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     // DD(range[0]);
 922     //   DD(range[1]);
 923     if ((range[0] == 0) && (range[1] == 1)) {
 924       presetComboBox->setCurrentIndex(5);// binary
 925     } else {
 926       // TODO
 927     }
 928   }
 929   QApplication::restoreOverrideCursor();
 930 }
 931 //------------------------------------------------------------------------------
 932
 933 //------------------------------------------------------------------------------
 934 void vvMainWindow::UpdateTree()
 935 {
 936   DataTree->resizeColumnToContents(COLUMN_TREE);
 937   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 938   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 939   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 940   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 941   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 942   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 943   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 944 }
 945 //------------------------------------------------------------------------------
 946
 947 //------------------------------------------------------------------------------
 948 void vvMainWindow::CurrentImageChanged(std::string id)
 949 {
 950   // DD("CurrentImageChanged");
 951 //   DD(id);
 952 //   DD(mCurrentSelectedImageId);
 953   if (id == mCurrentSelectedImageId) return; // Do nothing
 954   int selected = 0;
 955   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 956     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 957       selected = i;
 958     } else {
 959       DataTree->topLevelItem(i)->setSelected(0);
 960     }
 961     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 962       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 963
 964   }
 965   DataTree->topLevelItem(selected)->setSelected(1);
 966   // DD(mSlicerManagers[selected]->GetFileName());
 967   mCurrentSelectedImageId = id;
 968   emit SelectedImageHasChanged(mSlicerManagers[selected]);
 969 }
 970 //------------------------------------------------------------------------------
 971
 972 //------------------------------------------------------------------------------
 973 void vvMainWindow::ImageInfoChanged()
 974 {
 975   contextActions[6]->setEnabled(1);
 976   contextActions[5]->setEnabled(1);
 977   actionSave_As->setEnabled(1);
 978   actionAdd_VF_to_current_Image->setEnabled(1);
 979   actionAdd_fusion_image->setEnabled(1);
 980   actionNorth_East_Window->setEnabled(1);
 981   actionNorth_West_Window->setEnabled(1);
 982   actionSouth_East_Window->setEnabled(1);
 983   actionSouth_West_Window->setEnabled(1);
 984   inverseButton->setEnabled(1);
 985
 986   goToCursorPushButton->setEnabled(1);
 987
 988   if (DataTree->selectedItems().size()) {
 989     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 990
 991     colorMapComboBox->setEnabled(1);
 992     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
 993       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
 994           DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion") {
 995         colorMapComboBox->setEnabled(0);
 996         break;
 997       }
 998     }
 999
1000     std::vector<double> origin;
1001     std::vector<double> inputSpacing;
1002     std::vector<int> inputSize;
1003     std::vector<double> sizeMM;
1004     vtkSmartPointer<vtkMatrix4x4> transformation;
1005     int dimension=0;
1006     QString pixelType;
1007     QString inputSizeInBytes;
1008     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1009
1010     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1) {
1011       playButton->setEnabled(1);
1012       frameRateLabel->setEnabled(1);
1013       frameRateSpinBox->setEnabled(1);
1014     } else {
1015       playButton->setEnabled(0);
1016       frameRateLabel->setEnabled(0);
1017       frameRateSpinBox->setEnabled(0);
1018     }
1019
1020     //read image header
1021     int NPixel = 1;
1022
1023     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1024       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1025       dimension = imageSelected->GetNumberOfDimensions();
1026       origin.resize(dimension);
1027       inputSpacing.resize(dimension);
1028       inputSize.resize(dimension);
1029       sizeMM.resize(dimension);
1030       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1031       for (int i = 0; i < dimension; i++) {
1032         origin[i] = imageSelected->GetOrigin()[i];
1033         inputSpacing[i] = imageSelected->GetSpacing()[i];
1034         inputSize[i] = imageSelected->GetSize()[i];
1035         sizeMM[i] = inputSize[i]*inputSpacing[i];
1036         NPixel *= inputSize[i];
1037       }
1038       transformation = imageSelected->GetTransform()->GetMatrix();
1039       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1040     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1041       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1042       dimension = imageSelected->GetNumberOfDimensions();
1043       origin.resize(dimension);
1044       inputSpacing.resize(dimension);
1045       inputSize.resize(dimension);
1046       sizeMM.resize(dimension);
1047       pixelType = mSlicerManagers[index]->GetVF()->GetScalarTypeAsITKString().c_str();
1048       for (int i = 0; i < dimension; i++) {
1049         origin[i] = imageSelected->GetOrigin()[i];
1050         inputSpacing[i] = imageSelected->GetSpacing()[i];
1051         inputSize[i] = imageSelected->GetSize()[i];
1052         sizeMM[i] = inputSize[i]*inputSpacing[i];
1053         NPixel *= inputSize[i];
1054       }
1055       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1056     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1057       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1058       dimension = imageSelected->GetNumberOfDimensions();
1059       origin.resize(dimension);
1060       inputSpacing.resize(dimension);
1061       inputSize.resize(dimension);
1062       sizeMM.resize(dimension);
1063       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1064       for (int i = 0; i < dimension; i++) {
1065         origin[i] = imageSelected->GetOrigin()[i];
1066         inputSpacing[i] = imageSelected->GetSpacing()[i];
1067         inputSize[i] = imageSelected->GetSize()[i];
1068         sizeMM[i] = inputSize[i]*inputSpacing[i];
1069         NPixel *= inputSize[i];
1070       }
1071       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1072     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1073       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1074       dimension = imageSelected->GetNumberOfDimensions();
1075       origin.resize(dimension);
1076       inputSpacing.resize(dimension);
1077       inputSize.resize(dimension);
1078       sizeMM.resize(dimension);
1079       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1080       for (int i = 0; i < dimension; i++) {
1081         origin[i] = imageSelected->GetOrigin()[i];
1082         inputSpacing[i] = imageSelected->GetSpacing()[i];
1083         inputSize[i] = imageSelected->GetSize()[i];
1084         sizeMM[i] = inputSize[i]*inputSpacing[i];
1085         NPixel *= inputSize[i];
1086       }
1087       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1088     }
1089
1090     QString dim = QString::number(dimension) + " (";
1091     dim += pixelType + ")";
1092
1093     infoPanel->setFileName(image);
1094     infoPanel->setDimension(dim);
1095     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1096     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1097     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1098     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1099     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1100     infoPanel->setTransformation(Get4x4MatrixDoubleAsString(transformation));
1101
1102     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1103                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1104     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1105     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1106
1107     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1108     for (int i = 0; i < 4; i++) {
1109       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1110         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1111         break;
1112       }
1113     }
1114     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1115     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1116     // DD(mSlicerManagers[index]->GetColorMap());
1117     // DD(mSlicerManagers[index]->GetPreset());
1118     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1119     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1120
1121     infoPanel->setFileName(image);
1122     infoPanel->setDimension(dim);
1123     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1124     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1125     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1126     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1127     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1128
1129     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1130                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1131     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1132     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1133
1134     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1135     for (int i = 0; i < 4; i++) {
1136       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1137         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1138         break;
1139       }
1140     }
1141     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1142     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1143     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1144     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1145
1146     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1147       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1148       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1149                                   mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1150                                   mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1151     } else {
