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 #include "vtkMatrix4x4.h"
  71 #include "vtkTransform.h"
  72
  73 // Standard includes
  74 #include <iostream>
  75 #include <sstream>
  76 #include <iomanip>
  77
  78 #define COLUMN_TREE 0
  79 #define COLUMN_UL_VIEW 1
  80 #define COLUMN_UR_VIEW 2
  81 #define COLUMN_DL_VIEW 3
  82 #define COLUMN_DR_VIEW 4
  83 #define COLUMN_CLOSE_IMAGE 5
  84 #define COLUMN_RELOAD_IMAGE 6
  85 #define COLUMN_IMAGE_NAME 7
  86
  87 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.hdr *.vox *.his *.xdr *.SCAN )"
  88
  89 /*Data Tree values
  90   0,Qt::UserRole full filename
  91   1,Qt::CheckStateRole checkbutton UL View
  92   1,Qt::UserRole overlay, fusion or vector
  93   2,Qt::CheckStateRole checkbutton UR View
  94   3,Qt::CheckStateRole checkbutton DL View
  95   4,Qt::CheckStateRole checkbutton DR View
  96   5,0  short filename
  97   5,Qt::UserRole mSlicerManager id*/
  98
  99 //------------------------------------------------------------------------------
 100 vvMainWindow::vvMainWindow():vvMainWindowBase()
 101 {
 102   setupUi(this); // this sets up the GUI
 103
 104   mInputPathName = "";
 105   mMenuTools = menuTools;
 106   //  mMenuSegmentation = menuSegmentation;
 107   mContextMenu = &contextMenu;
 108   mMenuExperimentalTools = menuExperimental;
 109   mMainWidget = this;
 110   mCurrentTime = -1;
 111   mCurrentSelectedImageId = "";
 112
 113   //Init the contextMenu
 114   this->setContextMenuPolicy(Qt::CustomContextMenu);
 115   contextActions.resize(0);
 116   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 117                                   tr("O&pen new Image"));
 118   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 119   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 120   contextActions.push_back(actionOpen_new_image);
 121   contextMenu.addSeparator();
 122
 123   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 124                                tr("Close Current Image"));
 125   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 126   contextActions.push_back(actionClose_Image);
 127
 128   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 129                                 tr("Reload Current Image"));
 130   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 131   contextActions.push_back(actionReload_image);
 132
 133   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 134                               tr("Save Current Image"));
 135   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 136   contextActions.push_back(actionSave_image);
 137
 138   contextMenu.addSeparator();
 139
 140   contextMenu.addAction(actionAdd_VF_to_current_Image);
 141   contextActions.push_back(actionAdd_VF_to_current_Image);
 142
 143   QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 144       tr("Add overlay image to current image"));
 145   contextMenu.addAction(actionAdd_Overlay_to_current_Image);
 146   contextActions.push_back(actionAdd_Overlay_to_current_Image);
 147
 148   connect(actionAdd_Overlay_to_current_Image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 149
 150   contextMenu.addAction(actionAdd_fusion_image);
 151   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 152   contextActions.push_back(actionAdd_fusion_image);
 153
 154   // TRIAL DS
 155   /*
 156   QMenu * m = new QMenu(menubar);
 157   m->setTitle("TOTO");
 158   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 159   contextMenu.addMenu(m);
 160   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 161                      tr("BIDON"));
 162   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 163                      tr("BIDON2"));
 164   m->addAction(a);
 165   m->addAction(b);
 166   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 167   */
 168
 169   //init the DataTree
 170   mSlicerManagers.resize(0);
 171
 172   QStringList header;
 173   header.append("");
 174   header.append("TL");
 175   header.append("TR");
 176   header.append("BL");
 177   header.append("BR");
 178   header.append("");
 179   header.append("");
 180   header.append("Name");
 181
 182   DataTree->setHeaderLabels(header);
 183   DataTree->resizeColumnToContents(COLUMN_TREE);
 184   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 185   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 186   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 187   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 188   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 189   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 190   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 191
 192   viewMode = 1;
 193   documentation = new vvDocumentation();
 194   help_dialog = new vvHelpDialog();
 195   dicomSeriesSelector = new vvDicomSeriesSelector();
 196
 197   inverseButton->setEnabled(0);
 198   actionAdd_Overlay_to_current_Image->setEnabled(0);
 199   actionSave_As->setEnabled(0);
 200   actionAdd_VF_to_current_Image->setEnabled(0);
 201   actionAdd_fusion_image->setEnabled(0);
 202
 203   //init the sliders
 204   verticalSliders.push_back(NOVerticalSlider);
 205   verticalSliders.push_back(NEVerticalSlider);
 206   verticalSliders.push_back(SOVerticalSlider);
 207   verticalSliders.push_back(SEVerticalSlider);
 208
 209   for (int i =0; i < 4; i++)
 210     verticalSliders[i]->hide();
 211
 212   horizontalSliders.push_back(NOHorizontalSlider);
 213   horizontalSliders.push_back(NEHorizontalSlider);
 214   horizontalSliders.push_back(SOHorizontalSlider);
 215   horizontalSliders.push_back(SEHorizontalSlider);
 216
 217   for (int i =0; i < 4; i++)
 218     horizontalSliders[i]->hide();
 219
 220
 221   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 222   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 223   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 224   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 225
 226   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 227   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 228   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 229   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 230
 231   //connect everything
 232   connect(actionMaximum_Intensity_Projection,SIGNAL(triggered()),this,SLOT(ComputeMIP()));
 233   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 234   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 235   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 236   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 237   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 238   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 239   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 240   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 241   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 242   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 243   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 244   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 245   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 246   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 247   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 248   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 249
 250   ///////////////////////////////////////////////
 251   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 252   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 253   ///////////////////////////////////////////////
 254
 255   actionNorth_East_Window->setEnabled(0);
 256   actionNorth_West_Window->setEnabled(0);
 257   actionSouth_East_Window->setEnabled(0);
 258   actionSouth_West_Window->setEnabled(0);
 259
 260   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 261   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 262   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 263   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 264
 265   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 266   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 267           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 268
 269   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 270   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 271   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 272   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 273   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 274   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 275   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 276
 277
 278   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 279
 280   connect(linkPanel,SIGNAL(addLink(QString,QString)),this,SLOT(AddLink(QString,QString)));
 281   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 282   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int)),this,SLOT(SetVFProperty(int,int,int,int)));
 283   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int)),this,SLOT(SetOverlayProperty(int)));
 284   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,double,double)),
 285           this,SLOT(SetFusionProperty(int,int,double,double)));
 286   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 287
 288   playMode = 0;//pause
 289   mFrameRate = 10;
 290   playButton->setEnabled(0);
 291   frameRateLabel->setEnabled(0);
 292   frameRateSpinBox->setEnabled(0);
 293   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 294   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 295
 296   goToCursorPushButton->setEnabled(0);
 297   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 298
 299   NOViewWidget->hide();
 300   NEViewWidget->hide();
 301   SOViewWidget->hide();
 302   SEViewWidget->hide();
 303
 304   //Recently opened files
 305   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 306   if ( !recent_files.empty() ) {
 307     QMenu * rmenu = new QMenu("Recently opened files...");
 308     rmenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 309     menuFile->insertMenu(actionOpen_Image_With_Time,rmenu);
 310     menuFile->insertSeparator(actionOpen_Image_With_Time);
 311     for (std::list<std::string>::iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 312       QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")),
 313                                    (*i).c_str(),this);
 314       rmenu->addAction(current);
 315       connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 316     }
 317   }
 318
 319   // Adding all new tools (insertion in the menu)
 320   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 321
 322   if (!CLITK_EXPERIMENTAL)
 323     menuExperimental->menuAction()->setVisible(false);
 324
 325
 326   QTimer * timerMemory = new QTimer(this);
 327   //timerMemory->setInterval(5);
 328   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 329   timerMemory->start(2000);
 330 }
 331 //------------------------------------------------------------------------------
 332
 333
 334 //------------------------------------------------------------------------------
 335 void vvMainWindow::UpdateMemoryUsage()
 336 {
 337   //  clitk::PrintMemory(true);
 338   infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 339 }
 340 //------------------------------------------------------------------------------
 341
 342
 343 //------------------------------------------------------------------------------
 344 void vvMainWindow::ComputeMIP()
 345 {
 346   vvMaximumIntensityProjection mip;
 347   vvSlicerManager* selected_slicer = mSlicerManagers[GetSlicerIndexFromItem(DataTree->selectedItems()[0])];
 348   QFileInfo info(selected_slicer->GetFileName().c_str());
 349   mip.Compute(selected_slicer);
 350   if (!mip.error)
 351     AddImage(mip.GetOutput(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_mip.mhd");
 352 }
 353 //------------------------------------------------------------------------------
 354
 355
 356 //------------------------------------------------------------------------------
 357 void vvMainWindow::ComputeMidPosition()
 358 {
 359   bool ok;
 360   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 361   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 362                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 363   if (ok) {
 364     vvMidPosition midp;
 365     midp.slicer_manager = mSlicerManagers[index];
 366     midp.reference_image_index = ref;
 367     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 368     midp.Update();
 369     if (midp.error)
 370       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 371     else {
 372       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 373       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 374     }
 375     QApplication::restoreOverrideCursor();
 376   }
 377 }
 378 //------------------------------------------------------------------------------
 379
 380
 381 //------------------------------------------------------------------------------
 382 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 383 {
 384   QTreeWidgetItem *item = new QTreeWidgetItem();
 385   item->setData(0,Qt::UserRole,"filename.vtk");
 386   item->setData(1,Qt::UserRole,tr("contour"));
 387   QBrush brush;
 388   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 389   brush.setStyle(Qt::SolidPattern);
 390   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 391   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 392
 393   for (int j = 1; j <= 4; j++)
 394     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 395
 396   QTreePushButton* cButton = new QTreePushButton;
 397   cButton->setItem(item);
 398   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 399   cButton->setToolTip(tr("close image"));
 400   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 401   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 402           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 403
 404   QTreePushButton* rButton = new QTreePushButton;
 405   rButton->setItem(item);
 406   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 407   rButton->setToolTip(tr("reload image"));
 408   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 409   rButton->setEnabled(false);
 410   //Not implemented
 411   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 412   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 413
 414   DataTree->topLevelItem(image_index)->setExpanded(1);
 415   DataTree->topLevelItem(image_index)->addChild(item);
