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 #include <algorithm>
  19 #include <QMessageBox>
  20 #include <QInputDialog>
  21 #include <QTimer>
  22 #include "QTreePushButton.h"
  23
  24 // VV include
  25 #include "vvMainWindow.h"
  26 #include "vvHelpDialog.h"
  27 #include "vvDocumentation.h"
  28 #include "vvProgressDialog.h"
  29 #include "vvQDicomSeriesSelector.h"
  30 #include "vvSlicerManager.h"
  31 #include "clitkImageCommon.h"
  32 #include "vvSlicer.h"
  33 #include "vvInteractorStyleNavigator.h"
  34 #include "vvImageWriter.h"
  35 #include "vvResamplerDialog.h"
  36 #include "vvSegmentationDialog.h"
  37 #include "vvSurfaceViewerDialog.h"
  38 #include "vvDeformationDialog.h"
  39 #include "vvImageWarp.h"
  40 #include "vvUtils.h"
  41 #include "vvMaximumIntensityProjection.h"
  42 #include "vvMidPosition.h"
  43 #include "vvMesh.h"
  44 #include "vvStructSelector.h"
  45 #include "vvMeshReader.h"
  46 #include "vvConstants.h"
  47
  48 #ifdef CLITK_VV_USE_BDCM
  49 #include <bdcmDicomFilesSelectorDialog.h>
  50 #endif
  51
  52 // ITK include
  53 #include "itkImage.h"
  54 #include "itkImageFileReader.h"
  55 #include "itkByteSwapper.h"
  56 #include "itkCommand.h"
  57 #include "itkNumericSeriesFileNames.h"
  58
  59 // VTK include
  60 #include "vtkImageData.h"
  61 #include "vtkImageActor.h"
  62 #include "vtkCornerAnnotation.h"
  63 #include "vtkRenderWindow.h"
  64 #include "vtkRenderWindowInteractor.h"
  65 #include "vtkRenderer.h"
  66 #include "vtkRendererCollection.h"
  67 #include "vtkWindowToImageFilter.h"
  68 #include "vtkBMPWriter.h"
  69 #include "vtkTIFFWriter.h"
  70 #include "vtkPNMWriter.h"
  71 #include "vtkPNGWriter.h"
  72 #include "vtkJPEGWriter.h"
  73
  74 // Standard includes
  75 #include <iostream>
  76
  77 #define COLUMN_TREE 0
  78 #define COLUMN_UL_VIEW 1
  79 #define COLUMN_UR_VIEW 2
  80 #define COLUMN_DL_VIEW 3
  81 #define COLUMN_DR_VIEW 4
  82 #define COLUMN_CLOSE_IMAGE 5
  83 #define COLUMN_RELOAD_IMAGE 6
  84 #define COLUMN_IMAGE_NAME 7
  85
  86 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.hdr *.vox *.his *.xdr)"
  87
  88 /*Data Tree values
  89   0,Qt::UserRole full filename
  90   1,Qt::CheckStateRole checkbutton UL View
  91   1,Qt::UserRole overlay, fusion or vector
  92   2,Qt::CheckStateRole checkbutton UR View
  93   3,Qt::CheckStateRole checkbutton DL View
  94   4,Qt::CheckStateRole checkbutton DR View
  95   5,0  short filename
  96   5,Qt::UserRole mSlicerManager id*/
  97
  98 //------------------------------------------------------------------------------
  99 vvMainWindow::vvMainWindow():vvMainWindowBase() {
 100   setupUi(this); // this sets up the GUI
 101
 102   mInputPathName = "";
 103   mMenuTools = menuTools;
 104   mMenuExperimentalTools = menuExperimental;
 105   mMainWidget = this;
 106
 107   //Init the contextMenu
 108   this->setContextMenuPolicy(Qt::CustomContextMenu);
 109   contextActions.resize(0);
 110   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/fileopen.png")),
 111                                                         tr("O&pen new Image"));
 112   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 113   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 114   contextActions.push_back(actionOpen_new_image);
 115   contextMenu.addSeparator();
 116
 117   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")),
 118                                                      tr("Close Current Image"));
 119   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 120   contextActions.push_back(actionClose_Image);
 121
 122   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")),
 123                                                       tr("Reload Current Image"));
 124   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 125   contextActions.push_back(actionReload_image);
 126
 127   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/filesave.png")),
 128                                                     tr("Save Current Image"));
 129   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 130   contextActions.push_back(actionSave_image);
 131
 132   contextMenu.addSeparator();
 133
 134   // QAction* actionCrop_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/crop.png")),
 135   //                                                   tr("Crop Current Image"));
 136   // connect(actionCrop_image,SIGNAL(triggered()),this,SLOT(CropImage()));
 137   // contextActions.push_back(actionCrop_image);
 138
 139   QAction* actionSplit_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/cut.png")),
 140                                                      tr("Split Current Image"));
 141   connect(actionSplit_image,SIGNAL(triggered()),this,SLOT(SplitImage()));
 142   contextActions.push_back(actionSplit_image);
 143
 144   contextMenu.addSeparator();
 145
 146   contextMenu.addAction(actionAdd_VF_to_current_Image);
 147   contextActions.push_back(actionAdd_VF_to_current_Image);
 148
 149   QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/GPSup.png")),
 150                                                                        tr("Add overlay image to current image"));
 151   contextMenu.addAction(actionAdd_Overlay_to_current_Image);
 152   contextActions.push_back(actionAdd_Overlay_to_current_Image);
 153
 154   connect(actionAdd_Overlay_to_current_Image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 155
 156   contextMenu.addAction(actionAdd_fusion_image);
 157   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 158   contextActions.push_back(actionAdd_fusion_image);
 159
 160   //init the DataTree
 161   mSlicerManagers.resize(0);
 162
 163   QStringList header;
 164   header.append("");
 165   header.append("TL");
 166   header.append("TR");
 167   header.append("BL");
 168   header.append("BR");
 169   header.append("");
 170   header.append("");
 171   header.append("Name");
 172
 173   DataTree->setHeaderLabels(header);
 174   DataTree->resizeColumnToContents(COLUMN_TREE);
 175   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 176   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 177   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 178   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 179   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 180   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 181   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 182
 183   viewMode = 1;
 184   documentation = new vvDocumentation();
 185   help_dialog = new vvHelpDialog();
 186   dicomSeriesSelector = new vvDicomSeriesSelector();
 187
 188   inverseButton->setEnabled(0);
 189   actionAdd_Overlay_to_current_Image->setEnabled(0);
 190   actionSave_As->setEnabled(0);
 191   actionAdd_VF_to_current_Image->setEnabled(0);
 192   actionAdd_fusion_image->setEnabled(0);
 193
 194   //init the sliders
 195   verticalSliders.push_back(NOVerticalSlider);
 196   verticalSliders.push_back(NEVerticalSlider);
 197   verticalSliders.push_back(SOVerticalSlider);
 198   verticalSliders.push_back(SEVerticalSlider);
 199
 200   for (int i =0; i < 4; i++)
 201     verticalSliders[i]->hide();
 202
 203   horizontalSliders.push_back(NOHorizontalSlider);
 204   horizontalSliders.push_back(NEHorizontalSlider);
 205   horizontalSliders.push_back(SOHorizontalSlider);
 206   horizontalSliders.push_back(SEHorizontalSlider);
 207
 208   for (int i =0; i < 4; i++)
 209     horizontalSliders[i]->hide();
 210
 211
 212   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 213   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 214   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 215   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 216
 217   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 218   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 219   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 220   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 221
 222   //connect everything
 223   connect(actionMaximum_Intensity_Projection,SIGNAL(triggered()),this,SLOT(ComputeMIP()));
 224   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 225   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 226   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 227   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 228   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 229   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 230   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 231   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 232   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 233   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 234   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 235   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 236   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 237   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 238   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 239
 240   ///////////////////////////////////////////////
 241   contextMenu.addAction(actionResampler);
 242   connect(actionResampler,SIGNAL(triggered()),this,SLOT(ResampleCurrentImage()));
 243   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 244   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 245   ///////////////////////////////////////////////
 246
 247   actionNorth_East_Window->setEnabled(0);
 248   actionNorth_West_Window->setEnabled(0);
 249   actionSouth_East_Window->setEnabled(0);
 250   actionSouth_West_Window->setEnabled(0);
 251
 252   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 253   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 254   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 255   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 256
 257   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 258   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 259           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 260
 261   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 262   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 263   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 264   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 265   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 266   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 267
 268
 269   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 270
 271   connect(linkPanel,SIGNAL(addLink(QString,QString)),this,SLOT(AddLink(QString,QString)));
 272   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 273   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int)),this,SLOT(SetVFProperty(int,int,int)));
 274   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int)),this,SLOT(SetOverlayProperty(int)));
 275   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,double,double)),
 276           this,SLOT(SetFusionProperty(int,int,double,double)));
 277   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 278
 279   playMode = 0;//pause
 280   mFrameRate = 10;
 281   playButton->setEnabled(0);
 282   frameRateLabel->setEnabled(0);
 283   frameRateSpinBox->setEnabled(0);
 284   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 285   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 286
 287   goToCursorPushButton->setEnabled(0);
 288   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 289
 290   NOViewWidget->hide();
 291   NEViewWidget->hide();
 292   SOViewWidget->hide();
 293   SEViewWidget->hide();
 294
 295   //Recently opened files
 296   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 297   if ( !recent_files.empty() )
 298     {
 299       QMenu * rmenu = new QMenu("Recently opened files...");
 300       rmenu->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/open.png")));
 301       menuFile->insertMenu(actionOpen_Image_With_Time,rmenu);
 302       for (std::list<std::string>::iterator i = recent_files.begin();i!=recent_files.end();i++)
 303         {
 304           QAction* current=new QAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/open.png")),
 305                                        (*i).c_str(),this);
 306           rmenu->addAction(current);
 307           connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 308         }
 309     }
 310
 311   // Adding all new tools (insertion in the menu)
 312   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 313
 314   if (!CLITK_EXPERIMENTAL)
 315       menuExperimental->menuAction()->setVisible(false);
 316 }
 317 //------------------------------------------------------------------------------
 318
 319
 320 //------------------------------------------------------------------------------
 321 void vvMainWindow::ComputeMIP()
 322 {
 323   vvMaximumIntensityProjection mip;
 324   vvSlicerManager* selected_slicer = mSlicerManagers[GetSlicerIndexFromItem(DataTree->selectedItems()[0])];
 325   QFileInfo info(selected_slicer->GetFileName().c_str());
 326   mip.Compute(selected_slicer);
 327   AddImage(mip.GetOutput(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_mip.mhd");
 328 }
 329 //------------------------------------------------------------------------------
 330
 331
 332 //------------------------------------------------------------------------------
 333 void vvMainWindow::ComputeMidPosition()
 334 {
 335   bool ok;
 336   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 337   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 338                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 339   if (ok)
 340     {
 341       vvMidPosition midp;
 342       midp.slicer_manager = mSlicerManagers[index];
 343       midp.reference_image_index = ref;
 344       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 345       midp.Update();
 346       if (midp.error)
 347         QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 348       else
 349         {
 350           QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 351           AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 352         }
 353       QApplication::restoreOverrideCursor();
 354     }
 355 }
 356 //------------------------------------------------------------------------------
 357
 358
 359 //------------------------------------------------------------------------------
 360 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 361 {
 362   QTreeWidgetItem *item = new QTreeWidgetItem();
 363   item->setData(0,Qt::UserRole,"filename.vtk");
 364   item->setData(1,Qt::UserRole,tr("contour"));
 365   QBrush brush;
 366   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 367   brush.setStyle(Qt::SolidPattern);