1152       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1153       overlayPanel->getVFProperty(-1,-1,-1);
1154     }
1155     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1156       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1157       overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1158     } else {
1159       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1160       overlayPanel->getOverlayProperty(-1);
1161     }
1162     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1163       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1164       overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1165                                       mSlicerManagers[index]->GetFusionColorMap(),
1166                                       mSlicerManagers[index]->GetFusionWindow(),
1167                                       mSlicerManagers[index]->GetFusionLevel());
1168     } else {
1169       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1170       overlayPanel->getFusionProperty(-1, -1,-1,-1);
1171     }
1172   }
1173 }
1174 //------------------------------------------------------------------------------
1175
1176 //------------------------------------------------------------------------------
1177 void vvMainWindow::ShowDocumentation()
1178 {
1179   documentation->show();
1180 }
1181 //------------------------------------------------------------------------------
1182 void vvMainWindow::ShowHelpDialog()
1183 {
1184   help_dialog->show();
1185 }
1186 //------------------------------------------------------------------------------
1187
1188 //------------------------------------------------------------------------------
1189 void vvMainWindow::ChangeViewMode()
1190 {
1191   QListIterator<int> it0(splitter_3->sizes());
1192   QListIterator<int> it1(splitter_3->sizes());
1193   int max0 = 0;
1194   int max1 = 1;
1195   while (it0.hasNext()) {
1196     max0 += it0.next();
1197   }
1198   while (it1.hasNext()) {
1199     max1 += it1.next();
1200   }
1201   QList<int> size0;
1202   QList<int> size1;
1203   if (viewMode == 1) {
1204     viewMode = 0;
1205     size0.push_back(max0);
1206     size0.push_back(0);
1207     size1.push_back(max1);
1208     size1.push_back(0);
1209     splitter_3->setSizes(size0);
1210     OSplitter->setSizes(size1);
1211     DataTree->setColumnHidden(2,1);
1212     DataTree->setColumnHidden(3,1);
1213     DataTree->setColumnHidden(4,1);
1214   } else {
1215     viewMode = 1;
1216     size0.push_back(int(max0/2));
1217     size0.push_back(int(max0/2));
1218     size1.push_back(int(max1/2));
1219     size1.push_back(int(max1/2));
1220     splitter_3->setSizes(size0);
1221     OSplitter->setSizes(size1);
1222     DataTree->setColumnHidden(2,0);
1223     DataTree->setColumnHidden(3,0);
1224     DataTree->setColumnHidden(4,0);
1225   }
1226 }
1227 //------------------------------------------------------------------------------
1228
1229 //------------------------------------------------------------------------------
1230 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1231 {
1232   QString result = "";// QString::number(size);
1233   //result += " bytes (";
1234   if (size > 1000000000) {
1235     size /= 1000000000;
1236     result += QString::number(size);
1237     result += "Gb";//)";
1238   } else if (size > 1000000) {
1239     size /= 1000000;
1240     result += QString::number(size);
1241     result += "Mb";//)";
1242   } else if (size > 1000) {
1243     size /= 1000;
1244     result += QString::number(size);
1245     result += "kb";//)";
1246   }
1247   return result;
1248 }
1249 //------------------------------------------------------------------------------
1250
1251 //------------------------------------------------------------------------------
1252 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix)
1253 {
1254   std::ostringstream strmatrix;
1255
1256   for (unsigned int i = 0; i < 4; i++) {
1257     for (unsigned int j = 0; j < 4; j++) {
1258       strmatrix.flags(ios::showpos);
1259       strmatrix.width(10);
1260       strmatrix.precision(3);
1261       strmatrix.setf(ios::fixed,ios::floatfield);
1262       strmatrix.fill(' ');
1263       strmatrix << std::left << matrix->GetElement(i, j);
1264       //strmatrix.width(10);
1265       strmatrix << " ";
1266     }
1267     strmatrix << std::endl;
1268   }
1269   QString result = strmatrix.str().c_str();
1270   return result;
1271 }
1272 //------------------------------------------------------------------------------
1273
1274 //------------------------------------------------------------------------------
1275 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1276 {
1277   QString result;
1278   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1279     if (i != 0)
1280       result += " ";
1281     result += QString::number(vectorDouble[i]);
1282   }
1283   return result;
1284 }
1285 //------------------------------------------------------------------------------
1286
1287 //------------------------------------------------------------------------------
1288 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1289 {
1290   QString result;
1291   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1292     if (i != 0)
1293       result += " ";
1294     result += QString::number(vectorInt[i]);
1295   }
1296   return result;
1297 }
1298 //------------------------------------------------------------------------------
1299
1300 //------------------------------------------------------------------------------
1301 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1302 {
1303   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1304   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1305     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1306       return i;
1307   }
1308   return -1;
1309 }
1310 //------------------------------------------------------------------------------
1311
1312 //------------------------------------------------------------------------------
1313 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1314 {
1315   QString id = sm->GetId().c_str();
1316   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1317     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1318       return DataTree->topLevelItem(i);
1319   }
1320   return NULL;
1321 }
1322 //------------------------------------------------------------------------------
1323
1324 //------------------------------------------------------------------------------
1325 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clicked_item, int column)
1326 {
1327   int index = GetSlicerIndexFromItem(clicked_item);
1328   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1329     return;
1330   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1331     //Trick to avoid redoing twice the job for a key (sr)
1332     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()-> GetInteractor()->SetKeySym("Crap");
1333
1334     QTreeWidgetItem* current_row=DataTree->topLevelItem(i);
1335     if (DataTree->topLevelItem(index) == current_row) {
1336       vvSlicer* clicked_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1337       if (current_row == clicked_item) {
1338         //If we just activated a slicer
1339         if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1340           mSlicerManagers[i]->UpdateSlicer(column-1,clicked_item->data(column,Qt::CheckStateRole).toInt());
1341           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1342           DisplaySliders(i,column-1);
1343           std::map<std::string,int> overlay_counts;
1344           for (int child = 0; child < current_row->childCount(); child++) {
1345             std::string overlay_type =
1346               current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1347             overlay_counts[overlay_type]++;
1348             current_row->child(child)->setData(column,Qt::CheckStateRole,
1349                                                current_row->data(column,Qt::CheckStateRole));
1350             clicked_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,true);
1351           }
1352         } else { //We don't allow simply desactivating a slicer
1353           clicked_item->setData(column,Qt::CheckStateRole,2);
1354           return;
1355         }
1356       }
1357       //if we clicked on the vector(or overlay) and not the image
1358       else {
1359         if (clicked_item->data(column,Qt::CheckStateRole).toInt()) {
1360           current_row->setData(column,Qt::CheckStateRole,2);
1361           mSlicerManagers[i]->UpdateSlicer(column-1,2);
1362           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1363           DisplaySliders(i,column-1);
1364         }
1365         int vis = clicked_item->data(column,Qt::CheckStateRole).toInt();
1366         std::string overlay_type = clicked_item->data(1,Qt::UserRole).toString().toStdString();
1367         int overlay_index=0;
1368         for (int child = 0; child < current_row->childCount(); child++) {
1369           if (current_row->child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1370             overlay_index++;
1371           if (current_row->child(child) == clicked_item) break;
1372         }
1373         clicked_slicer->SetActorVisibility(
1374           clicked_item->data(1,Qt::UserRole).toString().toStdString(), overlay_index-1,vis);
1375       }
1376     } else if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1377       current_row->setData(column,Qt::CheckStateRole,0);
1378       mSlicerManagers[i]->UpdateSlicer(column-1,0);
1379       std::map<std::string,int> overlay_counts;
1380       for (int child = 0; child < current_row->childCount(); child++) {
1381         std::string overlay_type =
1382           current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1383         overlay_counts[overlay_type]++;
1384         current_row->child(child)->setData(column,Qt::CheckStateRole,0);
