[i];
1078             NPixel *= inputSize[i];
1079           }
1080         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1081       }
1082     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion")
1083       {
1084         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1085         dimension = imageSelected->GetNumberOfDimensions();
1086         origin.resize(dimension);
1087         inputSpacing.resize(dimension);
1088         inputSize.resize(dimension);
1089         sizeMM.resize(dimension);
1090         pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
1091         for (int i = 0;i < dimension;i++)
1092           {
1093             origin[i] = imageSelected->GetOrigin()[i];
1094             inputSpacing[i] = imageSelected->GetSpacing()[i];
1095             inputSize[i] = imageSelected->GetSize()[i];
1096             sizeMM[i] = inputSize[i]*inputSpacing[i];
1097             NPixel *= inputSize[i];
1098           }
1099         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1100       }
1101
1102     QString dim = QString::number(dimension) + " (";
1103     dim += pixelType + ")";
1104
1105     infoPanel->setFileName(image);
1106     infoPanel->setDimension(dim);
1107     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1108     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1109     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1110     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1111     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1112
1113     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1114                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1115     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1116     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1117
1118     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1119     for (int i = 0; i < 4;i++)
1120       {
1121         if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3)
1122           {
1123             mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1124             break;
1125           }
1126       }
1127     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1128     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1129     // DD(mSlicerManagers[index]->GetColorMap());
1130     // DD(mSlicerManagers[index]->GetPreset());
1131     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1132     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1133
1134     infoPanel->setFileName(image);
1135     infoPanel->setDimension(dim);
1136     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1137     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1138     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1139     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1140     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1141
1142     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1143                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1144     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1145     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1146
1147     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1148     for (int i = 0; i < 4;i++)
1149       {
1150         if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3)
1151           {
1152             mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1153             break;
1154           }
1155       }
1156     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1157     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1158     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1159     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1160
1161     if (mSlicerManagers[index]->GetSlicer(0)->GetVF())
1162       {
1163         overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1164         overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1165                                     mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1166                                     mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1167       }
1168     else
1169       {
1170         overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1171         overlayPanel->getVFProperty(-1,-1,-1);
1172       }
1173     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1174       {
1175         overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1176         overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1177       }
1178     else
1179       {
1180         overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1181         overlayPanel->getOverlayProperty(-1);
1182       }
1183     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion())
1184       {
1185         overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1186         overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1187                                         mSlicerManagers[index]->GetFusionColorMap(),
1188                                         mSlicerManagers[index]->GetFusionWindow(),
1189                                         mSlicerManagers[index]->GetFusionLevel());
1190       }
1191     else
1192       {
1193         overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1194         overlayPanel->getFusionProperty(-1, -1,-1,-1);
1195       }
1196   }
1197 }
1198 //------------------------------------------------------------------------------
1199
1200 //------------------------------------------------------------------------------
1201 void vvMainWindow::ShowDocumentation() {
1202   documentation->show();
1203 }
1204 //------------------------------------------------------------------------------
1205 void vvMainWindow::ShowHelpDialog() {
1206   help_dialog->show();
1207 }
1208 //------------------------------------------------------------------------------
1209
1210 //------------------------------------------------------------------------------
1211 void vvMainWindow::ChangeViewMode() {
1212   QListIterator<int> it0(splitter_3->sizes());
1213   QListIterator<int> it1(splitter_3->sizes());
1214   int max0 = 0;
1215   int max1 = 1;
1216   while (it0.hasNext())
1217     {
1218       max0 += it0.next();
1219     }
1220   while (it1.hasNext())
1221     {
1222       max1 += it1.next();
1223     }
1224   QList<int> size0;
1225   QList<int> size1;
1226   if (viewMode == 1)
1227     {
1228       viewMode = 0;
1229       size0.push_back(max0);
1230       size0.push_back(0);
1231       size1.push_back(max1);
1232       size1.push_back(0);
1233       splitter_3->setSizes(size0);
1234       OSplitter->setSizes(size1);
1235       DataTree->setColumnHidden(2,1);
1236       DataTree->setColumnHidden(3,1);
1237       DataTree->setColumnHidden(4,1);
1238     }
1239   else
1240     {
1241       viewMode = 1;
1242       size0.push_back(int(max0/2));
1243       size0.push_back(int(max0/2));
1244       size1.push_back(int(max1/2));
1245       size1.push_back(int(max1/2));
1246       splitter_3->setSizes(size0);
1247       OSplitter->setSizes(size1);
1248       DataTree->setColumnHidden(2,0);
1249       DataTree->setColumnHidden(3,0);
1250       DataTree->setColumnHidden(4,0);
1251     }
1252 }
1253 //------------------------------------------------------------------------------
1254
1255 //------------------------------------------------------------------------------
1256 QString vvMainWindow::GetSizeInBytes(unsigned long size) {
1257   QString result = "";// QString::number(size);
1258   //result += " bytes (";
1259   if (size > 1000000000)
1260     {
1261       size /= 1000000000;
1262       result += QString::number(size);
1263       result += "Gb";//)";
1264     }
1265   else if (size > 1000000)
1266     {
1267       size /= 1000000;
1268       result += QString::number(size);
1269       result += "Mb";//)";
1270     }
1271   else if (size > 1000)
1272     {
1273       size /= 1000;
1274       result += QString::number(size);
1275       result += "kb";//)";
1276     }
1277   return result;
1278 }
1279 //------------------------------------------------------------------------------
1280
1281 //------------------------------------------------------------------------------
1282 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble) {
1283   QString result;
1284   for (unsigned int i= 0; i < vectorDouble.size(); i++)
1285     {
1286       if (i != 0)
1287         result += " ";
1288       result += QString::number(vectorDouble[i]);
1289     }
1290   return result;
1291 }
1292 //------------------------------------------------------------------------------
1293
1294 //------------------------------------------------------------------------------
1295 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt) {
1296   QString result;
1297   for (unsigned int i= 0; i < vectorInt.size(); i++)
1298     {
1299       if (i != 0)
1300         result += " ";
1301       result += QString::number(vectorInt[i]);
1302     }
1303   return result;
1304 }
1305 //------------------------------------------------------------------------------
1306
1307 //------------------------------------------------------------------------------
1308 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item) {
1309   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1310   for (int i = 0; i < DataTree->topLevelItemCount(); i++)
1311     {
1312       if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1313         return i;
1314     }
1315   return -1;
1316 }
1317 //------------------------------------------------------------------------------
1318
1319 //------------------------------------------------------------------------------
1320 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm) {
1321     QString id = sm->GetId().c_str();
1322     for (int i = 0; i < DataTree->topLevelItemCount(); i++)
1323     {
1324         if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1325             return DataTree->topLevelItem(i);
1326     }
1327     return NULL;
1328 }
1329 //------------------------------------------------------------------------------
1330
1331 //------------------------------------------------------------------------------