 368   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 369   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 370
 371   for (int j = 1; j <= 4; j++)
 372     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 373
 374   QTreePushButton* cButton = new QTreePushButton;
 375   cButton->setItem(item);
 376   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 377   cButton->setToolTip(tr("close image"));
 378   cButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")));
 379   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 380           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 381
 382   QTreePushButton* rButton = new QTreePushButton;
 383   rButton->setItem(item);
 384   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 385   rButton->setToolTip(tr("reload image"));
 386   rButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")));
 387   rButton->setEnabled(false);
 388   //Not implemented
 389   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 390   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 391
 392   DataTree->topLevelItem(image_index)->setExpanded(1);
 393   DataTree->topLevelItem(image_index)->addChild(item);
 394   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 395   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 396   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 397   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 398
 399   UpdateTree();
 400   mSlicerManagers[image_index]->AddContour(contour,propagation);
 401   mSlicerManagers[image_index]->Render();
 402 }
 403 //------------------------------------------------------------------------------
 404
 405
 406 //------------------------------------------------------------------------------
 407 void vvMainWindow::OpenVTKContour()
 408 {
 409   if (mSlicerManagers.size() > 0)
 410     {
 411       QString Extensions = "Images ( *.vtk; *.obj)";
 412       Extensions += ";;All Files (*)";
 413       QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 414       if (file.isNull())
 415         return;
 416       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 417       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 418       vvMeshReader reader;
 419       reader.SetImage(mSlicerManagers[index]->GetImage());
 420       reader.SetModeToVTK();
 421       reader.SetFilename(file.toStdString());
 422       reader.Update();
 423       AddContour(index,reader.GetOutput()[0],false);
 424       QApplication::restoreOverrideCursor();
 425     }
 426 }
 427 //------------------------------------------------------------------------------
 428
 429
 430 //------------------------------------------------------------------------------
 431 void vvMainWindow::OpenDCStructContour()
 432 {
 433   if (mSlicerManagers.size() > 0)
 434     {
 435       QString Extensions = "Dicom Files ( *.dcm; RS*)";
 436       Extensions += ";;All Files (*)";
 437       QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 438       if (file.isNull())
 439         return;
 440       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 441       vvMeshReader reader;
 442       reader.SetFilename(file.toStdString());
 443       vvStructSelector selector;
 444       selector.SetStructures(reader.GetROINames());
 445       if (!mSlicerManagers[index]->GetVF().IsNull())
 446         selector.EnablePropagationCheckBox();
 447       if (selector.exec())
 448         {
 449           QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 450           reader.SetSelectedItems(selector.getSelectedItems());
 451           reader.SetImage(mSlicerManagers[index]->GetImage());
 452           if (selector.PropagationEnabled())
 453             reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 454           reader.Update();
 455           std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 456           for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 457                i!=contours.end();i++)
 458             AddContour(index,*i,selector.PropagationEnabled());
 459           QApplication::restoreOverrideCursor();
 460         }
 461     }
 462 }
 463 //------------------------------------------------------------------------------
 464
 465
 466 //------------------------------------------------------------------------------
 467 void vvMainWindow::ComputeDeformableRegistration()
 468 {
 469   if (mSlicerManagers.size() > 0)
 470     {
 471       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 472       vvDeformationDialog dialog(index,mSlicerManagers);
 473       if (dialog.exec())
 474         {
 475           std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 476           AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 477           WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 478         }
 479       else
 480         std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 481     }
 482   else QMessageBox::information(this, "Need to open image","You must open an image first.");
 483 }
 484 //------------------------------------------------------------------------------
 485
 486
 487 //------------------------------------------------------------------------------
 488 void vvMainWindow::WarpImage()
 489 {
 490   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 491   if (!mSlicerManagers[index]->GetVF().IsNull())
 492     {
 493       bool ok;
 494       int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 495                                          mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 496       if (ok)
 497         {
 498           WarpImage(mSlicerManagers[index],ref);
 499         }
 500     }
 501   else
 502     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 503 }
 504 //------------------------------------------------------------------------------
 505
 506
 507 //------------------------------------------------------------------------------
 508 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 509 {
 510   if (!selected_slicer->GetVF().IsNull())
 511     {
 512       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 513       QFileInfo info(selected_slicer->GetFileName().c_str());
 514       vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 515                        reference_phase,this);
 516       if (warp.ComputeWarpedImage())
 517         {
 518           AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 519           AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 520           AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 521           QApplication::restoreOverrideCursor();
 522         }
 523       else
 524         {
 525           QApplication::restoreOverrideCursor();
 526           QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 527         }
 528     }
 529   else
 530     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 531 }
 532 //------------------------------------------------------------------------------
 533
 534
 535 //------------------------------------------------------------------------------
 536 vvMainWindow::~vvMainWindow() {
 537   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
 538     {
 539       if (mSlicerManagers[i] != NULL)
 540         delete mSlicerManagers[i];
 541     }
 542 }
 543 //------------------------------------------------------------------------------
 544
 545
 546 //------------------------------------------------------------------------------
 547 void vvMainWindow::MergeImages() {
 548   QString Extensions = EXTENSIONS;
 549   Extensions += ";;All Files (*)";
 550   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 551   if (files.isEmpty())
 552     return;
 553   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 554   std::vector<std::string> vector;
 555
 556   unsigned int currentDim = 0;
 557   std::vector<double> currentSpacing;
 558   std::vector<int> currentSize;
 559   std::vector<double> currentOrigin;
 560
 561   for (int i = 0; i < files.size(); i++)
 562     {
 563       itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 564               files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 565       reader->SetFileName(files[i].toStdString().c_str());
 566       reader->ReadImageInformation();
 567       if (reader)        {
 568           //NOViewWidget->hide();
 569           //NEViewWidget->hide();
 570           //SOViewWidget->hide();
 571           //SEViewWidget->hide();
 572           if (i == 0)
 573               currentDim = reader->GetNumberOfDimensions();
 574           bool IsOk = true;
 575           for (unsigned int j = 0;j < currentDim; j++)
 576           {
 577               if (i == 0)
 578               {
 579                   if (j == 0)
 580                   {
 581                       currentSpacing.resize(currentDim);
 582                       currentSize.resize(currentDim);
 583                       currentOrigin.resize(currentDim);
 584                   }
 585                   currentOrigin[j] = reader->GetOrigin(j);
 586                   currentSpacing[j] = reader->GetSpacing(j);
 587                   currentSize[j] = reader->GetDimensions(j);
 588               }
 589               else if (currentDim != reader->GetNumberOfDimensions()
 590                       || currentSpacing[j] != reader->GetSpacing(j)
 591                       || currentSize[j] != (int)reader->GetDimensions(j)
 592                       || currentOrigin[j] != reader->GetOrigin(j))
 593               {
 594                   QString error = "Cannot read file (too different from others ";
 595                   error += files[i].toStdString().c_str();
 596                   QMessageBox::information(this,tr("Reading problem"),error);
 597                   IsOk = false;
 598                   break;
 599               }
 600           }
 601           if (IsOk)
 602               vector.push_back(files[i].toStdString());
 603       }
 604     }
 605   if (vector.size() > 0)
 606     LoadImages(vector, MERGED);
 607 }
 608 //------------------------------------------------------------------------------
 609
 610
 611 //------------------------------------------------------------------------------
 612 void vvMainWindow::MergeImagesWithTime() {
 613   QString Extensions = EXTENSIONS;
 614   Extensions += ";;All Files (*)";
 615   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 616   if (files.isEmpty())
 617     return;
 618   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 619   std::vector<std::string> vector;
 620
 621   unsigned int currentDim = 0;
 622   std::vector<double> currentSpacing;
 623   std::vector<int> currentSize;
 624   std::vector<double> currentOrigin;
 625
 626   for (int i = 0; i < files.size(); i++)
 627     {
 628       itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 629                                                                             files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 630       if (reader)
 631         {
 632           reader->SetFileName(files[i].toStdString().c_str());
 633           reader->ReadImageInformation();
 634           if (i == 0)
 635             currentDim = reader->GetNumberOfDimensions();
 636           bool IsOk = true;
 637           for (unsigned int j = 0;j < currentDim; j++)
 638             {
 639               if (i == 0)
 640                 {
 641                   if (j == 0)
 642                     {
 643                       currentSpacing.resize(currentDim);
 644                       currentSize.resize(currentDim);
 645                       currentOrigin.resize(currentDim);
 646                     }
 647                   currentOrigin[j] = reader->GetOrigin(j);
 648                   currentSpacing[j] = reader->GetSpacing(j);
 649                   currentSize[j] = reader->GetDimensions(j);
 650                 }
 651               else if (currentDim != reader->GetNumberOfDimensions()
 652                        || currentSpacing[j] != reader->GetSpacing(j)
 653                        || currentSize[j] != (int)reader->GetDimensions(j)
 654                        || currentOrigin[j] != reader->GetOrigin(j))
 655                 {
 656                   QString error = "Cannot read file (too different from others ";
 657                   error += files[i].toStdString().c_str();
 658                   QMessageBox::information(this,tr("Reading problem"),error);
 659                   IsOk = false;
 660                   break;
 661                 }
 662             }
 663           if (IsOk)
 664             vector.push_back(files[i].toStdString());
 665         }
 666       else
 667         {
 668           QString error = "Cannot read file info for ";
 669           error += files[i].toStdString().c_str();
 670           error += "\n";
 671           error += "Maybe you're trying to open an image in an unsupported format?\n";
 672           QMessageBox::information(this,tr("Reading problem"),error);
 673         }
 674     }
 675   sort(vector.begin(),vector.end());
 676   if (vector.size() > 1)
 677     LoadImages(vector, MERGEDWITHTIME);
 678   else
 679     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.");
 680 }
 681 //------------------------------------------------------------------------------
 682
 683
 684 //------------------------------------------------------------------------------
 685 void vvMainWindow::OpenDicom() {
 686   std::vector<std::string> files;
 687
 688 #ifdef CLITK_VV_USE_BDCM
 689   bool r = bdcm::OpenDicomFilesSelectorDialog(files,
 690                                               "DicomFilesSelectorDialog test",
 691                                               0,0,800,800,1);
 692
 693   if (r) {
 694     std::cout << "$$$$ main : user clicked 'OK' $$$$"<<std::endl;
 695     std::cout << "$$$$ selected files : "<<std::endl;
 696     std::vector<std::string>::iterator i;
 697     for (i=files.begin();i!=files.end();++i) {
 698       std::cout << *i << std::endl;
 699     }
 700     std::cout << "$$$$ "<<std::endl;
 701
 702     LoadImages(files,DICOM);
 703   }
 704   else {
 705     std::cout << "$$$$ main : user clicked 'CANCEL' $$$$"<<std::endl;
 706   }
 707 #else
 708   std::cout << "dicomSeriesSelector " << std::endl;
 709   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 710     files = *(dicomSeriesSelector->GetFilenames());
 711     LoadImages(files,DICOM);
 712   }
 713 #endif
 714
 715 }
 716 //------------------------------------------------------------------------------
 717
 718 //------------------------------------------------------------------------------
 719 void vvMainWindow::OpenImages() {
 720   QString Extensions = EXTENSIONS;
 721   Extensions += ";;All Files (*)";
 722
