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 #include "clitkConfiguration.h"
  48
  49 // ITK include
  50 #include "itkImage.h"
  51 #include "itkImageFileReader.h"
  52 #include "itkByteSwapper.h"
  53 #include "itkCommand.h"
  54 #include "itkNumericSeriesFileNames.h"
  55
  56 // VTK include
  57 #include "vtkImageData.h"
  58 #include "vtkImageActor.h"
  59 #include "vtkCornerAnnotation.h"
  60 #include "vtkRenderWindow.h"
  61 #include "vtkRenderWindowInteractor.h"
  62 #include "vtkRenderer.h"
  63 #include "vtkRendererCollection.h"
  64 #include "vtkWindowToImageFilter.h"
  65 #include "vtkBMPWriter.h"
  66 #include "vtkTIFFWriter.h"
  67 #include "vtkPNMWriter.h"
  68 #include "vtkPNGWriter.h"
  69 #include "vtkJPEGWriter.h"
  70
  71 // Standard includes
  72 #include <iostream>
  73
  74 #define COLUMN_TREE 0
  75 #define COLUMN_UL_VIEW 1
  76 #define COLUMN_UR_VIEW 2
  77 #define COLUMN_DL_VIEW 3
  78 #define COLUMN_DR_VIEW 4
  79 #define COLUMN_CLOSE_IMAGE 5
  80 #define COLUMN_RELOAD_IMAGE 6
  81 #define COLUMN_IMAGE_NAME 7
  82
  83 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.hdr *.vox *.his *.xdr *.SCAN )"
  84
  85 /*Data Tree values
  86   0,Qt::UserRole full filename
  87   1,Qt::CheckStateRole checkbutton UL View
  88   1,Qt::UserRole overlay, fusion or vector
  89   2,Qt::CheckStateRole checkbutton UR View
  90   3,Qt::CheckStateRole checkbutton DL View
  91   4,Qt::CheckStateRole checkbutton DR View
  92   5,0  short filename
  93   5,Qt::UserRole mSlicerManager id*/
  94
  95 //------------------------------------------------------------------------------
  96 vvMainWindow::vvMainWindow():vvMainWindowBase()
  97 {
  98   setupUi(this); // this sets up the GUI
  99
 100   mInputPathName = "";
 101   mMenuTools = menuTools;
 102   //  mMenuSegmentation = menuSegmentation;
 103   mContextMenu = &contextMenu;
 104   mMenuExperimentalTools = menuExperimental;
 105   mMainWidget = this;
 106   mCurrentTime = -1;
 107   mCurrentSelectedImageId = "";
 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   contextMenu.addAction(actionAdd_VF_to_current_Image);
 137   contextActions.push_back(actionAdd_VF_to_current_Image);
 138
 139   QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 140       tr("Add overlay image to current image"));
 141   contextMenu.addAction(actionAdd_Overlay_to_current_Image);
 142   contextActions.push_back(actionAdd_Overlay_to_current_Image);
 143
 144   connect(actionAdd_Overlay_to_current_Image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 145
 146   contextMenu.addAction(actionAdd_fusion_image);
 147   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 148   contextActions.push_back(actionAdd_fusion_image);
 149
 150   // TRIAL DS
 151   /*
 152   QMenu * m = new QMenu(menubar);
 153   m->setTitle("TOTO");
 154   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 155   contextMenu.addMenu(m);
 156   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 157                      tr("BIDON"));
 158   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 159                      tr("BIDON2"));
 160   m->addAction(a);
 161   m->addAction(b);
 162   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 163   */
 164
 165   //init the DataTree
 166   mSlicerManagers.resize(0);
 167
 168   QStringList header;
 169   header.append("");
 170   header.append("TL");
 171   header.append("TR");
 172   header.append("BL");
 173   header.append("BR");
 174   header.append("");
 175   header.append("");
 176   header.append("Name");
 177
 178   DataTree->setHeaderLabels(header);
 179   DataTree->resizeColumnToContents(COLUMN_TREE);
 180   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 181   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 182   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 183   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 184   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 185   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 186   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 187
 188   viewMode = 1;
 189   documentation = new vvDocumentation();
 190   help_dialog = new vvHelpDialog();
 191   dicomSeriesSelector = new vvDicomSeriesSelector();
 192
 193   inverseButton->setEnabled(0);
 194   actionAdd_Overlay_to_current_Image->setEnabled(0);
 195   actionSave_As->setEnabled(0);
 196   actionAdd_VF_to_current_Image->setEnabled(0);
 197   actionAdd_fusion_image->setEnabled(0);
 198
 199   //init the sliders
 200   verticalSliders.push_back(NOVerticalSlider);
 201   verticalSliders.push_back(NEVerticalSlider);
 202   verticalSliders.push_back(SOVerticalSlider);
 203   verticalSliders.push_back(SEVerticalSlider);
 204
 205   for (int i =0; i < 4; i++)
 206     verticalSliders[i]->hide();
 207
 208   horizontalSliders.push_back(NOHorizontalSlider);
 209   horizontalSliders.push_back(NEHorizontalSlider);
 210   horizontalSliders.push_back(SOHorizontalSlider);
 211   horizontalSliders.push_back(SEHorizontalSlider);
 212
 213   for (int i =0; i < 4; i++)
 214     horizontalSliders[i]->hide();
 215
 216
 217   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 218   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 219   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 220   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 221
 222   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 223   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 224   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 225   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 226
 227   //connect everything
 228   connect(actionMaximum_Intensity_Projection,SIGNAL(triggered()),this,SLOT(ComputeMIP()));
 229   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 230   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 231   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 232   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 233   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 234   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 235   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 236   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 237   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 238   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 239   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 240   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 241   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 242   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 243   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 244   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 245
 246   ///////////////////////////////////////////////
 247   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 248   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 249   ///////////////////////////////////////////////
 250
 251   actionNorth_East_Window->setEnabled(0);
 252   actionNorth_West_Window->setEnabled(0);
 253   actionSouth_East_Window->setEnabled(0);
 254   actionSouth_West_Window->setEnabled(0);
 255
 256   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 257   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 258   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 259   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 260
 261   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 262   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 263           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 264
 265   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 266   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 267   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 268   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 269   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 270   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 271   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 272
 273
 274   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 275
 276   connect(linkPanel,SIGNAL(addLink(QString,QString)),this,SLOT(AddLink(QString,QString)));
 277   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 278   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int)),this,SLOT(SetVFProperty(int,int,int,int)));
 279   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int)),this,SLOT(SetOverlayProperty(int)));
 280   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,double,double)),
 281           this,SLOT(SetFusionProperty(int,int,double,double)));
 282   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 283
 284   playMode = 0;//pause
 285   mFrameRate = 10;
 286   playButton->setEnabled(0);
 287   frameRateLabel->setEnabled(0);
 288   frameRateSpinBox->setEnabled(0);
 289   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 290   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 291
 292   goToCursorPushButton->setEnabled(0);
 293   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 294
 295   NOViewWidget->hide();
 296   NEViewWidget->hide();
 297   SOViewWidget->hide();
 298   SEViewWidget->hide();
 299
 300   //Recently opened files
 301   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 302   if ( !recent_files.empty() ) {
 303     QMenu * rmenu = new QMenu("Recently opened files...");
 304     rmenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 305     menuFile->insertMenu(actionOpen_Image_With_Time,rmenu);
 306     menuFile->insertSeparator(actionOpen_Image_With_Time);
 307     for (std::list<std::string>::iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 308       QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")),
 309                                    (*i).c_str(),this);
 310       rmenu->addAction(current);
 311       connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 312     }
 313   }
 314
 315   // Adding all new tools (insertion in the menu)
 316   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 317
 318   if (!CLITK_EXPERIMENTAL)
 319     menuExperimental->menuAction()->setVisible(false);
 320
 321
 322   QTimer * timerMemory = new QTimer(this);
 323   //timerMemory->setInterval(5);
 324   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 325   timerMemory->start(5000);
 326 }
 327 //------------------------------------------------------------------------------
 328
 329
 330 //------------------------------------------------------------------------------
 331 void vvMainWindow::UpdateMemoryUsage()
 332 {
 333   //  clitk::PrintMemory(true);
 334   infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" Mb");
 335 }
 336 //------------------------------------------------------------------------------
 337
 338
 339 //------------------------------------------------------------------------------
 340 void vvMainWindow::ComputeMIP()
 341 {
 342   vvMaximumIntensityProjection mip;
 343   vvSlicerManager* selected_slicer = mSlicerManagers[GetSlicerIndexFromItem(DataTree->selectedItems()[0])];
 344   QFileInfo info(selected_slicer->GetFileName().c_str());
 345   mip.Compute(selected_slicer);
 346   if (!mip.error)
 347     AddImage(mip.GetOutput(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_mip.mhd");
 348 }
 349 //------------------------------------------------------------------------------
 350
 351
 352 //------------------------------------------------------------------------------
 353 void vvMainWindow::ComputeMidPosition()
 354 {
 355   bool ok;
 356   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 357   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 358                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 359   if (ok) {
 360     vvMidPosition midp;
 361     midp.slicer_manager = mSlicerManagers[index];
 362     midp.reference_image_index = ref;
 363     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 364     midp.Update();
 365     if (midp.error)
 366       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 367     else {
 368       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 369       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 370     }
 371     QApplication::restoreOverrideCursor();
 372   }
 373 }
 374 //------------------------------------------------------------------------------
 375
 376
 377 //------------------------------------------------------------------------------
 378 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 379 {
 380   QTreeWidgetItem *item = new QTreeWidgetItem();
 381   item->setData(0,Qt::UserRole,"filename.vtk");
 382   item->setData(1,Qt::UserRole,tr("contour"));
 383   QBrush brush;
 384   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 385   brush.setStyle(Qt::SolidPattern);
 386   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 387   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 388
 389   for (int j = 1; j <= 4; j++)
 390     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 391
 392   QTreePushButton* cButton = new QTreePushButton;
 393   cButton->setItem(item);
 394   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 395   cButton->setToolTip(tr("close image"));
 396   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 397   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 398           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 399
 400   QTreePushButton* rButton = new QTreePushButton;
 401   rButton->setItem(item);
 402   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 403   rButton->setToolTip(tr("reload image"));
 404   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 405   rButton->setEnabled(false);
 406   //Not implemented
 407   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 408   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 409
 410   DataTree->topLevelItem(image_index)->setExpanded(1);
 411   DataTree->topLevelItem(image_index)->addChild(item);
 412   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 413   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 414   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 415   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 416