 416   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 417   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 418   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 419   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 420
 421   UpdateTree();
 422   mSlicerManagers[image_index]->AddContour(contour,propagation);
 423   mSlicerManagers[image_index]->Render();
 424 }
 425 //------------------------------------------------------------------------------
 426
 427
 428 //------------------------------------------------------------------------------
 429 void vvMainWindow::OpenVTKContour()
 430 {
 431   if (mSlicerManagers.size() > 0) {
 432     QString Extensions = "Images ( *.vtk *.obj)";
 433     Extensions += ";;All Files (*)";
 434     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 435     if (file.isNull())
 436       return;
 437     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 438     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 439     vvMeshReader reader;
 440     reader.SetImage(mSlicerManagers[index]->GetImage());
 441     reader.SetModeToVTK();
 442     reader.SetFilename(file.toStdString());
 443     reader.Update();
 444     AddContour(index,reader.GetOutput()[0],false);
 445     QApplication::restoreOverrideCursor();
 446   }
 447 }
 448 //------------------------------------------------------------------------------
 449
 450
 451 //------------------------------------------------------------------------------
 452 void vvMainWindow::OpenDCStructContour()
 453 {
 454   if (mSlicerManagers.size() > 0) {
 455     QString Extensions = "Dicom Files ( *.dcm RS*)";
 456     Extensions += ";;All Files (*)";
 457     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 458     if (file.isNull())
 459       return;
 460     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 461     vvMeshReader reader;
 462     reader.SetFilename(file.toStdString());
 463     vvStructSelector selector;
 464     selector.SetStructures(reader.GetROINames());
 465     if (!mSlicerManagers[index]->GetVF().IsNull())
 466       selector.EnablePropagationCheckBox();
 467     if (selector.exec()) {
 468       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 469       reader.SetSelectedItems(selector.getSelectedItems());
 470       reader.SetImage(mSlicerManagers[index]->GetImage());
 471       if (selector.PropagationEnabled())
 472         reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 473       reader.Update();
 474       std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 475       for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 476            i!=contours.end(); i++)
 477         AddContour(index,*i,selector.PropagationEnabled());
 478       QApplication::restoreOverrideCursor();
 479     }
 480   }
 481 }
 482 //------------------------------------------------------------------------------
 483
 484
 485 //------------------------------------------------------------------------------
 486 void vvMainWindow::ComputeDeformableRegistration()
 487 {
 488   if (mSlicerManagers.size() > 0) {
 489     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 490     vvDeformationDialog dialog(index,mSlicerManagers);
 491     if (dialog.exec()) {
 492       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 493       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 494       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 495     } else
 496       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 497   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 498 }
 499 //------------------------------------------------------------------------------
 500
 501
 502 //------------------------------------------------------------------------------
 503 void vvMainWindow::WarpImage()
 504 {
 505   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 506   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 507     bool ok;
 508     int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 509                                        mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 510     if (ok) {
 511       WarpImage(mSlicerManagers[index],ref);
 512     }
 513   } else
 514     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 515 }
 516 //------------------------------------------------------------------------------
 517
 518
 519 //------------------------------------------------------------------------------
 520 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 521 {
 522   if (!selected_slicer->GetVF().IsNull()) {
 523     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 524     QFileInfo info(selected_slicer->GetFileName().c_str());
 525     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 526                      reference_phase,this);
 527     if (warp.ComputeWarpedImage()) {
 528       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 529       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 530       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 531       QApplication::restoreOverrideCursor();
 532     } else {
 533       QApplication::restoreOverrideCursor();
 534       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 535     }
 536   } else
 537     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 538 }
 539 //------------------------------------------------------------------------------
 540
 541
 542 //------------------------------------------------------------------------------
 543 vvMainWindow::~vvMainWindow()
 544 {
 545   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 546     if (mSlicerManagers[i] != NULL)
 547       delete mSlicerManagers[i];
 548   }
 549 }
 550 //------------------------------------------------------------------------------
 551
 552 //------------------------------------------------------------------------------
 553 QTabWidget * vvMainWindow::GetTab()
 554 {
 555   return tabWidget;
 556 }
 557 //------------------------------------------------------------------------------
 558
 559
 560 //------------------------------------------------------------------------------
 561 void vvMainWindow::MergeImages()
 562 {
 563   QString Extensions = EXTENSIONS;
 564   Extensions += ";;All Files (*)";
 565   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 566   if (files.isEmpty())
 567     return;
 568   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 569   std::vector<std::string> vector;
 570
 571   unsigned int currentDim = 0;
 572   std::vector<double> currentSpacing;
 573   std::vector<int> currentSize;
 574   std::vector<double> currentOrigin;
 575
 576   for (int i = 0; i < files.size(); i++) {
 577     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 578                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 579     reader->SetFileName(files[i].toStdString().c_str());
 580     reader->ReadImageInformation();
 581     if (reader)        {
 582       //NOViewWidget->hide();
 583       //NEViewWidget->hide();
 584       //SOViewWidget->hide();
 585       //SEViewWidget->hide();
 586       if (i == 0)
 587         currentDim = reader->GetNumberOfDimensions();
 588       bool IsOk = true;
 589       for (unsigned int j = 0; j < currentDim; j++) {
 590         if (i == 0) {
 591           if (j == 0) {
 592             currentSpacing.resize(currentDim);
 593             currentSize.resize(currentDim);
 594             currentOrigin.resize(currentDim);
 595           }
 596           currentOrigin[j] = reader->GetOrigin(j);
 597           currentSpacing[j] = reader->GetSpacing(j);
 598           currentSize[j] = reader->GetDimensions(j);
 599         } else if (currentDim != reader->GetNumberOfDimensions()
 600                    || currentSpacing[j] != reader->GetSpacing(j)
 601                    || currentSize[j] != (int)reader->GetDimensions(j)
 602                    || currentOrigin[j] != reader->GetOrigin(j)) {
 603           QString error = "Cannot read file (too different from others ";
 604           error += files[i].toStdString().c_str();
 605           QMessageBox::information(this,tr("Reading problem"),error);
 606           IsOk = false;
 607           break;
 608         }
 609       }
 610       if (IsOk)
 611         vector.push_back(files[i].toStdString());
 612     }
 613   }
 614   if (vector.size() > 0)
 615     LoadImages(vector, MERGED);
 616 }
 617 //------------------------------------------------------------------------------
 618
 619 //------------------------------------------------------------------------------
 620 void vvMainWindow::SliceImages()
 621 {
 622   QString Extensions = EXTENSIONS;
 623   Extensions += ";;All Files (*)";
 624
 625   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 626   if (files.isEmpty())
 627     return;
 628   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 629   std::vector<std::string> vector;
 630   for (int i = 0; i < files.size(); i++)
 631     vector.push_back(files[i].toStdString());
 632   LoadImages(vector, SLICED);
 633 }
 634 //------------------------------------------------------------------------------
 635
 636 //------------------------------------------------------------------------------
 637 void vvMainWindow::MergeImagesWithTime()
 638 {
 639   QString Extensions = EXTENSIONS;
 640   Extensions += ";;All Files (*)";
 641   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 642   if (files.isEmpty())
 643     return;
 644   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 645   std::vector<std::string> vector;
 646
 647   unsigned int currentDim = 0;
 648   std::vector<double> currentSpacing;
 649   std::vector<int> currentSize;
 650   std::vector<double> currentOrigin;
 651
 652   for (int i = 0; i < files.size(); i++) {
 653     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 654                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 655     if (reader) {
 656       reader->SetFileName(files[i].toStdString().c_str());
 657       reader->ReadImageInformation();
 658       if (i == 0)
 659         currentDim = reader->GetNumberOfDimensions();
 660       bool IsOk = true;
 661       for (unsigned int j = 0; j < currentDim; j++) {
 662         if (i == 0) {
 663           if (j == 0) {
 664             currentSpacing.resize(currentDim);
 665             currentSize.resize(currentDim);
 666             currentOrigin.resize(currentDim);
 667           }
 668           currentOrigin[j] = reader->GetOrigin(j);
 669           currentSpacing[j] = reader->GetSpacing(j);
 670           currentSize[j] = reader->GetDimensions(j);
 671         } else if (currentDim != reader->GetNumberOfDimensions()
 672                    || currentSpacing[j] != reader->GetSpacing(j)
 673                    || currentSize[j] != (int)reader->GetDimensions(j)
 674                    || currentOrigin[j] != reader->GetOrigin(j)) {
 675           QString error = "Cannot read file (too different from others ";
 676           error += files[i].toStdString().c_str();
 677           QMessageBox::information(this,tr("Reading problem"),error);
 678           IsOk = false;
 679           break;
 680         }
 681       }
 682       if (IsOk)
 683         vector.push_back(files[i].toStdString());
 684     } else {
 685       QString error = "Cannot read file info for ";
 686       error += files[i].toStdString().c_str();
 687       error += "\n";
 688       error += "Maybe you're trying to open an image in an unsupported format?\n";
 689       QMessageBox::information(this,tr("Reading problem"),error);
 690     }
 691   }
 692   sort(vector.begin(),vector.end());
 693   if (vector.size() > 1)
 694     LoadImages(vector, MERGEDWITHTIME);
 695   else
 696     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.");
 697 }
 698 //------------------------------------------------------------------------------
 699
 700
 701 //------------------------------------------------------------------------------
 702 void vvMainWindow::OpenDicom()
 703 {
 704   std::vector<std::string> files;
 705
 706   std::cout << "dicomSeriesSelector " << std::endl;
 707   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 708     files = *(dicomSeriesSelector->GetFilenames());
 709     LoadImages(files,DICOM);
 710   }
 711 }
 712 //------------------------------------------------------------------------------
 713
 714 //------------------------------------------------------------------------------
 715 void vvMainWindow::OpenImages()
 716 {
 717   QString Extensions = EXTENSIONS;
 718   Extensions += ";;All Files (*)";
 719
 720   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 721   if (files.isEmpty())
 722     return;
 723   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 724   std::vector<std::string> vector;
 725   for (int i = 0; i < files.size(); i++)
 726     vector.push_back(files[i].toStdString());
 727   LoadImages(vector, IMAGE);
 728 }
 729 //------------------------------------------------------------------------------
 730 void vvMainWindow::OpenRecentImage()
 731 {
 732   QAction * caller = qobject_cast<QAction*>(sender());
 733   std::vector<std::string> images;
 734   images.push_back(caller->text().toStdString());
 735   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 736   LoadImages(images,IMAGE);
 737 }
 738 //------------------------------------------------------------------------------
 739
 740
 741 //------------------------------------------------------------------------------
 742 void vvMainWindow::OpenImageWithTime()
 743 {
 744   QString Extensions = EXTENSIONS;
 745   Extensions += ";;All Files (*)";
 746
 747   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 748   if (files.isEmpty())
 749     return;
 750   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 751   std::vector<std::string> vector;
 752   for (int i = 0; i < files.size(); i++) {
 753     vector.push_back(files[i].toStdString());
 754   }
 755   LoadImages(vector, IMAGEWITHTIME);
 756 }
 757 //------------------------------------------------------------------------------
 758
 759
 760 //------------------------------------------------------------------------------
 761 void vvMainWindow::LoadImages(std::vector<std::string> files, LoadedImageType filetype)
 762 {
 763   //Separate the way to open images and dicoms
 764   int fileSize;
 765   if (filetype == IMAGE || filetype == IMAGEWITHTIME)
 766     fileSize = files.size();