 723   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 724   if (files.isEmpty())
 725     return;
 726   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 727   std::vector<std::string> vector;
 728   for (int i = 0; i < files.size(); i++)
 729     vector.push_back(files[i].toStdString());
 730   LoadImages(vector, IMAGE);
 731 }
 732 //------------------------------------------------------------------------------
 733 void vvMainWindow::OpenRecentImage()
 734 {
 735   QAction * caller = qobject_cast<QAction*>(sender());
 736   std::vector<std::string> images;
 737   images.push_back(caller->text().toStdString());
 738   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 739   LoadImages(images,IMAGE);
 740 }
 741
 742 //------------------------------------------------------------------------------
 743 void vvMainWindow::OpenImageWithTime() {
 744   QString Extensions = EXTENSIONS;
 745   Extensions += ";;All Files (*)";
 746
 747   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 748   if (files.isEmpty())
 749     return;
 750   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 751   std::vector<std::string> vector;
 752   for (int i = 0; i < files.size(); i++)
 753     {
 754       vector.push_back(files[i].toStdString());
 755     }
 756   LoadImages(vector, IMAGEWITHTIME);
 757 }
 758 //------------------------------------------------------------------------------
 759
 760 //------------------------------------------------------------------------------
 761 void vvMainWindow::LoadImages(std::vector<std::string> files, LoadedImageType filetype) {
 762   //Separate the way to open images and dicoms
 763   int fileSize;
 764   if (filetype == IMAGE || filetype == IMAGEWITHTIME)
 765     fileSize = files.size();
 766   else
 767     fileSize = 1;
 768
 769   //Only add to the list of recently opened files when a single file is opened,
 770   //to avoid polluting the list of recently opened files
 771   if (files.size() == 1)
 772     {
 773       QFileInfo finfo=tr(files[0].c_str());
 774       AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 775     }
 776   //init the progress events
 777   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 778   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 779   qApp->processEvents();
 780
 781   int numberofsuccesulreads=0;
 782   //open images as 1 or multiples
 783   for (int i = 0; i < fileSize; i++) {
 784
 785     progress.Update("Opening " + files[i]);
 786     progress.SetProgress(i,fileSize);
 787     qApp->processEvents();
 788
 789     //read the image and put it in mSlicerManagers
 790     vvSlicerManager* imageManager = new vvSlicerManager(4);
 791     qApp->processEvents();
 792
 793     bool SetImageSucceed=false;
 794
 795     if (filetype == IMAGE || filetype == IMAGEWITHTIME)
 796       SetImageSucceed = imageManager->SetImage(files[i],filetype);
 797     else
 798       {
 799         SetImageSucceed = imageManager->SetImages(files,filetype);
 800       }
 801     if (SetImageSucceed == false)
 802       {
 803         QApplication::restoreOverrideCursor();
 804         QString error = "Cannot open file \n";
 805         error += imageManager->GetLastError().c_str();
 806         QMessageBox::information(this,tr("Reading problem"),error);
 807         delete imageManager;
 808       }
 809     else
 810       {
 811         mSlicerManagers.push_back(imageManager);
 812
 813         //create an item in the tree with good settings
 814         QTreeWidgetItem *item = new QTreeWidgetItem();
 815         item->setData(0,Qt::UserRole,files[i].c_str());
 816         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 817         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 818         qApp->processEvents();
 819
 820         //Create the buttons for reload and close
 821         qApp->processEvents();
 822         QTreePushButton* cButton = new QTreePushButton;
 823         cButton->setItem(item);
 824         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 825         cButton->setToolTip(tr("close image"));
 826         cButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")));
 827         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 828                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 829
 830         QTreePushButton* rButton = new QTreePushButton;
 831         rButton->setItem(item);
 832         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 833         rButton->setToolTip(tr("reload image"));
 834         rButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")));
 835         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 836                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 837
 838         DataTree->addTopLevelItem(item);
 839         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 840         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 841
 842         //set the id of the image
 843         QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 844         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 845         mSlicerManagers.back()->SetId(id.toStdString());
 846
 847         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 848
 849         connect(mSlicerManagers.back(),SIGNAL(currentImageChanged(std::string)),
 850                 this,SLOT(CurrentImageChanged(std::string)));
 851         connect(mSlicerManagers.back(),SIGNAL(
 852                                               UpdatePosition(int, double, double, double, double, double, double, double)),this,
 853                 SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 854         connect(mSlicerManagers.back(),SIGNAL(UpdateVector(int, double, double, double, double)),
 855                 this, SLOT(VectorChanged(int,double,double,double, double)));
 856         connect(mSlicerManagers.back(),SIGNAL(UpdateOverlay(int, double, double)),
 857                 this, SLOT(OverlayChanged(int,double,double)));
 858         connect(mSlicerManagers.back(),SIGNAL(UpdateFusion(int, double)),
 859                 this, SLOT(FusionChanged(int,double)));
 860         connect(mSlicerManagers.back(),SIGNAL(UpdateWindows(int, int, int)),
 861                 this,SLOT(WindowsChanged(int, int, int)));
 862         connect(mSlicerManagers.back(),SIGNAL(WindowLevelChanged(double, double,int, int)),
 863                 this,SLOT(WindowLevelChanged(double, double, int, int)));
 864         connect(mSlicerManagers.back(),SIGNAL(UpdateSlice(int,int)),
 865                 this,SLOT(UpdateSlice(int,int)));
 866         connect(mSlicerManagers.back(),SIGNAL(UpdateTSlice(int, int)),
 867                 this,SLOT(UpdateTSlice(int, int)));
 868         connect(mSlicerManagers.back(),SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 869                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 870         connect(mSlicerManagers.back(),SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 871                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 872         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 873         InitSlicers();
 874         numberofsuccesulreads++;
 875       }
 876   }
 877   if (numberofsuccesulreads)
 878     {
 879       NOViewWidget->show();
 880       NEViewWidget->show();
 881       SOViewWidget->show();
 882       SEViewWidget->show();
 883       UpdateTree();
 884       InitDisplay();
 885       ShowLastImage();
 886     }
 887   QApplication::restoreOverrideCursor();
 888
 889 }
 890 //------------------------------------------------------------------------------
 891
 892 //------------------------------------------------------------------------------
 893 void vvMainWindow::UpdateTree() {
 894   DataTree->resizeColumnToContents(COLUMN_TREE);
 895   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 896   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 897   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 898   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 899   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 900   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 901   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 902 }
 903 //------------------------------------------------------------------------------
 904
 905 //------------------------------------------------------------------------------
 906 void vvMainWindow::CurrentImageChanged(std::string id) {
 907   int selected = 0;
 908   for (int i = 0; i < DataTree->topLevelItemCount(); i++)
 909     {
 910       if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id)
 911         {
 912           selected = i;
 913         }
 914       else
 915         {
 916           DataTree->topLevelItem(i)->setSelected(0);
 917         }
 918       for (int child = 0; child < DataTree->topLevelItem(i)->childCount();child++)
 919         DataTree->topLevelItem(i)->child(child)->setSelected(0);
 920
 921     }
 922   DataTree->topLevelItem(selected)->setSelected(1);
 923 }
 924 //------------------------------------------------------------------------------
 925
 926 //------------------------------------------------------------------------------
 927 void vvMainWindow::ImageInfoChanged() {
 928   contextActions[7]->setEnabled(1);
 929   contextActions[6]->setEnabled(1);
 930   actionSave_As->setEnabled(1);
 931   actionAdd_VF_to_current_Image->setEnabled(1);
 932   actionAdd_fusion_image->setEnabled(1);
 933   actionNorth_East_Window->setEnabled(1);
 934   actionNorth_West_Window->setEnabled(1);
 935   actionSouth_East_Window->setEnabled(1);
 936   actionSouth_West_Window->setEnabled(1);
 937   inverseButton->setEnabled(1);
 938
 939   goToCursorPushButton->setEnabled(1);
 940
 941   if (DataTree->selectedItems().size()) {
 942     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 943
 944     colorMapComboBox->setEnabled(1);
 945     for (int i = 0; i < DataTree->topLevelItem(index)->childCount();i++)
 946       {
 947         if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
 948             DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion")
 949           {
 950             colorMapComboBox->setEnabled(0);
 951             break;
 952           }
 953       }
 954
 955     std::vector<double> origin;
 956     std::vector<double> inputSpacing;
 957     std::vector<int> inputSize;
 958     std::vector<double> sizeMM;
 959     int dimension=0;
 960     QString pixelType;
 961     QString inputSizeInBytes;
 962     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
 963
 964     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1)
 965       {
 966         playButton->setEnabled(1);
 967         frameRateLabel->setEnabled(1);
 968         frameRateSpinBox->setEnabled(1);
 969       }
 970     else
 971       {
 972         playButton->setEnabled(0);
 973         frameRateLabel->setEnabled(0);
 974         frameRateSpinBox->setEnabled(0);
 975       }
 976
 977     //read image header
 978     int NPixel = 1;
 979
 980     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0])
 981       {
 982         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
 983         dimension = imageSelected->GetNumberOfDimensions();
 984         origin.resize(dimension);
 985         inputSpacing.resize(dimension);
 986         inputSize.resize(dimension);
 987         sizeMM.resize(dimension);
 988         pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
 989         for (int i = 0;i < dimension;i++)
 990           {
 991             origin[i] = imageSelected->GetOrigin()[i];
 992             inputSpacing[i] = imageSelected->GetSpacing()[i];
 993             inputSize[i] = imageSelected->GetSize()[i];
 994             sizeMM[i] = inputSize[i]*inputSpacing[i];
 995             NPixel *= inputSize[i];
 996           }
 997         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
 998       }
 999     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector")
1000       {
1001         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1002         dimension = imageSelected->GetNumberOfDimensions();
1003         origin.resize(dimension);
1004         inputSpacing.resize(dimension);
1005         inputSize.resize(dimension);
1006         sizeMM.resize(dimension);
1007         pixelType = mSlicerManagers[index]->GetVF()->GetScalarTypeAsString().c_str();
1008         for (int i = 0;i < dimension;i++)
1009           {
1010             origin[i] = imageSelected->GetOrigin()[i];
1011             inputSpacing[i] = imageSelected->GetSpacing()[i];
1012             inputSize[i] = imageSelected->GetSize()[i];
1013             sizeMM[i] = inputSize[i]*inputSpacing[i];
1014             NPixel *= inputSize[i];
1015           }
1016         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1017       }
1018     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay")
1019       {
1020         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1021         dimension = imageSelected->GetNumberOfDimensions();
1022         origin.resize(dimension);
1023         inputSpacing.resize(dimension);
1024         inputSize.resize(dimension);
1025         sizeMM.resize(dimension);
1026         pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
1027         for (int i = 0;i < dimension;i++)
1028           {
1029             origin[i] = imageSelected->GetOrigin()[i];
1030             inputSpacing[i] = imageSelected->GetSpacing()[i];
1031             inputSize[i] = imageSelected->GetSize()[i];
1032             sizeMM[i] = inputSize[i]*inputSpacing[i];
1033             NPixel *= inputSize[i];
1034           }
1035         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1036       }
1037     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion")
1038       {
1039         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1040         dimension = imageSelected->GetNumberOfDimensions();
1041         origin.resize(dimension);
1042         inputSpacing.resize(dimension);
1043         inputSize.resize(dimension);
1044         sizeMM.resize(dimension);
1045         pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
1046         for (int i = 0;i < dimension;i++)
1047           {
1048             origin[i] = imageSelected->GetOrigin()[i];
1049             inputSpacing[i] = imageSelected->GetSpacing()[i];
1050             inputSize[i] = imageSelected->GetSize()[i];
1051             sizeMM[i] = inputSize[i]*inputSpacing[i];
1052             NPixel *= inputSize[i];
1053           }
1054         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1055       }
1056
1057     QString dim = QString::number(dimension) + " (";
1058     dim += pixelType + ")";