1332 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clicked_item, int column) {
1333   int index = GetSlicerIndexFromItem(clicked_item);
1334   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1335     return;
1336   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
1337     {
1338      //Trick to avoid redoing twice the job for a key (sr)
1339       mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()-> GetInteractor()->SetKeySym("Crap");
1340
1341       QTreeWidgetItem* current_row=DataTree->topLevelItem(i);
1342       if (DataTree->topLevelItem(index) == current_row)
1343         {
1344           vvSlicer* clicked_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1345           if (current_row == clicked_item)
1346             {
1347               //If we just activated a slicer
1348               if (current_row->data(column,Qt::CheckStateRole).toInt() > 0)
1349                 {
1350                   mSlicerManagers[i]->UpdateSlicer(column-1,clicked_item->data(column,Qt::CheckStateRole).toInt());
1351                   mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1352                   DisplaySliders(i,column-1);
1353                   std::map<std::string,int> overlay_counts;
1354                   for (int child = 0; child < current_row->childCount(); child++)
1355                     {
1356                       std::string overlay_type =
1357                         current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1358                       overlay_counts[overlay_type]++;
1359                       current_row->child(child)->setData(column,Qt::CheckStateRole,
1360                                                          current_row->data(column,Qt::CheckStateRole));
1361                       clicked_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,true);
1362                     }
1363                 }
1364               else //We don't allow simply desactivating a slicer
1365                 {
1366                   clicked_item->setData(column,Qt::CheckStateRole,2);
1367                   return;
1368                 }
1369             }
1370           //if we clicked on the vector(or overlay) and not the image
1371           else
1372             {
1373               if (clicked_item->data(column,Qt::CheckStateRole).toInt())
1374                 {
1375                   current_row->setData(column,Qt::CheckStateRole,2);
1376                   mSlicerManagers[i]->UpdateSlicer(column-1,2);
1377                   mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1378                   DisplaySliders(i,column-1);
1379                 }
1380               int vis = clicked_item->data(column,Qt::CheckStateRole).toInt();
1381               std::string overlay_type = clicked_item->data(1,Qt::UserRole).toString().toStdString();
1382               int overlay_index=0;
1383               for (int child = 0; child < current_row->childCount(); child++)
1384                 {
1385                   if (current_row->child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1386                     overlay_index++;
1387                   if (current_row->child(child) == clicked_item) break;
1388                 }
1389               clicked_slicer->SetActorVisibility(
1390                                                  clicked_item->data(1,Qt::UserRole).toString().toStdString(), overlay_index-1,vis);
1391             }
1392         }
1393       else if (current_row->data(column,Qt::CheckStateRole).toInt() > 0)
1394         {
1395           current_row->setData(column,Qt::CheckStateRole,0);
1396           mSlicerManagers[i]->UpdateSlicer(column-1,0);
1397           std::map<std::string,int> overlay_counts;
1398           for (int child = 0; child < current_row->childCount(); child++)
1399             {
1400               std::string overlay_type =
1401                 current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1402               overlay_counts[overlay_type]++;
1403               current_row->child(child)->setData(column,Qt::CheckStateRole,0);
1404               vvSlicer * current_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1405               current_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,false);
1406             }
1407         }
1408       //mSlicerManagers[i]->SetColorMap(-1);
1409       mSlicerManagers[i]->SetColorMap();
1410     }
1411   mSlicerManagers[index]->GetSlicer(column-1)->Render();
1412 }
1413 //------------------------------------------------------------------------------
1414
1415 void vvMainWindow::InitSlicers()
1416 {
1417   if (mSlicerManagers.size())
1418     {
1419       mSlicerManagers.back()->GenerateDefaultLookupTable();
1420
1421       mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1422       mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1423       mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1424       mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1425     }
1426 }
1427
1428 //------------------------------------------------------------------------------
1429 void vvMainWindow::InitDisplay() {
1430   if (mSlicerManagers.size())
1431     {
1432       //BE CAREFUL : this is absolutely necessary to set the interactor style
1433       //in order to have the same style instanciation for all SlicerManagers in
1434       // a same window
1435       for (int j = 0; j < 4; j++)
1436         {
1437           vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1438           style->SetAutoAdjustCameraClippingRange(1);
1439           bool AlreadySelected = false;
1440           for (int i = 0; i < DataTree->topLevelItemCount(); i++)
1441             {
1442               mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1443
1444               //select the image only if previous are not selected
1445               if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1)
1446                 {
1447                   mSlicerManagers[i]->UpdateSlicer(j,1);
1448                   AlreadySelected = true;
1449                 }
1450               else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected)
1451                 {
1452                   if (DataTree->selectedItems().size() == 0)
1453                     DataTree->topLevelItem(i)->setSelected(1);
1454                   DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1455                   mSlicerManagers[i]->UpdateSlicer(j,1);
1456                   DisplaySliders(i,j);
1457                 }
1458               else
1459                 {
1460                   DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1461                   mSlicerManagers[i]->UpdateSlicer(j,0);
1462                 }
1463             }
1464           style->Delete();
1465         }
1466     }
1467 }
1468 //------------------------------------------------------------------------------
1469
1470 //------------------------------------------------------------------------------
1471 void vvMainWindow::DisplaySliders(int slicer, int window) {
1472   int range[2];
1473   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1474   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1475
1476   int tRange[2];
1477   tRange[0] = 0;
1478   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1479   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1480   bool showHorizontal = false;
1481   bool showVertical = false;
1482   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1483       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1484           && mSlicerManagers[slicer]->GetType() != IMAGEWITHTIME
1485           && mSlicerManagers[slicer]->GetType() != MERGEDWITHTIME))
1486     showVertical = true;
1487   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1488       || mSlicerManagers[slicer]->GetType() == IMAGEWITHTIME
1489       || mSlicerManagers[slicer]->GetType() == MERGEDWITHTIME)
1490     showHorizontal = true;
1491
1492   if (showVertical)
1493     verticalSliders[window]->show();
1494   else
1495     verticalSliders[window]->hide();
1496   verticalSliders[window]->setRange(range[0],range[1]);
1497   verticalSliders[window]->setValue(position);
1498
1499   if (showHorizontal)
1500     horizontalSliders[window]->show();
1501   else
1502     horizontalSliders[window]->hide();
1503   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1504   horizontalSliders[window]->setValue(tPosition);
1505 }
1506 //------------------------------------------------------------------------------
1507
1508 //------------------------------------------------------------------------------
1509 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column) {
1510   int index = GetSlicerIndexFromItem(item);
1511
1512   if (DataTree->topLevelItem(index) != item)
1513     {
1514       QString warning = "Do you really want to close the overlay : ";
1515       warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1516       QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1517                          warning, 0, this);
1518       msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1519       msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1520       if (msgBox.exec() == QMessageBox::AcceptRole)
1521         {
1522           std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1523           int overlay_index=0;
1524           for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1525             {
1526               if (DataTree->topLevelItem(index)->\
1527                   child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1528                 overlay_index++;
1529               if (DataTree->topLevelItem(index)->child(child) == item) break;
1530             }
1531           mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1532           mSlicerManagers[index]->SetColorMap(0);
1533           DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1534           mSlicerManagers[index]->Render();
1535         }
1536     }
1537   else if (DataTree->topLevelItemCount() <= 1)
1538     {
1539       QString warning = "Do you really want to close the image : ";
1540       warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1541       warning += "\nThis is the last image, you're about to close vv !!!";
