vv/vvMainWindow.cxx

   1 /*=========================================================================
   2
   3   Program:   vv
   4   Module:    $RCSfile: vvMainWindow.cxx,v $
   5   Language:  C++
   6   Date:      $Date: 2010/03/24 13:59:01 $
   7   Version:   $Revision: 1.19 $
   8   Author :   Pierre Seroul (pierre.seroul@gmail.com)
   9
  10   Copyright (C) 200COLUMN_IMAGE_NAME
  11   Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
  12   CREATIS-LRMN http://www.creatis.insa-lyon.fr
  13
  14   This program is free software: you can redistribute it and/or modify
  15   it under the terms of the GNU General Public License as published by
  16   the Free Software Foundation, version 3 of the License.
  17
  18   This program is distributed in the hope that it will be useful,
  19   but WITHOUT ANY WARRANTY; without even the implied warranty of
  20   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  21   GNU General Public License for more details.
  22
  23   You should have received a copy of the GNU General Public License
  24   along with this program.  If not, see <http://www.gnu.org/licenses/>.
  25
  26   =========================================================================*/
  27
  28 // QT include
  29 #include <algorithm>
  30 #include <QMessageBox>
  31 #include <QInputDialog>
  32 #include <QTimer>
  33 #include "QTreePushButton.h"
  34
  35 // VV include
  36 #include "vvMainWindow.h"
  37 #include "vvHelpDialog.h"
  38 #include "vvDocumentation.h"
  39 #include "vvProgressDialog.h"
  40 #include "vvQDicomSeriesSelector.h"
  41 #include "vvSlicerManager.h"
  42 #include "clitkImageCommon.h"
  43 #include "vvSlicer.h"
  44 #include "vvInteractorStyleNavigator.h"
  45 #include "vvImageWriter.h"
  46 #include "vvResamplerDialog.h"
  47 #include "vvSegmentationDialog.h"
  48 #include "vvSurfaceViewerDialog.h"
  49 #include "vvDeformationDialog.h"
  50 #include "vvImageWarp.h"
  51 #include "vvUtils.h"
  52 #include "vvMaximumIntensityProjection.h"
  53 #include "vvMidPosition.h"
  54 #include "vvMesh.h"
  55 #include "vvStructSelector.h"
  56 #include "vvMeshReader.h"
  57 #include "vvConstants.h"
  58
  59 #ifdef CLITK_VV_USE_BDCM
  60 #include <bdcmDicomFilesSelectorDialog.h>
  61 #endif
  62
  63 // ITK include
  64 #include "itkImage.h"
  65 #include "itkImageFileReader.h"
  66 #include "itkByteSwapper.h"
  67 #include "itkCommand.h"
  68 #include "itkNumericSeriesFileNames.h"
  69
  70 // VTK include
  71 #include "vtkImageData.h"
  72 #include "vtkImageActor.h"
  73 #include "vtkCornerAnnotation.h"
  74 #include "vtkRenderWindow.h"
  75 #include "vtkRenderWindowInteractor.h"
  76 #include "vtkRenderer.h"
  77 #include "vtkRendererCollection.h"
  78 #include "vtkWindowToImageFilter.h"
  79 #include "vtkBMPWriter.h"
  80 #include "vtkTIFFWriter.h"
  81 #include "vtkPNMWriter.h"
  82 #include "vtkPNGWriter.h"
  83 #include "vtkJPEGWriter.h"
  84
  85 // Standard includes
  86 #include <iostream>
  87
  88 #define COLUMN_TREE 0
  89 #define COLUMN_UL_VIEW 1
  90 #define COLUMN_UR_VIEW 2
  91 #define COLUMN_DL_VIEW 3
  92 #define COLUMN_DR_VIEW 4
  93 #define COLUMN_CLOSE_IMAGE 5
  94 #define COLUMN_RELOAD_IMAGE 6
  95 #define COLUMN_IMAGE_NAME 7
  96
  97 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.hdr *.vox *.his *.xdr)"
  98
  99 /*Data Tree values
 100   0,Qt::UserRole full filename
 101   1,Qt::CheckStateRole checkbutton UL View
 102   1,Qt::UserRole overlay, fusion or vector
 103   2,Qt::CheckStateRole checkbutton UR View
 104   3,Qt::CheckStateRole checkbutton DL View
 105   4,Qt::CheckStateRole checkbutton DR View
 106   5,0  short filename
 107   5,Qt::UserRole mSlicerManager id*/
 108
 109 //------------------------------------------------------------------------------
 110 vvMainWindow::vvMainWindow():vvMainWindowBase() {
 111   setupUi(this); // this sets up the GUI
 112
 113   mInputPathName = "";
 114   mMenuTools = menuTools;
 115   mMenuExperimentalTools = menuExperimental;
 116   mMainWidget = this;
 117
 118   //Init the contextMenu
 119   this->setContextMenuPolicy(Qt::CustomContextMenu);
 120   contextActions.resize(0);
 121   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/fileopen.png")),
 122                                                         tr("O&pen new Image"));
 123   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 124   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 125   contextActions.push_back(actionOpen_new_image);
 126   contextMenu.addSeparator();
 127
 128   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")),
 129                                                      tr("Close Current Image"));
 130   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 131   contextActions.push_back(actionClose_Image);
 132
 133   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")),
 134                                                       tr("Reload Current Image"));
 135   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 136   contextActions.push_back(actionReload_image);
 137
 138   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/filesave.png")),
 139                                                     tr("Save Current Image"));
 140   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 141   contextActions.push_back(actionSave_image);
 142
 143   contextMenu.addSeparator();
 144
 145   // QAction* actionCrop_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/crop.png")),
 146   //                                                   tr("Crop Current Image"));
 147   // connect(actionCrop_image,SIGNAL(triggered()),this,SLOT(CropImage()));
 148   // contextActions.push_back(actionCrop_image);
 149
 150   QAction* actionSplit_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/cut.png")),
 151                                                      tr("Split Current Image"));
 152   connect(actionSplit_image,SIGNAL(triggered()),this,SLOT(SplitImage()));
 153   contextActions.push_back(actionSplit_image);
 154
 155   contextMenu.addSeparator();
 156
 157   contextMenu.addAction(actionAdd_VF_to_current_Image);
 158   contextActions.push_back(actionAdd_VF_to_current_Image);
 159
 160   QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/GPSup.png")),
 161                                                                        tr("Add overlay image to current image"));
 162   contextMenu.addAction(actionAdd_Overlay_to_current_Image);