1059
1060     infoPanel->setFileName(image);
1061     infoPanel->setDimension(dim);
1062     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1063     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1064     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1065     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1066     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1067
1068     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1069                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1070     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1071     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1072
1073     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1074     for (int i = 0; i < 4;i++)
1075       {
1076         if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3)
1077           {
1078             mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1079             break;
1080           }
1081       }
1082     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1083     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1084     // DD(mSlicerManagers[index]->GetColorMap());
1085     // DD(mSlicerManagers[index]->GetPreset());
1086     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1087     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1088
1089     infoPanel->setFileName(image);
1090     infoPanel->setDimension(dim);
1091     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1092     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1093     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1094     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1095     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1096
1097     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1098                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1099     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1100     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1101
1102     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1103     for (int i = 0; i < 4;i++)
1104       {
1105         if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3)
1106           {
1107             mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1108             break;
1109           }
1110       }
1111     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1112     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1113     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1114     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1115
1116     if (mSlicerManagers[index]->GetSlicer(0)->GetVF())
1117       {
1118         overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1119         overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1120                                     mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1121                                     mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1122       }
1123     else
1124       {
1125         overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1126         overlayPanel->getVFProperty(-1,-1,-1);
1127       }
1128     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1129       {
1130         overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1131         overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1132       }
1133     else
1134       {
1135         overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1136         overlayPanel->getOverlayProperty(-1);
1137       }
1138     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion())
1139       {
1140         overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1141         overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1142                                         mSlicerManagers[index]->GetFusionColorMap(),
1143                                         mSlicerManagers[index]->GetFusionWindow(),
1144                                         mSlicerManagers[index]->GetFusionLevel());
1145       }
1146     else
1147       {
1148         overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1149         overlayPanel->getFusionProperty(-1, -1,-1,-1);
1150       }
1151   }
1152 }
1153 //------------------------------------------------------------------------------
1154
1155 //------------------------------------------------------------------------------
1156 void vvMainWindow::ShowDocumentation() {
1157   documentation->show();
1158 }
1159 //------------------------------------------------------------------------------
1160 void vvMainWindow::ShowHelpDialog() {
1161   help_dialog->show();
1162 }
1163 //------------------------------------------------------------------------------
1164
1165 //------------------------------------------------------------------------------
1166 void vvMainWindow::ChangeViewMode() {
1167   QListIterator<int> it0(splitter_3->sizes());
1168   QListIterator<int> it1(splitter_3->sizes());
1169   int max0 = 0;
1170   int max1 = 1;
1171   while (it0.hasNext())
1172     {
1173       max0 += it0.next();
1174     }
1175   while (it1.hasNext())
1176     {
1177       max1 += it1.next();
1178     }
1179   QList<int> size0;
1180   QList<int> size1;
1181   if (viewMode == 1)
1182     {
1183       viewMode = 0;
1184       size0.push_back(max0);
1185       size0.push_back(0);
1186       size1.push_back(max1);
1187       size1.push_back(0);
1188       splitter_3->setSizes(size0);
1189       OSplitter->setSizes(size1);
1190       DataTree->setColumnHidden(2,1);
1191       DataTree->setColumnHidden(3,1);
1192       DataTree->setColumnHidden(4,1);
1193     }
1194   else
1195     {
1196       viewMode = 1;
1197       size0.push_back(int(max0/2));
1198       size0.push_back(int(max0/2));
1199       size1.push_back(int(max1/2));
1200       size1.push_back(int(max1/2));
1201       splitter_3->setSizes(size0);
1202       OSplitter->setSizes(size1);
1203       DataTree->setColumnHidden(2,0);
1204       DataTree->setColumnHidden(3,0);
1205       DataTree->setColumnHidden(4,0);
1206     }
1207 }
1208 //------------------------------------------------------------------------------
1209
1210 //------------------------------------------------------------------------------
1211 QString vvMainWindow::GetSizeInBytes(unsigned long size) {
1212   QString result = "";// QString::number(size);
1213   //result += " bytes (";
1214   if (size > 1000000000)
1215     {
1216       size /= 1000000000;
1217       result += QString::number(size);
1218       result += "Gb";//)";
1219     }
1220   else if (size > 1000000)
1221     {
1222       size /= 1000000;
1223       result += QString::number(size);
1224       result += "Mb";//)";
1225     }
1226   else if (size > 1000)
1227     {
1228       size /= 1000;
1229       result += QString::number(size);
1230       result += "kb";//)";
1231     }
1232   return result;
1233 }
1234 //------------------------------------------------------------------------------
1235
1236 //------------------------------------------------------------------------------
1237 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble) {
1238   QString result;
1239   for (unsigned int i= 0; i < vectorDouble.size(); i++)
1240     {
1241       if (i != 0)
1242         result += " ";
1243       result += QString::number(vectorDouble[i]);
1244     }
1245   return result;
1246 }
1247 //------------------------------------------------------------------------------
1248
1249 //------------------------------------------------------------------------------
1250 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt) {
1251   QString result;
1252   for (unsigned int i= 0; i < vectorInt.size(); i++)
1253     {
1254       if (i != 0)
1255         result += " ";
1256       result += QString::number(vectorInt[i]);
1257     }
1258   return result;
1259 }
1260 //------------------------------------------------------------------------------
1261
1262 //------------------------------------------------------------------------------
1263 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item) {
1264   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1265   for (int i = 0; i < DataTree->topLevelItemCount(); i++)
1266     {
1267       if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1268         return i;
1269     }
1270   return -1;
1271 }
1272 //------------------------------------------------------------------------------
1273
1274 //------------------------------------------------------------------------------
1275 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clicked_item, int column) {
1276   int index = GetSlicerIndexFromItem(clicked_item);
1277   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1278     return;
1279   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
1280     {
1281       QTreeWidgetItem* current_row=DataTree->topLevelItem(i);
1282       if (DataTree->topLevelItem(index) == current_row)
1283         {
1284           vvSlicer* clicked_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1285           if (current_row == clicked_item)
1286             {
1287               //If we just activated a slicer
1288               if (current_row->data(column,Qt::CheckStateRole).toInt() > 0)
1289                 {
1290                   mSlicerManagers[i]->UpdateSlicer(column-1,clicked_item->data(column,Qt::CheckStateRole).toInt());
1291                   mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1292                   DisplaySliders(i,column-1);
1293                   std::map<std::string,int> overlay_counts;
1294                   for (int child = 0; child < current_row->childCount(); child++)
1295                     {
1296                       std::string overlay_type =
1297                         current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1298                       overlay_counts[overlay_type]++;
1299                       current_row->child(child)->setData(column,Qt::CheckStateRole,
1300                                                          current_row->data(column,Qt::CheckStateRole));
1301                       clicked_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,true);
1302                     }
1303                 }
1304               else //We don't allow simply desactivating a slicer
1305                 {
1306                   clicked_item->setData(column,Qt::CheckStateRole,2);
1307                   return;
1308                 }
1309             }
1310           //if we clicked on the vector(or overlay) and not the image
1311           else
1312             {
1313               if (clicked_item->data(column,Qt::CheckStateRole).toInt())
1314                 {
1315                   current_row->setData(column,Qt::CheckStateRole,2);
1316                   mSlicerManagers[i]->UpdateSlicer(column-1,2);
1317                   mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1318                   DisplaySliders(i,column-1);
1319                 }
1320               int vis = clicked_item->data(column,Qt::CheckStateRole).toInt();
1321               std::string overlay_type = clicked_item->data(1,Qt::UserRole).toString().toStdString();
1322               int overlay_index=0;
1323               for (int child = 0; child < current_row->childCount(); child++)
1324                 {
1325                   if (current_row->child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1326                     overlay_index++;
1327                   if (current_row->child(child) == clicked_item) break;
1328                 }
1329               clicked_slicer->SetActorVisibility(
1330                                                  clicked_item->data(1,Qt::UserRole).toString().toStdString(), overlay_index-1,vis);
1331             }
1332         }
1333       else if (current_row->data(column,Qt::CheckStateRole).toInt() > 0)
1334         {
1335           current_row->setData(column,Qt::CheckStateRole,0);
1336           mSlicerManagers[i]->UpdateSlicer(column-1,0);
1337           std::map<std::string,int> overlay_counts;
1338           for (int child = 0; child < current_row->childCount(); child++)
1339             {
1340               std::string overlay_type =
1341                 current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1342               overlay_counts[overlay_type]++;
1343               current_row->child(child)->setData(column,Qt::CheckStateRole,0);
1344               vvSlicer * current_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1345               current_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,false);
1346             }
1347         }
1348       //mSlicerManagers[i]->SetColorMap(-1);
1349       mSlicerManagers[i]->SetColorMap();
1350     }
1351   mSlicerManagers[index]->GetSlicer(column-1)->Render();
1352 }
1353 //------------------------------------------------------------------------------
1354
1355 void vvMainWindow::InitSlicers()
1356 {
1357   if (mSlicerManagers.size())
1358     {
1359       mSlicerManagers.back()->GenerateDefaultLookupTable();
1360
1361       mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1362       mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1363       mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1364       mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1365     }
1366 }
1367
1368 //------------------------------------------------------------------------------
1369 void vvMainWindow::InitDisplay() {
1370   if (mSlicerManagers.size())
1371     {
1372       //BE CAREFUL : this is absolutely necessary to set the interactor style
1373       //in order to have the same style instanciation for all SlicerManagers in
1374       // a same window
1375       for (int j = 0; j < 4; j++)
1376         {
1377           vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1378           style->SetAutoAdjustCameraClippingRange(1);
1379           bool AlreadySelected = false;
1380           for (int i = 0; i < DataTree->topLevelItemCount(); i++)
1381             {
1382               mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1383
1384               //select the image only if previous are not selected
1385               if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1)
1386                 {
1387                   mSlicerManagers[i]->UpdateSlicer(j,1);
1388                   AlreadySelected = true;
1389                 }
1390               else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected)
1391                 {
1392                   if (DataTree->selectedItems().size() == 0)
1393                     DataTree->topLevelItem(i)->setSelected(1);