1385         vvSlicer * current_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1386         current_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,false);
1387       }
1388     }
1389     //mSlicerManagers[i]->SetColorMap(-1);
1390     mSlicerManagers[i]->SetColorMap();
1391   }
1392   mSlicerManagers[index]->GetSlicer(column-1)->Render();
1393 }
1394 //------------------------------------------------------------------------------
1395
1396 void vvMainWindow::InitSlicers()
1397 {
1398   if (mSlicerManagers.size()) {
1399     mSlicerManagers.back()->GenerateDefaultLookupTable();
1400
1401     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1402     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1403     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1404     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1405   }
1406 }
1407
1408 //------------------------------------------------------------------------------
1409 void vvMainWindow::InitDisplay()
1410 {
1411   if (mSlicerManagers.size()) {
1412     //BE CAREFUL : this is absolutely necessary to set the interactor style
1413     //in order to have the same style instanciation for all SlicerManagers in
1414     // a same window
1415     for (int j = 0; j < 4; j++) {
1416       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1417       style->SetAutoAdjustCameraClippingRange(1);
1418       bool AlreadySelected = false;
1419       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1420         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1421
1422         //select the image only if previous are not selected
1423         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1424           mSlicerManagers[i]->UpdateSlicer(j,1);
1425           AlreadySelected = true;
1426         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1427           if (DataTree->selectedItems().size() == 0)
1428             DataTree->topLevelItem(i)->setSelected(1);
1429           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1430           mSlicerManagers[i]->UpdateSlicer(j,1);
1431           DisplaySliders(i,j);
1432         } else {
1433           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1434           mSlicerManagers[i]->UpdateSlicer(j,0);
1435         }
1436       }
1437       style->Delete();
1438     }
1439   }
1440 }
1441 //------------------------------------------------------------------------------
1442
1443 //------------------------------------------------------------------------------
1444 void vvMainWindow::DisplaySliders(int slicer, int window)
1445 {
1446   int range[2];
1447   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1448   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1449
1450   int tRange[2];
1451   tRange[0] = 0;
1452   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1453   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1454   bool showHorizontal = false;
1455   bool showVertical = false;
1456   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1457       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1458           && mSlicerManagers[slicer]->GetType() != IMAGEWITHTIME
1459           && mSlicerManagers[slicer]->GetType() != MERGEDWITHTIME))
1460     showVertical = true;
1461   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1462       || mSlicerManagers[slicer]->GetType() == IMAGEWITHTIME
1463       || mSlicerManagers[slicer]->GetType() == MERGEDWITHTIME)
1464     showHorizontal = true;
1465
1466   if (showVertical)
1467     verticalSliders[window]->show();
1468   else
1469     verticalSliders[window]->hide();
1470   verticalSliders[window]->setRange(range[0],range[1]);
1471   verticalSliders[window]->setValue(position);
1472
1473   if (showHorizontal)
1474     horizontalSliders[window]->show();
1475   else
1476     horizontalSliders[window]->hide();
1477   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1478   horizontalSliders[window]->setValue(tPosition);
1479 }
1480 //------------------------------------------------------------------------------
1481
1482 //------------------------------------------------------------------------------
1483 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1484 {
1485   int index = GetSlicerIndexFromItem(item);
1486
1487   if (DataTree->topLevelItem(index) != item) {
1488     QString warning = "Do you really want to close the overlay : ";
1489     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1490     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1491                        warning, 0, this);
1492     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1493     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1494     if (msgBox.exec() == QMessageBox::AcceptRole) {
1495       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1496       int overlay_index=0;
1497       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1498         if (DataTree->topLevelItem(index)->\
1499             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1500           overlay_index++;
1501         if (DataTree->topLevelItem(index)->child(child) == item) break;
1502       }
1503       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1504       mSlicerManagers[index]->SetColorMap(0);
1505       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1506       mSlicerManagers[index]->Render();
1507     }
1508   } else if (DataTree->topLevelItemCount() <= 1) {
1509     QString warning = "Do you really want to close the image : ";
1510     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1511     warning += "\nThis is the last image, you're about to close vv !!!";
1512     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1513                        warning, 0, this);
1514     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1515     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1516     if (msgBox.exec() == QMessageBox::AcceptRole) {
1517       this->close();
1518     }
1519   } else {
1520     QString warning = "Do you really want to close the image : ";
1521     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1522     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1523                        warning, 0, this);
1524     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1525     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1526     if (msgBox.exec() == QMessageBox::AcceptRole) {
1527
1528       // Tell tools that we close an image
1529       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1530
1531       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1532       DataTree->takeTopLevelItem(index);
1533       for (int i = 0; i < index; i++) {
1534         Manageriter++;
1535       }
1536       linkPanel->removeImage(index);
1537       mSlicerManagers[index]->RemoveActors();
1538       delete mSlicerManagers[index];
1539       mSlicerManagers.erase(Manageriter);
1540
1541       //
1542       InitDisplay();
1543     }
1544   }
1545   ImageInfoChanged();
1546 }
1547 //------------------------------------------------------------------------------
1548
1549 //------------------------------------------------------------------------------
1550 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1551 {
1552   // int index = GetSlicerIndexFromItem(item);
1553   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1554   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1555   //     mSlicerManagers[index]->ReloadVF();
1556   //   else
1557   //     mSlicerManagers[index]->Reload();
1558
1559   //   QApplication::restoreOverrideCursor();
1560   int index = GetSlicerIndexFromItem(item);
1561   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1562   QString role=item->data(1,Qt::UserRole).toString();
1563   if ( role == "vector")
1564     mSlicerManagers[index]->ReloadVF();
1565   else if (role == "overlay")
1566     mSlicerManagers[index]->ReloadOverlay();
1567   else if (role == "fusion")
1568     mSlicerManagers[index]->ReloadFusion();
1569   else
1570     mSlicerManagers[index]->Reload();
1571
1572   // Update view and info
1573   ImageInfoChanged();
1574   mSlicerManagers[index]->Render();
1575   QApplication::restoreOverrideCursor();
1576 }
1577 //------------------------------------------------------------------------------
1578
1579 //------------------------------------------------------------------------------
1580 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1581 {
1582   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1583 }
1584 //------------------------------------------------------------------------------
1585
1586 //------------------------------------------------------------------------------
1587 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1588 {
1589   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1590 }
1591 //------------------------------------------------------------------------------
1592
1593 //------------------------------------------------------------------------------
1594 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1595 {
1596   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1597 }
1598 //------------------------------------------------------------------------------
1599
1600 //------------------------------------------------------------------------------
1601 void vvMainWindow::FusionChanged(int visibility, double value)
1602 {
1603   overlayPanel->getCurrentFusionInfo(visibility,value);
1604 }
1605 //------------------------------------------------------------------------------
1606
1607 //------------------------------------------------------------------------------
1608 void vvMainWindow::WindowsChanged(int window, int view, int slice)
1609 {
1610   infoPanel->setViews(window, view, slice);
1611 }
1612 //------------------------------------------------------------------------------
1613
1614 //------------------------------------------------------------------------------
1615 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap)
1616 {
1617   windowSpinBox->setValue(window);
1618   levelSpinBox->setValue(level);
1619   colorMapComboBox->setCurrentIndex(colormap);
1620   presetComboBox->setCurrentIndex(preset);