1542       QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1543                          warning, 0, this);
1544       msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1545       msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1546       if (msgBox.exec() == QMessageBox::AcceptRole)
1547         {
1548           this->close();
1549         }
1550     }
1551   else
1552     {
1553       QString warning = "Do you really want to close the image : ";
1554       warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1555       QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1556                          warning, 0, this);
1557       msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1558       msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1559       if (msgBox.exec() == QMessageBox::AcceptRole)
1560         {
1561
1562           // Tell tools that we close an image
1563           emit AnImageIsBeingClosed(mSlicerManagers[index]);
1564
1565           std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1566           DataTree->takeTopLevelItem(index);
1567           for (int i = 0; i < index; i++)
1568             {
1569               Manageriter++;
1570             }
1571           linkPanel->removeImage(index);
1572           mSlicerManagers[index]->RemoveActors();
1573           delete mSlicerManagers[index];
1574           mSlicerManagers.erase(Manageriter);
1575
1576           //
1577           InitDisplay();
1578         }
1579     }
1580 }
1581 //------------------------------------------------------------------------------
1582
1583 //------------------------------------------------------------------------------
1584 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column) {
1585   // int index = GetSlicerIndexFromItem(item);
1586   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1587   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1588   //     mSlicerManagers[index]->ReloadVF();
1589   //   else
1590   //     mSlicerManagers[index]->Reload();
1591
1592   //   QApplication::restoreOverrideCursor();
1593   int index = GetSlicerIndexFromItem(item);
1594   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1595   QString role=item->data(1,Qt::UserRole).toString();
1596   if ( role == "vector")
1597     mSlicerManagers[index]->ReloadVF();
1598   else if (role == "overlay")
1599     mSlicerManagers[index]->ReloadOverlay();
1600   else if (role == "fusion")
1601     mSlicerManagers[index]->ReloadFusion();
1602   else
1603     mSlicerManagers[index]->Reload();
1604
1605   // Update view and info
1606   ImageInfoChanged();
1607   mSlicerManagers[index]->Render();
1608   QApplication::restoreOverrideCursor();
1609 }
1610 //------------------------------------------------------------------------------
1611
1612 // void vvMainWindow::CropImage()
1613 // {
1614 //   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1615 //   vvCropDialog crop(mSlicerManagers,index);
1616 //   if(crop.exec())
1617 //     AddImage(crop.GetOutput(),"cropped.mhd");
1618 // }
1619
1620 //------------------------------------------------------------------------------
1621 void vvMainWindow::SplitImage() {
1622   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1623   int dim = mSlicerManagers[index]->GetDimension();
1624   QString warning = "Do you really want to split the ";
1625   warning += QString::number(dim) + "D image ";
1626   warning += DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString() + " into ";
1627   warning += QString::number(mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetSize()[dim-1]) + " ";
1628   warning += QString::number(dim-1) + "D images.";
1629   QMessageBox msgBox(QMessageBox::Warning, tr("Split Image"),
1630                      warning, 0, this);
1631   msgBox.addButton(tr("Split"), QMessageBox::AcceptRole);
1632   msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1633   if (msgBox.exec() == QMessageBox::AcceptRole)
1634     {
1635       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1636       if (dim > 2)
1637         {
1638           std::string filename = DataTree->selectedItems()[0]->data(0,Qt::UserRole).toString().toStdString();
1639           int numberOfSlice = mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetSize()[dim-1];
1640           std::string path = itksys::SystemTools::GetFilenamePath(
1641                                                                   filename);
1642           path += "/";
1643           path += DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString().toStdString();
1644           path += "%03d";
1645           path += itksys::SystemTools::GetFilenameLastExtension(
1646                                                                 filename).c_str();
1647
1648           typedef itk::NumericSeriesFileNames NameGeneratorType;
1649           NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
1650           nameGenerator->SetSeriesFormat(path.c_str());
1651           nameGenerator->SetStartIndex(0);
1652           nameGenerator->SetEndIndex(numberOfSlice-1);
1653           nameGenerator->SetIncrementIndex(1);
1654
1655           for (int i = 0; i < numberOfSlice; i++)
1656             {
1657               vvSlicerManager* imageManager = new vvSlicerManager(4);
1658               imageManager->SetExtractedImage(nameGenerator->GetFileNames()[i],
1659                                               mSlicerManagers[index]->GetSlicer(0)->GetImage(), i);
1660               mSlicerManagers.push_back(imageManager);
1661
1662               //create an item in the tree with good settings
1663               QTreeWidgetItem *item = new QTreeWidgetItem();
1664               item->setData(0,Qt::UserRole,nameGenerator->GetFileNames()[i].c_str());
1665               std::string fileI = itksys::SystemTools::GetFilenameWithoutLastExtension(
1666                                                                                        nameGenerator->GetFileNames()[i]).c_str();
1667               item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileI.c_str());
1668               for (int j = 1; j <= 4; j++)
1669                 {
1670                   for (int i = 0; i < DataTree->topLevelItemCount(); i++)
1671                     {
1672                       DataTree->topLevelItem(i)->setData(j,Qt::CheckStateRole,0);
1673                     }
1674                   item->setData(j,Qt::CheckStateRole,2);
1675                 }
1676
1677               //Create the buttons for reload and close
1678               QTreePushButton* cButton = new QTreePushButton;
1679               cButton->setItem(item);
1680               cButton->setColumn(COLUMN_CLOSE_IMAGE);
1681               cButton->setToolTip(tr("close image"));
1682               cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1683               connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1684                       this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1685
1686               QTreePushButton* rButton = new QTreePushButton;
1687               rButton->setItem(item);
1688               rButton->setColumn(COLUMN_RELOAD_IMAGE);
1689               rButton->setToolTip(tr("reload image"));
1690               rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1691               rButton->setEnabled(false);
1692               connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1693                       this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1694
1695               DataTree->addTopLevelItem(item);
1696               DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1697               DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1698
1699               //set the id of the image
1700               QString id = nameGenerator->GetFileNames()[i].c_str() + QString::number(mSlicerManagers.size()-1);
1701               item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1702               mSlicerManagers.back()->SetId(id.toStdString());
1703               linkPanel->addImage(fileI, id.toStdString());
1704               connect(mSlicerManagers.back(),SIGNAL(currentImageChanged(std::string)),
1705                       this,SLOT(CurrentImageChanged(std::string)));
1706               connect(mSlicerManagers.back(),SIGNAL(
1707                                                     UpdatePosition(int, double, double, double, double, double, double, double)),this,
1708                       SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
1709               connect(mSlicerManagers.back(),SIGNAL(UpdateVector(int, double, double, double, double)),
1710                       this, SLOT(VectorChanged(int,double,double,double, double)));
1711               connect(mSlicerManagers.back(),SIGNAL(UpdateOverlay(int, double, double)),
1712                       this, SLOT(OverlayChanged(int,double,double)));
1713               connect(mSlicerManagers.back(),SIGNAL(UpdateFusion(int, double)),
1714                       this, SLOT(FusionChanged(int,double)));
1715               connect(mSlicerManagers.back(),SIGNAL(UpdateWindows(int, int, int)),
1716                       this,SLOT(WindowsChanged(int, int, int)));
1717               connect(mSlicerManagers.back(),SIGNAL(WindowLevelChanged(double, double,int, int)),
1718                       this,SLOT(WindowLevelChanged(double, double, int, int)));
1719               connect(mSlicerManagers.back(),SIGNAL(UpdateSlice(int,int)),
1720                       this,SLOT(UpdateSlice(int,int)));
1721               connect(mSlicerManagers.back(),SIGNAL(UpdateTSlice(int, int)),
1722                       this,SLOT(UpdateTSlice(int, int)));
1723               connect(mSlicerManagers.back(),SIGNAL(UpdateSliceRange(int,int,int,int,int)),
1724                       this,SLOT(UpdateSliceRange(int,int,int,int,int)));
1725               connect(mSlicerManagers.back(),SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
1726                       this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
1727               connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
1728               UpdateTree();