 767   else
 768     fileSize = 1;
 769
 770   // For SLICED, we need the number of slices (ndim and #slices)
 771   std::vector<unsigned int> nSlices;
 772   nSlices.resize(files.size());
 773   std::fill(nSlices.begin(), nSlices.end(), 1);
 774   if (filetype == SLICED) {
 775     for (int i = 0; i < fileSize; i++) {
 776       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 777       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 778       if (!header) {
 779         nSlices[i] = 0;
 780         QString error = "Cannot open file \n";
 781         error += files[i].c_str();
 782         QMessageBox::information(this,tr("Reading problem"),error);
 783         return;
 784       }
 785       if (header->GetNumberOfDimensions() < 3) {
 786         nSlices[i] = 0;
 787         QString error = "Dimension problem. Cannot slice \n";
 788         error += files[i].c_str();
 789         QMessageBox::information(this,tr("Reading problem"),error);
 790         return;
 791       }
 792       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 793     }
 794   }
 795
 796   //Only add to the list of recently opened files when a single file is opened,
 797   //to avoid polluting the list of recently opened files
 798   if (files.size() == 1) {
 799     QFileInfo finfo=tr(files[0].c_str());
 800     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 801   }
 802   //init the progress events
 803   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 804   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 805   qApp->processEvents();
 806
 807   int numberofsuccesulreads=0;
 808   //open images as 1 or multiples
 809   for (int i = 0; i < fileSize; i++) {
 810
 811     progress.SetText("Opening " + files[i]);
 812     progress.SetProgress(i,fileSize);
 813     qApp->processEvents();
 814
 815     for (unsigned int j = 0; j < nSlices[i]; j++) {
 816       //read the image and put it in mSlicerManagers
 817       vvSlicerManager* imageManager = new vvSlicerManager(4);
 818       qApp->processEvents();
 819
 820       bool SetImageSucceed=false;
 821
 822       // Change filename if an image with the same already exist
 823       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 824
 825       if (filetype == IMAGE || filetype == IMAGEWITHTIME || filetype == SLICED)
 826         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 827       else {
 828         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 829       }
 830       if (SetImageSucceed == false) {
 831         QApplication::restoreOverrideCursor();
 832         QString error = "Cannot open file \n";
 833         error += imageManager->GetLastError().c_str();
 834         QMessageBox::information(this,tr("Reading problem"),error);
 835         delete imageManager;
 836       } else {
 837         mSlicerManagers.push_back(imageManager);
 838
 839         //create an item in the tree with good settings
 840         QTreeWidgetItem *item = new QTreeWidgetItem();
 841         item->setData(0,Qt::UserRole,files[i].c_str());
 842         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 843         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 844         item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
 845         qApp->processEvents();
 846
 847         //Create the buttons for reload and close
 848         qApp->processEvents();
 849         QTreePushButton* cButton = new QTreePushButton;
 850         cButton->setItem(item);
 851         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 852         cButton->setToolTip(tr("close image"));
 853         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 854         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 855                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 856
 857         QTreePushButton* rButton = new QTreePushButton;
 858         rButton->setItem(item);
 859         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 860         rButton->setToolTip(tr("reload image"));
 861         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 862         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 863                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 864
 865         DataTree->addTopLevelItem(item);
 866         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 867         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 868
 869         //set the id of the image
 870         QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 871         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 872         mSlicerManagers.back()->SetId(id.toStdString());
 873
 874         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 875
 876         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 877                 this,SLOT(CurrentImageChanged(std::string)));
 878         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 879                 this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 880         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 881                 this, SLOT(VectorChanged(int,double,double,double, double)));
 882         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 883                 this, SLOT(OverlayChanged(int,double,double)));
 884         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 885                 this, SLOT(FusionChanged(int,double)));
 886         connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
 887                 this,SLOT(WindowsChanged(int, int, int)));
 888         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
 889                 this,SLOT(WindowLevelChanged(double, double, int, int)));
 890         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 891                 this,SLOT(UpdateSlice(int,int)));
 892         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 893                 this,SLOT(UpdateTSlice(int, int)));
 894         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 895                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 896         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 897                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 898         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*)),
 899                 this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*)));
 900         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 901                 this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 902         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 903         InitSlicers();
 904       }
 905       numberofsuccesulreads++;
 906     }
 907   }
 908   if (numberofsuccesulreads) {
 909     NOViewWidget->show();
 910     NEViewWidget->show();
 911     SOViewWidget->show();
 912     SEViewWidget->show();
 913     UpdateTree();
 914     InitDisplay();
 915     ShowLastImage();
 916
 917     // Try to guess default WindowLevel
 918     double range[2];
 919     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 920     // DD(range[0]);
 921     //   DD(range[1]);
 922     if ((range[0] == 0) && (range[1] == 1)) {
 923       presetComboBox->setCurrentIndex(5);// binary
 924     } else {
 925       // TODO
 926     }
 927   }
 928   QApplication::restoreOverrideCursor();
 929 }
 930 //------------------------------------------------------------------------------
 931
 932 //------------------------------------------------------------------------------
 933 void vvMainWindow::UpdateTree()
 934 {
 935   DataTree->resizeColumnToContents(COLUMN_TREE);
 936   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 937   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 938   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 939   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 940   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 941   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 942   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 943 }
 944 //------------------------------------------------------------------------------
 945
 946 //------------------------------------------------------------------------------
 947 void vvMainWindow::CurrentImageChanged(std::string id)
 948 {
 949   // DD("CurrentImageChanged");
 950 //   DD(id);
 951 //   DD(mCurrentSelectedImageId);
 952   if (id == mCurrentSelectedImageId) return; // Do nothing
 953   int selected = 0;
 954   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 955     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 956       selected = i;
 957     } else {
 958       DataTree->topLevelItem(i)->setSelected(0);
 959     }
 960     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 961       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 962
 963   }
 964   DataTree->topLevelItem(selected)->setSelected(1);
 965   // DD(mSlicerManagers[selected]->GetFileName());
 966   mCurrentSelectedImageId = id;
 967   emit SelectedImageHasChanged(mSlicerManagers[selected]);
 968 }
 969 //------------------------------------------------------------------------------
 970
 971 //------------------------------------------------------------------------------
 972 void vvMainWindow::ImageInfoChanged()
 973 {
 974   contextActions[6]->setEnabled(1);
 975   contextActions[5]->setEnabled(1);
 976   actionSave_As->setEnabled(1);
 977   actionAdd_VF_to_current_Image->setEnabled(1);
 978   actionAdd_fusion_image->setEnabled(1);
 979   actionNorth_East_Window->setEnabled(1);
 980   actionNorth_West_Window->setEnabled(1);
 981   actionSouth_East_Window->setEnabled(1);
 982   actionSouth_West_Window->setEnabled(1);
 983   inverseButton->setEnabled(1);
 984
 985   goToCursorPushButton->setEnabled(1);
 986
 987   if (DataTree->selectedItems().size()) {
 988     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 989
 990     colorMapComboBox->setEnabled(1);
 991     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
 992       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
 993           DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion") {
 994         colorMapComboBox->setEnabled(0);
 995         break;
 996       }
 997     }
 998
 999     std::vector<double> origin;
1000     std::vector<double> inputSpacing;
1001     std::vector<int> inputSize;
1002     std::vector<double> sizeMM;
1003     vtkSmartPointer<vtkMatrix4x4> transformation;
1004     int dimension=0;
1005     QString pixelType;
1006     QString inputSizeInBytes;
1007     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1008
1009     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1) {
1010       playButton->setEnabled(1);
1011       frameRateLabel->setEnabled(1);
1012       frameRateSpinBox->setEnabled(1);
1013     } else {
1014       playButton->setEnabled(0);
1015       frameRateLabel->setEnabled(0);
1016       frameRateSpinBox->setEnabled(0);
1017     }
1018
1019     //read image header
1020     int NPixel = 1;
1021
1022     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1023       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1024       dimension = imageSelected->GetNumberOfDimensions();
1025       origin.resize(dimension);
1026       inputSpacing.resize(dimension);
1027       inputSize.resize(dimension);
1028       sizeMM.resize(dimension);
1029       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1030       for (int i = 0; i < dimension; i++) {
1031         origin[i] = imageSelected->GetOrigin()[i];
1032         inputSpacing[i] = imageSelected->GetSpacing()[i];
1033         inputSize[i] = imageSelected->GetSize()[i];
1034         sizeMM[i] = inputSize[i]*inputSpacing[i];
1035         NPixel *= inputSize[i];
1036       }
1037       transformation = imageSelected->GetTransform()->GetMatrix();
1038       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1039     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1040       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1041       dimension = imageSelected->GetNumberOfDimensions();
1042       origin.resize(dimension);
1043       inputSpacing.resize(dimension);
1044       inputSize.resize(dimension);
1045       sizeMM.resize(dimension);
1046       pixelType = mSlicerManagers[index]->GetVF()->GetScalarTypeAsITKString().c_str();
1047       for (int i = 0; i < dimension; i++) {
1048         origin[i] = imageSelected->GetOrigin()[i];
1049         inputSpacing[i] = imageSelected->GetSpacing()[i];
1050         inputSize[i] = imageSelected->GetSize()[i];
1051         sizeMM[i] = inputSize[i]*inputSpacing[i];
1052         NPixel *= inputSize[i];
1053       }
1054       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1055     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1056       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1057       dimension = imageSelected->GetNumberOfDimensions();
1058       origin.resize(dimension);
1059       inputSpacing.resize(dimension);
1060       inputSize.resize(dimension);
1061       sizeMM.resize(dimension);
1062       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1063       for (int i = 0; i < dimension; i++) {
1064         origin[i] = imageSelected->GetOrigin()[i];
1065         inputSpacing[i] = imageSelected->GetSpacing()[i];
1066         inputSize[i] = imageSelected->GetSize()[i];
1067         sizeMM[i] = inputSize[i]*inputSpacing[i];
1068         NPixel *= inputSize[i];
1069       }
1070       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1071     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1072       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1073       dimension = imageSelected->GetNumberOfDimensions();
1074       origin.resize(dimension);
1075       inputSpacing.resize(dimension);
1076       inputSize.resize(dimension);
1077       sizeMM.resize(dimension);
1078       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1079       for (int i = 0; i < dimension; i++) {
1080         origin[i] = imageSelected->GetOrigin()[i];
1081         inputSpacing[i] = imageSelected->GetSpacing()[i];
1082         inputSize[i] = imageSelected->GetSize()[i];
1083         sizeMM[i] = inputSize[i]*inputSpacing[i];
1084         NPixel *= inputSize[i];
1085       }
1086       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1087     }
1088
1089     QString dim = QString::number(dimension) + " (";
1090     dim += pixelType + ")";
1091
1092     infoPanel->setFileName(image);
1093     infoPanel->setDimension(dim);