1621 }
1622 //------------------------------------------------------------------------------
1623
1624 //------------------------------------------------------------------------------
1625 void vvMainWindow::WindowLevelEdited()
1626 {
1627   presetComboBox->setCurrentIndex(6);
1628   UpdateWindowLevel();
1629 }
1630 //------------------------------------------------------------------------------
1631
1632 //------------------------------------------------------------------------------
1633 void vvMainWindow::UpdateWindowLevel()
1634 {
1635   if (DataTree->selectedItems().size()) {
1636     if (presetComboBox->currentIndex() == 7) //For ventilation
1637       colorMapComboBox->setCurrentIndex(5);
1638     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1639     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1640     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1641     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1642     mSlicerManagers[index]->Render();
1643   }
1644 }
1645 //------------------------------------------------------------------------------
1646
1647 //------------------------------------------------------------------------------
1648 void vvMainWindow::UpdateColorMap()
1649 {
1650   if (DataTree->selectedItems().size()) {
1651     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1652     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1653     mSlicerManagers[index]->Render();
1654   }
1655 }
1656 //------------------------------------------------------------------------------
1657 void vvMainWindow::SwitchWindowLevel()
1658 {
1659   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1660   int window = mSlicerManagers[index]->GetColorWindow();
1661   presetComboBox->setCurrentIndex(6);
1662   windowSpinBox->setValue(-window);
1663   UpdateWindowLevel();
1664 }
1665 //------------------------------------------------------------------------------
1666
1667 //------------------------------------------------------------------------------
1668 void vvMainWindow::ApplyWindowLevelToAllImages()
1669 {
1670   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1671     if (mSlicerManagers[i] == NULL)
1672       continue;
1673     mSlicerManagers[i]->SetColorWindow(windowSpinBox->value());
1674     mSlicerManagers[i]->SetColorLevel(levelSpinBox->value());
1675     mSlicerManagers[i]->SetPreset(6);
1676     mSlicerManagers[i]->Render();
1677   }
1678 }
1679 //------------------------------------------------------------------------------
1680
1681 //------------------------------------------------------------------------------
1682 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1683 {
1684   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1685     if (mSlicerManagers[i]->GetId() == id) {
1686       //mSlicerManagers[i]->SetTSlice(temps);
1687       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1688       mSlicerManagers[i]->UpdateViews(0,slicer);
1689       break;
1690     }
1691   }
1692 }
1693 //------------------------------------------------------------------------------
1694
1695 //------------------------------------------------------------------------------
1696 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm)
1697 {
1698   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1699     if (id == mSlicerManagers[i]->GetId()) {
1700       mSlicerManagers[i]->UpdateLinkedNavigation(sm->GetSlicer(0));
1701     }
1702   }
1703 }
1704 //------------------------------------------------------------------------------
1705
1706 //------------------------------------------------------------------------------
1707 void vvMainWindow::ShowContextMenu(QPoint point)
1708 {
1709   if (!DataTree->selectedItems().size()) {
1710     contextActions[1]->setEnabled(0);
1711     contextActions[2]->setEnabled(0);
1712     contextActions[3]->setEnabled(0);
1713     contextActions[4]->setEnabled(0);
1714     contextActions[5]->setEnabled(0);
1715     contextActions[6]->setEnabled(0);
1716   } else {
1717     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1718     contextActions[1]->setEnabled(1);
1719     contextActions[2]->setEnabled(
1720       DataTree->itemWidget(DataTree->selectedItems()[0],
1721                            COLUMN_RELOAD_IMAGE)->isEnabled());
1722     contextActions[3]->setEnabled(1);
1723     contextActions[5]->setEnabled(1);
1724     contextActions[6]->setEnabled(1);
1725
1726     if (mSlicerManagers[index]->GetDimension() < 3)
1727       contextActions[4]->setEnabled(0);
1728     else
1729       contextActions[4]->setEnabled(1);
1730   }
1731   contextMenu.exec(QCursor::pos());
1732 }
1733 //------------------------------------------------------------------------------
1734
1735 //------------------------------------------------------------------------------
1736 void vvMainWindow::CloseImage()
1737 {
1738   CloseImage(DataTree->selectedItems()[0],0);
1739 }
1740 //------------------------------------------------------------------------------
1741
1742 //------------------------------------------------------------------------------
1743 void vvMainWindow::ReloadImage()
1744 {
1745   ReloadImage(DataTree->selectedItems()[0],0);
1746 }
1747 //------------------------------------------------------------------------------
1748
1749 //------------------------------------------------------------------------------
1750 void vvMainWindow::SelectOverlayImage()
1751 {
1752   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1753
1754   //check if one overlay image is added
1755   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1756     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1757       QString error = "Cannot add more than one compared image\n";
1758       error += "Please remove first ";
1759       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1760       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1761       return;
1762     }
1763
1764   QString Extensions = EXTENSIONS;
1765   Extensions += ";;All Files (*)";
1766   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1767   if (!file.isEmpty())
1768     AddOverlayImage(index,file);
1769 }
1770 //------------------------------------------------------------------------------
1771
1772 //------------------------------------------------------------------------------
1773 void vvMainWindow::AddOverlayImage(int index, QString file)
1774 {
1775
1776   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1777   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1778                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1779   reader->SetFileName(file.toStdString().c_str());
1780   reader->ReadImageInformation();
1781   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1782   int dimension = reader->GetNumberOfDimensions();
1783   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1784   vvProgressDialog progress("Opening " + file.toStdString());
1785   qApp->processEvents();
1786
1787   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1788   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component)) {
1789     //create an item in the tree with good settings
1790     QTreeWidgetItem *item = new QTreeWidgetItem();
1791     item->setData(0,Qt::UserRole,file.toStdString().c_str());
1792     item->setData(1,Qt::UserRole,tr("overlay"));
1793     QFileInfo fileinfo(file); //Do not show the path
1794     item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1795     item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1796     qApp->processEvents();
1797
1798     for (int j = 1; j <= 4; j++) {
1799       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1800       mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("overlay",0,
1801           DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1802     }
1803
1804     //Create the buttons for reload and close
1805     qApp->processEvents();
1806     QTreePushButton* cButton = new QTreePushButton;
1807     cButton->setItem(item);
1808     cButton->setColumn(COLUMN_CLOSE_IMAGE);
1809     cButton->setToolTip(tr("close image"));
1810     cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1811     connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1812             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1813
1814     QTreePushButton* rButton = new QTreePushButton;
1815     rButton->setItem(item);
1816     rButton->setColumn(COLUMN_RELOAD_IMAGE);
1817     rButton->setToolTip(tr("reload image"));
1818     rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1819     connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1820             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1821
1822     DataTree->topLevelItem(index)->setExpanded(1);
1823     DataTree->topLevelItem(index)->addChild(item);
1824     DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1825     DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1826
1827     //set the id of the image
1828     QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1829     item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1830     UpdateTree();
1831     qApp->processEvents();
1832     ImageInfoChanged();
1833     QApplication::restoreOverrideCursor();
1834   } else {
1835     QApplication::restoreOverrideCursor();
1836     QString error = "Cannot import the new image.\n";
1837     error += mSlicerManagers[index]->GetLastError().c_str();
1838     QMessageBox::information(this,tr("Problem reading image !"),error);
1839   }
1840 }
1841 //------------------------------------------------------------------------------
1842
1843
1844 //------------------------------------------------------------------------------
1845 void vvMainWindow::AddROI(int index, QString file)
1846 {
1847   DD("AddImageAndROI");
1848   /*
1849   // Get slice manager
1850
1851   // Load image
1852
1853   vvImageReader * mReader = new vvImageReader;
1854   mReader->SetInputFilename(filename.toStdString());
1855   mReader->Update(IMAGE);
1856   if (mReader->GetLastError().size() != 0) {
1857     std::cerr << "Error while reading " << filename.toStdString() << std::endl;
1858     QString error = "Cannot open file \n";