 417   UpdateTree();
 418   mSlicerManagers[image_index]->AddContour(contour,propagation);
 419   mSlicerManagers[image_index]->Render();
 420 }
 421 //------------------------------------------------------------------------------
 422
 423
 424 //------------------------------------------------------------------------------
 425 void vvMainWindow::OpenVTKContour()
 426 {
 427   if (mSlicerManagers.size() > 0) {
 428     QString Extensions = "Images ( *.vtk *.obj)";
 429     Extensions += ";;All Files (*)";
 430     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 431     if (file.isNull())
 432       return;
 433     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 434     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 435     vvMeshReader reader;
 436     reader.SetImage(mSlicerManagers[index]->GetImage());
 437     reader.SetModeToVTK();
 438     reader.SetFilename(file.toStdString());
 439     reader.Update();
 440     AddContour(index,reader.GetOutput()[0],false);
 441     QApplication::restoreOverrideCursor();
 442   }
 443 }
 444 //------------------------------------------------------------------------------
 445
 446
 447 //------------------------------------------------------------------------------
 448 void vvMainWindow::OpenDCStructContour()
 449 {
 450   if (mSlicerManagers.size() > 0) {
 451     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       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 465       reader.SetSelectedItems(selector.getSelectedItems());
 466       reader.SetImage(mSlicerManagers[index]->GetImage());
 467       if (selector.PropagationEnabled())
 468         reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 469       reader.Update();
 470       std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 471       for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 472            i!=contours.end(); i++)
 473         AddContour(index,*i,selector.PropagationEnabled());
 474       QApplication::restoreOverrideCursor();
 475     }
 476   }
 477 }
 478 //------------------------------------------------------------------------------
 479
 480
 481 //------------------------------------------------------------------------------
 482 void vvMainWindow::ComputeDeformableRegistration()
 483 {
 484   if (mSlicerManagers.size() > 0) {
 485     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 486     vvDeformationDialog dialog(index,mSlicerManagers);
 487     if (dialog.exec()) {
 488       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 489       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 490       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 491     } else
 492       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 493   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 494 }
 495 //------------------------------------------------------------------------------
 496
 497
 498 //------------------------------------------------------------------------------
 499 void vvMainWindow::WarpImage()
 500 {
 501   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 502   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 503     bool ok;
 504     int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 505                                        mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 506     if (ok) {
 507       WarpImage(mSlicerManagers[index],ref);
 508     }
 509   } else
 510     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 511 }
 512 //------------------------------------------------------------------------------
 513
 514
 515 //------------------------------------------------------------------------------
 516 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 517 {
 518   if (!selected_slicer->GetVF().IsNull()) {
 519     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 520     QFileInfo info(selected_slicer->GetFileName().c_str());
 521     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 522                      reference_phase,this);
 523     if (warp.ComputeWarpedImage()) {
 524       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 525       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 526       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 527       QApplication::restoreOverrideCursor();
 528     } else {
 529       QApplication::restoreOverrideCursor();
 530       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 531     }
 532   } else
 533     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 534 }
 535 //------------------------------------------------------------------------------
 536
 537
 538 //------------------------------------------------------------------------------
 539 vvMainWindow::~vvMainWindow()
 540 {
 541   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 542     if (mSlicerManagers[i] != NULL)
 543       delete mSlicerManagers[i];
 544   }
 545 }
 546 //------------------------------------------------------------------------------
 547
 548 //------------------------------------------------------------------------------
 549 QTabWidget * vvMainWindow::GetTab()
 550 {
 551   return tabWidget;
 552 }
 553 //------------------------------------------------------------------------------
 554
 555
 556 //------------------------------------------------------------------------------
 557 void vvMainWindow::MergeImages()
 558 {
 559   QString Extensions = EXTENSIONS;
 560   Extensions += ";;All Files (*)";
 561   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 562   if (files.isEmpty())
 563     return;
 564   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 565   std::vector<std::string> vector;
 566
 567   unsigned int currentDim = 0;
 568   std::vector<double> currentSpacing;
 569   std::vector<int> currentSize;
 570   std::vector<double> currentOrigin;
 571
 572   for (int i = 0; i < files.size(); i++) {
 573     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 574                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 575     reader->SetFileName(files[i].toStdString().c_str());
 576     reader->ReadImageInformation();
 577     if (reader)        {
 578       //NOViewWidget->hide();
 579       //NEViewWidget->hide();
 580       //SOViewWidget->hide();
 581       //SEViewWidget->hide();
 582       if (i == 0)
 583         currentDim = reader->GetNumberOfDimensions();
 584       bool IsOk = true;
 585       for (unsigned int j = 0; j < currentDim; j++) {
 586         if (i == 0) {
 587           if (j == 0) {
 588             currentSpacing.resize(currentDim);
 589             currentSize.resize(currentDim);
 590             currentOrigin.resize(currentDim);
 591           }
 592           currentOrigin[j] = reader->GetOrigin(j);
 593           currentSpacing[j] = reader->GetSpacing(j);
 594           currentSize[j] = reader->GetDimensions(j);
 595         } else if (currentDim != reader->GetNumberOfDimensions()
 596                    || currentSpacing[j] != reader->GetSpacing(j)
 597                    || currentSize[j] != (int)reader->GetDimensions(j)
 598                    || currentOrigin[j] != reader->GetOrigin(j)) {
 599           QString error = "Cannot read file (too different from others ";
 600           error += files[i].toStdString().c_str();
 601           QMessageBox::information(this,tr("Reading problem"),error);
 602           IsOk = false;
 603           break;
 604         }
 605       }
 606       if (IsOk)
 607         vector.push_back(files[i].toStdString());
 608     }
 609   }
 610   if (vector.size() > 0)
 611     LoadImages(vector, MERGED);
 612 }
 613 //------------------------------------------------------------------------------
 614
 615 //------------------------------------------------------------------------------
 616 void vvMainWindow::SliceImages()
 617 {
 618   QString Extensions = EXTENSIONS;
 619   Extensions += ";;All Files (*)";
 620
 621   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 622   if (files.isEmpty())
 623     return;
 624   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 625   std::vector<std::string> vector;
 626   for (int i = 0; i < files.size(); i++)
 627     vector.push_back(files[i].toStdString());
 628   LoadImages(vector, SLICED);
 629 }
 630 //------------------------------------------------------------------------------
 631
 632 //------------------------------------------------------------------------------
 633 void vvMainWindow::MergeImagesWithTime()
 634 {
 635   QString Extensions = EXTENSIONS;
 636   Extensions += ";;All Files (*)";
 637   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 638   if (files.isEmpty())
 639     return;
 640   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 641   std::vector<std::string> vector;
 642
 643   unsigned int currentDim = 0;
 644   std::vector<double> currentSpacing;
 645   std::vector<int> currentSize;
 646   std::vector<double> currentOrigin;
 647
 648   for (int i = 0; i < files.size(); i++) {
 649     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 650                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 651     if (reader) {
 652       reader->SetFileName(files[i].toStdString().c_str());
 653       reader->ReadImageInformation();
 654       if (i == 0)
 655         currentDim = reader->GetNumberOfDimensions();
 656       bool IsOk = true;
 657       for (unsigned int j = 0; j < currentDim; j++) {
 658         if (i == 0) {
 659           if (j == 0) {
 660             currentSpacing.resize(currentDim);
 661             currentSize.resize(currentDim);
 662             currentOrigin.resize(currentDim);
 663           }
 664           currentOrigin[j] = reader->GetOrigin(j);
 665           currentSpacing[j] = reader->GetSpacing(j);
 666           currentSize[j] = reader->GetDimensions(j);
 667         } 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           QString error = "Cannot read file (too different from others ";
 672           error += files[i].toStdString().c_str();
 673           QMessageBox::information(this,tr("Reading problem"),error);
 674           IsOk = false;
 675           break;
 676         }
 677       }
 678       if (IsOk)
 679         vector.push_back(files[i].toStdString());
 680     } else {
 681       QString error = "Cannot read file info for ";
 682       error += files[i].toStdString().c_str();
 683       error += "\n";
 684       error += "Maybe you're trying to open an image in an unsupported format?\n";
 685       QMessageBox::information(this,tr("Reading problem"),error);
 686     }
 687   }
 688   sort(vector.begin(),vector.end());
 689   if (vector.size() > 1)
 690     LoadImages(vector, MERGEDWITHTIME);
 691   else
 692     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.");
 693 }
 694 //------------------------------------------------------------------------------
 695
 696
 697 //------------------------------------------------------------------------------
 698 void vvMainWindow::OpenDicom()
 699 {
 700   std::vector<std::string> files;
 701
 702   std::cout << "dicomSeriesSelector " << std::endl;
 703   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 704     files = *(dicomSeriesSelector->GetFilenames());
 705     LoadImages(files,DICOM);
 706   }
 707 }
 708 //------------------------------------------------------------------------------
 709
 710 //------------------------------------------------------------------------------
 711 void vvMainWindow::OpenImages()
 712 {
 713   QString Extensions = EXTENSIONS;
 714   Extensions += ";;All Files (*)";
 715
 716   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 717   if (files.isEmpty())
 718     return;
 719   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 720   std::vector<std::string> vector;
 721   for (int i = 0; i < files.size(); i++)
 722     vector.push_back(files[i].toStdString());
 723   LoadImages(vector, IMAGE);
 724 }
 725 //------------------------------------------------------------------------------
 726 void vvMainWindow::OpenRecentImage()
 727 {
 728   QAction * caller = qobject_cast<QAction*>(sender());
 729   std::vector<std::string> images;
 730   images.push_back(caller->text().toStdString());
 731   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 732   LoadImages(images,IMAGE);
 733 }
 734 //------------------------------------------------------------------------------
 735
 736
 737 //------------------------------------------------------------------------------
 738 void vvMainWindow::OpenImageWithTime()
 739 {
 740   QString Extensions = EXTENSIONS;
 741   Extensions += ";;All Files (*)";
 742
 743   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 744   if (files.isEmpty())
 745     return;
 746   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 747   std::vector<std::string> vector;
 748   for (int i = 0; i < files.size(); i++) {
 749     vector.push_back(files[i].toStdString());
 750   }
 751   LoadImages(vector, IMAGEWITHTIME);
 752 }
 753 //------------------------------------------------------------------------------
 754
 755
 756 //------------------------------------------------------------------------------
 757 void vvMainWindow::LoadImages(std::vector<std::string> files, LoadedImageType filetype)
 758 {
 759   //Separate the way to open images and dicoms
 760   int fileSize;
 761   if (filetype == IMAGE || filetype == IMAGEWITHTIME)
 762     fileSize = files.size();
 763   else
 764     fileSize = 1;
 765
 766   // For SLICED, we need the number of slices (ndim and #slices)
 767   std::vector<unsigned int> nSlices;
 768   nSlices.resize(files.size());
 769   std::fill(nSlices.begin(), nSlices.end(), 1);
 770   if (filetype == SLICED) {
 771     for (int i = 0; i < fileSize; i++) {
 772       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 773       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 774       if (!header) {
 775         nSlices[i] = 0;
 776         QString error = "Cannot open file \n";
 777         error += files[i].c_str();
 778         QMessageBox::information(this,tr("Reading problem"),error);