1729               qApp->processEvents();
1730               InitSlicers();
1731               InitDisplay();
1732               qApp->processEvents();
1733             }
1734           QApplication::restoreOverrideCursor();
1735         }
1736       else
1737         {
1738           QApplication::restoreOverrideCursor();
1739           QString error = "Cannot split file (dimensions must be greater than 2) ";
1740           QMessageBox::information(this,tr("Splitting problem"),error);
1741         }
1742     }
1743 }
1744 //------------------------------------------------------------------------------
1745
1746 //------------------------------------------------------------------------------
1747 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value) {
1748   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1749 }
1750 //------------------------------------------------------------------------------
1751
1752 //------------------------------------------------------------------------------
1753 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value) {
1754   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1755 }
1756 //------------------------------------------------------------------------------
1757
1758 //------------------------------------------------------------------------------
1759 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef) {
1760   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1761 }
1762 //------------------------------------------------------------------------------
1763
1764 //------------------------------------------------------------------------------
1765 void vvMainWindow::FusionChanged(int visibility, double value) {
1766   overlayPanel->getCurrentFusionInfo(visibility,value);
1767 }
1768 //------------------------------------------------------------------------------
1769
1770 //------------------------------------------------------------------------------
1771 void vvMainWindow::WindowsChanged(int window, int view, int slice) {
1772   infoPanel->setViews(window, view, slice);
1773 }
1774 //------------------------------------------------------------------------------
1775
1776 //------------------------------------------------------------------------------
1777 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap) {
1778   windowSpinBox->setValue(window);
1779   levelSpinBox->setValue(level);
1780   colorMapComboBox->setCurrentIndex(colormap);
1781   presetComboBox->setCurrentIndex(preset);
1782 }
1783 //------------------------------------------------------------------------------
1784
1785 //------------------------------------------------------------------------------
1786 void vvMainWindow::WindowLevelEdited() {
1787   presetComboBox->setCurrentIndex(6);
1788   UpdateWindowLevel();
1789 }
1790 //------------------------------------------------------------------------------
1791
1792 //------------------------------------------------------------------------------
1793 void vvMainWindow::UpdateWindowLevel() {
1794   if (DataTree->selectedItems().size())
1795     {
1796       if (presetComboBox->currentIndex() == 7) //For ventilation
1797         colorMapComboBox->setCurrentIndex(5);
1798       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1799       mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1800       mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1801       mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1802       mSlicerManagers[index]->Render();
1803     }
1804 }
1805 //------------------------------------------------------------------------------
1806
1807 //------------------------------------------------------------------------------
1808 void vvMainWindow::UpdateColorMap() {
1809   if (DataTree->selectedItems().size())
1810     {
1811       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1812       mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1813       mSlicerManagers[index]->Render();
1814     }
1815 }
1816 //------------------------------------------------------------------------------
1817 void vvMainWindow::SwitchWindowLevel() {
1818   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1819   int window = mSlicerManagers[index]->GetColorWindow();
1820   presetComboBox->setCurrentIndex(6);
1821   windowSpinBox->setValue(-window);
1822   UpdateWindowLevel();
1823 }
1824 //------------------------------------------------------------------------------
1825
1826 //------------------------------------------------------------------------------
1827 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps) {
1828   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
1829     {
1830       if (mSlicerManagers[i]->GetId() == id)
1831         {
1832           //mSlicerManagers[i]->SetTSlice(temps);
1833           mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1834           mSlicerManagers[i]->UpdateViews(0,slicer);
1835           break;
1836         }
1837     }
1838 }
1839 //------------------------------------------------------------------------------
1840
1841 //------------------------------------------------------------------------------
1842 void vvMainWindow::ShowContextMenu(QPoint point) {
1843   if (!DataTree->selectedItems().size())
1844     {
1845       contextActions[1]->setEnabled(0);
1846       contextActions[2]->setEnabled(0);
1847       contextActions[3]->setEnabled(0);
1848       contextActions[4]->setEnabled(0);
1849       contextActions[5]->setEnabled(0);
1850       contextActions[6]->setEnabled(0);
1851       contextActions[7]->setEnabled(0);
1852     }
1853   else
1854     {
1855       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1856       contextActions[1]->setEnabled(1);
1857       contextActions[2]->setEnabled(
1858                                     DataTree->itemWidget(DataTree->selectedItems()[0],
1859                                                          COLUMN_RELOAD_IMAGE)->isEnabled());
1860       contextActions[3]->setEnabled(1);
1861       contextActions[5]->setEnabled(1);
1862       contextActions[6]->setEnabled(1);
1863       contextActions[7]->setEnabled(1);
1864
1865       if (mSlicerManagers[index]->GetDimension() < 3)
1866         contextActions[4]->setEnabled(0);
1867       else
1868         contextActions[4]->setEnabled(1);
1869     }
1870   contextMenu.exec(QCursor::pos());
1871 }
1872 //------------------------------------------------------------------------------
1873
1874 //------------------------------------------------------------------------------
1875 void vvMainWindow::CloseImage() {
1876   CloseImage(DataTree->selectedItems()[0],0);
1877 }
1878 //------------------------------------------------------------------------------
1879
1880 //------------------------------------------------------------------------------
1881 void vvMainWindow::ReloadImage() {
1882   ReloadImage(DataTree->selectedItems()[0],0);
1883 }
1884 //------------------------------------------------------------------------------
1885
1886 //------------------------------------------------------------------------------
1887 void vvMainWindow::SelectOverlayImage() {
1888   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1889
1890   //check if one overlay image is added
1891   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1892     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay")
1893       {
1894         QString error = "Cannot add more than one compared image\n";
1895         error += "Please remove first ";
1896         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1897         QMessageBox::information(this,tr("Problem adding compared image !"),error);
1898         return;
1899       }
1900
1901   QString Extensions = EXTENSIONS;
1902   Extensions += ";;All Files (*)";
1903   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1904   if (!file.isEmpty())
1905     AddOverlayImage(index,file);
1906 }
1907 //------------------------------------------------------------------------------
1908
1909 //------------------------------------------------------------------------------
1910 void vvMainWindow::AddOverlayImage(int index, QString file) {
1911
1912   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1913   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1914                                                                         file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1915   reader->SetFileName(file.toStdString().c_str());
1916   reader->ReadImageInformation();
1917   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1918   int dimension = reader->GetNumberOfDimensions();
1919   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1920   vvProgressDialog progress("Opening " + file.toStdString());
1921   qApp->processEvents();
1922
1923   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1924   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component))
1925     {
1926       //create an item in the tree with good settings
1927       QTreeWidgetItem *item = new QTreeWidgetItem();
1928       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1929       item->setData(1,Qt::UserRole,tr("overlay"));
1930       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
1931       qApp->processEvents();
1932
1933       for (int j = 1; j <= 4; j++)
1934         {
1935           item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1936           mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("overlay",0,
1937                                                                     DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1938         }
1939
1940       //Create the buttons for reload and close
1941       qApp->processEvents();
1942       QTreePushButton* cButton = new QTreePushButton;
1943       cButton->setItem(item);
1944       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1945       cButton->setToolTip(tr("close image"));
1946       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1947       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1948               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1949
1950       QTreePushButton* rButton = new QTreePushButton;
1951       rButton->setItem(item);