1859     error += mReader->GetLastError().c_str();
1860     QMessageBox::information(this,tr("Reading problem"),error);
1861     delete mReader;
1862     return;
1863   }
1864   vvImage::Pointer roi = mReader->GetOutput();
1865
1866   // Create roi in new tool
1867   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
1868 */
1869 }
1870 //------------------------------------------------------------------------------
1871
1872 //------------------------------------------------------------------------------
1873 void vvMainWindow::SelectFusionImage()
1874 {
1875   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1876
1877   //check if one fusion image is added
1878   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1879     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
1880       QString error = "Cannot add more than one fusion image\n";
1881       error += "Please remove first ";
1882       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1883       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1884       return;
1885     }
1886
1887   QString Extensions = EXTENSIONS;
1888   Extensions += ";;All Files (*)";
1889   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1890   if (!file.isEmpty())
1891     AddFusionImage(index,file);
1892 }
1893 //------------------------------------------------------------------------------
1894
1895 //------------------------------------------------------------------------------
1896 void vvMainWindow::AddFusionImage(int index, QString file)
1897 {
1898   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1899   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1900                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1901   reader->SetFileName(file.toStdString().c_str());
1902   reader->ReadImageInformation();
1903   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1904   if (reader) {
1905     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1906     vvProgressDialog progress("Opening fusion");
1907     qApp->processEvents();
1908
1909     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1910     if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1911                                           reader->GetNumberOfDimensions(), component)) {
1912       //create an item in the tree with good settings
1913       QTreeWidgetItem *item = new QTreeWidgetItem();
1914       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1915       item->setData(1,Qt::UserRole,tr("fusion"));
1916       QFileInfo fileinfo(filename.c_str()); //Do not show the path
1917       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1918       item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1919       qApp->processEvents();
1920
1921       for (int j = 1; j <= 4; j++) {
1922         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1923         mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("fusion",0,
1924             DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1925       }
1926
1927       //Create the buttons for reload and close
1928       qApp->processEvents();
1929       QTreePushButton* cButton = new QTreePushButton;
1930       cButton->setItem(item);
1931       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1932       cButton->setToolTip(tr("close image"));
1933       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1934       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1935               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1936
1937       QTreePushButton* rButton = new QTreePushButton;
1938       rButton->setItem(item);
1939       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1940       rButton->setToolTip(tr("reload image"));
1941       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1942       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1943               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1944
1945       DataTree->topLevelItem(index)->setExpanded(1);
1946       DataTree->topLevelItem(index)->addChild(item);
1947       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1948       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1949
1950       //set the id of the image
1951       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1952       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1953       UpdateTree();
1954       qApp->processEvents();
1955       ImageInfoChanged();
1956       QApplication::restoreOverrideCursor();
1957     } else {
1958       QApplication::restoreOverrideCursor();
1959       QString error = "Cannot import the new image.\n";
1960       error += mSlicerManagers[index]->GetLastError().c_str();
1961       QMessageBox::information(this,tr("Problem reading image !"),error);
1962     }
1963   } else {
1964     QString error = "Cannot import the new image.\n";
1965     QMessageBox::information(this,tr("Problem reading image !"),error);
1966   }
1967 }
1968 //------------------------------------------------------------------------------
1969
1970
1971 //------------------------------------------------------------------------------
1972 void vvMainWindow::OpenField()
1973 {
1974   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1975   //check if a vector field has already been added
1976   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1977     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
1978       QString error = "Cannot add more than one vector field\n";
1979       error += "Please remove first ";
1980       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1981       QMessageBox::information(this,tr("Problem adding vector field!"),error);
1982       return;
1983     }
1984
1985   QString Extensions = "Images ( *.mhd)";
1986   Extensions += ";;Images ( *.vf)";
1987   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
1988   if (!file.isEmpty())
1989     AddField(file,index);
1990 }
1991 //------------------------------------------------------------------------------
1992
1993
1994 //------------------------------------------------------------------------------
1995 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
1996 {
1997   //create an item in the tree with good settings
1998   QTreeWidgetItem *item = new QTreeWidgetItem();
1999   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2000   item->setData(1,Qt::UserRole,tr("vector"));
2001   QFileInfo fileinfo(filename); //Do not show the path
2002   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2003   item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
2004   qApp->processEvents();
2005
2006   for (int j = 1; j <= 4; j++) {
2007     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2008     mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("vector",0,
2009         DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
2010   }
2011
2012   //Create the buttons for reload and close
2013   qApp->processEvents();
2014   QTreePushButton* cButton = new QTreePushButton;
2015   cButton->setItem(item);
2016   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2017   cButton->setToolTip(tr("close vector field"));
2018   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2019   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2020           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2021
2022   QTreePushButton* rButton = new QTreePushButton;
2023   rButton->setItem(item);
2024   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2025   rButton->setToolTip(tr("reload vector field"));
2026   rButton->setEnabled(from_disk);
2027   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2028   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2029           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2030
2031   DataTree->topLevelItem(index)->setExpanded(1);
2032   DataTree->topLevelItem(index)->addChild(item);
2033   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2034   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2035
2036   //set the id of the image
2037   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2038   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2039   UpdateTree();
2040   qApp->processEvents();
2041   ImageInfoChanged();
2042   QApplication::restoreOverrideCursor();
2043 }
2044 //------------------------------------------------------------------------------
2045
2046
2047 //------------------------------------------------------------------------------
2048 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2049 {
2050   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2051   vvSlicerManager* imageManager = mSlicerManagers[index];
2052   if (imageManager->SetVF(vf,file.toStdString())) {
2053     AddFieldEntry(file,index,false);
2054   } else {
2055     QString error = "Cannot import the vector field for this image.\n";
2056     error += imageManager->GetLastError().c_str();
2057     QMessageBox::information(this,tr("Problem reading VF !"),error);
2058   }
2059   QApplication::restoreOverrideCursor();
2060 }
2061 //------------------------------------------------------------------------------
2062
2063
2064 //------------------------------------------------------------------------------
2065 void vvMainWindow::AddField(QString file,int index)
2066 {
2067   if (QFile::exists(file)) {
2068     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2069
2070     //init the progress events
2071     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2072     vvProgressDialog progress("Opening " + file.toStdString());
2073     qApp->processEvents();
2074
2075     //read the vector and put it in the current mSlicerManager
2076     vvSlicerManager* imageManager = mSlicerManagers[index];
2077     qApp->processEvents();
2078
2079     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2080     if (imageManager->SetVF(file.toStdString())) {
2081       imageManager->Render();
2082       AddFieldEntry(file,index,true);
2083     } else {
2084       QApplication::restoreOverrideCursor();
2085       QString error = "Cannot import the vector field for this image.\n";
2086       error += imageManager->GetLastError().c_str();