1094     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1095     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1096     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1097     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1098     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1099     infoPanel->setTransformation(Get4x4MatrixDoubleAsString(transformation));
1100
1101     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1102                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1103     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1104     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1105
1106     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1107     for (int i = 0; i < 4; i++) {
1108       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1109         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1110         break;
1111       }
1112     }
1113     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1114     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1115     // DD(mSlicerManagers[index]->GetColorMap());
1116     // DD(mSlicerManagers[index]->GetPreset());
1117     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1118     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1119
1120     infoPanel->setFileName(image);
1121     infoPanel->setDimension(dim);
1122     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1123     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1124     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1125     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1126     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1127
1128     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1129                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1130     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1131     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1132
1133     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1134     for (int i = 0; i < 4; i++) {
1135       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1136         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1137         break;
1138       }
1139     }
1140     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1141     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1142     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1143     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1144
1145     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1146       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1147       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1148                                   mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1149                                   mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1150     } else {
1151       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1152       overlayPanel->getVFProperty(-1,-1,-1);
1153     }
1154     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1155       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1156       overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1157     } else {
1158       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1159       overlayPanel->getOverlayProperty(-1);
1160     }
1161     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1162       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1163       overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1164                                       mSlicerManagers[index]->GetFusionColorMap(),
1165                                       mSlicerManagers[index]->GetFusionWindow(),
1166                                       mSlicerManagers[index]->GetFusionLevel());
1167     } else {
1168       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1169       overlayPanel->getFusionProperty(-1, -1,-1,-1);
1170     }
1171   }
1172 }
1173 //------------------------------------------------------------------------------
1174
1175 //------------------------------------------------------------------------------
1176 void vvMainWindow::ShowDocumentation()
1177 {
1178   documentation->show();
1179 }
1180 //------------------------------------------------------------------------------
1181 void vvMainWindow::ShowHelpDialog()
1182 {
1183   help_dialog->show();
1184 }
1185 //------------------------------------------------------------------------------
1186
1187 //------------------------------------------------------------------------------
1188 void vvMainWindow::ChangeViewMode()
1189 {
1190   QListIterator<int> it0(splitter_3->sizes());
1191   QListIterator<int> it1(splitter_3->sizes());
1192   int max0 = 0;
1193   int max1 = 1;
1194   while (it0.hasNext()) {
1195     max0 += it0.next();
1196   }
1197   while (it1.hasNext()) {
1198     max1 += it1.next();
1199   }
1200   QList<int> size0;
1201   QList<int> size1;
1202   if (viewMode == 1) {
1203     viewMode = 0;
1204     size0.push_back(max0);
1205     size0.push_back(0);
1206     size1.push_back(max1);
1207     size1.push_back(0);
1208     splitter_3->setSizes(size0);
1209     OSplitter->setSizes(size1);
1210     DataTree->setColumnHidden(2,1);
1211     DataTree->setColumnHidden(3,1);
1212     DataTree->setColumnHidden(4,1);
1213   } else {
1214     viewMode = 1;
1215     size0.push_back(int(max0/2));
1216     size0.push_back(int(max0/2));
1217     size1.push_back(int(max1/2));
1218     size1.push_back(int(max1/2));
1219     splitter_3->setSizes(size0);
1220     OSplitter->setSizes(size1);
1221     DataTree->setColumnHidden(2,0);
1222     DataTree->setColumnHidden(3,0);
1223     DataTree->setColumnHidden(4,0);
1224   }
1225 }
1226 //------------------------------------------------------------------------------
1227
1228 //------------------------------------------------------------------------------
1229 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1230 {
1231   QString result = "";// QString::number(size);
1232   //result += " bytes (";
1233   if (size > 1000000000) {
1234     size /= 1000000000;
1235     result += QString::number(size);
1236     result += "Gb";//)";
1237   } else if (size > 1000000) {
1238     size /= 1000000;
1239     result += QString::number(size);
1240     result += "Mb";//)";
1241   } else if (size > 1000) {
1242     size /= 1000;
1243     result += QString::number(size);
1244     result += "kb";//)";
1245   }
1246   return result;
1247 }
1248 //------------------------------------------------------------------------------
1249
1250 //------------------------------------------------------------------------------
1251 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix)
1252 {
1253   std::ostringstream strmatrix;
1254
1255   for (unsigned int i = 0; i < 4; i++) {
1256     for (unsigned int j = 0; j < 4; j++) {
1257       strmatrix.flags(ios::showpos);
1258       strmatrix.width(10);
1259       strmatrix.precision(3);
1260       strmatrix.setf(ios::fixed,ios::floatfield);
1261       strmatrix.fill(' ');
1262       strmatrix << std::left << matrix->GetElement(i, j);
1263       //strmatrix.width(10);
1264       strmatrix << " ";
1265     }
1266     strmatrix << std::endl;
1267   }
1268   QString result = strmatrix.str().c_str();
1269   return result;
1270 }
1271 //------------------------------------------------------------------------------
1272
1273 //------------------------------------------------------------------------------
1274 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1275 {
1276   QString result;
1277   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1278     if (i != 0)
1279       result += " ";
1280     result += QString::number(vectorDouble[i]);
1281   }
1282   return result;
1283 }
1284 //------------------------------------------------------------------------------
1285
1286 //------------------------------------------------------------------------------
1287 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1288 {
1289   QString result;
1290   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1291     if (i != 0)
1292       result += " ";
1293     result += QString::number(vectorInt[i]);
1294   }
1295   return result;
1296 }
1297 //------------------------------------------------------------------------------
1298
1299 //------------------------------------------------------------------------------
1300 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1301 {
1302   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1303   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1304     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1305       return i;
1306   }
1307   return -1;
1308 }
1309 //------------------------------------------------------------------------------
1310
1311 //------------------------------------------------------------------------------
1312 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1313 {
1314   QString id = sm->GetId().c_str();
1315   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1316     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1317       return DataTree->topLevelItem(i);
1318   }
1319   return NULL;
1320 }
1321 //------------------------------------------------------------------------------
1322
1323 //------------------------------------------------------------------------------
1324 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clicked_item, int column)
1325 {
1326   int index = GetSlicerIndexFromItem(clicked_item);
1327   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1328     return;
1329   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1330     //Trick to avoid redoing twice the job for a key (sr)
1331     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()-> GetInteractor()->SetKeySym("Crap");
1332
1333     QTreeWidgetItem* current_row=DataTree->topLevelItem(i);
1334     if (DataTree->topLevelItem(index) == current_row) {
1335       vvSlicer* clicked_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1336       if (current_row == clicked_item) {
1337         //If we just activated a slicer
1338         if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1339           mSlicerManagers[i]->UpdateSlicer(column-1,clicked_item->data(column,Qt::CheckStateRole).toInt());
1340           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1341           DisplaySliders(i,column-1);
1342           std::map<std::string,int> overlay_counts;
1343           for (int child = 0; child < current_row->childCount(); child++) {
1344             std::string overlay_type =
1345               current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1346             overlay_counts[overlay_type]++;
1347             current_row->child(child)->setData(column,Qt::CheckStateRole,
1348                                                current_row->data(column,Qt::CheckStateRole));
1349             clicked_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,true);
1350           }
1351         } else { //We don't allow simply desactivating a slicer
1352           clicked_item->setData(column,Qt::CheckStateRole,2);
1353           return;
1354         }
1355       }
1356       //if we clicked on the vector(or overlay) and not the image
1357       else {
1358         if (clicked_item->data(column,Qt::CheckStateRole).toInt()) {
1359           current_row->setData(column,Qt::CheckStateRole,2);
1360           mSlicerManagers[i]->UpdateSlicer(column-1,2);
1361           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1362           DisplaySliders(i,column-1);
1363         }
1364         int vis = clicked_item->data(column,Qt::CheckStateRole).toInt();
1365         std::string overlay_type = clicked_item->data(1,Qt::UserRole).toString().toStdString();
1366         int overlay_index=0;
1367         for (int child = 0; child < current_row->childCount(); child++) {
1368           if (current_row->child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1369             overlay_index++;
1370           if (current_row->child(child) == clicked_item) break;
1371         }
1372         clicked_slicer->SetActorVisibility(
1373           clicked_item->data(1,Qt::UserRole).toString().toStdString(), overlay_index-1,vis);
1374       }
1375     } else if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1376       current_row->setData(column,Qt::CheckStateRole,0);
1377       mSlicerManagers[i]->UpdateSlicer(column-1,0);
1378       std::map<std::string,int> overlay_counts;
1379       for (int child = 0; child < current_row->childCount(); child++) {
1380         std::string overlay_type =
1381           current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1382         overlay_counts[overlay_type]++;
1383         current_row->child(child)->setData(column,Qt::CheckStateRole,0);
1384         vvSlicer * current_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1385         current_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,false);
1386       }
1387     }
1388     //mSlicerManagers[i]->SetColorMap(-1);
1389     mSlicerManagers[i]->SetColorMap();
1390   }
1391   mSlicerManagers[index]->GetSlicer(column-1)->Render();
1392 }
1393 //------------------------------------------------------------------------------
1394
1395 void vvMainWindow::InitSlicers()
1396 {
1397   if (mSlicerManagers.size()) {
1398     mSlicerManagers.back()->GenerateDefaultLookupTable();
1399
1400     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1401     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1402     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1403     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1404   }
1405 }
1406
1407 //------------------------------------------------------------------------------
1408 void vvMainWindow::InitDisplay()
1409 {
1410   if (mSlicerManagers.size()) {
1411     //BE CAREFUL : this is absolutely necessary to set the interactor style
1412     //in order to have the same style instanciation for all SlicerManagers in
1413     // a same window
1414     for (int j = 0; j < 4; j++) {
1415       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1416       style->SetAutoAdjustCameraClippingRange(1);
1417       bool AlreadySelected = false;
1418       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1419         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1420
1421         //select the image only if previous are not selected