 779         return;
 780       }
 781       if (header->GetNumberOfDimensions() < 3) {
 782         nSlices[i] = 0;
 783         QString error = "Dimension problem. Cannot slice \n";
 784         error += files[i].c_str();
 785         QMessageBox::information(this,tr("Reading problem"),error);
 786         return;
 787       }
 788       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 789     }
 790   }
 791
 792   //Only add to the list of recently opened files when a single file is opened,
 793   //to avoid polluting the list of recently opened files
 794   if (files.size() == 1) {
 795     QFileInfo finfo=tr(files[0].c_str());
 796     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 797   }
 798   //init the progress events
 799   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 800   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 801   qApp->processEvents();
 802
 803   int numberofsuccesulreads=0;
 804   //open images as 1 or multiples
 805   for (int i = 0; i < fileSize; i++) {
 806
 807     progress.SetText("Opening " + files[i]);
 808     progress.SetProgress(i,fileSize);
 809     qApp->processEvents();
 810
 811     for (unsigned int j = 0; j < nSlices[i]; j++) {
 812       //read the image and put it in mSlicerManagers
 813       vvSlicerManager* imageManager = new vvSlicerManager(4);
 814       qApp->processEvents();
 815
 816       bool SetImageSucceed=false;
 817
 818       // Change filename if an image with the same already exist
 819       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 820
 821       if (filetype == IMAGE || filetype == IMAGEWITHTIME || filetype == SLICED)
 822         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 823       else {
 824         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 825       }
 826       if (SetImageSucceed == false) {
 827         QApplication::restoreOverrideCursor();
 828         QString error = "Cannot open file \n";
 829         error += imageManager->GetLastError().c_str();
 830         QMessageBox::information(this,tr("Reading problem"),error);
 831         delete imageManager;
 832       } else {
 833         mSlicerManagers.push_back(imageManager);
 834
 835         //create an item in the tree with good settings
 836         QTreeWidgetItem *item = new QTreeWidgetItem();
 837         item->setData(0,Qt::UserRole,files[i].c_str());
 838         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 839         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 840         item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
 841         qApp->processEvents();
 842
 843         //Create the buttons for reload and close
 844         qApp->processEvents();
 845         QTreePushButton* cButton = new QTreePushButton;
 846         cButton->setItem(item);
 847         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 848         cButton->setToolTip(tr("close image"));
 849         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 850         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 851                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 852
 853         QTreePushButton* rButton = new QTreePushButton;
 854         rButton->setItem(item);
 855         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 856         rButton->setToolTip(tr("reload image"));
 857         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 858         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 859                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 860
 861         DataTree->addTopLevelItem(item);
 862         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 863         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 864
 865         //set the id of the image
 866         QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 867         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 868         mSlicerManagers.back()->SetId(id.toStdString());
 869
 870         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 871
 872         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 873                 this,SLOT(CurrentImageChanged(std::string)));
 874         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 875                 this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 876         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 877                 this, SLOT(VectorChanged(int,double,double,double, double)));
 878         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 879                 this, SLOT(OverlayChanged(int,double,double)));
 880         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 881                 this, SLOT(FusionChanged(int,double)));
 882         connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
 883                 this,SLOT(WindowsChanged(int, int, int)));
 884         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
 885                 this,SLOT(WindowLevelChanged(double, double, int, int)));
 886         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 887                 this,SLOT(UpdateSlice(int,int)));
 888         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 889                 this,SLOT(UpdateTSlice(int, int)));
 890         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 891                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 892         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 893                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 894         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*)),
 895                 this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*)));
 896         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 897                 this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 898         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 899         InitSlicers();
 900       }
 901       numberofsuccesulreads++;
 902     }
 903   }
 904   if (numberofsuccesulreads) {
 905     NOViewWidget->show();
 906     NEViewWidget->show();
 907     SOViewWidget->show();
 908     SEViewWidget->show();
 909     UpdateTree();
 910     InitDisplay();
 911     ShowLastImage();
 912
 913     // Try to guess default WindowLevel
 914     double range[2];
 915     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 916     // DD(range[0]);
 917     //   DD(range[1]);
 918     if ((range[0] == 0) && (range[1] == 1)) {
 919       presetComboBox->setCurrentIndex(5);// binary
 920     } else {
 921       // TODO
 922     }
 923   }
 924   QApplication::restoreOverrideCursor();
 925 }
 926 //------------------------------------------------------------------------------
 927
 928 //------------------------------------------------------------------------------
 929 void vvMainWindow::UpdateTree()
 930 {
 931   DataTree->resizeColumnToContents(COLUMN_TREE);
 932   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 933   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 934   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 935   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 936   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 937   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 938   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 939 }
 940 //------------------------------------------------------------------------------
 941
 942 //------------------------------------------------------------------------------
 943 void vvMainWindow::CurrentImageChanged(std::string id)
 944 {
 945   // DD("CurrentImageChanged");
 946 //   DD(id);
 947 //   DD(mCurrentSelectedImageId);
 948   if (id == mCurrentSelectedImageId) return; // Do nothing
 949   int selected = 0;
 950   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 951     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 952       selected = i;
 953     } else {
 954       DataTree->topLevelItem(i)->setSelected(0);
 955     }
 956     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 957       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 958
 959   }
 960   DataTree->topLevelItem(selected)->setSelected(1);
 961   // DD(mSlicerManagers[selected]->GetFileName());
 962   mCurrentSelectedImageId = id;
 963   emit SelectedImageHasChanged(mSlicerManagers[selected]);
 964 }
 965 //------------------------------------------------------------------------------
 966
 967 //------------------------------------------------------------------------------
 968 void vvMainWindow::ImageInfoChanged()
 969 {
 970   contextActions[6]->setEnabled(1);
 971   contextActions[5]->setEnabled(1);
 972   actionSave_As->setEnabled(1);
 973   actionAdd_VF_to_current_Image->setEnabled(1);
 974   actionAdd_fusion_image->setEnabled(1);
 975   actionNorth_East_Window->setEnabled(1);
 976   actionNorth_West_Window->setEnabled(1);
 977   actionSouth_East_Window->setEnabled(1);
 978   actionSouth_West_Window->setEnabled(1);
 979   inverseButton->setEnabled(1);
 980
 981   goToCursorPushButton->setEnabled(1);
 982
 983   if (DataTree->selectedItems().size()) {
 984     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 985
 986     colorMapComboBox->setEnabled(1);
 987     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
 988       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
 989           DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion") {
 990         colorMapComboBox->setEnabled(0);
 991         break;
 992       }
 993     }
 994
 995     std::vector<double> origin;
 996     std::vector<double> inputSpacing;
 997     std::vector<int> inputSize;
 998     std::vector<double> sizeMM;
 999     int dimension=0;
1000     QString pixelType;
1001     QString inputSizeInBytes;
1002     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1003
1004     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1) {
1005       playButton->setEnabled(1);
1006       frameRateLabel->setEnabled(1);
1007       frameRateSpinBox->setEnabled(1);
1008     } else {
1009       playButton->setEnabled(0);
1010       frameRateLabel->setEnabled(0);
1011       frameRateSpinBox->setEnabled(0);
1012     }
1013
1014     //read image header
1015     int NPixel = 1;
1016
1017     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1018       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1019       dimension = imageSelected->GetNumberOfDimensions();
1020       origin.resize(dimension);
1021       inputSpacing.resize(dimension);
1022       inputSize.resize(dimension);
1023       sizeMM.resize(dimension);
1024       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1025       for (int i = 0; i < dimension; i++) {
1026         origin[i] = imageSelected->GetOrigin()[i];
1027         inputSpacing[i] = imageSelected->GetSpacing()[i];
1028         inputSize[i] = imageSelected->GetSize()[i];
1029         sizeMM[i] = inputSize[i]*inputSpacing[i];
1030         NPixel *= inputSize[i];
1031       }
1032       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1033     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1034       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1035       dimension = imageSelected->GetNumberOfDimensions();
1036       origin.resize(dimension);
1037       inputSpacing.resize(dimension);
1038       inputSize.resize(dimension);
1039       sizeMM.resize(dimension);
1040       pixelType = mSlicerManagers[index]->GetVF()->GetScalarTypeAsITKString().c_str();
1041       for (int i = 0; i < dimension; i++) {
1042         origin[i] = imageSelected->GetOrigin()[i];
1043         inputSpacing[i] = imageSelected->GetSpacing()[i];
1044         inputSize[i] = imageSelected->GetSize()[i];
1045         sizeMM[i] = inputSize[i]*inputSpacing[i];
1046         NPixel *= inputSize[i];
1047       }
1048       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1049     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1050       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1051       dimension = imageSelected->GetNumberOfDimensions();
1052       origin.resize(dimension);
1053       inputSpacing.resize(dimension);
1054       inputSize.resize(dimension);
1055       sizeMM.resize(dimension);
1056       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1057       for (int i = 0; i < dimension; i++) {
1058         origin[i] = imageSelected->GetOrigin()[i];
1059         inputSpacing[i] = imageSelected->GetSpacing()[i];
1060         inputSize[i] = imageSelected->GetSize()[i];
1061         sizeMM[i] = inputSize[i]*inputSpacing[i];
1062         NPixel *= inputSize[i];
1063       }
1064       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1065     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1066       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1067       dimension = imageSelected->GetNumberOfDimensions();
1068       origin.resize(dimension);
1069       inputSpacing.resize(dimension);
1070       inputSize.resize(dimension);
1071       sizeMM.resize(dimension);
1072       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1073       for (int i = 0; i < dimension; i++) {
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
1083     QString dim = QString::number(dimension) + " (";
1084     dim += pixelType + ")";
1085
1086     infoPanel->setFileName(image);
1087     infoPanel->setDimension(dim);
1088     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1089     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1090     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1091     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1092     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1093
1094     infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" Mb");
1095
1096
1097     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1098                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1099     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1100     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1101
1102     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1103     for (int i = 0; i < 4; i++) {