1952       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1953       rButton->setToolTip(tr("reload image"));
1954       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1955       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1956               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1957
1958       DataTree->topLevelItem(index)->setExpanded(1);
1959       DataTree->topLevelItem(index)->addChild(item);
1960       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1961       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1962
1963       //set the id of the image
1964       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1965       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1966       UpdateTree();
1967       qApp->processEvents();
1968       ImageInfoChanged();
1969       QApplication::restoreOverrideCursor();
1970     }
1971   else
1972     {
1973       QApplication::restoreOverrideCursor();
1974       QString error = "Cannot import the new image.\n";
1975       error += mSlicerManagers[index]->GetLastError().c_str();
1976       QMessageBox::information(this,tr("Problem reading image !"),error);
1977     }
1978 }
1979
1980 void vvMainWindow::AddFusionImage()
1981 {
1982   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1983
1984   //check if one fusion image is added
1985   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1986     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion")
1987       {
1988         QString error = "Cannot add more than one fusion image\n";
1989         error += "Please remove first ";
1990         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1991         QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1992         return;
1993       }
1994
1995   QString Extensions = EXTENSIONS;
1996   Extensions += ";;All Files (*)";
1997   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1998   if (!file.isEmpty())
1999     {
2000       mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2001       itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2002                                                                             file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2003       reader->SetFileName(file.toStdString().c_str());
2004       reader->ReadImageInformation();
2005       std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2006       if (reader)
2007         {
2008           QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2009           vvProgressDialog progress("Opening fusion");
2010           qApp->processEvents();
2011
2012           std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2013           if (mSlicerManagers[index]->SetFusion(file.toStdString(),
2014                                                 reader->GetNumberOfDimensions(), component))
2015             {
2016               //create an item in the tree with good settings
2017               QTreeWidgetItem *item = new QTreeWidgetItem();
2018               item->setData(0,Qt::UserRole,file.toStdString().c_str());
2019               item->setData(1,Qt::UserRole,tr("fusion"));
2020               item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
2021               qApp->processEvents();
2022
2023               for (int j = 1; j <= 4; j++)
2024                 {
2025                   item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2026                   mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("fusion",0,
2027                                                                              DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
2028                 }
2029
2030               //Create the buttons for reload and close
2031               qApp->processEvents();
2032               QTreePushButton* cButton = new QTreePushButton;
2033               cButton->setItem(item);
2034               cButton->setColumn(COLUMN_CLOSE_IMAGE);
2035               cButton->setToolTip(tr("close image"));
2036               cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2037               connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2038                       this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2039
2040               QTreePushButton* rButton = new QTreePushButton;
2041               rButton->setItem(item);
2042               rButton->setColumn(COLUMN_RELOAD_IMAGE);
2043               rButton->setToolTip(tr("reload image"));
2044               rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2045               connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2046                       this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2047
2048               DataTree->topLevelItem(index)->setExpanded(1);
2049               DataTree->topLevelItem(index)->addChild(item);
2050               DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2051               DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2052
2053               //set the id of the image
2054               QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2055               item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2056               UpdateTree();
2057               qApp->processEvents();
2058               ImageInfoChanged();
2059               QApplication::restoreOverrideCursor();
2060             }
2061           else
2062             {
2063               QApplication::restoreOverrideCursor();
2064               QString error = "Cannot import the new image.\n";
2065               error += mSlicerManagers[index]->GetLastError().c_str();
2066               QMessageBox::information(this,tr("Problem reading image !"),error);
2067             }
2068         }
2069       else
2070         {
2071           QString error = "Cannot import the new image.\n";
2072           QMessageBox::information(this,tr("Problem reading image !"),error);
2073         }
2074     }
2075 }
2076 //------------------------------------------------------------------------------
2077
2078
2079 //------------------------------------------------------------------------------
2080 void vvMainWindow::OpenField()
2081 {
2082   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2083   //check if a vector field has already been added
2084   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2085     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector")
2086       {
2087         QString error = "Cannot add more than one vector field\n";
2088         error += "Please remove first ";
2089         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2090         QMessageBox::information(this,tr("Problem adding vector field!"),error);
2091         return;
2092       }
2093
2094   QString Extensions = "Images ( *.mhd)";
2095   Extensions += ";;Images ( *.vf)";
2096   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2097   if (!file.isEmpty())
2098     AddField(file,index);
2099 }
2100 //------------------------------------------------------------------------------
2101
2102
2103 //------------------------------------------------------------------------------
2104 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2105 {
2106   //create an item in the tree with good settings
2107   QTreeWidgetItem *item = new QTreeWidgetItem();
2108   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2109   item->setData(1,Qt::UserRole,tr("vector"));
2110   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename);
2111   qApp->processEvents();
2112
2113   for (int j = 1; j <= 4; j++)
2114     {
2115       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2116       mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("vector",0,
2117                                                                  DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
2118     }
2119
2120   //Create the buttons for reload and close
2121   qApp->processEvents();
2122   QTreePushButton* cButton = new QTreePushButton;
2123   cButton->setItem(item);
2124   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2125   cButton->setToolTip(tr("close vector field"));
2126   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2127   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2128           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2129
2130   QTreePushButton* rButton = new QTreePushButton;
2131   rButton->setItem(item);
2132   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2133   rButton->setToolTip(tr("reload vector field"));
2134   rButton->setEnabled(from_disk);
2135   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2136   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2137           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2138
2139   DataTree->topLevelItem(index)->setExpanded(1);
2140   DataTree->topLevelItem(index)->addChild(item);
2141   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2142   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2143
2144   //set the id of the image
2145   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2146   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2147   UpdateTree();
2148   qApp->processEvents();
2149   ImageInfoChanged();
2150   QApplication::restoreOverrideCursor();
2151 }
2152 //------------------------------------------------------------------------------
2153
2154
2155 //------------------------------------------------------------------------------
2156 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2157 {
2158   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2159   vvSlicerManager* imageManager = mSlicerManagers[index];
2160   if (imageManager->SetVF(vf,file.toStdString()))
2161     {
2162       AddFieldEntry(file,index,false);
2163     }
2164   else
2165     {
2166       QString error = "Cannot import the vector field for this image.\n";
2167       error += imageManager->GetLastError().c_str();
2168       QMessageBox::information(this,tr("Problem reading VF !"),error);
2169     }
2170   QApplication::restoreOverrideCursor();
2171 }
2172 //------------------------------------------------------------------------------
2173
2174
2175 //------------------------------------------------------------------------------
