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