1422         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1423           mSlicerManagers[i]->UpdateSlicer(j,1);
1424           AlreadySelected = true;
1425         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1426           if (DataTree->selectedItems().size() == 0)
1427             DataTree->topLevelItem(i)->setSelected(1);
1428           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1429           mSlicerManagers[i]->UpdateSlicer(j,1);
1430           DisplaySliders(i,j);
1431         } else {
1432           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1433           mSlicerManagers[i]->UpdateSlicer(j,0);
1434         }
1435       }
1436       style->Delete();
1437     }
1438   }
1439 }
1440 //------------------------------------------------------------------------------
1441
1442 //------------------------------------------------------------------------------
1443 void vvMainWindow::DisplaySliders(int slicer, int window)
1444 {
1445   int range[2];
1446   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1447   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1448
1449   int tRange[2];
1450   tRange[0] = 0;
1451   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1452   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1453   bool showHorizontal = false;
1454   bool showVertical = false;
1455   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1456       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1457           && mSlicerManagers[slicer]->GetType() != IMAGEWITHTIME
1458           && mSlicerManagers[slicer]->GetType() != MERGEDWITHTIME))
1459     showVertical = true;
1460   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1461       || mSlicerManagers[slicer]->GetType() == IMAGEWITHTIME
1462       || mSlicerManagers[slicer]->GetType() == MERGEDWITHTIME)
1463     showHorizontal = true;
1464
1465   if (showVertical)
1466     verticalSliders[window]->show();
1467   else
1468     verticalSliders[window]->hide();
1469   verticalSliders[window]->setRange(range[0],range[1]);
1470   verticalSliders[window]->setValue(position);
1471
1472   if (showHorizontal)
1473     horizontalSliders[window]->show();
1474   else
1475     horizontalSliders[window]->hide();
1476   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1477   horizontalSliders[window]->setValue(tPosition);
1478 }
1479 //------------------------------------------------------------------------------
1480
1481 //------------------------------------------------------------------------------
1482 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1483 {
1484   int index = GetSlicerIndexFromItem(item);
1485
1486   if (DataTree->topLevelItem(index) != item) {
1487     QString warning = "Do you really want to close the overlay : ";
1488     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1489     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1490                        warning, 0, this);
1491     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1492     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1493     if (msgBox.exec() == QMessageBox::AcceptRole) {
1494       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1495       int overlay_index=0;
1496       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1497         if (DataTree->topLevelItem(index)->\
1498             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1499           overlay_index++;
1500         if (DataTree->topLevelItem(index)->child(child) == item) break;
1501       }
1502       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1503       mSlicerManagers[index]->SetColorMap(0);
1504       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1505       mSlicerManagers[index]->Render();
1506     }
1507   } else if (DataTree->topLevelItemCount() <= 1) {
1508     QString warning = "Do you really want to close the image : ";
1509     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1510     warning += "\nThis is the last image, you're about to close vv !!!";
1511     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1512                        warning, 0, this);
1513     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1514     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1515     if (msgBox.exec() == QMessageBox::AcceptRole) {
1516       this->close();
1517     }
1518   } else {
1519     QString warning = "Do you really want to close the image : ";
1520     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1521     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1522                        warning, 0, this);
1523     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1524     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1525     if (msgBox.exec() == QMessageBox::AcceptRole) {
1526
1527       // Tell tools that we close an image
1528       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1529
1530       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1531       DataTree->takeTopLevelItem(index);
1532       for (int i = 0; i < index; i++) {
1533         Manageriter++;
1534       }
1535       linkPanel->removeImage(index);
1536       mSlicerManagers[index]->RemoveActors();
1537       delete mSlicerManagers[index];
1538       mSlicerManagers.erase(Manageriter);
1539
1540       //
1541       InitDisplay();
1542     }
1543   }
1544   ImageInfoChanged();
1545 }
1546 //------------------------------------------------------------------------------
1547
1548 //------------------------------------------------------------------------------
1549 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1550 {
1551   // int index = GetSlicerIndexFromItem(item);
1552   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1553   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1554   //     mSlicerManagers[index]->ReloadVF();
1555   //   else
1556   //     mSlicerManagers[index]->Reload();
1557
1558   //   QApplication::restoreOverrideCursor();
1559   int index = GetSlicerIndexFromItem(item);
1560   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1561   QString role=item->data(1,Qt::UserRole).toString();
1562   if ( role == "vector")
1563     mSlicerManagers[index]->ReloadVF();
1564   else if (role == "overlay")
1565     mSlicerManagers[index]->ReloadOverlay();
1566   else if (role == "fusion")
1567     mSlicerManagers[index]->ReloadFusion();
1568   else
1569     mSlicerManagers[index]->Reload();
1570
1571   // Update view and info
1572   ImageInfoChanged();
1573   mSlicerManagers[index]->Render();
1574   QApplication::restoreOverrideCursor();
1575 }
1576 //------------------------------------------------------------------------------
1577
1578 //------------------------------------------------------------------------------
1579 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1580 {
1581   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1582 }
1583 //------------------------------------------------------------------------------
1584
1585 //------------------------------------------------------------------------------
1586 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1587 {
1588   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1589 }
1590 //------------------------------------------------------------------------------
1591
1592 //------------------------------------------------------------------------------
1593 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1594 {
1595   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1596 }
1597 //------------------------------------------------------------------------------
1598
1599 //------------------------------------------------------------------------------
1600 void vvMainWindow::FusionChanged(int visibility, double value)
1601 {
1602   overlayPanel->getCurrentFusionInfo(visibility,value);
1603 }
1604 //------------------------------------------------------------------------------
1605
1606 //------------------------------------------------------------------------------
1607 void vvMainWindow::WindowsChanged(int window, int view, int slice)
1608 {
1609   infoPanel->setViews(window, view, slice);
1610 }
1611 //------------------------------------------------------------------------------
1612
1613 //------------------------------------------------------------------------------
1614 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap)
1615 {
1616   windowSpinBox->setValue(window);
1617   levelSpinBox->setValue(level);
1618   colorMapComboBox->setCurrentIndex(colormap);
1619   presetComboBox->setCurrentIndex(preset);
1620 }
1621 //------------------------------------------------------------------------------
1622
1623 //------------------------------------------------------------------------------
1624 void vvMainWindow::WindowLevelEdited()
1625 {
1626   presetComboBox->setCurrentIndex(6);
1627   UpdateWindowLevel();
1628 }
1629 //------------------------------------------------------------------------------
1630
1631 //------------------------------------------------------------------------------
1632 void vvMainWindow::UpdateWindowLevel()
1633 {
1634   if (DataTree->selectedItems().size()) {
1635     if (presetComboBox->currentIndex() == 7) //For ventilation
1636       colorMapComboBox->setCurrentIndex(5);
1637     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1638     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1639     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1640     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1641     mSlicerManagers[index]->Render();
1642   }
1643 }
1644 //------------------------------------------------------------------------------
1645
1646 //------------------------------------------------------------------------------
1647 void vvMainWindow::UpdateColorMap()
1648 {
1649   if (DataTree->selectedItems().size()) {
1650     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1651     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1652     mSlicerManagers[index]->Render();
1653   }
1654 }
1655 //------------------------------------------------------------------------------
1656 void vvMainWindow::SwitchWindowLevel()
1657 {
1658   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1659   int window = mSlicerManagers[index]->GetColorWindow();
1660   presetComboBox->setCurrentIndex(6);
1661   windowSpinBox->setValue(-window);
1662   UpdateWindowLevel();
1663 }
1664 //------------------------------------------------------------------------------
1665
1666 //------------------------------------------------------------------------------
1667 void vvMainWindow::ApplyWindowLevelToAllImages()
1668 {
1669   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1670     if (mSlicerManagers[i] == NULL)
1671       continue;
1672     mSlicerManagers[i]->SetColorWindow(windowSpinBox->value());
1673     mSlicerManagers[i]->SetColorLevel(levelSpinBox->value());
1674     mSlicerManagers[i]->SetPreset(6);
1675     mSlicerManagers[i]->Render();
1676   }
1677 }
1678 //------------------------------------------------------------------------------
1679
1680 //------------------------------------------------------------------------------
1681 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1682 {
1683   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1684     if (mSlicerManagers[i]->GetId() == id) {
1685       //mSlicerManagers[i]->SetTSlice(temps);
1686       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1687       mSlicerManagers[i]->UpdateViews(0,slicer);
1688       break;
1689     }
1690   }
1691 }
1692 //------------------------------------------------------------------------------
1693
1694 //------------------------------------------------------------------------------
1695 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm)
1696 {
1697   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1698     if (id == mSlicerManagers[i]->GetId()) {
1699       mSlicerManagers[i]->UpdateLinkedNavigation(sm->GetSlicer(0));
1700     }
1701   }
1702 }
1703 //------------------------------------------------------------------------------
1704
1705 //------------------------------------------------------------------------------
1706 void vvMainWindow::ShowContextMenu(QPoint point)
1707 {
1708   if (!DataTree->selectedItems().size()) {
1709     contextActions[1]->setEnabled(0);
1710     contextActions[2]->setEnabled(0);
1711     contextActions[3]->setEnabled(0);
1712     contextActions[4]->setEnabled(0);
1713     contextActions[5]->setEnabled(0);
1714     contextActions[6]->setEnabled(0);
1715   } else {
1716     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1717     contextActions[1]->setEnabled(1);
1718     contextActions[2]->setEnabled(
1719       DataTree->itemWidget(DataTree->selectedItems()[0],
1720                            COLUMN_RELOAD_IMAGE)->isEnabled());
1721     contextActions[3]->setEnabled(1);
1722     contextActions[5]->setEnabled(1);
1723     contextActions[6]->setEnabled(1);
1724
1725     if (mSlicerManagers[index]->GetDimension() < 3)
1726       contextActions[4]->setEnabled(0);
1727     else
1728       contextActions[4]->setEnabled(1);
1729   }
1730   contextMenu.exec(QCursor::pos());
1731 }
1732 //------------------------------------------------------------------------------
1733
1734 //------------------------------------------------------------------------------
1735 void vvMainWindow::CloseImage()
1736 {
1737   CloseImage(DataTree->selectedItems()[0],0);
1738 }
1739 //------------------------------------------------------------------------------
1740
1741 //------------------------------------------------------------------------------
1742 void vvMainWindow::ReloadImage()
1743 {
1744   ReloadImage(DataTree->selectedItems()[0],0);
1745 }
1746 //------------------------------------------------------------------------------
1747
1748 //------------------------------------------------------------------------------
1749 void vvMainWindow::SelectOverlayImage()
1750 {
1751   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1752
1753   //check if one overlay image is added
1754   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1755     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1756       QString error = "Cannot add more than one compared image\n";
1757       error += "Please remove first ";
1758       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1759       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1760       return;