2087       QMessageBox::information(this,tr("Problem reading VF !"),error);
2088     }
2089   } else
2090     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2091
2092 }
2093 //------------------------------------------------------------------------------
2094
2095
2096 //------------------------------------------------------------------------------
2097 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width)
2098 {
2099   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2100   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2101     for (int i = 0; i < 4; i++) {
2102       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2103       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2104       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2105       if (log > 0)
2106         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2107       else
2108         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2109     }
2110   }
2111 }
2112 //------------------------------------------------------------------------------
2113
2114
2115 //------------------------------------------------------------------------------
2116 void vvMainWindow::SetOverlayProperty(int color)
2117 {
2118   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2119   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2120     mSlicerManagers[index]->SetOverlayColor(color);
2121     mSlicerManagers[index]->SetColorMap(0);
2122     mSlicerManagers[index]->Render();
2123   }
2124 }
2125 //------------------------------------------------------------------------------
2126
2127 //------------------------------------------------------------------------------
2128 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level)
2129 {
2130   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2131   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2132     mSlicerManagers[index]->SetFusionOpacity(opacity);
2133     mSlicerManagers[index]->SetFusionColorMap(colormap);
2134     mSlicerManagers[index]->SetFusionWindow(window);
2135     mSlicerManagers[index]->SetFusionLevel(level);
2136     mSlicerManagers[index]->SetColorMap(0);
2137     mSlicerManagers[index]->Render();
2138   }
2139 }
2140 //------------------------------------------------------------------------------
2141
2142 //------------------------------------------------------------------------------
2143 void vvMainWindow::SaveAs()
2144 {
2145   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2146     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2147     return;
2148   }
2149
2150   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2151   int dimension = mSlicerManagers[index]->GetDimension();
2152   QStringList OutputListeFormat;
2153   OutputListeFormat.clear();
2154   if (dimension == 1) {
2155     OutputListeFormat.push_back(".mhd");
2156   }
2157   if (dimension == 2) {
2158     OutputListeFormat.push_back(".bmp");
2159     OutputListeFormat.push_back(".png");
2160     OutputListeFormat.push_back(".jpeg");
2161     OutputListeFormat.push_back(".tif");
2162     OutputListeFormat.push_back(".mhd");
2163     OutputListeFormat.push_back(".hdr");
2164     OutputListeFormat.push_back(".vox");
2165   } else if (dimension == 3) {
2166     OutputListeFormat.push_back(".mhd");
2167     OutputListeFormat.push_back(".hdr");
2168     OutputListeFormat.push_back(".vox");
2169   } else if (dimension == 4) {
2170     OutputListeFormat.push_back(".mhd");
2171   }
2172   QString Extensions = "AllFiles(*.*)";
2173   for (int i = 0; i < OutputListeFormat.count(); i++) {
2174     Extensions += ";;Images ( *";
2175     Extensions += OutputListeFormat[i];
2176     Extensions += ")";
2177   }
2178   QString fileName = QFileDialog::getSaveFileName(this,
2179                      tr("Save As"),
2180                      mSlicerManagers[index]->GetFileName().c_str(),
2181                      Extensions);
2182   if (!fileName.isEmpty()) {
2183     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2184     if (OutputListeFormat.contains(
2185           fileformat.c_str())) {
2186       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2187       std::string action = "Saving";
2188       vvProgressDialog progress("Saving "+fileName.toStdString());
2189       qApp->processEvents();
2190       vvImageWriter *writer = new vvImageWriter;
2191       writer->SetOutputFileName(fileName.toStdString());
2192       writer->SetInput(mSlicerManagers[index]->GetImage());
2193       writer->Update();
2194       QApplication::restoreOverrideCursor();
2195       if (writer->GetLastError().size()) {
2196         QString error = "Saving did not succeed\n";
2197         error += writer->GetLastError().c_str();
2198         QMessageBox::information(this,tr("Saving Problem"),error);
2199         SaveAs();
2200       }
2201     } else {
2202       QString error = fileformat.c_str();
2203       if (error.isEmpty())
2204         error += "no file format specified !";
2205       else
2206         error += " format unknown !!!\n";
2207       QMessageBox::information(this,tr("Saving Problem"),error);
2208       SaveAs();
2209     }
2210   }
2211 }
2212 //------------------------------------------------------------------------------
2213
2214
2215 //------------------------------------------------------------------------------
2216 void vvMainWindow::AddLink(QString image1,QString image2)
2217 {
2218   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2219     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2220       mSlicerManagers[i]->AddLink(image2.toStdString());
2221     }
2222     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2223       mSlicerManagers[i]->AddLink(image1.toStdString());
2224     }
2225   }
2226 }
2227 //------------------------------------------------------------------------------
2228
2229
2230 //------------------------------------------------------------------------------
2231 void vvMainWindow::RemoveLink(QString image1,QString image2)
2232 {
2233   // DD("vvMainWindow:RemoveLink");
2234   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2235     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2236       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2237     }
2238     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2239       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2240     }
2241   }
2242 }
2243 //------------------------------------------------------------------------------
2244
2245 //------------------------------------------------------------------------------
2246 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2247 {
2248   int index = 0;
2249   while(sm != mSlicerManagers[index])
2250     index++;
2251   index = (index+offset) % mSlicerManagers.size();
2252
2253   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2254   //CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2255   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2256   DisplayChanged(item,slicer+1);
2257 }
2258 //------------------------------------------------------------------------------
2259
2260 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2261 {
2262   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2263     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2264       for (int j = 0; j < 4; j++) {
2265         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2266         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2267         //UpdateTSlice(j,value);
2268       }
2269       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2270       break;
2271     }
2272   }
2273 }
2274 //------------------------------------------------------------------------------
2275
2276
2277 //------------------------------------------------------------------------------
2278 void vvMainWindow::NOHorizontalSliderMoved()
2279 {
2280   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2281   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2282 //  mCurrentTime = NOHorizontalSlider->value();
2283 }
2284 //------------------------------------------------------------------------------
2285
2286
2287 //------------------------------------------------------------------------------
2288 void vvMainWindow::NEHorizontalSliderMoved()
2289 {
2290   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2291   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2292 //  mCurrentTime = NEHorizontalSlider->value();
2293 }
2294 //------------------------------------------------------------------------------
2295
2296
2297 //------------------------------------------------------------------------------
2298 void vvMainWindow::SOHorizontalSliderMoved()
2299 {
2300   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2301   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2302   // mCurrentTime = SOHorizontalSlider->value();
2303 }
2304 //------------------------------------------------------------------------------
2305
2306
2307 //------------------------------------------------------------------------------
2308 void vvMainWindow::SEHorizontalSliderMoved()
2309 {
2310   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2311   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2312   // mCurrentTime = SEHorizontalSlider->value();
2313 }
2314 //------------------------------------------------------------------------------
2315
2316 //------------------------------------------------------------------------------
2317 void vvMainWindow::NOVerticalSliderChanged()
2318 {
2319   static int value=-1;
2320   if (value == NOVerticalSlider->value()) return;
2321   else value = NOVerticalSlider->value();
2322   //  int value = NOVerticalSlider->value();
2323   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2324     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2325       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2326         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2327         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2328
2329         // If nor Update/Render -> slider not work
2330         // only render = ok navigation, but for contour Update needed but slower ?