1394                   DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1395                   mSlicerManagers[i]->UpdateSlicer(j,1);
1396                   DisplaySliders(i,j);
1397                 }
1398               else
1399                 {
1400                   DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1401                   mSlicerManagers[i]->UpdateSlicer(j,0);
1402                 }
1403             }
1404           style->Delete();
1405         }
1406     }
1407 }
1408 //------------------------------------------------------------------------------
1409
1410 //------------------------------------------------------------------------------
1411 void vvMainWindow::DisplaySliders(int slicer, int window) {
1412   int range[2];
1413   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1414   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1415
1416   int tRange[2];
1417   tRange[0] = 0;
1418   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1419   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1420   bool showHorizontal = false;
1421   bool showVertical = false;
1422   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1423       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1424           && mSlicerManagers[slicer]->GetType() != IMAGEWITHTIME
1425           && mSlicerManagers[slicer]->GetType() != MERGEDWITHTIME))
1426     showVertical = true;
1427   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1428       || mSlicerManagers[slicer]->GetType() == IMAGEWITHTIME
1429       || mSlicerManagers[slicer]->GetType() == MERGEDWITHTIME)
1430     showHorizontal = true;
1431
1432   if (showVertical)
1433     verticalSliders[window]->show();
1434   else
1435     verticalSliders[window]->hide();
1436   verticalSliders[window]->setRange(range[0],range[1]);
1437   verticalSliders[window]->setValue(position);
1438
1439   if (showHorizontal)
1440     horizontalSliders[window]->show();
1441   else
1442     horizontalSliders[window]->hide();
1443   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1444   horizontalSliders[window]->setValue(tPosition);
1445 }
1446 //------------------------------------------------------------------------------
1447
1448 //------------------------------------------------------------------------------
1449 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column) {
1450   int index = GetSlicerIndexFromItem(item);
1451
1452   if (DataTree->topLevelItem(index) != item)
1453     {
1454       QString warning = "Do you really want to close the overlay : ";
1455       warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1456       QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1457                          warning, 0, this);
1458       msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1459       msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1460       if (msgBox.exec() == QMessageBox::AcceptRole)
1461         {
1462           std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1463           int overlay_index=0;
1464           for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1465             {
1466               if (DataTree->topLevelItem(index)->\
1467                   child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1468                 overlay_index++;
1469               if (DataTree->topLevelItem(index)->child(child) == item) break;
1470             }
1471           mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1472           mSlicerManagers[index]->SetColorMap(0);
1473           DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1474           mSlicerManagers[index]->Render();
1475         }
1476     }
1477   else if (DataTree->topLevelItemCount() <= 1)
1478     {
1479       QString warning = "Do you really want to close the image : ";
1480       warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1481       warning += "\nThis is the last image, you're about to close vv !!!";
1482       QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1483                          warning, 0, this);
1484       msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1485       msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1486       if (msgBox.exec() == QMessageBox::AcceptRole)
1487         {
1488           this->close();
1489         }
1490     }
1491   else
1492     {
1493       QString warning = "Do you really want to close the image : ";
1494       warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1495       QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1496                          warning, 0, this);
1497       msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1498       msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1499       if (msgBox.exec() == QMessageBox::AcceptRole)
1500         {
1501
1502           // Tell tools that we close an image
1503           emit AnImageIsBeingClosed(mSlicerManagers[index]);
1504
1505           std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1506           DataTree->takeTopLevelItem(index);
1507           for (int i = 0; i < index; i++)
1508             {
1509               Manageriter++;
1510             }
1511           linkPanel->removeImage(index);
1512           mSlicerManagers[index]->RemoveActors();
1513           delete mSlicerManagers[index];
1514           mSlicerManagers.erase(Manageriter);
1515
1516           //
1517           InitDisplay();
1518         }
1519     }
1520 }
1521 //------------------------------------------------------------------------------
1522
1523 //------------------------------------------------------------------------------
1524 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column) {
1525   // int index = GetSlicerIndexFromItem(item);
1526   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1527   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1528   //     mSlicerManagers[index]->ReloadVF();
1529   //   else
1530   //     mSlicerManagers[index]->Reload();
1531
1532   //   QApplication::restoreOverrideCursor();
1533   int index = GetSlicerIndexFromItem(item);
1534   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1535   QString role=item->data(1,Qt::UserRole).toString();
1536   if ( role == "vector")
1537     mSlicerManagers[index]->ReloadVF();
1538   else if (role == "overlay")
1539     mSlicerManagers[index]->ReloadOverlay();
1540   else if (role == "fusion")
1541     mSlicerManagers[index]->ReloadFusion();
1542   else
1543     mSlicerManagers[index]->Reload();
1544   QApplication::restoreOverrideCursor();
1545 }
1546 //------------------------------------------------------------------------------
1547
1548 // void vvMainWindow::CropImage()
1549 // {
1550 //   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1551 //   vvCropDialog crop(mSlicerManagers,index);
1552 //   if(crop.exec())
1553 //     AddImage(crop.GetOutput(),"cropped.mhd");
1554 // }
1555
1556 //------------------------------------------------------------------------------
1557 void vvMainWindow::SplitImage() {
1558   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1559   int dim = mSlicerManagers[index]->GetDimension();
1560   QString warning = "Do you really want to split the ";
1561   warning += QString::number(dim) + "D image ";
1562   warning += DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString() + " into ";
1563   warning += QString::number(mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetSize()[dim-1]) + " ";
1564   warning += QString::number(dim-1) + "D images.";
1565   QMessageBox msgBox(QMessageBox::Warning, tr("Split Image"),
1566                      warning, 0, this);
1567   msgBox.addButton(tr("Split"), QMessageBox::AcceptRole);
1568   msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1569   if (msgBox.exec() == QMessageBox::AcceptRole)
1570     {
1571       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1572       if (dim > 2)
1573         {
1574           std::string filename = DataTree->selectedItems()[0]->data(0,Qt::UserRole).toString().toStdString();
1575           int numberOfSlice = mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetSize()[dim-1];
1576           std::string path = itksys::SystemTools::GetFilenamePath(
1577                                                                   filename);
1578           path += "/";
1579           path += DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString().toStdString();
1580           path += "%03d";
1581           path += itksys::SystemTools::GetFilenameLastExtension(
1582                                                                 filename).c_str();
1583
1584           typedef itk::NumericSeriesFileNames NameGeneratorType;
1585           NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
1586           nameGenerator->SetSeriesFormat(path.c_str());
1587           nameGenerator->SetStartIndex(0);
1588           nameGenerator->SetEndIndex(numberOfSlice-1);
1589           nameGenerator->SetIncrementIndex(1);
1590
1591           for (int i = 0; i < numberOfSlice; i++)
1592             {
1593               vvSlicerManager* imageManager = new vvSlicerManager(4);
1594               imageManager->SetExtractedImage(nameGenerator->GetFileNames()[i],
1595                                               mSlicerManagers[index]->GetSlicer(0)->GetImage(), i);
1596               mSlicerManagers.push_back(imageManager);
1597
1598               //create an item in the tree with good settings
1599               QTreeWidgetItem *item = new QTreeWidgetItem();
1600               item->setData(0,Qt::UserRole,nameGenerator->GetFileNames()[i].c_str());
1601               std::string fileI = itksys::SystemTools::GetFilenameWithoutLastExtension(
1602                                                                                        nameGenerator->GetFileNames()[i]).c_str();
1603               item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileI.c_str());
1604               for (int j = 1; j <= 4; j++)
1605                 {
1606                   for (int i = 0; i < DataTree->topLevelItemCount(); i++)
1607                     {
1608                       DataTree->topLevelItem(i)->setData(j,Qt::CheckStateRole,0);
1609                     }
1610                   item->setData(j,Qt::CheckStateRole,2);
1611                 }
1612
1613               //Create the buttons for reload and close
1614               QTreePushButton* cButton = new QTreePushButton;
1615               cButton->setItem(item);
1616               cButton->setColumn(COLUMN_CLOSE_IMAGE);
1617               cButton->setToolTip(tr("close image"));
1618               cButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")));
1619               connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1620                       this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1621
1622               QTreePushButton* rButton = new QTreePushButton;
1623               rButton->setItem(item);
1624               rButton->setColumn(COLUMN_RELOAD_IMAGE);
1625               rButton->setToolTip(tr("reload image"));
1626               rButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")));
1627               rButton->setEnabled(false);
1628               connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1629                       this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1630
1631               DataTree->addTopLevelItem(item);
1632               DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1633               DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1634
1635               //set the id of the image
1636               QString id = nameGenerator->GetFileNames()[i].c_str() + QString::number(mSlicerManagers.size()-1);
1637               item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1638               mSlicerManagers.back()->SetId(id.toStdString());
1639               linkPanel->addImage(fileI, id.toStdString());
1640               connect(mSlicerManagers.back(),SIGNAL(currentImageChanged(std::string)),
1641                       this,SLOT(CurrentImageChanged(std::string)));
1642               connect(mSlicerManagers.back(),SIGNAL(
1643                                                     UpdatePosition(int, double, double, double, double, double, double, double)),this,
1644                       SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
1645               connect(mSlicerManagers.back(),SIGNAL(UpdateVector(int, double, double, double, double)),
1646                       this, SLOT(VectorChanged(int,double,double,double, double)));
1647               connect(mSlicerManagers.back(),SIGNAL(UpdateOverlay(int, double, double)),
1648                       this, SLOT(OverlayChanged(int,double,double)));
1649               connect(mSlicerManagers.back(),SIGNAL(UpdateFusion(int, double)),
1650                       this, SLOT(FusionChanged(int,double)));
1651               connect(mSlicerManagers.back(),SIGNAL(UpdateWindows(int, int, int)),
1652                       this,SLOT(WindowsChanged(int, int, int)));
1653               connect(mSlicerManagers.back(),SIGNAL(WindowLevelChanged(double, double,int, int)),
1654                       this,SLOT(WindowLevelChanged(double, double, int, int)));
1655               connect(mSlicerManagers.back(),SIGNAL(UpdateSlice(int,int)),
1656                       this,SLOT(UpdateSlice(int,int)));
1657               connect(mSlicerManagers.back(),SIGNAL(UpdateTSlice(int, int)),
1658                       this,SLOT(UpdateTSlice(int, int)));
1659               connect(mSlicerManagers.back(),SIGNAL(UpdateSliceRange(int,int,int,int,int)),
1660                       this,SLOT(UpdateSliceRange(int,int,int,int,int)));
1661               connect(mSlicerManagers.back(),SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
1662                       this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
1663               connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
1664               UpdateTree();
1665               qApp->processEvents();
1666               InitSlicers();
1667               InitDisplay();
1668               qApp->processEvents();
1669             }
1670           QApplication::restoreOverrideCursor();
1671         }
1672       else
1673         {
1674           QApplication::restoreOverrideCursor();
1675           QString error = "Cannot split file (dimensions must be greater than 2) ";
1676           QMessageBox::information(this,tr("Splitting problem"),error);
1677         }
1678     }
1679 }
1680 //------------------------------------------------------------------------------
1681
1682 //------------------------------------------------------------------------------