1761     }
1762
1763   QString Extensions = EXTENSIONS;
1764   Extensions += ";;All Files (*)";
1765   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1766   if (!file.isEmpty())
1767     AddOverlayImage(index,file);
1768 }
1769 //------------------------------------------------------------------------------
1770
1771 //------------------------------------------------------------------------------
1772 void vvMainWindow::AddOverlayImage(int index, QString file)
1773 {
1774
1775   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1776   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1777                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1778   reader->SetFileName(file.toStdString().c_str());
1779   reader->ReadImageInformation();
1780   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1781   int dimension = reader->GetNumberOfDimensions();
1782   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1783   vvProgressDialog progress("Opening " + file.toStdString());
1784   qApp->processEvents();
1785
1786   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1787   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component)) {
1788     //create an item in the tree with good settings
1789     QTreeWidgetItem *item = new QTreeWidgetItem();
1790     item->setData(0,Qt::UserRole,file.toStdString().c_str());
1791     item->setData(1,Qt::UserRole,tr("overlay"));
1792     QFileInfo fileinfo(file); //Do not show the path
1793     item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1794     item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1795     qApp->processEvents();
1796
1797     for (int j = 1; j <= 4; j++) {
1798       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1799       mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("overlay",0,
1800           DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1801     }
1802
1803     //Create the buttons for reload and close
1804     qApp->processEvents();
1805     QTreePushButton* cButton = new QTreePushButton;
1806     cButton->setItem(item);
1807     cButton->setColumn(COLUMN_CLOSE_IMAGE);
1808     cButton->setToolTip(tr("close image"));
1809     cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1810     connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1811             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1812
1813     QTreePushButton* rButton = new QTreePushButton;
1814     rButton->setItem(item);
1815     rButton->setColumn(COLUMN_RELOAD_IMAGE);
1816     rButton->setToolTip(tr("reload image"));
1817     rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1818     connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1819             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1820
1821     DataTree->topLevelItem(index)->setExpanded(1);
1822     DataTree->topLevelItem(index)->addChild(item);
1823     DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1824     DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1825
1826     //set the id of the image
1827     QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1828     item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1829     UpdateTree();
1830     qApp->processEvents();
1831     ImageInfoChanged();
1832     QApplication::restoreOverrideCursor();
1833   } else {
1834     QApplication::restoreOverrideCursor();
1835     QString error = "Cannot import the new image.\n";
1836     error += mSlicerManagers[index]->GetLastError().c_str();
1837     QMessageBox::information(this,tr("Problem reading image !"),error);
1838   }
1839 }
1840 //------------------------------------------------------------------------------
1841
1842
1843 //------------------------------------------------------------------------------
1844 void vvMainWindow::AddROI(int index, QString file)
1845 {
1846   DD("AddImageAndROI");
1847   /*
1848   // Get slice manager
1849
1850   // Load image
1851
1852   vvImageReader * mReader = new vvImageReader;
1853   mReader->SetInputFilename(filename.toStdString());
1854   mReader->Update(IMAGE);
1855   if (mReader->GetLastError().size() != 0) {
1856     std::cerr << "Error while reading " << filename.toStdString() << std::endl;
1857     QString error = "Cannot open file \n";
1858     error += mReader->GetLastError().c_str();
1859     QMessageBox::information(this,tr("Reading problem"),error);
1860     delete mReader;
1861     return;
1862   }
1863   vvImage::Pointer roi = mReader->GetOutput();
1864
1865   // Create roi in new tool
1866   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
1867 */
1868 }
1869 //------------------------------------------------------------------------------
1870
1871 //------------------------------------------------------------------------------
1872 void vvMainWindow::SelectFusionImage()
1873 {
1874   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1875
1876   //check if one fusion image is added
1877   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1878     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
1879       QString error = "Cannot add more than one fusion image\n";
1880       error += "Please remove first ";
1881       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1882       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1883       return;
1884     }
1885
1886   QString Extensions = EXTENSIONS;
1887   Extensions += ";;All Files (*)";
1888   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1889   if (!file.isEmpty())
1890     AddFusionImage(index,file);
1891 }
1892 //------------------------------------------------------------------------------
1893
1894 //------------------------------------------------------------------------------
1895 void vvMainWindow::AddFusionImage(int index, QString file)
1896 {
1897   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1898   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1899                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1900   reader->SetFileName(file.toStdString().c_str());
1901   reader->ReadImageInformation();
1902   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1903   if (reader) {
1904     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1905     vvProgressDialog progress("Opening fusion");
1906     qApp->processEvents();
1907
1908     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1909     if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1910                                           reader->GetNumberOfDimensions(), component)) {
1911       //create an item in the tree with good settings
1912       QTreeWidgetItem *item = new QTreeWidgetItem();
1913       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1914       item->setData(1,Qt::UserRole,tr("fusion"));
1915       QFileInfo fileinfo(filename.c_str()); //Do not show the path
1916       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1917       item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1918       qApp->processEvents();
1919
1920       for (int j = 1; j <= 4; j++) {
1921         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1922         mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("fusion",0,
1923             DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1924       }
1925
1926       //Create the buttons for reload and close
1927       qApp->processEvents();
1928       QTreePushButton* cButton = new QTreePushButton;
1929       cButton->setItem(item);
1930       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1931       cButton->setToolTip(tr("close image"));
1932       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1933       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1934               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1935
1936       QTreePushButton* rButton = new QTreePushButton;
1937       rButton->setItem(item);
1938       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1939       rButton->setToolTip(tr("reload image"));
1940       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1941       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1942               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1943
1944       DataTree->topLevelItem(index)->setExpanded(1);
1945       DataTree->topLevelItem(index)->addChild(item);
1946       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1947       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1948
1949       //set the id of the image
1950       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1951       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1952       UpdateTree();
1953       qApp->processEvents();
1954       ImageInfoChanged();
1955       QApplication::restoreOverrideCursor();
1956     } else {
1957       QApplication::restoreOverrideCursor();
1958       QString error = "Cannot import the new image.\n";
1959       error += mSlicerManagers[index]->GetLastError().c_str();
1960       QMessageBox::information(this,tr("Problem reading image !"),error);
1961     }
1962   } else {
1963     QString error = "Cannot import the new image.\n";
1964     QMessageBox::information(this,tr("Problem reading image !"),error);
1965   }
1966 }
1967 //------------------------------------------------------------------------------
1968
1969
1970 //------------------------------------------------------------------------------
1971 void vvMainWindow::OpenField()
1972 {
1973   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1974   //check if a vector field has already been added
1975   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1976     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
1977       QString error = "Cannot add more than one vector field\n";
1978       error += "Please remove first ";
1979       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1980       QMessageBox::information(this,tr("Problem adding vector field!"),error);
1981       return;
1982     }
1983
1984   QString Extensions = "Images ( *.mhd)";
1985   Extensions += ";;Images ( *.vf)";
1986   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
1987   if (!file.isEmpty())
1988     AddField(file,index);
1989 }
1990 //------------------------------------------------------------------------------
1991
1992
1993 //------------------------------------------------------------------------------
1994 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
1995 {
1996   //create an item in the tree with good settings
1997   QTreeWidgetItem *item = new QTreeWidgetItem();
1998   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
1999   item->setData(1,Qt::UserRole,tr("vector"));
2000   QFileInfo fileinfo(filename); //Do not show the path
2001   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2002   item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
2003   qApp->processEvents();
2004
2005   for (int j = 1; j <= 4; j++) {
2006     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2007     mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("vector",0,
2008         DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
2009   }
2010
2011   //Create the buttons for reload and close
2012   qApp->processEvents();
2013   QTreePushButton* cButton = new QTreePushButton;
2014   cButton->setItem(item);
2015   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2016   cButton->setToolTip(tr("close vector field"));
2017   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2018   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2019           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2020
2021   QTreePushButton* rButton = new QTreePushButton;
2022   rButton->setItem(item);
2023   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2024   rButton->setToolTip(tr("reload vector field"));
2025   rButton->setEnabled(from_disk);
2026   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2027   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2028           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2029
2030   DataTree->topLevelItem(index)->setExpanded(1);
2031   DataTree->topLevelItem(index)->addChild(item);
2032   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2033   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2034
2035   //set the id of the image
2036   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2037   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2038   UpdateTree();
2039   qApp->processEvents();
2040   ImageInfoChanged();
2041   QApplication::restoreOverrideCursor();
2042 }
2043 //------------------------------------------------------------------------------
2044
2045
2046 //------------------------------------------------------------------------------
2047 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2048 {
2049   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2050   vvSlicerManager* imageManager = mSlicerManagers[index];
2051   if (imageManager->SetVF(vf,file.toStdString())) {
2052     AddFieldEntry(file,index,false);
2053   } else {
2054     QString error = "Cannot import the vector field for this image.\n";
2055     error += imageManager->GetLastError().c_str();
2056     QMessageBox::information(this,tr("Problem reading VF !"),error);
2057   }
2058   QApplication::restoreOverrideCursor();
2059 }
2060 //------------------------------------------------------------------------------
2061
2062
2063 //------------------------------------------------------------------------------
2064 void vvMainWindow::AddField(QString file,int index)
2065 {
2066   if (QFile::exists(file)) {
2067     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2068
2069     //init the progress events
2070     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2071     vvProgressDialog progress("Opening " + file.toStdString());
2072     qApp->processEvents();
2073
2074     //read the vector and put it in the current mSlicerManager
2075     vvSlicerManager* imageManager = mSlicerManagers[index];
2076     qApp->processEvents();
2077
2078     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2079     if (imageManager->SetVF(file.toStdString())) {
2080       imageManager->Render();
2081       AddFieldEntry(file,index,true);
2082     } else {
2083       QApplication::restoreOverrideCursor();
2084       QString error = "Cannot import the vector field for this image.\n";
2085       error += imageManager->GetLastError().c_str();