2331
2332         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2333         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2334       }
2335       break;
2336     }
2337   }
2338 }
2339 //------------------------------------------------------------------------------
2340
2341
2342 //------------------------------------------------------------------------------
2343 void vvMainWindow::NEVerticalSliderChanged()
2344 {
2345   static int value=-1;
2346   if (value == NEVerticalSlider->value()) return;
2347   else value = NEVerticalSlider->value();
2348   //  int value = NEVerticalSlider->value();
2349   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2350     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2351       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2352         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2353         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2354         mSlicerManagers[i]->UpdateSlice(1);
2355         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2356       }
2357       break;
2358     }
2359   }
2360 }
2361 //------------------------------------------------------------------------------
2362
2363
2364 //------------------------------------------------------------------------------
2365 void vvMainWindow::SOVerticalSliderChanged()
2366 {
2367   static int value=-1;
2368   // DD(value);
2369 //   DD(SOVerticalSlider->value());
2370   if (value == SOVerticalSlider->value()) return;
2371   else value = SOVerticalSlider->value();
2372   //int value = SOVerticalSlider->value();
2373   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2374     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2375       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2376         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2377         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2378         mSlicerManagers[i]->UpdateSlice(2);
2379         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2380       }
2381       // else { DD("avoid SOVerticalSlider slicer update"); }
2382       break;
2383     }
2384   }
2385 }
2386 //------------------------------------------------------------------------------
2387
2388
2389 //------------------------------------------------------------------------------
2390 void vvMainWindow::SEVerticalSliderChanged()
2391 {
2392   static int value=-1;
2393   if (value == SEVerticalSlider->value()) return;
2394   else value = SEVerticalSlider->value();
2395   // int value = SEVerticalSlider->value();
2396   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2397     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2398       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2399         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2400         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2401         mSlicerManagers[i]->UpdateSlice(3);
2402         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2403       }
2404       break;
2405     }
2406   }
2407 }
2408 //------------------------------------------------------------------------------
2409
2410
2411 //------------------------------------------------------------------------------
2412 void vvMainWindow::UpdateSlice(int slicer, int slice)
2413 {
2414   // DD("vvMainWindow::UpdateSlice");
2415 //   DD(slicer);
2416 //   DD(slice);
2417   if (slicer == 0) {
2418     //    if (slice != NOVerticalSlider->value())
2419     NOVerticalSlider->setValue(slice);
2420   } else {
2421     if (slicer == 1)
2422       NEVerticalSlider->setValue(slice);
2423     else {
2424       if (slicer == 2)
2425         SOVerticalSlider->setValue(slice);
2426       else {
2427         if (slicer == 3)
2428           SEVerticalSlider->setValue(slice);
2429       }
2430     }
2431   }
2432   // DD("vvMainWindow:UpdateSlice END");
2433 }
2434 //------------------------------------------------------------------------------
2435
2436
2437 //------------------------------------------------------------------------------
2438 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2439 {
2440   switch (slicer) {
2441   case 0:
2442     NOHorizontalSlider->setValue(slice);
2443     break;
2444   case 1:
2445     NEHorizontalSlider->setValue(slice);
2446     break;
2447   case 2:
2448     SOHorizontalSlider->setValue(slice);
2449     break;
2450   case 3:
2451     SEHorizontalSlider->setValue(slice);
2452     break;
2453   }
2454 }
2455 //------------------------------------------------------------------------------
2456
2457
2458 //------------------------------------------------------------------------------
2459 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2460 {
2461   int position = int((min+max)/2);
2462   int tPosition = int((tmin+tmax)/2);
2463   if (slicer == 0) {
2464     NOVerticalSlider->setValue(position);
2465     NOVerticalSlider->setRange(min,max);
2466     NOHorizontalSlider->setRange(tmin,tmax);
2467     NOHorizontalSlider->setValue(tPosition);
2468   } else if (slicer == 1) {
2469     NEVerticalSlider->setValue(position);
2470     NEVerticalSlider->setRange(min,max);
2471     NEHorizontalSlider->setRange(tmin,tmax);
2472     NEHorizontalSlider->setValue(tPosition);
2473   } else if (slicer == 2) {
2474     SOVerticalSlider->setValue(position);
2475     SOVerticalSlider->setRange(min,max);
2476     SOHorizontalSlider->setRange(tmin,tmax);
2477     SOHorizontalSlider->setValue(tPosition);
2478   } else if (slicer == 3) {
2479     SEVerticalSlider->setValue(position);
2480     SEVerticalSlider->setRange(min,max);
2481     SEHorizontalSlider->setRange(tmin,tmax);
2482     SEHorizontalSlider->setValue(tPosition);
2483   }
2484 }
2485 //------------------------------------------------------------------------------
2486
2487
2488 //------------------------------------------------------------------------------
2489 void vvMainWindow::SaveNOScreenshot()
2490 {
2491   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2492   w2i->SetInput(NOViewWidget->GetRenderWindow());
2493   w2i->Update();
2494   SaveScreenshot(w2i->GetOutput());
2495   w2i->Delete();
2496 }
2497 //------------------------------------------------------------------------------
2498
2499
2500 //------------------------------------------------------------------------------
2501 void vvMainWindow::SaveNEScreenshot()
2502 {
2503   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2504   w2i->SetInput(NEViewWidget->GetRenderWindow());
2505   w2i->Update();
2506   SaveScreenshot(w2i->GetOutput());
2507   w2i->Delete();
2508 }
2509 //------------------------------------------------------------------------------
2510
2511
2512 //------------------------------------------------------------------------------
2513 void vvMainWindow::SaveSOScreenshot()
2514 {
2515   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2516   w2i->SetInput(SOViewWidget->GetRenderWindow());
2517   w2i->Update();
2518   SaveScreenshot(w2i->GetOutput());
2519   w2i->Delete();
2520 }
2521 //------------------------------------------------------------------------------
2522
2523
2524 //------------------------------------------------------------------------------
2525 void vvMainWindow::SaveSEScreenshot()
2526 {
2527   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2528   w2i->SetInput(SEViewWidget->GetRenderWindow());
2529   w2i->Update();
2530   SaveScreenshot(w2i->GetOutput());
2531   w2i->Delete();
2532 }
2533 //------------------------------------------------------------------------------
2534
2535
2536 //------------------------------------------------------------------------------
2537 void vvMainWindow::SaveScreenshot(vtkImageData* image)
2538 {
2539   QString Extensions = "Images( *.png);;";
2540   Extensions += "Images( *.jpg);;";
2541   Extensions += "Images( *.bmp);;";
2542   Extensions += "Images( *.tif);;";
2543   Extensions += "Images( *.ppm)";
2544   QString fileName = QFileDialog::getSaveFileName(this,
2545                      tr("Save As"),
2546                      itksys::SystemTools::GetFilenamePath(
2547                        mSlicerManagers[0]->GetFileName()).c_str(),
2548                      Extensions);
2549   if (!fileName.isEmpty()) {
2550     const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2551     if (!strcmp(ext, ".bmp")) {
2552       vtkBMPWriter *bmp = vtkBMPWriter::New();
2553       bmp->SetInput(image);
2554       bmp->SetFileName(fileName.toStdString().c_str());
2555       bmp->Write();
2556       bmp->Delete();
2557     } else if (!strcmp(ext, ".tif")) {
2558       vtkTIFFWriter *tif = vtkTIFFWriter::New();
2559       tif->SetInput(image);
2560       tif->SetFileName(fileName.toStdString().c_str());
2561       tif->Write();
2562       tif->Delete();
2563     } else if (!strcmp(ext, ".ppm")) {
2564       vtkPNMWriter *pnm = vtkPNMWriter::New();
2565       pnm->SetInput(image);
2566       pnm->SetFileName(fileName.toStdString().c_str());
2567       pnm->Write();
2568       pnm->Delete();
2569     } else if (!strcmp(ext, ".png")) {
2570       vtkPNGWriter *png = vtkPNGWriter::New();
2571       png->SetInput(image);
2572       png->SetFileName(fileName.toStdString().c_str());
2573       png->Write();
2574       png->Delete();
2575     } else if (!strcmp(ext, ".jpg")) {
2576       vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2577       jpg->SetInput(image);