1683 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value) {
1684   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1685 }
1686 //------------------------------------------------------------------------------
1687
1688 //------------------------------------------------------------------------------
1689 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value) {
1690   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1691 }
1692 //------------------------------------------------------------------------------
1693
1694 //------------------------------------------------------------------------------
1695 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef) {
1696   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1697 }
1698 //------------------------------------------------------------------------------
1699
1700 //------------------------------------------------------------------------------
1701 void vvMainWindow::FusionChanged(int visibility, double value) {
1702   overlayPanel->getCurrentFusionInfo(visibility,value);
1703 }
1704 //------------------------------------------------------------------------------
1705
1706 //------------------------------------------------------------------------------
1707 void vvMainWindow::WindowsChanged(int window, int view, int slice) {
1708   infoPanel->setViews(window, view, slice);
1709 }
1710 //------------------------------------------------------------------------------
1711
1712 //------------------------------------------------------------------------------
1713 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap) {
1714   windowSpinBox->setValue(window);
1715   levelSpinBox->setValue(level);
1716   colorMapComboBox->setCurrentIndex(colormap);
1717   presetComboBox->setCurrentIndex(preset);
1718 }
1719 //------------------------------------------------------------------------------
1720
1721 //------------------------------------------------------------------------------
1722 void vvMainWindow::WindowLevelEdited() {
1723   presetComboBox->setCurrentIndex(6);
1724   UpdateWindowLevel();
1725 }
1726 //------------------------------------------------------------------------------
1727
1728 //------------------------------------------------------------------------------
1729 void vvMainWindow::UpdateWindowLevel() {
1730   if (DataTree->selectedItems().size())
1731     {
1732       if (presetComboBox->currentIndex() == 7) //For ventilation
1733         colorMapComboBox->setCurrentIndex(5);
1734       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1735       mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1736       mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1737       mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1738       mSlicerManagers[index]->Render();
1739     }
1740 }
1741 //------------------------------------------------------------------------------
1742
1743 //------------------------------------------------------------------------------
1744 void vvMainWindow::UpdateColorMap() {
1745   if (DataTree->selectedItems().size())
1746     {
1747       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1748       mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1749       mSlicerManagers[index]->Render();
1750     }
1751 }
1752 //------------------------------------------------------------------------------
1753 void vvMainWindow::SwitchWindowLevel() {
1754   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1755   int window = mSlicerManagers[index]->GetColorWindow();
1756   presetComboBox->setCurrentIndex(6);
1757   windowSpinBox->setValue(-window);
1758   UpdateWindowLevel();
1759 }
1760 //------------------------------------------------------------------------------
1761
1762 //------------------------------------------------------------------------------
1763 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps) {
1764   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
1765     {
1766       if (mSlicerManagers[i]->GetId() == id)
1767         {
1768           //mSlicerManagers[i]->SetTSlice(temps);
1769           mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1770           mSlicerManagers[i]->UpdateViews(0,slicer);
1771           break;
1772         }
1773     }
1774 }
1775 //------------------------------------------------------------------------------
1776
1777 //------------------------------------------------------------------------------
1778 void vvMainWindow::ShowContextMenu(QPoint point) {
1779   if (!DataTree->selectedItems().size())
1780     {
1781       contextActions[1]->setEnabled(0);
1782       contextActions[2]->setEnabled(0);
1783       contextActions[3]->setEnabled(0);
1784       contextActions[4]->setEnabled(0);
1785       contextActions[5]->setEnabled(0);
1786       contextActions[6]->setEnabled(0);
1787       contextActions[7]->setEnabled(0);
1788     }
1789   else
1790     {
1791       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1792       contextActions[1]->setEnabled(1);
1793       contextActions[2]->setEnabled(
1794                                     DataTree->itemWidget(DataTree->selectedItems()[0],
1795                                                          COLUMN_RELOAD_IMAGE)->isEnabled());
1796       contextActions[3]->setEnabled(1);
1797       contextActions[5]->setEnabled(1);
1798       contextActions[6]->setEnabled(1);
1799       contextActions[7]->setEnabled(1);
1800
1801       if (mSlicerManagers[index]->GetDimension() < 3)
1802         contextActions[4]->setEnabled(0);
1803       else
1804         contextActions[4]->setEnabled(1);
1805     }
1806   contextMenu.exec(QCursor::pos());
1807 }
1808 //------------------------------------------------------------------------------
1809
1810 //------------------------------------------------------------------------------
1811 void vvMainWindow::CloseImage() {
1812   CloseImage(DataTree->selectedItems()[0],0);
1813 }
1814 //------------------------------------------------------------------------------
1815
1816 //------------------------------------------------------------------------------
1817 void vvMainWindow::ReloadImage() {
1818   ReloadImage(DataTree->selectedItems()[0],0);
1819 }
1820 //------------------------------------------------------------------------------
1821
1822 //------------------------------------------------------------------------------
1823 void vvMainWindow::SelectOverlayImage() {
1824   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1825
1826   //check if one overlay image is added
1827   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1828     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay")
1829       {
1830         QString error = "Cannot add more than one compared image\n";
1831         error += "Please remove first ";
1832         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1833         QMessageBox::information(this,tr("Problem adding compared image !"),error);
1834         return;
1835       }
1836
1837   QString Extensions = EXTENSIONS;
1838   Extensions += ";;All Files (*)";
1839   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1840   if (!file.isEmpty())
1841     AddOverlayImage(index,file);
1842 }
1843 //------------------------------------------------------------------------------
1844
1845 //------------------------------------------------------------------------------
1846 void vvMainWindow::AddOverlayImage(int index, QString file) {
1847   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1848   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1849                                                                         file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1850   reader->SetFileName(file.toStdString().c_str());
1851   reader->ReadImageInformation();
1852   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1853   int dimension = reader->GetNumberOfDimensions();
1854   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1855   vvProgressDialog progress("Opening " + file.toStdString());
1856   qApp->processEvents();
1857
1858   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1859   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component))
1860     {
1861       //create an item in the tree with good settings
1862       QTreeWidgetItem *item = new QTreeWidgetItem();
1863       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1864       item->setData(1,Qt::UserRole,tr("overlay"));
1865       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
1866       qApp->processEvents();
1867
1868       for (int j = 1; j <= 4; j++)
1869         {
1870           item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1871           mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("overlay",0,
1872                                                                      DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1873         }
1874
1875       //Create the buttons for reload and close
1876       qApp->processEvents();
1877       QTreePushButton* cButton = new QTreePushButton;
1878       cButton->setItem(item);
1879       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1880       cButton->setToolTip(tr("close image"));
1881       cButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")));
1882       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1883               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1884
1885       QTreePushButton* rButton = new QTreePushButton;
1886       rButton->setItem(item);
1887       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1888       rButton->setToolTip(tr("reload image"));
1889       rButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")));
1890       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1891               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1892
1893       DataTree->topLevelItem(index)->setExpanded(1);
1894       DataTree->topLevelItem(index)->addChild(item);
1895       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1896       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1897
1898       //set the id of the image
1899       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1900       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1901       UpdateTree();
1902       qApp->processEvents();
1903       ImageInfoChanged();
1904       QApplication::restoreOverrideCursor();
1905     }
1906   else
1907     {
1908       QApplication::restoreOverrideCursor();
1909       QString error = "Cannot import the new image.\n";
1910       error += mSlicerManagers[index]->GetLastError().c_str();
1911       QMessageBox::information(this,tr("Problem reading image !"),error);
1912     }
1913 }
1914
1915 void vvMainWindow::AddFusionImage()
1916 {
1917   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1918
1919   //check if one fusion image is added
1920   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1921     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion")
1922       {
1923         QString error = "Cannot add more than one fusion image\n";
1924         error += "Please remove first ";
1925         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1926         QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1927         return;
1928       }
1929
1930   QString Extensions = EXTENSIONS;
1931   Extensions += ";;All Files (*)";
1932   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1933   if (!file.isEmpty())
1934     {
1935       mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1936       itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1937                                                                             file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1938       reader->SetFileName(file.toStdString().c_str());
1939       reader->ReadImageInformation();
1940       std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1941       if (reader)
1942         {
1943           QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1944           vvProgressDialog progress("Opening fusion");
1945           qApp->processEvents();
1946
1947           std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1948           if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1949                                                 reader->GetNumberOfDimensions(), component))
1950             {
1951               //create an item in the tree with good settings
1952               QTreeWidgetItem *item = new QTreeWidgetItem();
1953               item->setData(0,Qt::UserRole,file.toStdString().c_str());
1954               item->setData(1,Qt::UserRole,tr("fusion"));
1955               item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
1956               qApp->processEvents();
1957
1958               for (int j = 1; j <= 4; j++)
1959                 {
1960                   item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1961                   mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("fusion",0,
1962                                                                              DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1963                 }
1964
1965               //Create the buttons for reload and close
1966               qApp->processEvents();
1967               QTreePushButton* cButton = new QTreePushButton;
1968               cButton->setItem(item);
1969               cButton->setColumn(COLUMN_CLOSE_IMAGE);
1970               cButton->setToolTip(tr("close image"));
1971               cButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")));
1972               connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1973                       this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1974
1975               QTreePushButton* rButton = new QTreePushButton;
1976               rButton->setItem(item);
1977               rButton->setColumn(COLUMN_RELOAD_IMAGE);
1978               rButton->setToolTip(tr("reload image"));
1979               rButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")));
1980               connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1981                       this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1982
1983               DataTree->topLevelItem(index)->setExpanded(1);
1984               DataTree->topLevelItem(index)->addChild(item);
1985               DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1986               DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1987
1988               //set the id of the image
1989               QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1990               item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1991               UpdateTree();