2176 void vvMainWindow::AddField(QString file,int index)
2177 {
2178   if (QFile::exists(file))
2179     {
2180       mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2181
2182       //init the progress events
2183       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2184       vvProgressDialog progress("Opening " + file.toStdString());
2185       qApp->processEvents();
2186
2187       //read the vector and put it in the current mSlicerManager
2188       vvSlicerManager* imageManager = mSlicerManagers[index];
2189       qApp->processEvents();
2190
2191       std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2192       if (imageManager->SetVF(file.toStdString()))
2193         {
2194           imageManager->Render();
2195           AddFieldEntry(file,index,true);
2196         }
2197       else
2198         {
2199           QApplication::restoreOverrideCursor();
2200           QString error = "Cannot import the vector field for this image.\n";
2201           error += imageManager->GetLastError().c_str();
2202           QMessageBox::information(this,tr("Problem reading VF !"),error);
2203         }
2204     }
2205   else
2206     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2207
2208 }
2209 //------------------------------------------------------------------------------
2210
2211
2212 //------------------------------------------------------------------------------
2213 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width) {
2214   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2215   if (mSlicerManagers[index]->GetSlicer(0)->GetVF())
2216     {
2217       for (int i = 0; i < 4; i++)
2218         {
2219           mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2220           mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2221           mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2222           if (log > 0)
2223             mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2224           else
2225             mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2226         }
2227     }
2228 }
2229 //------------------------------------------------------------------------------
2230
2231
2232 //------------------------------------------------------------------------------
2233 void vvMainWindow::SetOverlayProperty(int color) {
2234   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2235   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
2236     {
2237       mSlicerManagers[index]->SetOverlayColor(color);
2238       mSlicerManagers[index]->SetColorMap(0);
2239       mSlicerManagers[index]->Render();
2240     }
2241 }
2242 //------------------------------------------------------------------------------
2243
2244 //------------------------------------------------------------------------------
2245 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level) {
2246   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2247   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion())
2248     {
2249       mSlicerManagers[index]->SetFusionOpacity(opacity);
2250       mSlicerManagers[index]->SetFusionColorMap(colormap);
2251       mSlicerManagers[index]->SetFusionWindow(window);
2252       mSlicerManagers[index]->SetFusionLevel(level);
2253       mSlicerManagers[index]->SetColorMap(0);
2254       mSlicerManagers[index]->Render();
2255     }
2256 }
2257 //------------------------------------------------------------------------------
2258
2259 //------------------------------------------------------------------------------
2260 void vvMainWindow::SaveAs() {
2261   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector")
2262     {
2263       QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2264       return;
2265     }
2266
2267   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2268   int dimension = mSlicerManagers[index]->GetDimension();
2269   QStringList OutputListeFormat;
2270   OutputListeFormat.clear();
2271   if (dimension == 1)
2272     {
2273       OutputListeFormat.push_back(".mhd");
2274     }
2275   if (dimension == 2)
2276     {
2277       OutputListeFormat.push_back(".bmp");
2278       OutputListeFormat.push_back(".png");
2279       OutputListeFormat.push_back(".jpeg");
2280       OutputListeFormat.push_back(".tif");
2281       OutputListeFormat.push_back(".mhd");
2282       OutputListeFormat.push_back(".hdr");
2283       OutputListeFormat.push_back(".vox");
2284     }
2285   else if (dimension == 3)
2286     {
2287       OutputListeFormat.push_back(".mhd");
2288       OutputListeFormat.push_back(".hdr");
2289       OutputListeFormat.push_back(".vox");
2290     }
2291   else if (dimension == 4)
2292     {
2293       OutputListeFormat.push_back(".mhd");
2294     }
2295   QString Extensions = "AllFiles(*.*)";
2296   for (int i = 0; i < OutputListeFormat.count(); i++)
2297     {
2298       Extensions += ";;Images ( *";
2299       Extensions += OutputListeFormat[i];
2300       Extensions += ")";
2301     }
2302   QString fileName = QFileDialog::getSaveFileName(this,
2303                                                   tr("Save As"),
2304                                                   mSlicerManagers[index]->GetFileName().c_str(),
2305                                                   Extensions);
2306   if (!fileName.isEmpty())
2307     {
2308       std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2309       if (OutputListeFormat.contains(
2310                                      fileformat.c_str()))
2311         {
2312           QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2313           std::string action = "Saving";
2314           vvProgressDialog progress("Saving "+fileName.toStdString());
2315           qApp->processEvents();
2316           vvImageWriter *writer = new vvImageWriter;
2317           writer->SetOutputFileName(fileName.toStdString());
2318           writer->SetInput(mSlicerManagers[index]->GetImage());
2319           writer->Update();
2320           QApplication::restoreOverrideCursor();
2321           if (writer->GetLastError().size())
2322             {
2323               QString error = "Saving did not succeed\n";
2324               error += writer->GetLastError().c_str();
2325               QMessageBox::information(this,tr("Saving Problem"),error);
2326               SaveAs();
2327             }
2328         }
2329       else
2330         {
2331           QString error = fileformat.c_str();
2332           if (error.isEmpty())
2333             error += "no file format specified !";
2334           else
2335             error += " format unknown !!!\n";
2336           QMessageBox::information(this,tr("Saving Problem"),error);
2337           SaveAs();
2338         }
2339     }
2340 }
2341 //------------------------------------------------------------------------------
2342
2343
2344 //------------------------------------------------------------------------------
2345 void vvMainWindow::AddLink(QString image1,QString image2) {
2346   for (unsigned int i = 0; i < mSlicerManagers.size();i++)
2347     {
2348       if (image1.toStdString() == mSlicerManagers[i]->GetId())
2349         {
2350           mSlicerManagers[i]->AddLink(image2.toStdString());
2351         }
2352       if (image2.toStdString() == mSlicerManagers[i]->GetId())
2353         {
2354           mSlicerManagers[i]->AddLink(image1.toStdString());
2355         }
2356     }
2357 }
2358 //------------------------------------------------------------------------------
2359
2360
2361 //------------------------------------------------------------------------------
2362 void vvMainWindow::RemoveLink(QString image1,QString image2) {
2363   // DD("vvMainWindow:RemoveLink");
2364   for (unsigned int i = 0; i < mSlicerManagers.size();i++)
2365     {
2366       if (image1.toStdString() == mSlicerManagers[i]->GetId())
2367         {
2368           mSlicerManagers[i]->RemoveLink(image2.toStdString());
2369         }
2370       if (image2.toStdString() == mSlicerManagers[i]->GetId())
2371         {
2372           mSlicerManagers[i]->RemoveLink(image1.toStdString());
2373         }
2374     }
2375 }
2376 //------------------------------------------------------------------------------
2377
2378 //------------------------------------------------------------------------------
2379 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2380 {
2381     int index = 0;
2382     while(sm != mSlicerManagers[index])
2383         index++;
2384     index = (index+offset) % mSlicerManagers.size();
2385
2386     QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2387     //CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2388     item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2389     DisplayChanged(item,slicer+1);
2390 }
2391 //------------------------------------------------------------------------------
2392
2393 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2394 {
2395   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2396     {
2397       if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1)
2398         {
2399           for (int j = 0; j < 4; j++)
2400             {
2401               mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2402               //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2403               //UpdateTSlice(j,value);
2404             }
2405           mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2406           break;
2407         }
2408     }
2409 }
2410 //------------------------------------------------------------------------------
2411
2412
2413 //------------------------------------------------------------------------------
2414 void vvMainWindow::NOHorizontalSliderMoved() {
2415   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2416   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2417  //  mCurrentTime = NOHorizontalSlider->value();
2418 }
2419 //------------------------------------------------------------------------------
2420
2421
2422 //------------------------------------------------------------------------------
2423 void vvMainWindow::NEHorizontalSliderMoved() {