1104       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1105         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1106         break;
1107       }
1108     }
1109     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1110     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1111     // DD(mSlicerManagers[index]->GetColorMap());
1112     // DD(mSlicerManagers[index]->GetPreset());
1113     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1114     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1115
1116     infoPanel->setFileName(image);
1117     infoPanel->setDimension(dim);
1118     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1119     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1120     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1121     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1122     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1123
1124     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1125                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1126     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1127     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1128
1129     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1130     for (int i = 0; i < 4; i++) {
1131       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1132         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1133         break;
1134       }
1135     }
1136     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1137     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1138     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1139     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1140
1141     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1142       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1143       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1144                                   mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1145                                   mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1146     } else {
1147       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1148       overlayPanel->getVFProperty(-1,-1,-1);
1149     }
1150     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1151       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1152       overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1153     } else {
1154       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1155       overlayPanel->getOverlayProperty(-1);
1156     }
1157     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1158       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1159       overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1160                                       mSlicerManagers[index]->GetFusionColorMap(),
1161                                       mSlicerManagers[index]->GetFusionWindow(),
1162                                       mSlicerManagers[index]->GetFusionLevel());
1163     } else {
1164       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1165       overlayPanel->getFusionProperty(-1, -1,-1,-1);
1166     }
1167   }
1168 }
1169 //------------------------------------------------------------------------------
1170
1171 //------------------------------------------------------------------------------
1172 void vvMainWindow::ShowDocumentation()
1173 {
1174   documentation->show();
1175 }
1176 //------------------------------------------------------------------------------
1177 void vvMainWindow::ShowHelpDialog()
1178 {
1179   help_dialog->show();
1180 }
1181 //------------------------------------------------------------------------------
1182
1183 //------------------------------------------------------------------------------
1184 void vvMainWindow::ChangeViewMode()
1185 {
1186   QListIterator<int> it0(splitter_3->sizes());
1187   QListIterator<int> it1(splitter_3->sizes());
1188   int max0 = 0;
1189   int max1 = 1;
1190   while (it0.hasNext()) {
1191     max0 += it0.next();
1192   }
1193   while (it1.hasNext()) {
1194     max1 += it1.next();
1195   }
1196   QList<int> size0;
1197   QList<int> size1;
1198   if (viewMode == 1) {
1199     viewMode = 0;
1200     size0.push_back(max0);
1201     size0.push_back(0);
1202     size1.push_back(max1);
1203     size1.push_back(0);
1204     splitter_3->setSizes(size0);
1205     OSplitter->setSizes(size1);
1206     DataTree->setColumnHidden(2,1);
1207     DataTree->setColumnHidden(3,1);
1208     DataTree->setColumnHidden(4,1);
1209   } else {
1210     viewMode = 1;
1211     size0.push_back(int(max0/2));
1212     size0.push_back(int(max0/2));
1213     size1.push_back(int(max1/2));
1214     size1.push_back(int(max1/2));
1215     splitter_3->setSizes(size0);
1216     OSplitter->setSizes(size1);
1217     DataTree->setColumnHidden(2,0);
1218     DataTree->setColumnHidden(3,0);
1219     DataTree->setColumnHidden(4,0);
1220   }
1221 }
1222 //------------------------------------------------------------------------------
1223
1224 //------------------------------------------------------------------------------
1225 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1226 {
1227   QString result = "";// QString::number(size);
1228   //result += " bytes (";
1229   if (size > 1000000000) {
1230     size /= 1000000000;
1231     result += QString::number(size);
1232     result += "Gb";//)";
1233   } else if (size > 1000000) {
1234     size /= 1000000;
1235     result += QString::number(size);
1236     result += "Mb";//)";
1237   } else if (size > 1000) {
1238     size /= 1000;
1239     result += QString::number(size);
1240     result += "kb";//)";
1241   }
1242   return result;
1243 }
1244 //------------------------------------------------------------------------------
1245
1246 //------------------------------------------------------------------------------
1247 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1248 {
1249   QString result;
1250   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1251     if (i != 0)
1252       result += " ";
1253     result += QString::number(vectorDouble[i]);
1254   }
1255   return result;
1256 }
1257 //------------------------------------------------------------------------------
1258
1259 //------------------------------------------------------------------------------
1260 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1261 {
1262   QString result;
1263   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1264     if (i != 0)
1265       result += " ";
1266     result += QString::number(vectorInt[i]);
1267   }
1268   return result;
1269 }
1270 //------------------------------------------------------------------------------
1271
1272 //------------------------------------------------------------------------------
1273 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1274 {
1275   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1276   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1277     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1278       return i;
1279   }
1280   return -1;
1281 }
1282 //------------------------------------------------------------------------------
1283
1284 //------------------------------------------------------------------------------
1285 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1286 {
1287   QString id = sm->GetId().c_str();
1288   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1289     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1290       return DataTree->topLevelItem(i);
1291   }
1292   return NULL;
1293 }
1294 //------------------------------------------------------------------------------
1295
1296 //------------------------------------------------------------------------------
1297 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clicked_item, int column)
1298 {
1299   int index = GetSlicerIndexFromItem(clicked_item);
1300   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1301     return;
1302   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1303     //Trick to avoid redoing twice the job for a key (sr)
1304     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()-> GetInteractor()->SetKeySym("Crap");
1305
1306     QTreeWidgetItem* current_row=DataTree->topLevelItem(i);
1307     if (DataTree->topLevelItem(index) == current_row) {
1308       vvSlicer* clicked_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1309       if (current_row == clicked_item) {
1310         //If we just activated a slicer
1311         if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1312           mSlicerManagers[i]->UpdateSlicer(column-1,clicked_item->data(column,Qt::CheckStateRole).toInt());
1313           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1314           DisplaySliders(i,column-1);
1315           std::map<std::string,int> overlay_counts;
1316           for (int child = 0; child < current_row->childCount(); child++) {
1317             std::string overlay_type =
1318               current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1319             overlay_counts[overlay_type]++;
1320             current_row->child(child)->setData(column,Qt::CheckStateRole,
1321                                                current_row->data(column,Qt::CheckStateRole));
1322             clicked_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,true);
1323           }
1324         } else { //We don't allow simply desactivating a slicer
1325           clicked_item->setData(column,Qt::CheckStateRole,2);
1326           return;
1327         }
1328       }
1329       //if we clicked on the vector(or overlay) and not the image
1330       else {
1331         if (clicked_item->data(column,Qt::CheckStateRole).toInt()) {
1332           current_row->setData(column,Qt::CheckStateRole,2);
1333           mSlicerManagers[i]->UpdateSlicer(column-1,2);
1334           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1335           DisplaySliders(i,column-1);
1336         }
1337         int vis = clicked_item->data(column,Qt::CheckStateRole).toInt();
1338         std::string overlay_type = clicked_item->data(1,Qt::UserRole).toString().toStdString();
1339         int overlay_index=0;
1340         for (int child = 0; child < current_row->childCount(); child++) {
1341           if (current_row->child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1342             overlay_index++;
1343           if (current_row->child(child) == clicked_item) break;
1344         }
1345         clicked_slicer->SetActorVisibility(
1346           clicked_item->data(1,Qt::UserRole).toString().toStdString(), overlay_index-1,vis);
1347       }
1348     } else if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1349       current_row->setData(column,Qt::CheckStateRole,0);
1350       mSlicerManagers[i]->UpdateSlicer(column-1,0);
1351       std::map<std::string,int> overlay_counts;
1352       for (int child = 0; child < current_row->childCount(); child++) {
1353         std::string overlay_type =
1354           current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1355         overlay_counts[overlay_type]++;
1356         current_row->child(child)->setData(column,Qt::CheckStateRole,0);
1357         vvSlicer * current_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1358         current_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,false);
1359       }
1360     }
1361     //mSlicerManagers[i]->SetColorMap(-1);
1362     mSlicerManagers[i]->SetColorMap();
1363   }
1364   mSlicerManagers[index]->GetSlicer(column-1)->Render();
1365 }
1366 //------------------------------------------------------------------------------
1367
1368 void vvMainWindow::InitSlicers()
1369 {
1370   if (mSlicerManagers.size()) {
1371     mSlicerManagers.back()->GenerateDefaultLookupTable();
1372
1373     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1374     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1375     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1376     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1377   }
1378 }
1379
1380 //------------------------------------------------------------------------------
1381 void vvMainWindow::InitDisplay()
1382 {
1383   if (mSlicerManagers.size()) {
1384     //BE CAREFUL : this is absolutely necessary to set the interactor style
1385     //in order to have the same style instanciation for all SlicerManagers in
1386     // a same window
1387     for (int j = 0; j < 4; j++) {
1388       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1389       style->SetAutoAdjustCameraClippingRange(1);
1390       bool AlreadySelected = false;
1391       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1392         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1393
1394         //select the image only if previous are not selected
1395         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1396           mSlicerManagers[i]->UpdateSlicer(j,1);
1397           AlreadySelected = true;
1398         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1399           if (DataTree->selectedItems().size() == 0)
1400             DataTree->topLevelItem(i)->setSelected(1);
1401           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1402           mSlicerManagers[i]->UpdateSlicer(j,1);
1403           DisplaySliders(i,j);
1404         } else {
1405           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1406           mSlicerManagers[i]->UpdateSlicer(j,0);
1407         }
1408       }
1409       style->Delete();
1410     }
1411   }
1412 }
1413 //------------------------------------------------------------------------------
1414
1415 //------------------------------------------------------------------------------
1416 void vvMainWindow::DisplaySliders(int slicer, int window)
1417 {
1418   int range[2];
1419   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1420   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1421
1422   int tRange[2];
1423   tRange[0] = 0;
1424   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1425   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1426   bool showHorizontal = false;