1992               qApp->processEvents();
1993               ImageInfoChanged();
1994               QApplication::restoreOverrideCursor();
1995             }
1996           else
1997             {
1998               QApplication::restoreOverrideCursor();
1999               QString error = "Cannot import the new image.\n";
2000               error += mSlicerManagers[index]->GetLastError().c_str();
2001               QMessageBox::information(this,tr("Problem reading image !"),error);
2002             }
2003         }
2004       else
2005         {
2006           QString error = "Cannot import the new image.\n";
2007           QMessageBox::information(this,tr("Problem reading image !"),error);
2008         }
2009     }
2010 }
2011
2012
2013 void vvMainWindow::OpenField()
2014 {
2015   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2016   //check if a vector field has already been added
2017   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2018     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector")
2019       {
2020         QString error = "Cannot add more than one vector field\n";
2021         error += "Please remove first ";
2022         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2023         QMessageBox::information(this,tr("Problem adding vector field!"),error);
2024         return;
2025       }
2026
2027   QString Extensions = "Images ( *.mhd)";
2028   Extensions += ";;Images ( *.vf)";
2029   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2030   if (!file.isEmpty())
2031     AddField(file,index);
2032 }
2033
2034 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2035 {
2036   //create an item in the tree with good settings
2037   QTreeWidgetItem *item = new QTreeWidgetItem();
2038   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2039   item->setData(1,Qt::UserRole,tr("vector"));
2040   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename);
2041   qApp->processEvents();
2042
2043   for (int j = 1; j <= 4; j++)
2044     {
2045       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2046       mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("vector",0,
2047                                                                  DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
2048     }
2049
2050   //Create the buttons for reload and close
2051   qApp->processEvents();
2052   QTreePushButton* cButton = new QTreePushButton;
2053   cButton->setItem(item);
2054   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2055   cButton->setToolTip(tr("close vector field"));
2056   cButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")));
2057   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2058           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2059
2060   QTreePushButton* rButton = new QTreePushButton;
2061   rButton->setItem(item);
2062   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2063   rButton->setToolTip(tr("reload vector field"));
2064   rButton->setEnabled(from_disk);
2065   rButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")));
2066   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2067           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2068
2069   DataTree->topLevelItem(index)->setExpanded(1);
2070   DataTree->topLevelItem(index)->addChild(item);
2071   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2072   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2073
2074   //set the id of the image
2075   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2076   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2077   UpdateTree();
2078   qApp->processEvents();
2079   ImageInfoChanged();
2080   QApplication::restoreOverrideCursor();
2081 }
2082
2083 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2084 {
2085   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2086   vvSlicerManager* imageManager = mSlicerManagers[index];
2087   if (imageManager->SetVF(vf,file.toStdString()))
2088     {
2089       AddFieldEntry(file,index,false);
2090     }
2091   else
2092     {
2093       QString error = "Cannot import the vector field for this image.\n";
2094       error += imageManager->GetLastError().c_str();
2095       QMessageBox::information(this,tr("Problem reading VF !"),error);
2096     }
2097   QApplication::restoreOverrideCursor();
2098 }
2099
2100 void vvMainWindow::AddField(QString file,int index)
2101 {
2102   if (QFile::exists(file))
2103     {
2104       mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2105
2106       //init the progress events
2107       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2108       vvProgressDialog progress("Opening " + file.toStdString());
2109       qApp->processEvents();
2110
2111       //read the vector and put it in the current mSlicerManager
2112       vvSlicerManager* imageManager = mSlicerManagers[index];
2113       qApp->processEvents();
2114
2115       std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2116       if (imageManager->SetVF(file.toStdString()))
2117         {
2118           imageManager->Render();
2119           AddFieldEntry(file,index,true);
2120         }
2121       else
2122         {
2123           QApplication::restoreOverrideCursor();
2124           QString error = "Cannot import the vector field for this image.\n";
2125           error += imageManager->GetLastError().c_str();
2126           QMessageBox::information(this,tr("Problem reading VF !"),error);
2127         }
2128     }
2129   else
2130     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2131
2132 }
2133 //------------------------------------------------------------------------------
2134
2135 //------------------------------------------------------------------------------
2136 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log) {
2137   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2138   if (mSlicerManagers[index]->GetSlicer(0)->GetVF())
2139     {
2140       for (int i = 0; i < 4; i++)
2141         {
2142           mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2143           mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2144           if (log > 0)
2145             mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2146           else
2147             mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2148         }
2149     }
2150 }
2151 //------------------------------------------------------------------------------
2152
2153 //------------------------------------------------------------------------------
2154 void vvMainWindow::SetOverlayProperty(int color) {
2155   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2156   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
2157     {
2158       mSlicerManagers[index]->SetOverlayColor(color);
2159       mSlicerManagers[index]->SetColorMap(0);
2160       mSlicerManagers[index]->Render();
2161     }
2162 }
2163 //------------------------------------------------------------------------------
2164
2165 //------------------------------------------------------------------------------
2166 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level) {
2167   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2168   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion())
2169     {
2170       mSlicerManagers[index]->SetFusionOpacity(opacity);
2171       mSlicerManagers[index]->SetFusionColorMap(colormap);
2172       mSlicerManagers[index]->SetFusionWindow(window);
2173       mSlicerManagers[index]->SetFusionLevel(level);
2174       mSlicerManagers[index]->SetColorMap(0);
2175       mSlicerManagers[index]->Render();
2176     }
2177 }
2178 //------------------------------------------------------------------------------
2179
2180 //------------------------------------------------------------------------------
2181 void vvMainWindow::SaveAs() {
2182   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector")
2183     {
2184       QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2185       return;
2186     }
2187
2188   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2189   int dimension = mSlicerManagers[index]->GetDimension();
2190   QStringList OutputListeFormat;
2191   OutputListeFormat.clear();
2192   if (dimension == 1)
2193     {
2194       OutputListeFormat.push_back(".mhd");
2195     }
2196   if (dimension == 2)
2197     {
2198       OutputListeFormat.push_back(".bmp");
2199       OutputListeFormat.push_back(".png");
2200       OutputListeFormat.push_back(".jpeg");
2201       OutputListeFormat.push_back(".tif");
2202       OutputListeFormat.push_back(".mhd");
2203       OutputListeFormat.push_back(".hdr");
2204       OutputListeFormat.push_back(".vox");
2205     }
2206   else if (dimension == 3)
2207     {
2208       OutputListeFormat.push_back(".mhd");
2209       OutputListeFormat.push_back(".hdr");
2210       OutputListeFormat.push_back(".vox");
2211     }
2212   else if (dimension == 4)
2213     {
2214       OutputListeFormat.push_back(".mhd");
2215     }
2216   QString Extensions = "AllFiles(*.*)";
2217   for (int i = 0; i < OutputListeFormat.count(); i++)
2218     {
2219       Extensions += ";;Images ( *";
2220       Extensions += OutputListeFormat[i];
2221       Extensions += ")";
2222     }
2223   QString fileName = QFileDialog::getSaveFileName(this,
2224                                                   tr("Save As"),
2225                                                   mSlicerManagers[index]->GetFileName().c_str(),
2226                                                   Extensions);
2227   if (!fileName.isEmpty())
2228     {
2229       std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2230       if (OutputListeFormat.contains(
2231                                      fileformat.c_str()))
2232         {
2233           QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2234           std::string action = "Saving";
2235           vvProgressDialog progress("Saving "+fileName.toStdString());
2236           qApp->processEvents();
2237           vvImageWriter *writer = new vvImageWriter;
2238           writer->SetOutputFileName(fileName.toStdString());
2239           writer->SetInput(mSlicerManagers[index]->GetImage());
2240           writer->Update();
2241           QApplication::restoreOverrideCursor();
2242           if (writer->GetLastError().size())
2243             {
2244               QString error = "Saving did not succeed\n";
2245               error += writer->GetLastError().c_str();
2246               QMessageBox::information(this,tr("Saving Problem"),error);
2247               SaveAs();
2248             }
2249         }
2250       else
2251         {
2252           QString error = fileformat.c_str();
2253           if (error.isEmpty())
2254             error += "no file format specified !";
2255           else
2256             error += " format unknown !!!\n";
2257           QMessageBox::information(this,tr("Saving Problem"),error);
2258           SaveAs();
2259         }
2260     }
2261 }
2262 //------------------------------------------------------------------------------
2263
2264 //------------------------------------------------------------------------------
2265 void vvMainWindow::AddLink(QString image1,QString image2) {
2266   for (unsigned int i = 0; i < mSlicerManagers.size();i++)
2267     {
2268       if (image1.toStdString() == mSlicerManagers[i]->GetId())
2269         {
2270           mSlicerManagers[i]->AddLink(image2.toStdString());
2271         }
2272       if (image2.toStdString() == mSlicerManagers[i]->GetId())
2273         {
2274           mSlicerManagers[i]->AddLink(image1.toStdString());
2275         }
2276     }
2277 }
2278 //------------------------------------------------------------------------------
2279
2280 //------------------------------------------------------------------------------
2281 void vvMainWindow::RemoveLink(QString image1,QString image2) {
2282   for (unsigned int i = 0; i < mSlicerManagers.size();i++)
2283     {
2284       if (image1.toStdString() == mSlicerManagers[i]->GetId())
2285         {
2286           mSlicerManagers[i]->RemoveLink(image2.toStdString());
2287         }
2288       if (image2.toStdString() == mSlicerManagers[i]->GetId())
2289         {
2290           mSlicerManagers[i]->RemoveLink(image1.toStdString());
2291         }
2292     }
2293 }
2294 //------------------------------------------------------------------------------
2295
2296 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2297 {
2298   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2299     {
2300       if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1)
2301         {
2302           for (int j = 0; j < 4; j++)
2303             {
2304               mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2305               //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2306               //UpdateTSlice(j,value);
2307             }
2308           mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2309           break;
2310         }
2311     }
2312 }
2313
2314 //------------------------------------------------------------------------------
2315 void vvMainWindow::NOHorizontalSliderMoved() {
2316   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2317 }
2318 //------------------------------------------------------------------------------
2319
2320 //------------------------------------------------------------------------------
2321 void vvMainWindow::NEHorizontalSliderMoved() {
2322   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2323 }
2324 //------------------------------------------------------------------------------
2325
2326 //------------------------------------------------------------------------------
2327 void vvMainWindow::SOHorizontalSliderMoved() {
2328   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2329 }
2330 //------------------------------------------------------------------------------
2331
2332 //------------------------------------------------------------------------------
2333 void vvMainWindow::SEHorizontalSliderMoved() {
2334   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2335 }
2336 //------------------------------------------------------------------------------
2337
2338 //------------------------------------------------------------------------------
2339 void vvMainWindow::NOVerticalSliderChanged() {
2340   int value = NOVerticalSlider->value();
2341   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2342     {
2343       if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
2344         {
2345           mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2346           mSlicerManagers[i]->UpdateSlice(0); // <-- DS add this. Not too much update ?