2086       QMessageBox::information(this,tr("Problem reading VF !"),error);
2087     }
2088   } else
2089     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2090
2091 }
2092 //------------------------------------------------------------------------------
2093
2094
2095 //------------------------------------------------------------------------------
2096 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width)
2097 {
2098   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2099   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2100     for (int i = 0; i < 4; i++) {
2101       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2102       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2103       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2104       if (log > 0)
2105         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2106       else
2107         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2108     }
2109   }
2110 }
2111 //------------------------------------------------------------------------------
2112
2113
2114 //------------------------------------------------------------------------------
2115 void vvMainWindow::SetOverlayProperty(int color)
2116 {
2117   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2118   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2119     mSlicerManagers[index]->SetOverlayColor(color);
2120     mSlicerManagers[index]->SetColorMap(0);
2121     mSlicerManagers[index]->Render();
2122   }
2123 }
2124 //------------------------------------------------------------------------------
2125
2126 //------------------------------------------------------------------------------
2127 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level)
2128 {
2129   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2130   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2131     mSlicerManagers[index]->SetFusionOpacity(opacity);
2132     mSlicerManagers[index]->SetFusionColorMap(colormap);
2133     mSlicerManagers[index]->SetFusionWindow(window);
2134     mSlicerManagers[index]->SetFusionLevel(level);
2135     mSlicerManagers[index]->SetColorMap(0);
2136     mSlicerManagers[index]->Render();
2137   }
2138 }
2139 //------------------------------------------------------------------------------
2140
2141 //------------------------------------------------------------------------------
2142 void vvMainWindow::SaveAs()
2143 {
2144   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2145     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2146     return;
2147   }
2148
2149   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2150   int dimension = mSlicerManagers[index]->GetDimension();
2151   QStringList OutputListeFormat;
2152   OutputListeFormat.clear();
2153   if (dimension == 1) {
2154     OutputListeFormat.push_back(".mhd");
2155   }
2156   if (dimension == 2) {
2157     OutputListeFormat.push_back(".bmp");
2158     OutputListeFormat.push_back(".png");
2159     OutputListeFormat.push_back(".jpeg");
2160     OutputListeFormat.push_back(".tif");
2161     OutputListeFormat.push_back(".mhd");
2162     OutputListeFormat.push_back(".hdr");
2163     OutputListeFormat.push_back(".vox");
2164   } else if (dimension == 3) {
2165     OutputListeFormat.push_back(".mhd");
2166     OutputListeFormat.push_back(".hdr");
2167     OutputListeFormat.push_back(".vox");
2168   } else if (dimension == 4) {
2169     OutputListeFormat.push_back(".mhd");
2170   }
2171   QString Extensions = "AllFiles(*.*)";
2172   for (int i = 0; i < OutputListeFormat.count(); i++) {
2173     Extensions += ";;Images ( *";
2174     Extensions += OutputListeFormat[i];
2175     Extensions += ")";
2176   }
2177   QString fileName = QFileDialog::getSaveFileName(this,
2178                      tr("Save As"),
2179                      mSlicerManagers[index]->GetFileName().c_str(),
2180                      Extensions);
2181   if (!fileName.isEmpty()) {
2182     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2183     if (OutputListeFormat.contains(
2184           fileformat.c_str())) {
2185       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2186       std::string action = "Saving";
2187       vvProgressDialog progress("Saving "+fileName.toStdString());
2188       qApp->processEvents();
2189       vvImageWriter *writer = new vvImageWriter;
2190       writer->SetOutputFileName(fileName.toStdString());
2191       writer->SetInput(mSlicerManagers[index]->GetImage());
2192       writer->Update();
2193       QApplication::restoreOverrideCursor();
2194       if (writer->GetLastError().size()) {
2195         QString error = "Saving did not succeed\n";
2196         error += writer->GetLastError().c_str();
2197         QMessageBox::information(this,tr("Saving Problem"),error);
2198         SaveAs();
2199       }
2200     } else {
2201       QString error = fileformat.c_str();
2202       if (error.isEmpty())
2203         error += "no file format specified !";
2204       else
2205         error += " format unknown !!!\n";
2206       QMessageBox::information(this,tr("Saving Problem"),error);
2207       SaveAs();
2208     }
2209   }
2210 }
2211 //------------------------------------------------------------------------------
2212
2213
2214 //------------------------------------------------------------------------------
2215 void vvMainWindow::AddLink(QString image1,QString image2)
2216 {
2217   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2218     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2219       mSlicerManagers[i]->AddLink(image2.toStdString());
2220     }
2221     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2222       mSlicerManagers[i]->AddLink(image1.toStdString());
2223     }
2224   }
2225 }
2226 //------------------------------------------------------------------------------
2227
2228
2229 //------------------------------------------------------------------------------
2230 void vvMainWindow::RemoveLink(QString image1,QString image2)
2231 {
2232   // DD("vvMainWindow:RemoveLink");
2233   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2234     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2235       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2236     }
2237     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2238       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2239     }
2240   }
2241 }
2242 //------------------------------------------------------------------------------
2243
2244 //------------------------------------------------------------------------------
2245 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2246 {
2247   int index = 0;
2248   while(sm != mSlicerManagers[index])
2249     index++;
2250   index = (index+offset) % mSlicerManagers.size();
2251
2252   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2253   //CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2254   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2255   DisplayChanged(item,slicer+1);
2256 }
2257 //------------------------------------------------------------------------------
2258
2259 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2260 {
2261   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2262     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2263       for (int j = 0; j < 4; j++) {
2264         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2265         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2266         //UpdateTSlice(j,value);
2267       }
2268       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2269       break;
2270     }
2271   }
2272 }
2273 //------------------------------------------------------------------------------
2274
2275
2276 //------------------------------------------------------------------------------
2277 void vvMainWindow::NOHorizontalSliderMoved()
2278 {
2279   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2280   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2281 //  mCurrentTime = NOHorizontalSlider->value();
2282 }
2283 //------------------------------------------------------------------------------
2284
2285
2286 //------------------------------------------------------------------------------
2287 void vvMainWindow::NEHorizontalSliderMoved()
2288 {
2289   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2290   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2291 //  mCurrentTime = NEHorizontalSlider->value();
2292 }
2293 //------------------------------------------------------------------------------
2294
2295
2296 //------------------------------------------------------------------------------
2297 void vvMainWindow::SOHorizontalSliderMoved()
2298 {
2299   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2300   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2301   // mCurrentTime = SOHorizontalSlider->value();
2302 }
2303 //------------------------------------------------------------------------------
2304
2305
2306 //------------------------------------------------------------------------------
2307 void vvMainWindow::SEHorizontalSliderMoved()
2308 {
2309   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2310   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2311   // mCurrentTime = SEHorizontalSlider->value();
2312 }
2313 //------------------------------------------------------------------------------
2314
2315 //------------------------------------------------------------------------------
2316 void vvMainWindow::NOVerticalSliderChanged()
2317 {
2318   static int value=-1;
2319   if (value == NOVerticalSlider->value()) return;
2320   else value = NOVerticalSlider->value();
2321   //  int value = NOVerticalSlider->value();
2322   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2323     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2324       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2325         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2326         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2327
2328         // If nor Update/Render -> slider not work
2329         // only render = ok navigation, but for contour Update needed but slower ?
2330
2331         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2332         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2333       }
2334       break;
2335     }
2336   }
2337 }
2338 //------------------------------------------------------------------------------
2339
2340
2341 //------------------------------------------------------------------------------
2342 void vvMainWindow::NEVerticalSliderChanged()
2343 {
2344   static int value=-1;
2345   if (value == NEVerticalSlider->value()) return;
2346   else value = NEVerticalSlider->value();
2347   //  int value = NEVerticalSlider->value();
2348   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2349     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2350       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2351         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2352         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2353         mSlicerManagers[i]->UpdateSlice(1);
2354         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2355       }
2356       break;
2357     }
2358   }
2359 }
2360 //------------------------------------------------------------------------------
2361
2362
2363 //------------------------------------------------------------------------------
2364 void vvMainWindow::SOVerticalSliderChanged()
2365 {
2366   static int value=-1;
2367   // DD(value);
2368 //   DD(SOVerticalSlider->value());
2369   if (value == SOVerticalSlider->value()) return;
2370   else value = SOVerticalSlider->value();
2371   //int value = SOVerticalSlider->value();
2372   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2373     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2374       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2375         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2376         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2377         mSlicerManagers[i]->UpdateSlice(2);
2378         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2379       }
2380       // else { DD("avoid SOVerticalSlider slicer update"); }
2381       break;
2382     }
2383   }
2384 }
2385 //------------------------------------------------------------------------------
2386
2387
2388 //------------------------------------------------------------------------------
2389 void vvMainWindow::SEVerticalSliderChanged()
2390 {
2391   static int value=-1;
2392   if (value == SEVerticalSlider->value()) return;
2393   else value = SEVerticalSlider->value();
2394   // int value = SEVerticalSlider->value();
2395   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2396     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2397       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2398         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2399         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2400         mSlicerManagers[i]->UpdateSlice(3);
2401         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2402       }
2403       break;
2404     }
2405   }
2406 }
2407 //------------------------------------------------------------------------------
2408
2409
2410 //------------------------------------------------------------------------------
2411 void vvMainWindow::UpdateSlice(int slicer, int slice)
2412 {
2413   // DD("vvMainWindow::UpdateSlice");
2414 //   DD(slicer);
2415 //   DD(slice);
2416   if (slicer == 0) {
2417     //    if (slice != NOVerticalSlider->value())
2418     NOVerticalSlider->setValue(slice);
2419   } else {
2420     if (slicer == 1)
2421       NEVerticalSlider->setValue(slice);
2422     else {
2423       if (slicer == 2)
2424         SOVerticalSlider->setValue(slice);
2425       else {
2426         if (slicer == 3)
2427           SEVerticalSlider->setValue(slice);
2428       }
2429     }
2430   }
2431   // DD("vvMainWindow:UpdateSlice END");
2432 }
2433 //------------------------------------------------------------------------------
2434
2435
2436 //------------------------------------------------------------------------------
2437 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2438 {
2439   switch (slicer) {
2440   case 0:
2441     NOHorizontalSlider->setValue(slice);
2442     break;
2443   case 1:
2444     NEHorizontalSlider->setValue(slice);
2445     break;
2446   case 2:
2447     SOHorizontalSlider->setValue(slice);
2448     break;
2449   case 3:
2450     SEHorizontalSlider->setValue(slice);
2451     break;
2452   }
2453 }
2454 //------------------------------------------------------------------------------
2455
2456
2457 //------------------------------------------------------------------------------
2458 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2459 {
2460   int position = int((min+max)/2);
2461   int tPosition = int((tmin+tmax)/2);
2462   if (slicer == 0) {
2463     NOVerticalSlider->setValue(position);
2464     NOVerticalSlider->setRange(min,max);
2465     NOHorizontalSlider->setRange(tmin,tmax);
2466     NOHorizontalSlider->setValue(tPosition);
2467   } else if (slicer == 1) {
2468     NEVerticalSlider->setValue(position);
2469     NEVerticalSlider->setRange(min,max);
2470     NEHorizontalSlider->setRange(tmin,tmax);
2471     NEHorizontalSlider->setValue(tPosition);
2472   } else if (slicer == 2) {
2473     SOVerticalSlider->setValue(position);
2474     SOVerticalSlider->setRange(min,max);
2475     SOHorizontalSlider->setRange(tmin,tmax);
2476     SOHorizontalSlider->setValue(tPosition);
2477   } else if (slicer == 3) {
2478     SEVerticalSlider->setValue(position);
2479     SEVerticalSlider->setRange(min,max);
2480     SEHorizontalSlider->setRange(tmin,tmax);
2481     SEHorizontalSlider->setValue(tPosition);
2482   }
2483 }
2484 //------------------------------------------------------------------------------
2485
2486
2487 //------------------------------------------------------------------------------
2488 void vvMainWindow::SaveNOScreenshot()
2489 {
2490   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2491   w2i->SetInput(NOViewWidget->GetRenderWindow());
2492   w2i->Update();
2493   SaveScreenshot(w2i->GetOutput());
2494   w2i->Delete();
2495 }
2496 //------------------------------------------------------------------------------
2497
2498
2499 //------------------------------------------------------------------------------
2500 void vvMainWindow::SaveNEScreenshot()
2501 {
2502   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2503   w2i->SetInput(NEViewWidget->GetRenderWindow());
2504   w2i->Update();
2505   SaveScreenshot(w2i->GetOutput());
2506   w2i->Delete();
2507 }
2508 //------------------------------------------------------------------------------
2509
2510
2511 //------------------------------------------------------------------------------
2512 void vvMainWindow::SaveSOScreenshot()
2513 {
2514   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2515   w2i->SetInput(SOViewWidget->GetRenderWindow());
2516   w2i->Update();
2517   SaveScreenshot(w2i->GetOutput());
2518   w2i->Delete();
2519 }
2520 //------------------------------------------------------------------------------
2521
2522
2523 //------------------------------------------------------------------------------
2524 void vvMainWindow::SaveSEScreenshot()
2525 {
2526   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2527   w2i->SetInput(SEViewWidget->GetRenderWindow());
2528   w2i->Update();
2529   SaveScreenshot(w2i->GetOutput());
2530   w2i->Delete();
2531 }
2532 //------------------------------------------------------------------------------
2533
2534
2535 //------------------------------------------------------------------------------
2536 void vvMainWindow::SaveScreenshot(vtkImageData* image)
2537 {
2538   QString Extensions = "Images( *.png);;";
2539   Extensions += "Images( *.jpg);;";
2540   Extensions += "Images( *.bmp);;";
2541   Extensions += "Images( *.tif);;";
2542   Extensions += "Images( *.ppm)";
2543   QString fileName = QFileDialog::getSaveFileName(this,
2544                      tr("Save As"),
2545                      itksys::SystemTools::GetFilenamePath(
2546                        mSlicerManagers[0]->GetFileName()).c_str(),
2547                      Extensions);
2548   if (!fileName.isEmpty()) {
2549     const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2550     if (!strcmp(ext, ".bmp")) {
2551       vtkBMPWriter *bmp = vtkBMPWriter::New();
2552       bmp->SetInput(image);
2553       bmp->SetFileName(fileName.toStdString().c_str());
2554       bmp->Write();
2555       bmp->Delete();
2556     } else if (!strcmp(ext, ".tif")) {
2557       vtkTIFFWriter *tif = vtkTIFFWriter::New();
2558       tif->SetInput(image);
2559       tif->SetFileName(fileName.toStdString().c_str());
2560       tif->Write();
2561       tif->Delete();
2562     } else if (!strcmp(ext, ".ppm")) {
2563       vtkPNMWriter *pnm = vtkPNMWriter::New();
2564       pnm->SetInput(image);
2565       pnm->SetFileName(fileName.toStdString().c_str());
2566       pnm->Write();
2567       pnm->Delete();
2568     } else if (!strcmp(ext, ".png")) {
2569       vtkPNGWriter *png = vtkPNGWriter::New();
2570       png->SetInput(image);
2571       png->SetFileName(fileName.toStdString().c_str());
2572       png->Write();
2573       png->Delete();
2574     } else if (!strcmp(ext, ".jpg")) {
2575       vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2576       jpg->SetInput(image);
2577       jpg->SetFileName(fileName.toStdString().c_str());
2578       jpg->Write();
2579       jpg->Delete();
2580     } else {
2581       QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2582     }
2583   }
2584
2585 }
2586 //------------------------------------------------------------------------------
2587
2588
2589 //------------------------------------------------------------------------------
2590 void vvMainWindow::GoToCursor()
2591 {
2592   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2593   for (int column = 1; column < 5; column++) {
2594     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
2595       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2596       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2597         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2598       mSlicerManagers[index]->UpdateViews(1,column-1);
2599       mSlicerManagers[index]->UpdateLinked(column-1);
2600       break;
2601     }
2602   }
2603 }
2604 //------------------------------------------------------------------------------
2605
2606 //------------------------------------------------------------------------------
2607 void vvMainWindow::PlayPause()
2608 {
2609   if (playMode) {
2610     playMode = 0;
2611     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2612     ImageInfoChanged();
2613     return;
2614   } else {
2615     int image_number=DataTree->topLevelItemCount();
2616     bool has_temporal;
2617     for (int i=0; i<image_number; i++)
2618       if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1) {
2619         has_temporal=true;
2620         break;
2621       }
2622     if (has_temporal) {
2623       playMode = 1;
2624       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2625       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2626     }
2627   }
2628 }
2629 //------------------------------------------------------------------------------
2630
2631 //------------------------------------------------------------------------------
2632 void vvMainWindow::PlayNext()
2633 {
2634   if (playMode && !this->isHidden()) {
2635     int image_number=DataTree->topLevelItemCount();
2636     ///Only play one slicer per SM, and only if the SM is being displayed
2637     for (int i=0; i<image_number; i++)
2638       for (int j=0; j<4; j++)
2639         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2640             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
2641           mSlicerManagers[i]->SetNextTSlice(j);
2642           break;
2643         }
2644     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2645   }
2646 }
2647 //------------------------------------------------------------------------------
2648
2649 void vvMainWindow::ShowLastImage()
2650 {
2651   if (mSlicerManagers.size() > 1) {
2652     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2653     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2654     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2655     DisplayChanged(item,1);
2656   }
2657 }
2658
2659 //------------------------------------------------------------------------------
2660 void vvMainWindow::UpdateRenderWindows()
2661 {
2662   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2663   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2664   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2665   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2666 }
2667 //------------------------------------------------------------------------------
2668
2669 //------------------------------------------------------------------------------
2670 void vvMainWindow::SegmentationOnCurrentImage()
2671 {
2672   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2673
2674   vvSegmentationDialog segmentation;
2675   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2676   segmentation.exec();
2677 }
2678 //------------------------------------------------------------------------------
2679
2680 void vvMainWindow::SurfaceViewerLaunch()
2681 {
2682   vvSurfaceViewerDialog surfaceViewer;
2683   surfaceViewer.exec();
2684 }
2685 //------------------------------------------------------------------------------
2686
2687
2688 //------------------------------------------------------------------------------
2689 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
2690 {
2691   int number=0;
2692   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
2693     vvSlicerManager * v = mSlicerManagers[l];
2694     if (v->GetBaseFileName() ==
2695         vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
2696       number = std::max(number, v->GetBaseFileNameNumber()+1);
2697     }
2698   }
2699   return number;
2700 }
2701 //------------------------------------------------------------------------------
2702
2703
2704 //------------------------------------------------------------------------------
2705 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2706 {
2707   // Change filename if another image exist with the same name
2708   int number = GetImageDuplicateFilenameNumber(filename);
2709
2710   // Create new SliceManager
2711   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
2712   slicer_manager->SetImage(image);//, IMAGE, number);
2713   //  filename = filename+"_"+clitk::toString(number);
2714   slicer_manager->SetFilename(filename, number);
2715   mSlicerManagers.push_back(slicer_manager);
2716
2717   //create an item in the tree with good settings
2718   QTreeWidgetItem *item = new QTreeWidgetItem();
2719   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2720   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
2721   qApp->processEvents();
2722
2723   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2724
2725   //Create the buttons for reload and close
2726   qApp->processEvents();
2727   QTreePushButton* cButton = new QTreePushButton;
2728   cButton->setItem(item);
2729   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2730   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2731   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2732           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2733
2734   QTreePushButton* rButton = new QTreePushButton;
2735   rButton->setItem(item);
2736   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2737   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2738   rButton->setEnabled(0);
2739   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2740           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2741
2742   DataTree->addTopLevelItem(item);
2743   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2744   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2745
2746   //set the id of the image
2747   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2748   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2749   mSlicerManagers.back()->SetId(id.toStdString());
2750
2751   linkPanel->addImage(filename, id.toStdString());
2752
2753   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
2754           this, SLOT(CurrentImageChanged(std::string)));
2755   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
2756           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2757   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
2758           this, SLOT(VectorChanged(int,double,double,double, double)));
2759   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
2760           this, SLOT(OverlayChanged(int,double,double)));
2761   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
2762           this, SLOT(FusionChanged(int,double)));
2763   connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
2764           this,SLOT(WindowsChanged(int, int, int)));
2765   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
2766           this,SLOT(WindowLevelChanged(double, double, int, int)));
2767   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
2768           this,SLOT(UpdateSlice(int,int)));
2769   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
2770           this,SLOT(UpdateTSlice(int, int)));
2771   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2772           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2773   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2774           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2775   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*)),
2776           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*)));
2777   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
2778           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
2779   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2780   UpdateTree();
2781   qApp->processEvents();
2782   InitSlicers();
2783   ShowLastImage();
2784   InitDisplay();
2785   qApp->processEvents();
2786
2787   // End
2788   ImageInfoChanged();
2789   return slicer_manager;
2790 }
2791 //------------------------------------------------------------------------------
2792
2793
2794 //------------------------------------------------------------------------------
2795 void vvMainWindow::UpdateCurrentSlicer()
2796 {
2797   int index = -1;
2798   if (DataTree->selectedItems().size() > 0) {
2799     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2800   }
2801   mSlicerManagerCurrentIndex = index;
2802 }
2803 //------------------------------------------------------------------------------
2804