2424   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2425   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2426  //  mCurrentTime = NEHorizontalSlider->value();
2427 }
2428 //------------------------------------------------------------------------------
2429
2430
2431 //------------------------------------------------------------------------------
2432 void vvMainWindow::SOHorizontalSliderMoved() {
2433   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2434   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2435   // mCurrentTime = SOHorizontalSlider->value();
2436 }
2437 //------------------------------------------------------------------------------
2438
2439
2440 //------------------------------------------------------------------------------
2441 void vvMainWindow::SEHorizontalSliderMoved() {
2442   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2443   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2444   // mCurrentTime = SEHorizontalSlider->value();
2445 }
2446 //------------------------------------------------------------------------------
2447
2448 //------------------------------------------------------------------------------
2449 void vvMainWindow::NOVerticalSliderChanged() {
2450   static int value=-1;
2451   if (value == NOVerticalSlider->value()) return;
2452   else value = NOVerticalSlider->value();
2453   //  int value = NOVerticalSlider->value();
2454   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2455     {
2456       if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
2457         {
2458           if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2459             mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2460             mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2461             mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2462             //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2463           }
2464           break;
2465         }
2466     }
2467 }
2468 //------------------------------------------------------------------------------
2469
2470
2471 //------------------------------------------------------------------------------
2472 void vvMainWindow::NEVerticalSliderChanged() {
2473   static int value=-1;
2474   if (value == NEVerticalSlider->value()) return;
2475   else value = NEVerticalSlider->value();
2476   //  int value = NEVerticalSlider->value();
2477   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2478     {
2479       if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1)
2480         {
2481           if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2482             mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2483             mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2484             mSlicerManagers[i]->UpdateSlice(1);
2485             //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2486           }
2487           break;
2488         }
2489     }
2490 }
2491 //------------------------------------------------------------------------------
2492
2493
2494 //------------------------------------------------------------------------------
2495 void vvMainWindow::SOVerticalSliderChanged() {
2496   // DD("SOVerticalSliderChanged");
2497   static int value=-1;
2498   // DD(value);
2499 //   DD(SOVerticalSlider->value());
2500   if (value == SOVerticalSlider->value()) return;
2501   else value = SOVerticalSlider->value();
2502   //int value = SOVerticalSlider->value();
2503   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2504     {
2505       if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
2506         {
2507           if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2508             mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2509             mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2510             mSlicerManagers[i]->UpdateSlice(2);
2511             //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2512           }
2513           // else { DD("avoid SOVerticalSlider slicer update"); }
2514           break;
2515         }
2516     }
2517 }
2518 //------------------------------------------------------------------------------
2519
2520
2521 //------------------------------------------------------------------------------
2522 void vvMainWindow::SEVerticalSliderChanged() {
2523   static int value=-1;
2524   if (value == SEVerticalSlider->value()) return;
2525   else value = SEVerticalSlider->value();
2526   // int value = SEVerticalSlider->value();
2527   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2528     {
2529       if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1)
2530         {
2531           if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2532             mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2533             mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2534             mSlicerManagers[i]->UpdateSlice(3);
2535             //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2536           }
2537           break;
2538         }
2539     }
2540 }
2541 //------------------------------------------------------------------------------
2542
2543
2544 //------------------------------------------------------------------------------
2545 void vvMainWindow::UpdateSlice(int slicer, int slice) {
2546   // DD("vvMainWindow::UpdateSlice");
2547 //   DD(slicer);
2548 //   DD(slice);
2549   if (slicer == 0) {
2550     //    if (slice != NOVerticalSlider->value())
2551     NOVerticalSlider->setValue(slice);
2552   }
2553   else {
2554     if (slicer == 1)
2555     NEVerticalSlider->setValue(slice);
2556     else {
2557       if (slicer == 2)
2558         SOVerticalSlider->setValue(slice);
2559       else {
2560         if (slicer == 3)
2561           SEVerticalSlider->setValue(slice);
2562       }
2563     }
2564   }
2565   // DD("vvMainWindow:UpdateSlice END");
2566 }
2567 //------------------------------------------------------------------------------
2568
2569
2570 //------------------------------------------------------------------------------
2571 void vvMainWindow::UpdateTSlice(int slicer, int slice) {
2572   switch (slicer)
2573     {
2574     case 0:
2575       NOHorizontalSlider->setValue(slice);
2576       break;
2577     case 1:
2578       NEHorizontalSlider->setValue(slice);
2579       break;
2580     case 2:
2581       SOHorizontalSlider->setValue(slice);
2582       break;
2583     case 3:
2584       SEHorizontalSlider->setValue(slice);
2585       break;
2586     }
2587 }
2588 //------------------------------------------------------------------------------
2589
2590
2591 //------------------------------------------------------------------------------
2592 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax) {
2593   int position = int((min+max)/2);
2594   int tPosition = int((tmin+tmax)/2);
2595   if (slicer == 0)
2596     {
2597       NOVerticalSlider->setValue(position);
2598       NOVerticalSlider->setRange(min,max);
2599       NOHorizontalSlider->setRange(tmin,tmax);
2600       NOHorizontalSlider->setValue(tPosition);
2601     }
2602   else if (slicer == 1)
2603     {
2604       NEVerticalSlider->setValue(position);
2605       NEVerticalSlider->setRange(min,max);
2606       NEHorizontalSlider->setRange(tmin,tmax);
2607       NEHorizontalSlider->setValue(tPosition);
2608     }
2609   else if (slicer == 2)
2610     {
2611       SOVerticalSlider->setValue(position);
2612       SOVerticalSlider->setRange(min,max);
2613       SOHorizontalSlider->setRange(tmin,tmax);
2614       SOHorizontalSlider->setValue(tPosition);
2615     }
2616   else if (slicer == 3)
2617     {
2618       SEVerticalSlider->setValue(position);
2619       SEVerticalSlider->setRange(min,max);
2620       SEHorizontalSlider->setRange(tmin,tmax);
2621       SEHorizontalSlider->setValue(tPosition);
2622     }
2623 }
2624 //------------------------------------------------------------------------------
2625
2626
2627 //------------------------------------------------------------------------------
2628 void vvMainWindow::SaveNOScreenshot() {
2629   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2630   w2i->SetInput(NOViewWidget->GetRenderWindow());
2631   w2i->Update();
2632   SaveScreenshot(w2i->GetOutput());
2633   w2i->Delete();
2634 }
2635 //------------------------------------------------------------------------------
2636
2637
2638 //------------------------------------------------------------------------------
2639 void vvMainWindow::SaveNEScreenshot() {
2640   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2641   w2i->SetInput(NEViewWidget->GetRenderWindow());
2642   w2i->Update();
2643   SaveScreenshot(w2i->GetOutput());
2644   w2i->Delete();
2645 }
2646 //------------------------------------------------------------------------------
2647
2648
2649 //------------------------------------------------------------------------------
2650 void vvMainWindow::SaveSOScreenshot() {
2651   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2652   w2i->SetInput(SOViewWidget->GetRenderWindow());
2653   w2i->Update();
2654   SaveScreenshot(w2i->GetOutput());
2655   w2i->Delete();
2656 }
2657 //------------------------------------------------------------------------------
2658
2659
2660 //------------------------------------------------------------------------------
2661 void vvMainWindow::SaveSEScreenshot() {
2662   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2663   w2i->SetInput(SEViewWidget->GetRenderWindow());
2664   w2i->Update();
2665   SaveScreenshot(w2i->GetOutput());
2666   w2i->Delete();
2667 }
2668 //------------------------------------------------------------------------------
2669
2670
2671 //------------------------------------------------------------------------------
2672 void vvMainWindow::SaveScreenshot(vtkImageData* image) {
2673   QString Extensions = "Images( *.png);;";
2674   Extensions += "Images( *.jpg);;";
2675   Extensions += "Images( *.bmp);;";
2676   Extensions += "Images( *.tif);;";
2677   Extensions += "Images( *.ppm)";
2678   QString fileName = QFileDialog::getSaveFileName(this,
2679                                                   tr("Save As"),
2680                                                   itksys::SystemTools::GetFilenamePath(