2347           break;
2348         }
2349     }
2350 }
2351 //------------------------------------------------------------------------------
2352
2353 //------------------------------------------------------------------------------
2354 void vvMainWindow::NEVerticalSliderChanged() {
2355   int value = NEVerticalSlider->value();
2356   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2357     {
2358       if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1)
2359         {
2360           mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2361           break;
2362         }
2363     }
2364 }
2365 //------------------------------------------------------------------------------
2366
2367 //------------------------------------------------------------------------------
2368 void vvMainWindow::SOVerticalSliderChanged() {
2369   int value = SOVerticalSlider->value();
2370   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2371     {
2372       if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
2373         {
2374           mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2375           break;
2376         }
2377     }
2378 }
2379 //------------------------------------------------------------------------------
2380
2381 //------------------------------------------------------------------------------
2382 void vvMainWindow::SEVerticalSliderChanged() {
2383   int value = SEVerticalSlider->value();
2384   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2385     {
2386       if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1)
2387         {
2388           mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2389           break;
2390         }
2391     }
2392 }
2393 //------------------------------------------------------------------------------
2394
2395 //------------------------------------------------------------------------------
2396 void vvMainWindow::UpdateSlice(int slicer, int slice) {
2397   if (slicer == 0) {
2398     if (slice != NOVerticalSlider->value())
2399       NOVerticalSlider->setValue(slice);
2400   }
2401   else if (slicer == 1)
2402     NEVerticalSlider->setValue(slice);
2403   else if (slicer == 2)
2404     SOVerticalSlider->setValue(slice);
2405   else if (slicer == 3)
2406     SEVerticalSlider->setValue(slice);
2407 }
2408 //------------------------------------------------------------------------------
2409
2410 //------------------------------------------------------------------------------
2411 void vvMainWindow::UpdateTSlice(int slicer, int slice) {
2412   switch (slicer)
2413     {
2414     case 0:
2415       NOHorizontalSlider->setValue(slice);
2416       break;
2417     case 1:
2418       NEHorizontalSlider->setValue(slice);
2419       break;
2420     case 2:
2421       SOHorizontalSlider->setValue(slice);
2422       break;
2423     case 3:
2424       SEHorizontalSlider->setValue(slice);
2425       break;
2426     }
2427 }
2428 //------------------------------------------------------------------------------
2429
2430 //------------------------------------------------------------------------------
2431 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax) {
2432   int position = int((min+max)/2);
2433   int tPosition = int((tmin+tmax)/2);
2434   if (slicer == 0)
2435     {
2436       NOVerticalSlider->setValue(position);
2437       NOVerticalSlider->setRange(min,max);
2438       NOHorizontalSlider->setRange(tmin,tmax);
2439       NOHorizontalSlider->setValue(tPosition);
2440     }
2441   else if (slicer == 1)
2442     {
2443       NEVerticalSlider->setValue(position);
2444       NEVerticalSlider->setRange(min,max);
2445       NEHorizontalSlider->setRange(tmin,tmax);
2446       NEHorizontalSlider->setValue(tPosition);
2447     }
2448   else if (slicer == 2)
2449     {
2450       SOVerticalSlider->setValue(position);
2451       SOVerticalSlider->setRange(min,max);
2452       SOHorizontalSlider->setRange(tmin,tmax);
2453       SOHorizontalSlider->setValue(tPosition);
2454     }
2455   else if (slicer == 3)
2456     {
2457       SEVerticalSlider->setValue(position);
2458       SEVerticalSlider->setRange(min,max);
2459       SEHorizontalSlider->setRange(tmin,tmax);
2460       SEHorizontalSlider->setValue(tPosition);
2461     }
2462 }
2463 //------------------------------------------------------------------------------
2464
2465 //------------------------------------------------------------------------------
2466 void vvMainWindow::SaveNOScreenshot() {
2467   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2468   w2i->SetInput(NOViewWidget->GetRenderWindow());
2469   w2i->Update();
2470   SaveScreenshot(w2i->GetOutput());
2471   w2i->Delete();
2472 }
2473 //------------------------------------------------------------------------------
2474
2475 //------------------------------------------------------------------------------
2476 void vvMainWindow::SaveNEScreenshot() {
2477   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2478   w2i->SetInput(NEViewWidget->GetRenderWindow());
2479   w2i->Update();
2480   SaveScreenshot(w2i->GetOutput());
2481   w2i->Delete();
2482 }
2483 //------------------------------------------------------------------------------
2484
2485 //------------------------------------------------------------------------------
2486 void vvMainWindow::SaveSOScreenshot() {
2487   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2488   w2i->SetInput(SOViewWidget->GetRenderWindow());
2489   w2i->Update();
2490   SaveScreenshot(w2i->GetOutput());
2491   w2i->Delete();
2492 }
2493 //------------------------------------------------------------------------------
2494
2495 //------------------------------------------------------------------------------
2496 void vvMainWindow::SaveSEScreenshot() {
2497   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2498   w2i->SetInput(SEViewWidget->GetRenderWindow());
2499   w2i->Update();
2500   SaveScreenshot(w2i->GetOutput());
2501   w2i->Delete();
2502 }
2503 //------------------------------------------------------------------------------
2504
2505 //------------------------------------------------------------------------------
2506 void vvMainWindow::SaveScreenshot(vtkImageData* image) {
2507   QString Extensions = "Images( *.png);;";
2508   Extensions += "Images( *.jpg);;";
2509   Extensions += "Images( *.bmp);;";
2510   Extensions += "Images( *.tif);;";
2511   Extensions += "Images( *.ppm)";
2512   QString fileName = QFileDialog::getSaveFileName(this,
2513                                                   tr("Save As"),
2514                                                   itksys::SystemTools::GetFilenamePath(
2515                                                                                        mSlicerManagers[0]->GetFileName()).c_str(),
2516                                                   Extensions);
2517   if (!fileName.isEmpty())
2518     {
2519       const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2520       if (!strcmp(ext, ".bmp"))
2521         {
2522           vtkBMPWriter *bmp = vtkBMPWriter::New();
2523           bmp->SetInput(image);
2524           bmp->SetFileName(fileName.toStdString().c_str());
2525           bmp->Write();
2526           bmp->Delete();
2527         }
2528       else if (!strcmp(ext, ".tif"))
2529         {
2530           vtkTIFFWriter *tif = vtkTIFFWriter::New();
2531           tif->SetInput(image);
2532           tif->SetFileName(fileName.toStdString().c_str());
2533           tif->Write();
2534           tif->Delete();
2535         }
2536       else if (!strcmp(ext, ".ppm"))
2537         {
2538           vtkPNMWriter *pnm = vtkPNMWriter::New();
2539           pnm->SetInput(image);
2540           pnm->SetFileName(fileName.toStdString().c_str());
2541           pnm->Write();
2542           pnm->Delete();
2543         }
2544       else if (!strcmp(ext, ".png"))
2545         {
2546           vtkPNGWriter *png = vtkPNGWriter::New();
2547           png->SetInput(image);
2548           png->SetFileName(fileName.toStdString().c_str());
2549           png->Write();
2550           png->Delete();
2551         }
2552       else if (!strcmp(ext, ".jpg"))
2553         {
2554           vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2555           jpg->SetInput(image);
2556           jpg->SetFileName(fileName.toStdString().c_str());
2557           jpg->Write();
2558           jpg->Delete();
2559         }
2560       else
2561         {
2562           QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2563         }
2564     }
2565
2566 }
2567 //------------------------------------------------------------------------------
2568
2569 //------------------------------------------------------------------------------
2570 void vvMainWindow::GoToCursor() {
2571   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2572   for (int column = 1; column < 5; column++)
2573     {
2574       if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1)
2575         {
2576           double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2577           mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2578                                                                           cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2579           mSlicerManagers[index]->UpdateViews(1,column-1);
2580           mSlicerManagers[index]->UpdateLinked(column-1);
2581           break;
2582         }
2583     }
2584 }
2585 //------------------------------------------------------------------------------
2586
2587 //------------------------------------------------------------------------------
2588 void vvMainWindow::PlayPause() {
2589   if (playMode)
2590     {
2591       playMode = 0;
2592       playButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/player_play.png")));
2593       ImageInfoChanged();
2594       return;
2595     }
2596   else
2597     {
2598       int image_number=DataTree->topLevelItemCount();
2599       bool has_temporal;
2600       for (int i=0;i<image_number;i++)
2601         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1)
2602           {
2603             has_temporal=true;
2604             break;
2605           }
2606       if (has_temporal)
2607         {
2608           playMode = 1;
2609           playButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/player_pause.png")));
2610           QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2611         }
2612     }
2613 }
2614 //------------------------------------------------------------------------------
2615
2616 //------------------------------------------------------------------------------
2617 void vvMainWindow::PlayNext() {
2618   if (playMode && !this->isHidden())
2619     {
2620       int image_number=DataTree->topLevelItemCount();
2621       ///Only play one slicer per SM, and only if the SM is being displayed
2622       for (int i=0;i<image_number;i++)
2623         for (int j=0;j<4;j++)
2624           if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2625               DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0)
2626             {
2627               mSlicerManagers[i]->SetNextTSlice(j);
2628               break;
2629             }
2630       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2631     }
2632 }
2633 //------------------------------------------------------------------------------
2634
2635 void vvMainWindow::ShowLastImage()
2636 {
2637   if (mSlicerManagers.size() > 1)
2638     {
2639       QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2640       CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2641       item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2642       DisplayChanged(item,1);
2643     }
2644 }
2645
2646 //------------------------------------------------------------------------------
2647 void vvMainWindow::UpdateRenderWindows() {
2648   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2649   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2650   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2651   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2652 }
2653 //------------------------------------------------------------------------------
2654
2655 //------------------------------------------------------------------------------
2656 void vvMainWindow::ResampleCurrentImage() {
2657   vvResamplerDialog resampler;
2658   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2659   resampler.SetSlicerManagers(mSlicerManagers,index);
2660   if (resampler.exec())
2661     AddImage(resampler.GetOutput(),resampler.GetOutputFileName());
2662 }
2663 //------------------------------------------------------------------------------
2664
2665 //------------------------------------------------------------------------------
2666 void vvMainWindow::SegmentationOnCurrentImage() {
2667   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2668
2669   vvSegmentationDialog segmentation;
2670   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2671   segmentation.exec();
2672 }
2673 //------------------------------------------------------------------------------
2674
2675 void vvMainWindow::SurfaceViewerLaunch()
2676 {
2677   vvSurfaceViewerDialog surfaceViewer;
2678   surfaceViewer.exec();
2679 }
2680
2681 //------------------------------------------------------------------------------
2682 void vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2683 {
2684   vvSlicerManager* m = new vvSlicerManager(4);
2685   m->SetImage(image);
2686   m->SetFilename(filename);
2687   AddImage(m);
2688 }
2689
2690 //------------------------------------------------------------------------------
2691 void vvMainWindow::AddImage(vvSlicerManager * slicer_manager) {
2692   mSlicerManagers.push_back(slicer_manager);
2693
2694   std::string filename = slicer_manager->GetFileName();
2695
2696   //create an item in the tree with good settings
2697   QTreeWidgetItem *item = new QTreeWidgetItem();
2698   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2699   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
2700   qApp->processEvents();
2701
2702   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2703
2704   //Create the buttons for reload and close
2705   qApp->processEvents();
2706   QTreePushButton* cButton = new QTreePushButton;
2707   cButton->setItem(item);
2708   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2709   cButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")));
2710   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2711           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2712
2713   QTreePushButton* rButton = new QTreePushButton;
2714   rButton->setItem(item);
2715   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2716   rButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")));
2717   rButton->setEnabled(0);
2718   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2719           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2720
2721   DataTree->addTopLevelItem(item);
2722   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2723   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2724
2725   //set the id of the image
2726   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2727   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2728   mSlicerManagers.back()->SetId(id.toStdString());
2729
2730   linkPanel->addImage(filename, id.toStdString());
2731
2732   connect(mSlicerManagers.back(),SIGNAL(currentImageChanged(std::string)),
2733           this,SLOT(CurrentImageChanged(std::string)));
2734   connect(mSlicerManagers.back(),SIGNAL(
2735                                         UpdatePosition(int, double, double, double, double, double, double, double)),this,
2736           SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2737   connect(mSlicerManagers.back(),SIGNAL(UpdateVector(int, double, double, double, double)),
2738           this, SLOT(VectorChanged(int,double,double,double, double)));
2739   connect(mSlicerManagers.back(),SIGNAL(UpdateOverlay(int, double, double)),
2740           this, SLOT(OverlayChanged(int,double,double)));
2741   connect(mSlicerManagers.back(),SIGNAL(UpdateFusion(int, double)),
2742           this, SLOT(FusionChanged(int,double)));
2743   connect(mSlicerManagers.back(),SIGNAL(UpdateWindows(int, int, int)),
2744           this,SLOT(WindowsChanged(int, int, int)));
2745   connect(mSlicerManagers.back(),SIGNAL(WindowLevelChanged(double, double,int, int)),
2746           this,SLOT(WindowLevelChanged(double, double, int, int)));
2747   connect(mSlicerManagers.back(),SIGNAL(UpdateSlice(int,int)),
2748           this,SLOT(UpdateSlice(int,int)));
2749   connect(mSlicerManagers.back(),SIGNAL(UpdateTSlice(int, int)),
2750           this,SLOT(UpdateTSlice(int, int)));
2751   connect(mSlicerManagers.back(),SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2752           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2753   connect(mSlicerManagers.back(),SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2754           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2755   connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2756   UpdateTree();
2757   qApp->processEvents();
2758   InitSlicers();
2759   ShowLastImage();
2760   InitDisplay();
2761   qApp->processEvents();
2762 }
2763 //------------------------------------------------------------------------------
2764
2765
2766 //------------------------------------------------------------------------------
2767 void vvMainWindow::UpdateCurrentSlicer() {
2768   int index = -1;
2769   if (DataTree->selectedItems().size() > 0) {
2770     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2771   }
2772   mSlicerManagerCurrentIndex = index;
2773 }
2774 //------------------------------------------------------------------------------
2775