2578       jpg->SetFileName(fileName.toStdString().c_str());
2579       jpg->Write();
2580       jpg->Delete();
2581     } else {
2582       QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2583     }
2584   }
2585
2586 }
2587 //------------------------------------------------------------------------------
2588
2589
2590 //------------------------------------------------------------------------------
2591 void vvMainWindow::GoToCursor()
2592 {
2593   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2594   for (int column = 1; column < 5; column++) {
2595     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
2596       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2597       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2598         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2599       mSlicerManagers[index]->UpdateViews(1,column-1);
2600       mSlicerManagers[index]->UpdateLinked(column-1);
2601       break;
2602     }
2603   }
2604 }
2605 //------------------------------------------------------------------------------
2606
2607 //------------------------------------------------------------------------------
2608 void vvMainWindow::PlayPause()
2609 {
2610   if (playMode) {
2611     playMode = 0;
2612     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2613     ImageInfoChanged();
2614     return;
2615   } else {
2616     int image_number=DataTree->topLevelItemCount();
2617     bool has_temporal;
2618     for (int i=0; i<image_number; i++)
2619       if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1) {
2620         has_temporal=true;
2621         break;
2622       }
2623     if (has_temporal) {
2624       playMode = 1;
2625       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2626       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2627     }
2628   }
2629 }
2630 //------------------------------------------------------------------------------
2631
2632 //------------------------------------------------------------------------------
2633 void vvMainWindow::PlayNext()
2634 {
2635   if (playMode && !this->isHidden()) {
2636     int image_number=DataTree->topLevelItemCount();
2637     ///Only play one slicer per SM, and only if the SM is being displayed
2638     for (int i=0; i<image_number; i++)
2639       for (int j=0; j<4; j++)
2640         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2641             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
2642           mSlicerManagers[i]->SetNextTSlice(j);
2643           break;
2644         }
2645     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2646   }
2647 }
2648 //------------------------------------------------------------------------------
2649
2650 void vvMainWindow::ShowLastImage()
2651 {
2652   if (mSlicerManagers.size() > 1) {
2653     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2654     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2655     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2656     DisplayChanged(item,1);
2657   }
2658 }
2659
2660 //------------------------------------------------------------------------------
2661 void vvMainWindow::UpdateRenderWindows()
2662 {
2663   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2664   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2665   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2666   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2667 }
2668 //------------------------------------------------------------------------------
2669
2670 //------------------------------------------------------------------------------
2671 void vvMainWindow::SegmentationOnCurrentImage()
2672 {
2673   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2674
2675   vvSegmentationDialog segmentation;
2676   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2677   segmentation.exec();
2678 }
2679 //------------------------------------------------------------------------------
2680
2681 void vvMainWindow::SurfaceViewerLaunch()
2682 {
2683   vvSurfaceViewerDialog surfaceViewer;
2684   surfaceViewer.exec();
2685 }
2686 //------------------------------------------------------------------------------
2687
2688
2689 //------------------------------------------------------------------------------
2690 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
2691 {
2692   int number=0;
2693   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
2694     vvSlicerManager * v = mSlicerManagers[l];
2695     if (v->GetBaseFileName() ==
2696         vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
2697       number = std::max(number, v->GetBaseFileNameNumber()+1);
2698     }
2699   }
2700   return number;
2701 }
2702 //------------------------------------------------------------------------------
2703
2704
2705 //------------------------------------------------------------------------------
2706 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2707 {
2708   // Change filename if another image exist with the same name
2709   int number = GetImageDuplicateFilenameNumber(filename);
2710
2711   // Create new SliceManager
2712   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
2713   slicer_manager->SetImage(image);//, IMAGE, number);
2714   //  filename = filename+"_"+clitk::toString(number);
2715   slicer_manager->SetFilename(filename, number);
2716   mSlicerManagers.push_back(slicer_manager);
2717
2718   //create an item in the tree with good settings
2719   QTreeWidgetItem *item = new QTreeWidgetItem();
2720   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2721   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
2722   qApp->processEvents();
2723
2724   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2725
2726   //Create the buttons for reload and close
2727   qApp->processEvents();
2728   QTreePushButton* cButton = new QTreePushButton;
2729   cButton->setItem(item);
2730   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2731   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2732   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2733           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2734
2735   QTreePushButton* rButton = new QTreePushButton;
2736   rButton->setItem(item);
2737   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2738   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2739   rButton->setEnabled(0);
2740   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2741           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2742
2743   DataTree->addTopLevelItem(item);
2744   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2745   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2746
2747   //set the id of the image
2748   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2749   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2750   mSlicerManagers.back()->SetId(id.toStdString());
2751
2752   linkPanel->addImage(filename, id.toStdString());
2753
2754   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
2755           this, SLOT(CurrentImageChanged(std::string)));
2756   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
2757           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2758   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
2759           this, SLOT(VectorChanged(int,double,double,double, double)));
2760   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
2761           this, SLOT(OverlayChanged(int,double,double)));
2762   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
2763           this, SLOT(FusionChanged(int,double)));
2764   connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
2765           this,SLOT(WindowsChanged(int, int, int)));
2766   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
2767           this,SLOT(WindowLevelChanged(double, double, int, int)));
2768   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
2769           this,SLOT(UpdateSlice(int,int)));
2770   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
2771           this,SLOT(UpdateTSlice(int, int)));
2772   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2773           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2774   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2775           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2776   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*)),
2777           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*)));
2778   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
2779           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
2780   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2781   UpdateTree();
2782   qApp->processEvents();
2783   InitSlicers();
2784   ShowLastImage();
2785   InitDisplay();
2786   qApp->processEvents();
2787
2788   // End
2789   ImageInfoChanged();
2790   return slicer_manager;
2791 }
2792 //------------------------------------------------------------------------------
2793
2794
2795 //------------------------------------------------------------------------------
2796 void vvMainWindow::UpdateCurrentSlicer()
2797 {
2798   int index = -1;
2799   if (DataTree->selectedItems().size() > 0) {
2800     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2801   }
2802   mSlicerManagerCurrentIndex = index;
2803 }
2804 //------------------------------------------------------------------------------
2805