2681                                                                                        mSlicerManagers[0]->GetFileName()).c_str(),
2682                                                   Extensions);
2683   if (!fileName.isEmpty())
2684     {
2685       const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2686       if (!strcmp(ext, ".bmp"))
2687         {
2688           vtkBMPWriter *bmp = vtkBMPWriter::New();
2689           bmp->SetInput(image);
2690           bmp->SetFileName(fileName.toStdString().c_str());
2691           bmp->Write();
2692           bmp->Delete();
2693         }
2694       else if (!strcmp(ext, ".tif"))
2695         {
2696           vtkTIFFWriter *tif = vtkTIFFWriter::New();
2697           tif->SetInput(image);
2698           tif->SetFileName(fileName.toStdString().c_str());
2699           tif->Write();
2700           tif->Delete();
2701         }
2702       else if (!strcmp(ext, ".ppm"))
2703         {
2704           vtkPNMWriter *pnm = vtkPNMWriter::New();
2705           pnm->SetInput(image);
2706           pnm->SetFileName(fileName.toStdString().c_str());
2707           pnm->Write();
2708           pnm->Delete();
2709         }
2710       else if (!strcmp(ext, ".png"))
2711         {
2712           vtkPNGWriter *png = vtkPNGWriter::New();
2713           png->SetInput(image);
2714           png->SetFileName(fileName.toStdString().c_str());
2715           png->Write();
2716           png->Delete();
2717         }
2718       else if (!strcmp(ext, ".jpg"))
2719         {
2720           vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2721           jpg->SetInput(image);
2722           jpg->SetFileName(fileName.toStdString().c_str());
2723           jpg->Write();
2724           jpg->Delete();
2725         }
2726       else
2727         {
2728           QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2729         }
2730     }
2731
2732 }
2733 //------------------------------------------------------------------------------
2734
2735
2736 //------------------------------------------------------------------------------
2737 void vvMainWindow::GoToCursor() {
2738   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2739   for (int column = 1; column < 5; column++)
2740     {
2741       if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1)
2742         {
2743           double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2744           mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2745                                                                           cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2746           mSlicerManagers[index]->UpdateViews(1,column-1);
2747           mSlicerManagers[index]->UpdateLinked(column-1);
2748           break;
2749         }
2750     }
2751 }
2752 //------------------------------------------------------------------------------
2753
2754 //------------------------------------------------------------------------------
2755 void vvMainWindow::PlayPause() {
2756   if (playMode)
2757     {
2758       playMode = 0;
2759       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2760       ImageInfoChanged();
2761       return;
2762     }
2763   else
2764     {
2765       int image_number=DataTree->topLevelItemCount();
2766       bool has_temporal;
2767       for (int i=0;i<image_number;i++)
2768         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1)
2769           {
2770             has_temporal=true;
2771             break;
2772           }
2773       if (has_temporal)
2774         {
2775           playMode = 1;
2776           playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2777           QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2778         }
2779     }
2780 }
2781 //------------------------------------------------------------------------------
2782
2783 //------------------------------------------------------------------------------
2784 void vvMainWindow::PlayNext() {
2785   if (playMode && !this->isHidden())
2786     {
2787       int image_number=DataTree->topLevelItemCount();
2788       ///Only play one slicer per SM, and only if the SM is being displayed
2789       for (int i=0;i<image_number;i++)
2790         for (int j=0;j<4;j++)
2791           if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2792               DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0)
2793             {
2794               mSlicerManagers[i]->SetNextTSlice(j);
2795               break;
2796             }
2797       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2798     }
2799 }
2800 //------------------------------------------------------------------------------
2801
2802 void vvMainWindow::ShowLastImage()
2803 {
2804   if (mSlicerManagers.size() > 1)
2805     {
2806       QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2807       CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2808       item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2809       DisplayChanged(item,1);
2810     }
2811 }
2812
2813 //------------------------------------------------------------------------------
2814 void vvMainWindow::UpdateRenderWindows() {
2815   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2816   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2817   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2818   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2819 }
2820 //------------------------------------------------------------------------------
2821
2822 //------------------------------------------------------------------------------
2823 void vvMainWindow::SegmentationOnCurrentImage() {
2824   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2825
2826   vvSegmentationDialog segmentation;
2827   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2828   segmentation.exec();
2829 }
2830 //------------------------------------------------------------------------------
2831
2832 void vvMainWindow::SurfaceViewerLaunch()
2833 {
2834   vvSurfaceViewerDialog surfaceViewer;
2835   surfaceViewer.exec();
2836 }
2837
2838 //------------------------------------------------------------------------------
2839 void vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2840 {
2841   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
2842   slicer_manager->SetImage(image);
2843   slicer_manager->SetFilename(filename);
2844   mSlicerManagers.push_back(slicer_manager);
2845
2846   //create an item in the tree with good settings
2847   QTreeWidgetItem *item = new QTreeWidgetItem();
2848   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2849   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
2850   qApp->processEvents();
2851
2852   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2853
2854   //Create the buttons for reload and close
2855   qApp->processEvents();
2856   QTreePushButton* cButton = new QTreePushButton;
2857   cButton->setItem(item);
2858   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2859   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2860   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2861           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2862
2863   QTreePushButton* rButton = new QTreePushButton;
2864   rButton->setItem(item);
2865   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2866   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2867   rButton->setEnabled(0);
2868   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2869           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2870
2871   DataTree->addTopLevelItem(item);
2872   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2873   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2874
2875   //set the id of the image
2876   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2877   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2878   mSlicerManagers.back()->SetId(id.toStdString());
2879
2880   linkPanel->addImage(filename, id.toStdString());
2881
2882   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
2883           this, SLOT(CurrentImageChanged(std::string)));
2884   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
2885           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2886   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
2887           this, SLOT(VectorChanged(int,double,double,double, double)));
2888   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
2889           this, SLOT(OverlayChanged(int,double,double)));
2890   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
2891           this, SLOT(FusionChanged(int,double)));
2892   connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
2893           this,SLOT(WindowsChanged(int, int, int)));
2894   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
2895           this,SLOT(WindowLevelChanged(double, double, int, int)));
2896   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
2897           this,SLOT(UpdateSlice(int,int)));
2898   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
2899           this,SLOT(UpdateTSlice(int, int)));
2900   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2901           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2902   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2903           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2904   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
2905           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
2906   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2907   UpdateTree();
2908   qApp->processEvents();
2909   InitSlicers();
2910   ShowLastImage();
2911   InitDisplay();
2912   qApp->processEvents();
2913 }
2914 //------------------------------------------------------------------------------
2915
2916
2917 //------------------------------------------------------------------------------
2918 void vvMainWindow::UpdateCurrentSlicer() {
2919   int index = -1;
2920   if (DataTree->selectedItems().size() > 0) {
2921     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2922   }
2923   mSlicerManagerCurrentIndex = index;
2924 }
2925 //------------------------------------------------------------------------------
2926