1427   bool showVertical = false;
1428   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1429       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1430           && mSlicerManagers[slicer]->GetType() != IMAGEWITHTIME
1431           && mSlicerManagers[slicer]->GetType() != MERGEDWITHTIME))
1432     showVertical = true;
1433   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1434       || mSlicerManagers[slicer]->GetType() == IMAGEWITHTIME
1435       || mSlicerManagers[slicer]->GetType() == MERGEDWITHTIME)
1436     showHorizontal = true;
1437
1438   if (showVertical)
1439     verticalSliders[window]->show();
1440   else
1441     verticalSliders[window]->hide();
1442   verticalSliders[window]->setRange(range[0],range[1]);
1443   verticalSliders[window]->setValue(position);
1444
1445   if (showHorizontal)
1446     horizontalSliders[window]->show();
1447   else
1448     horizontalSliders[window]->hide();
1449   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1450   horizontalSliders[window]->setValue(tPosition);
1451 }
1452 //------------------------------------------------------------------------------
1453
1454 //------------------------------------------------------------------------------
1455 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1456 {
1457   int index = GetSlicerIndexFromItem(item);
1458
1459   if (DataTree->topLevelItem(index) != item) {
1460     QString warning = "Do you really want to close the overlay : ";
1461     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1462     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1463                        warning, 0, this);
1464     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1465     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1466     if (msgBox.exec() == QMessageBox::AcceptRole) {
1467       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1468       int overlay_index=0;
1469       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1470         if (DataTree->topLevelItem(index)->\
1471             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1472           overlay_index++;
1473         if (DataTree->topLevelItem(index)->child(child) == item) break;
1474       }
1475       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1476       mSlicerManagers[index]->SetColorMap(0);
1477       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1478       mSlicerManagers[index]->Render();
1479     }
1480   } else if (DataTree->topLevelItemCount() <= 1) {
1481     QString warning = "Do you really want to close the image : ";
1482     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1483     warning += "\nThis is the last image, you're about to close vv !!!";
1484     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1485                        warning, 0, this);
1486     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1487     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1488     if (msgBox.exec() == QMessageBox::AcceptRole) {
1489       this->close();
1490     }
1491   } else {
1492     QString warning = "Do you really want to close the image : ";
1493     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1494     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1495                        warning, 0, this);
1496     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1497     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1498     if (msgBox.exec() == QMessageBox::AcceptRole) {
1499
1500       // Tell tools that we close an image
1501       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1502
1503       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1504       DataTree->takeTopLevelItem(index);
1505       for (int i = 0; i < index; i++) {
1506         Manageriter++;
1507       }
1508       linkPanel->removeImage(index);
1509       mSlicerManagers[index]->RemoveActors();
1510       delete mSlicerManagers[index];
1511       mSlicerManagers.erase(Manageriter);
1512
1513       //
1514       InitDisplay();
1515     }
1516   }
1517   ImageInfoChanged();
1518 }
1519 //------------------------------------------------------------------------------
1520
1521 //------------------------------------------------------------------------------
1522 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1523 {
1524   // int index = GetSlicerIndexFromItem(item);
1525   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1526   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1527   //     mSlicerManagers[index]->ReloadVF();
1528   //   else
1529   //     mSlicerManagers[index]->Reload();
1530
1531   //   QApplication::restoreOverrideCursor();
1532   int index = GetSlicerIndexFromItem(item);
1533   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1534   QString role=item->data(1,Qt::UserRole).toString();
1535   if ( role == "vector")
1536     mSlicerManagers[index]->ReloadVF();
1537   else if (role == "overlay")
1538     mSlicerManagers[index]->ReloadOverlay();
1539   else if (role == "fusion")
1540     mSlicerManagers[index]->ReloadFusion();
1541   else
1542     mSlicerManagers[index]->Reload();
1543
1544   // Update view and info
1545   ImageInfoChanged();
1546   mSlicerManagers[index]->Render();
1547   QApplication::restoreOverrideCursor();
1548 }
1549 //------------------------------------------------------------------------------
1550
1551 //------------------------------------------------------------------------------
1552 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1553 {
1554   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1555 }
1556 //------------------------------------------------------------------------------
1557
1558 //------------------------------------------------------------------------------
1559 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1560 {
1561   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1562 }
1563 //------------------------------------------------------------------------------
1564
1565 //------------------------------------------------------------------------------
1566 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1567 {
1568   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1569 }
1570 //------------------------------------------------------------------------------
1571
1572 //------------------------------------------------------------------------------
1573 void vvMainWindow::FusionChanged(int visibility, double value)
1574 {
1575   overlayPanel->getCurrentFusionInfo(visibility,value);
1576 }
1577 //------------------------------------------------------------------------------
1578
1579 //------------------------------------------------------------------------------
1580 void vvMainWindow::WindowsChanged(int window, int view, int slice)
1581 {
1582   infoPanel->setViews(window, view, slice);
1583 }
1584 //------------------------------------------------------------------------------
1585
1586 //------------------------------------------------------------------------------
1587 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap)
1588 {
1589   windowSpinBox->setValue(window);
1590   levelSpinBox->setValue(level);
1591   colorMapComboBox->setCurrentIndex(colormap);
1592   presetComboBox->setCurrentIndex(preset);
1593 }
1594 //------------------------------------------------------------------------------
1595
1596 //------------------------------------------------------------------------------
1597 void vvMainWindow::WindowLevelEdited()
1598 {
1599   presetComboBox->setCurrentIndex(6);
1600   UpdateWindowLevel();
1601 }
1602 //------------------------------------------------------------------------------
1603
1604 //------------------------------------------------------------------------------
1605 void vvMainWindow::UpdateWindowLevel()
1606 {
1607   if (DataTree->selectedItems().size()) {
1608     if (presetComboBox->currentIndex() == 7) //For ventilation
1609       colorMapComboBox->setCurrentIndex(5);
1610     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1611     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1612     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1613     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1614     mSlicerManagers[index]->Render();
1615   }
1616 }
1617 //------------------------------------------------------------------------------
1618
1619 //------------------------------------------------------------------------------
1620 void vvMainWindow::UpdateColorMap()
1621 {
1622   if (DataTree->selectedItems().size()) {
1623     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1624     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1625     mSlicerManagers[index]->Render();
1626   }
1627 }
1628 //------------------------------------------------------------------------------
1629 void vvMainWindow::SwitchWindowLevel()
1630 {
1631   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1632   int window = mSlicerManagers[index]->GetColorWindow();
1633   presetComboBox->setCurrentIndex(6);
1634   windowSpinBox->setValue(-window);
1635   UpdateWindowLevel();
1636 }
1637 //------------------------------------------------------------------------------
1638
1639 //------------------------------------------------------------------------------
1640 void vvMainWindow::ApplyWindowLevelToAllImages()
1641 {
1642   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1643     if (mSlicerManagers[i] == NULL)
1644       continue;
1645     mSlicerManagers[i]->SetColorWindow(windowSpinBox->value());
1646     mSlicerManagers[i]->SetColorLevel(levelSpinBox->value());
1647     mSlicerManagers[i]->SetPreset(6);
1648     mSlicerManagers[i]->Render();
1649   }
1650 }
1651 //------------------------------------------------------------------------------
1652
1653 //------------------------------------------------------------------------------
1654 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1655 {
1656   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1657     if (mSlicerManagers[i]->GetId() == id) {
1658       //mSlicerManagers[i]->SetTSlice(temps);
1659       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1660       mSlicerManagers[i]->UpdateViews(0,slicer);
1661       break;
1662     }
1663   }
1664 }
1665 //------------------------------------------------------------------------------
1666
1667 //------------------------------------------------------------------------------
1668 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm)
1669 {
1670   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1671     if (id == mSlicerManagers[i]->GetId()) {
1672       mSlicerManagers[i]->UpdateLinkedNavigation(sm->GetSlicer(0));
1673     }
1674   }
1675 }
1676 //------------------------------------------------------------------------------
1677
1678 //------------------------------------------------------------------------------
1679 void vvMainWindow::ShowContextMenu(QPoint point)
1680 {
1681   if (!DataTree->selectedItems().size()) {
1682     contextActions[1]->setEnabled(0);
1683     contextActions[2]->setEnabled(0);
1684     contextActions[3]->setEnabled(0);
1685     contextActions[4]->setEnabled(0);
1686     contextActions[5]->setEnabled(0);
1687     contextActions[6]->setEnabled(0);
1688   } else {
1689     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1690     contextActions[1]->setEnabled(1);
1691     contextActions[2]->setEnabled(
1692       DataTree->itemWidget(DataTree->selectedItems()[0],
1693                            COLUMN_RELOAD_IMAGE)->isEnabled());
1694     contextActions[3]->setEnabled(1);
1695     contextActions[5]->setEnabled(1);
1696     contextActions[6]->setEnabled(1);
1697
1698     if (mSlicerManagers[index]->GetDimension() < 3)
1699       contextActions[4]->setEnabled(0);
1700     else
1701       contextActions[4]->setEnabled(1);
1702   }
1703   contextMenu.exec(QCursor::pos());
1704 }
1705 //------------------------------------------------------------------------------
1706
1707 //------------------------------------------------------------------------------
1708 void vvMainWindow::CloseImage()
1709 {
1710   CloseImage(DataTree->selectedItems()[0],0);
1711 }
1712 //------------------------------------------------------------------------------
1713
1714 //------------------------------------------------------------------------------
1715 void vvMainWindow::ReloadImage()
1716 {
1717   ReloadImage(DataTree->selectedItems()[0],0);
1718 }
1719 //------------------------------------------------------------------------------
1720
1721 //------------------------------------------------------------------------------
1722 void vvMainWindow::SelectOverlayImage()
1723 {
1724   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1725
1726   //check if one overlay image is added
1727   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1728     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1729       QString error = "Cannot add more than one compared image\n";
1730       error += "Please remove first ";
1731       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1732       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1733       return;
1734     }
1735
1736   QString Extensions = EXTENSIONS;
1737   Extensions += ";;All Files (*)";
1738   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1739   if (!file.isEmpty())
1740     AddOverlayImage(index,file);
1741 }
1742 //------------------------------------------------------------------------------
1743
1744 //------------------------------------------------------------------------------
1745 void vvMainWindow::AddOverlayImage(int index, QString file)
1746 {
1747
1748   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1749   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1750                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1751   reader->SetFileName(file.toStdString().c_str());
1752   reader->ReadImageInformation();
1753   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1754   int dimension = reader->GetNumberOfDimensions();
1755   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1756   vvProgressDialog progress("Opening " + file.toStdString());
1757   qApp->processEvents();
1758
1759   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1760   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component)) {
1761     //create an item in the tree with good settings
1762     QTreeWidgetItem *item = new QTreeWidgetItem();
1763     item->setData(0,Qt::UserRole,file.toStdString().c_str());
1764     item->setData(1,Qt::UserRole,tr("overlay"));
1765     QFileInfo fileinfo(file); //Do not show the path
1766     item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1767     item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1768     qApp->processEvents();
1769
1770     for (int j = 1; j <= 4; j++) {
1771       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1772       mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("overlay",0,
1773           DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1774     }
1775
1776     //Create the buttons for reload and close
1777     qApp->processEvents();
1778     QTreePushButton* cButton = new QTreePushButton;
1779     cButton->setItem(item);
1780     cButton->setColumn(COLUMN_CLOSE_IMAGE);
1781     cButton->setToolTip(tr("close image"));
1782     cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1783     connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1784             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1785
1786     QTreePushButton* rButton = new QTreePushButton;
1787     rButton->setItem(item);
1788     rButton->setColumn(COLUMN_RELOAD_IMAGE);
1789     rButton->setToolTip(tr("reload image"));
1790     rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1791     connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1792             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1793
1794     DataTree->topLevelItem(index)->setExpanded(1);
1795     DataTree->topLevelItem(index)->addChild(item);
1796     DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1797     DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1798
1799     //set the id of the image
1800     QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1801     item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1802     UpdateTree();
1803     qApp->processEvents();
1804     ImageInfoChanged();
1805     QApplication::restoreOverrideCursor();
1806   } else {
1807     QApplication::restoreOverrideCursor();
1808     QString error = "Cannot import the new image.\n";
1809     error += mSlicerManagers[index]->GetLastError().c_str();
1810     QMessageBox::information(this,tr("Problem reading image !"),error);
1811   }
1812 }
1813 //------------------------------------------------------------------------------
1814
1815
1816 //------------------------------------------------------------------------------
1817 void vvMainWindow::AddROI(int index, QString file)
1818 {
1819   DD("AddImageAndROI");
1820   /*
1821   // Get slice manager
1822
1823   // Load image
1824
1825   vvImageReader * mReader = new vvImageReader;
1826   mReader->SetInputFilename(filename.toStdString());
1827   mReader->Update(IMAGE);
1828   if (mReader->GetLastError().size() != 0) {
1829     std::cerr << "Error while reading " << filename.toStdString() << std::endl;
1830     QString error = "Cannot open file \n";
1831     error += mReader->GetLastError().c_str();
1832     QMessageBox::information(this,tr("Reading problem"),error);
1833     delete mReader;
1834     return;
1835   }
1836   vvImage::Pointer roi = mReader->GetOutput();
1837
1838   // Create roi in new tool
1839   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
1840 */
1841 }
1842 //------------------------------------------------------------------------------
1843
1844 //------------------------------------------------------------------------------
1845 void vvMainWindow::SelectFusionImage()
1846 {
1847   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1848
1849   //check if one fusion image is added
1850   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1851     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
1852       QString error = "Cannot add more than one fusion image\n";
1853       error += "Please remove first ";
1854       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1855       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1856       return;
1857     }
1858
1859   QString Extensions = EXTENSIONS;
1860   Extensions += ";;All Files (*)";
1861   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1862   if (!file.isEmpty())
1863     AddFusionImage(index,file);
1864 }
1865 //------------------------------------------------------------------------------
1866
1867 //------------------------------------------------------------------------------
1868 void vvMainWindow::AddFusionImage(int index, QString file)
1869 {
1870   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1871   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1872                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1873   reader->SetFileName(file.toStdString().c_str());
1874   reader->ReadImageInformation();
1875   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1876   if (reader) {
1877     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1878     vvProgressDialog progress("Opening fusion");
1879     qApp->processEvents();
1880
1881     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1882     if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1883                                           reader->GetNumberOfDimensions(), component)) {
1884       //create an item in the tree with good settings
1885       QTreeWidgetItem *item = new QTreeWidgetItem();
1886       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1887       item->setData(1,Qt::UserRole,tr("fusion"));
1888       QFileInfo fileinfo(filename.c_str()); //Do not show the path
1889       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1890       item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1891       qApp->processEvents();
1892
1893       for (int j = 1; j <= 4; j++) {
1894         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1895         mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("fusion",0,
1896             DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1897       }
1898
1899       //Create the buttons for reload and close
1900       qApp->processEvents();
1901       QTreePushButton* cButton = new QTreePushButton;
1902       cButton->setItem(item);
1903       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1904       cButton->setToolTip(tr("close image"));
1905       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1906       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1907               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1908
1909       QTreePushButton* rButton = new QTreePushButton;
1910       rButton->setItem(item);
1911       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1912       rButton->setToolTip(tr("reload image"));
1913       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1914       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1915               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1916
1917       DataTree->topLevelItem(index)->setExpanded(1);
1918       DataTree->topLevelItem(index)->addChild(item);
1919       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1920       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1921
1922       //set the id of the image
1923       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1924       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1925       UpdateTree();
1926       qApp->processEvents();
1927       ImageInfoChanged();
1928       QApplication::restoreOverrideCursor();
1929     } else {
1930       QApplication::restoreOverrideCursor();
1931       QString error = "Cannot import the new image.\n";
1932       error += mSlicerManagers[index]->GetLastError().c_str();
1933       QMessageBox::information(this,tr("Problem reading image !"),error);
1934     }
1935   } else {
1936     QString error = "Cannot import the new image.\n";
1937     QMessageBox::information(this,tr("Problem reading image !"),error);
1938   }
1939 }
1940 //------------------------------------------------------------------------------
1941
1942
1943 //------------------------------------------------------------------------------
1944 void vvMainWindow::OpenField()
1945 {
1946   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1947   //check if a vector field has already been added
1948   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1949     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
1950       QString error = "Cannot add more than one vector field\n";
1951       error += "Please remove first ";
1952       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1953       QMessageBox::information(this,tr("Problem adding vector field!"),error);
1954       return;
1955     }
1956
1957   QString Extensions = "Images ( *.mhd)";
1958   Extensions += ";;Images ( *.vf)";
1959   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
1960   if (!file.isEmpty())
1961     AddField(file,index);
1962 }
1963 //------------------------------------------------------------------------------
1964
1965
1966 //------------------------------------------------------------------------------
1967 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
1968 {
1969   //create an item in the tree with good settings
1970   QTreeWidgetItem *item = new QTreeWidgetItem();
1971   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
1972   item->setData(1,Qt::UserRole,tr("vector"));
1973   QFileInfo fileinfo(filename); //Do not show the path
1974   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1975   item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1976   qApp->processEvents();
1977
1978   for (int j = 1; j <= 4; j++) {
1979     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1980     mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("vector",0,
1981         DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1982   }
1983
1984   //Create the buttons for reload and close
1985   qApp->processEvents();
1986   QTreePushButton* cButton = new QTreePushButton;
1987   cButton->setItem(item);
1988   cButton->setColumn(COLUMN_CLOSE_IMAGE);
1989   cButton->setToolTip(tr("close vector field"));
1990   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1991   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1992           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1993
1994   QTreePushButton* rButton = new QTreePushButton;
1995   rButton->setItem(item);
1996   rButton->setColumn(COLUMN_RELOAD_IMAGE);
1997   rButton->setToolTip(tr("reload vector field"));
1998   rButton->setEnabled(from_disk);
1999   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2000   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2001           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2002
2003   DataTree->topLevelItem(index)->setExpanded(1);
2004   DataTree->topLevelItem(index)->addChild(item);
2005   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2006   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2007
2008   //set the id of the image
2009   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2010   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2011   UpdateTree();
2012   qApp->processEvents();
2013   ImageInfoChanged();
2014   QApplication::restoreOverrideCursor();
2015 }
2016 //------------------------------------------------------------------------------
2017
2018
2019 //------------------------------------------------------------------------------
2020 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2021 {
2022   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2023   vvSlicerManager* imageManager = mSlicerManagers[index];
2024   if (imageManager->SetVF(vf,file.toStdString())) {
2025     AddFieldEntry(file,index,false);
2026   } else {
2027     QString error = "Cannot import the vector field for this image.\n";
2028     error += imageManager->GetLastError().c_str();
2029     QMessageBox::information(this,tr("Problem reading VF !"),error);
2030   }
2031   QApplication::restoreOverrideCursor();
2032 }
2033 //------------------------------------------------------------------------------
2034
2035
2036 //------------------------------------------------------------------------------
2037 void vvMainWindow::AddField(QString file,int index)
2038 {
2039   if (QFile::exists(file)) {
2040     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2041
2042     //init the progress events
2043     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2044     vvProgressDialog progress("Opening " + file.toStdString());
2045     qApp->processEvents();
2046
2047     //read the vector and put it in the current mSlicerManager
2048     vvSlicerManager* imageManager = mSlicerManagers[index];
2049     qApp->processEvents();
2050
2051     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2052     if (imageManager->SetVF(file.toStdString())) {
2053       imageManager->Render();
2054       AddFieldEntry(file,index,true);
2055     } else {
2056       QApplication::restoreOverrideCursor();
2057       QString error = "Cannot import the vector field for this image.\n";
2058       error += imageManager->GetLastError().c_str();
2059       QMessageBox::information(this,tr("Problem reading VF !"),error);
2060     }
2061   } else
2062     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2063
2064 }
2065 //------------------------------------------------------------------------------
2066
2067
2068 //------------------------------------------------------------------------------
2069 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width)
2070 {
2071   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2072   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2073     for (int i = 0; i < 4; i++) {
2074       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2075       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2076       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2077       if (log > 0)
2078         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2079       else
2080         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2081     }
2082   }
2083 }
2084 //------------------------------------------------------------------------------
2085
2086
2087 //------------------------------------------------------------------------------
2088 void vvMainWindow::SetOverlayProperty(int color)
2089 {
2090   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2091   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2092     mSlicerManagers[index]->SetOverlayColor(color);
2093     mSlicerManagers[index]->SetColorMap(0);
2094     mSlicerManagers[index]->Render();
2095   }
2096 }
2097 //------------------------------------------------------------------------------
2098
2099 //------------------------------------------------------------------------------
2100 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level)
2101 {
2102   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2103   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2104     mSlicerManagers[index]->SetFusionOpacity(opacity);
2105     mSlicerManagers[index]->SetFusionColorMap(colormap);
2106     mSlicerManagers[index]->SetFusionWindow(window);
2107     mSlicerManagers[index]->SetFusionLevel(level);
2108     mSlicerManagers[index]->SetColorMap(0);
2109     mSlicerManagers[index]->Render();
2110   }
2111 }
2112 //------------------------------------------------------------------------------
2113
2114 //------------------------------------------------------------------------------
2115 void vvMainWindow::SaveAs()
2116 {
2117   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2118     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2119     return;
2120   }
2121
2122   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2123   int dimension = mSlicerManagers[index]->GetDimension();
2124   QStringList OutputListeFormat;
2125   OutputListeFormat.clear();
2126   if (dimension == 1) {
2127     OutputListeFormat.push_back(".mhd");
2128   }
2129   if (dimension == 2) {
2130     OutputListeFormat.push_back(".bmp");
2131     OutputListeFormat.push_back(".png");
2132     OutputListeFormat.push_back(".jpeg");
2133     OutputListeFormat.push_back(".tif");
2134     OutputListeFormat.push_back(".mhd");
2135     OutputListeFormat.push_back(".hdr");
2136     OutputListeFormat.push_back(".vox");
2137   } else if (dimension == 3) {
2138     OutputListeFormat.push_back(".mhd");
2139     OutputListeFormat.push_back(".hdr");
2140     OutputListeFormat.push_back(".vox");
2141   } else if (dimension == 4) {
2142     OutputListeFormat.push_back(".mhd");
2143   }
2144   QString Extensions = "AllFiles(*.*)";
2145   for (int i = 0; i < OutputListeFormat.count(); i++) {
2146     Extensions += ";;Images ( *";
2147     Extensions += OutputListeFormat[i];
2148     Extensions += ")";
2149   }
2150   QString fileName = QFileDialog::getSaveFileName(this,
2151                      tr("Save As"),
2152                      mSlicerManagers[index]->GetFileName().c_str(),
2153                      Extensions);
2154   if (!fileName.isEmpty()) {
2155     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2156     if (OutputListeFormat.contains(
2157           fileformat.c_str())) {
2158       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2159       std::string action = "Saving";
2160       vvProgressDialog progress("Saving "+fileName.toStdString());
2161       qApp->processEvents();
2162       vvImageWriter *writer = new vvImageWriter;
2163       writer->SetOutputFileName(fileName.toStdString());
2164       writer->SetInput(mSlicerManagers[index]->GetImage());
2165       writer->Update();
2166       QApplication::restoreOverrideCursor();
2167       if (writer->GetLastError().size()) {
2168         QString error = "Saving did not succeed\n";
2169         error += writer->GetLastError().c_str();
2170         QMessageBox::information(this,tr("Saving Problem"),error);
2171         SaveAs();
2172       }
2173     } else {
2174       QString error = fileformat.c_str();
2175       if (error.isEmpty())
2176         error += "no file format specified !";
2177       else
2178         error += " format unknown !!!\n";
2179       QMessageBox::information(this,tr("Saving Problem"),error);
2180       SaveAs();
2181     }
2182   }
2183 }
2184 //------------------------------------------------------------------------------
2185
2186
2187 //------------------------------------------------------------------------------
2188 void vvMainWindow::AddLink(QString image1,QString image2)
2189 {
2190   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2191     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2192       mSlicerManagers[i]->AddLink(image2.toStdString());
2193     }
2194     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2195       mSlicerManagers[i]->AddLink(image1.toStdString());
2196     }
2197   }
2198 }
2199 //------------------------------------------------------------------------------
2200
2201
2202 //------------------------------------------------------------------------------
2203 void vvMainWindow::RemoveLink(QString image1,QString image2)
2204 {
2205   // DD("vvMainWindow:RemoveLink");
2206   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2207     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2208       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2209     }
2210     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2211       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2212     }
2213   }
2214 }
2215 //------------------------------------------------------------------------------
2216
2217 //------------------------------------------------------------------------------
2218 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2219 {
2220   int index = 0;
2221   while(sm != mSlicerManagers[index])
2222     index++;
2223   index = (index+offset) % mSlicerManagers.size();
2224
2225   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2226   //CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2227   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2228   DisplayChanged(item,slicer+1);
2229 }
2230 //------------------------------------------------------------------------------
2231
2232 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2233 {
2234   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2235     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2236       for (int j = 0; j < 4; j++) {
2237         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2238         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2239         //UpdateTSlice(j,value);
2240       }
2241       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2242       break;
2243     }
2244   }
2245 }
2246 //------------------------------------------------------------------------------
2247
2248
2249 //------------------------------------------------------------------------------
2250 void vvMainWindow::NOHorizontalSliderMoved()
2251 {
2252   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2253   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2254 //  mCurrentTime = NOHorizontalSlider->value();
2255 }
2256 //------------------------------------------------------------------------------
2257
2258
2259 //------------------------------------------------------------------------------
2260 void vvMainWindow::NEHorizontalSliderMoved()
2261 {
2262   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2263   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2264 //  mCurrentTime = NEHorizontalSlider->value();
2265 }
2266 //------------------------------------------------------------------------------
2267
2268
2269 //------------------------------------------------------------------------------
2270 void vvMainWindow::SOHorizontalSliderMoved()
2271 {
2272   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2273   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2274   // mCurrentTime = SOHorizontalSlider->value();
2275 }
2276 //------------------------------------------------------------------------------
2277
2278
2279 //------------------------------------------------------------------------------
2280 void vvMainWindow::SEHorizontalSliderMoved()
2281 {
2282   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2283   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2284   // mCurrentTime = SEHorizontalSlider->value();
2285 }
2286 //------------------------------------------------------------------------------
2287
2288 //------------------------------------------------------------------------------
2289 void vvMainWindow::NOVerticalSliderChanged()
2290 {
2291   static int value=-1;
2292   if (value == NOVerticalSlider->value()) return;
2293   else value = NOVerticalSlider->value();
2294   //  int value = NOVerticalSlider->value();
2295   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2296     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2297       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2298         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2299         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2300
2301         // If nor Update/Render -> slider not work
2302         // only render = ok navigation, but for contour Update needed but slower ?
2303
2304         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2305         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2306       }
2307       break;
2308     }
2309   }
2310 }
2311 //------------------------------------------------------------------------------
2312
2313
2314 //------------------------------------------------------------------------------
2315 void vvMainWindow::NEVerticalSliderChanged()
2316 {
2317   static int value=-1;
2318   if (value == NEVerticalSlider->value()) return;
2319   else value = NEVerticalSlider->value();
2320   //  int value = NEVerticalSlider->value();
2321   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2322     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2323       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2324         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2325         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2326         mSlicerManagers[i]->UpdateSlice(1);
2327         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2328       }
2329       break;
2330     }
2331   }
2332 }
2333 //------------------------------------------------------------------------------
2334
2335
2336 //------------------------------------------------------------------------------
2337 void vvMainWindow::SOVerticalSliderChanged()
2338 {
2339   static int value=-1;
2340   // DD(value);
2341 //   DD(SOVerticalSlider->value());
2342   if (value == SOVerticalSlider->value()) return;
2343   else value = SOVerticalSlider->value();
2344   //int value = SOVerticalSlider->value();
2345   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2346     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2347       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2348         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2349         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2350         mSlicerManagers[i]->UpdateSlice(2);
2351         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2352       }
2353       // else { DD("avoid SOVerticalSlider slicer update"); }
2354       break;
2355     }
2356   }
2357 }
2358 //------------------------------------------------------------------------------
2359
2360
2361 //------------------------------------------------------------------------------
2362 void vvMainWindow::SEVerticalSliderChanged()
2363 {
2364   static int value=-1;
2365   if (value == SEVerticalSlider->value()) return;
2366   else value = SEVerticalSlider->value();
2367   // int value = SEVerticalSlider->value();
2368   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2369     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2370       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2371         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2372         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2373         mSlicerManagers[i]->UpdateSlice(3);
2374         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2375       }
2376       break;
2377     }
2378   }
2379 }
2380 //------------------------------------------------------------------------------
2381
2382
2383 //------------------------------------------------------------------------------
2384 void vvMainWindow::UpdateSlice(int slicer, int slice)
2385 {
2386   // DD("vvMainWindow::UpdateSlice");
2387 //   DD(slicer);
2388 //   DD(slice);
2389   if (slicer == 0) {
2390     //    if (slice != NOVerticalSlider->value())
2391     NOVerticalSlider->setValue(slice);
2392   } else {
2393     if (slicer == 1)
2394       NEVerticalSlider->setValue(slice);
2395     else {
2396       if (slicer == 2)
2397         SOVerticalSlider->setValue(slice);
2398       else {
2399         if (slicer == 3)
2400           SEVerticalSlider->setValue(slice);
2401       }
2402     }
2403   }
2404   // DD("vvMainWindow:UpdateSlice END");
2405 }
2406 //------------------------------------------------------------------------------
2407
2408
2409 //------------------------------------------------------------------------------
2410 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2411 {
2412   switch (slicer) {
2413   case 0:
2414     NOHorizontalSlider->setValue(slice);
2415     break;
2416   case 1:
2417     NEHorizontalSlider->setValue(slice);
2418     break;
2419   case 2:
2420     SOHorizontalSlider->setValue(slice);
2421     break;
2422   case 3:
2423     SEHorizontalSlider->setValue(slice);
2424     break;
2425   }
2426 }
2427 //------------------------------------------------------------------------------
2428
2429
2430 //------------------------------------------------------------------------------
2431 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2432 {
2433   int position = int((min+max)/2);
2434   int tPosition = int((tmin+tmax)/2);
2435   if (slicer == 0) {
2436     NOVerticalSlider->setValue(position);
2437     NOVerticalSlider->setRange(min,max);
2438     NOHorizontalSlider->setRange(tmin,tmax);
2439     NOHorizontalSlider->setValue(tPosition);
2440   } else if (slicer == 1) {
2441     NEVerticalSlider->setValue(position);
2442     NEVerticalSlider->setRange(min,max);
2443     NEHorizontalSlider->setRange(tmin,tmax);
2444     NEHorizontalSlider->setValue(tPosition);
2445   } else if (slicer == 2) {
2446     SOVerticalSlider->setValue(position);
2447     SOVerticalSlider->setRange(min,max);
2448     SOHorizontalSlider->setRange(tmin,tmax);
2449     SOHorizontalSlider->setValue(tPosition);
2450   } else if (slicer == 3) {
2451     SEVerticalSlider->setValue(position);
2452     SEVerticalSlider->setRange(min,max);
2453     SEHorizontalSlider->setRange(tmin,tmax);
2454     SEHorizontalSlider->setValue(tPosition);
2455   }
2456 }
2457 //------------------------------------------------------------------------------
2458
2459
2460 //------------------------------------------------------------------------------
2461 void vvMainWindow::SaveNOScreenshot()
2462 {
2463   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2464   w2i->SetInput(NOViewWidget->GetRenderWindow());
2465   w2i->Update();
2466   SaveScreenshot(w2i->GetOutput());
2467   w2i->Delete();
2468 }
2469 //------------------------------------------------------------------------------
2470
2471
2472 //------------------------------------------------------------------------------
2473 void vvMainWindow::SaveNEScreenshot()
2474 {
2475   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2476   w2i->SetInput(NEViewWidget->GetRenderWindow());
2477   w2i->Update();
2478   SaveScreenshot(w2i->GetOutput());
2479   w2i->Delete();
2480 }
2481 //------------------------------------------------------------------------------
2482
2483
2484 //------------------------------------------------------------------------------
2485 void vvMainWindow::SaveSOScreenshot()
2486 {
2487   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2488   w2i->SetInput(SOViewWidget->GetRenderWindow());
2489   w2i->Update();
2490   SaveScreenshot(w2i->GetOutput());
2491   w2i->Delete();
2492 }
2493 //------------------------------------------------------------------------------
2494
2495
2496 //------------------------------------------------------------------------------
2497 void vvMainWindow::SaveSEScreenshot()
2498 {
2499   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2500   w2i->SetInput(SEViewWidget->GetRenderWindow());
2501   w2i->Update();
2502   SaveScreenshot(w2i->GetOutput());
2503   w2i->Delete();
2504 }
2505 //------------------------------------------------------------------------------
2506
2507
2508 //------------------------------------------------------------------------------
2509 void vvMainWindow::SaveScreenshot(vtkImageData* image)
2510 {
2511   QString Extensions = "Images( *.png);;";
2512   Extensions += "Images( *.jpg);;";
2513   Extensions += "Images( *.bmp);;";
2514   Extensions += "Images( *.tif);;";
2515   Extensions += "Images( *.ppm)";
2516   QString fileName = QFileDialog::getSaveFileName(this,
2517                      tr("Save As"),
2518                      itksys::SystemTools::GetFilenamePath(
2519                        mSlicerManagers[0]->GetFileName()).c_str(),
2520                      Extensions);
2521   if (!fileName.isEmpty()) {
2522     const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2523     if (!strcmp(ext, ".bmp")) {
2524       vtkBMPWriter *bmp = vtkBMPWriter::New();
2525       bmp->SetInput(image);
2526       bmp->SetFileName(fileName.toStdString().c_str());
2527       bmp->Write();
2528       bmp->Delete();
2529     } else if (!strcmp(ext, ".tif")) {
2530       vtkTIFFWriter *tif = vtkTIFFWriter::New();
2531       tif->SetInput(image);
2532       tif->SetFileName(fileName.toStdString().c_str());
2533       tif->Write();
2534       tif->Delete();
2535     } else if (!strcmp(ext, ".ppm")) {
2536       vtkPNMWriter *pnm = vtkPNMWriter::New();
2537       pnm->SetInput(image);
2538       pnm->SetFileName(fileName.toStdString().c_str());
2539       pnm->Write();
2540       pnm->Delete();
2541     } else if (!strcmp(ext, ".png")) {
2542       vtkPNGWriter *png = vtkPNGWriter::New();
2543       png->SetInput(image);
2544       png->SetFileName(fileName.toStdString().c_str());
2545       png->Write();
2546       png->Delete();
2547     } else if (!strcmp(ext, ".jpg")) {
2548       vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2549       jpg->SetInput(image);
2550       jpg->SetFileName(fileName.toStdString().c_str());
2551       jpg->Write();
2552       jpg->Delete();
2553     } else {
2554       QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2555     }
2556   }
2557
2558 }
2559 //------------------------------------------------------------------------------
2560
2561
2562 //------------------------------------------------------------------------------
2563 void vvMainWindow::GoToCursor()
2564 {
2565   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2566   for (int column = 1; column < 5; column++) {
2567     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
2568       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2569       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2570         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2571       mSlicerManagers[index]->UpdateViews(1,column-1);
2572       mSlicerManagers[index]->UpdateLinked(column-1);
2573       break;
2574     }
2575   }
2576 }
2577 //------------------------------------------------------------------------------
2578
2579 //------------------------------------------------------------------------------
2580 void vvMainWindow::PlayPause()
2581 {
2582   if (playMode) {
2583     playMode = 0;
2584     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2585     ImageInfoChanged();
2586     return;
2587   } else {
2588     int image_number=DataTree->topLevelItemCount();
2589     bool has_temporal;
2590     for (int i=0; i<image_number; i++)
2591       if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1) {
2592         has_temporal=true;
2593         break;
2594       }
2595     if (has_temporal) {
2596       playMode = 1;
2597       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2598       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2599     }
2600   }
2601 }
2602 //------------------------------------------------------------------------------
2603
2604 //------------------------------------------------------------------------------
2605 void vvMainWindow::PlayNext()
2606 {
2607   if (playMode && !this->isHidden()) {
2608     int image_number=DataTree->topLevelItemCount();
2609     ///Only play one slicer per SM, and only if the SM is being displayed
2610     for (int i=0; i<image_number; i++)
2611       for (int j=0; j<4; j++)
2612         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2613             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
2614           mSlicerManagers[i]->SetNextTSlice(j);
2615           break;
2616         }
2617     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2618   }
2619 }
2620 //------------------------------------------------------------------------------
2621
2622 void vvMainWindow::ShowLastImage()
2623 {
2624   if (mSlicerManagers.size() > 1) {
2625     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2626     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2627     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2628     DisplayChanged(item,1);
2629   }
2630 }
2631
2632 //------------------------------------------------------------------------------
2633 void vvMainWindow::UpdateRenderWindows()
2634 {
2635   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2636   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2637   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2638   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2639 }
2640 //------------------------------------------------------------------------------
2641
2642 //------------------------------------------------------------------------------
2643 void vvMainWindow::SegmentationOnCurrentImage()
2644 {
2645   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2646
2647   vvSegmentationDialog segmentation;
2648   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2649   segmentation.exec();
2650 }
2651 //------------------------------------------------------------------------------
2652
2653 void vvMainWindow::SurfaceViewerLaunch()
2654 {
2655   vvSurfaceViewerDialog surfaceViewer;
2656   surfaceViewer.exec();
2657 }
2658 //------------------------------------------------------------------------------
2659
2660
2661 //------------------------------------------------------------------------------
2662 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
2663 {
2664   int number=0;
2665   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
2666     vvSlicerManager * v = mSlicerManagers[l];
2667     if (v->GetBaseFileName() ==
2668         vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
2669       number = std::max(number, v->GetBaseFileNameNumber()+1);
2670     }
2671   }
2672   return number;
2673 }
2674 //------------------------------------------------------------------------------
2675
2676
2677 //------------------------------------------------------------------------------
2678 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2679 {
2680   // Change filename if another image exist with the same name
2681   int number = GetImageDuplicateFilenameNumber(filename);
2682
2683   // Create new SliceManager
2684   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
2685   slicer_manager->SetImage(image);//, IMAGE, number);
2686   //  filename = filename+"_"+clitk::toString(number);
2687   slicer_manager->SetFilename(filename, number);
2688   mSlicerManagers.push_back(slicer_manager);
2689
2690   //create an item in the tree with good settings
2691   QTreeWidgetItem *item = new QTreeWidgetItem();
2692   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2693   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
2694   qApp->processEvents();
2695
2696   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2697
2698   //Create the buttons for reload and close
2699   qApp->processEvents();
2700   QTreePushButton* cButton = new QTreePushButton;
2701   cButton->setItem(item);
2702   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2703   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2704   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2705           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2706
2707   QTreePushButton* rButton = new QTreePushButton;
2708   rButton->setItem(item);
2709   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2710   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2711   rButton->setEnabled(0);
2712   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2713           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2714
2715   DataTree->addTopLevelItem(item);
2716   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2717   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2718
2719   //set the id of the image
2720   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2721   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2722   mSlicerManagers.back()->SetId(id.toStdString());
2723
2724   linkPanel->addImage(filename, id.toStdString());
2725
2726   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
2727           this, SLOT(CurrentImageChanged(std::string)));
2728   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
2729           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2730   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
2731           this, SLOT(VectorChanged(int,double,double,double, double)));
2732   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
2733           this, SLOT(OverlayChanged(int,double,double)));
2734   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
2735           this, SLOT(FusionChanged(int,double)));
2736   connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
2737           this,SLOT(WindowsChanged(int, int, int)));
2738   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
2739           this,SLOT(WindowLevelChanged(double, double, int, int)));
2740   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
2741           this,SLOT(UpdateSlice(int,int)));
2742   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
2743           this,SLOT(UpdateTSlice(int, int)));
2744   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2745           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2746   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2747           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2748   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*)),
2749           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*)));
2750   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
2751           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
2752   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2753   UpdateTree();
2754   qApp->processEvents();
2755   InitSlicers();
2756   ShowLastImage();
2757   InitDisplay();
2758   qApp->processEvents();
2759
2760   // End
2761   ImageInfoChanged();
2762   return slicer_manager;
2763 }
2764 //------------------------------------------------------------------------------
2765
2766
2767 //------------------------------------------------------------------------------
2768 void vvMainWindow::UpdateCurrentSlicer()
2769 {
2770   int index = -1;
2771   if (DataTree->selectedItems().size() > 0) {
2772     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2773   }
2774   mSlicerManagerCurrentIndex = index;
2775 }
2776 //------------------------------------------------------------------------------
2777