 163   contextActions.push_back(actionAdd_Overlay_to_current_Image);
 164
 165   connect(actionAdd_Overlay_to_current_Image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 166
 167   contextMenu.addAction(actionAdd_fusion_image);
 168   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 169   contextActions.push_back(actionAdd_fusion_image);
 170
 171   //init the DataTree
 172   mSlicerManagers.resize(0);
 173
 174   QStringList header;
 175   header.append("");
 176   header.append("TL");
 177   header.append("TR");
 178   header.append("BL");
 179   header.append("BR");
 180   header.append("");
 181   header.append("");
 182   header.append("Name");
 183
 184   DataTree->setHeaderLabels(header);
 185   DataTree->resizeColumnToContents(COLUMN_TREE);
 186   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 187   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 188   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 189   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 190   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 191   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 192   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 193
 194   viewMode = 1;
 195   documentation = new vvDocumentation();
 196   help_dialog = new vvHelpDialog();
 197   dicomSeriesSelector = new vvDicomSeriesSelector();
 198
 199   inverseButton->setEnabled(0);
 200   actionAdd_Overlay_to_current_Image->setEnabled(0);
 201   actionSave_As->setEnabled(0);
 202   actionAdd_VF_to_current_Image->setEnabled(0);
 203   actionAdd_fusion_image->setEnabled(0);
 204
 205   //init the sliders
 206   verticalSliders.push_back(NOVerticalSlider);
 207   verticalSliders.push_back(NEVerticalSlider);
 208   verticalSliders.push_back(SOVerticalSlider);
 209   verticalSliders.push_back(SEVerticalSlider);
 210
 211   for (int i =0; i < 4; i++)
 212     verticalSliders[i]->hide();
 213
 214   horizontalSliders.push_back(NOHorizontalSlider);
 215   horizontalSliders.push_back(NEHorizontalSlider);
 216   horizontalSliders.push_back(SOHorizontalSlider);
 217   horizontalSliders.push_back(SEHorizontalSlider);
 218
 219   for (int i =0; i < 4; i++)
 220     horizontalSliders[i]->hide();
 221
 222
 223   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 224   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 225   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 226   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 227
 228   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 229   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 230   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 231   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 232
 233   //connect everything
 234   connect(actionMaximum_Intensity_Projection,SIGNAL(triggered()),this,SLOT(ComputeMIP()));
 235   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 236   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 237   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 238   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 239   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 240   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 241   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 242   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 243   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 244   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 245   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 246   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 247   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 248   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 249   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 250
 251   ///////////////////////////////////////////////
 252   contextMenu.addAction(actionResampler);
 253   connect(actionResampler,SIGNAL(triggered()),this,SLOT(ResampleCurrentImage()));
 254   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 255   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 256   ///////////////////////////////////////////////
 257
 258   actionNorth_East_Window->setEnabled(0);
 259   actionNorth_West_Window->setEnabled(0);
 260   actionSouth_East_Window->setEnabled(0);
 261   actionSouth_West_Window->setEnabled(0);
 262
 263   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 264   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 265   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 266   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 267
 268   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 269   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 270           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 271
 272   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 273   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 274   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 275   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 276   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 277   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 278
 279
 280   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 281
 282   connect(linkPanel,SIGNAL(addLink(QString,QString)),this,SLOT(AddLink(QString,QString)));
 283   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 284   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int)),this,SLOT(SetVFProperty(int,int,int)));
 285   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int)),this,SLOT(SetOverlayProperty(int)));
 286   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,double,double)),
 287           this,SLOT(SetFusionProperty(int,int,double,double)));
 288   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 289
 290   playMode = 0;//pause
 291   mFrameRate = 10;
 292   playButton->setEnabled(0);
 293   frameRateLabel->setEnabled(0);
 294   frameRateSpinBox->setEnabled(0);
 295   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 296   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 297
 298   goToCursorPushButton->setEnabled(0);
 299   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 300
 301   NOViewWidget->hide();
 302   NEViewWidget->hide();
 303   SOViewWidget->hide();
 304   SEViewWidget->hide();
 305
 306   //Recently opened files
 307   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 308   if ( !recent_files.empty() )
 309     {
 310       QMenu * rmenu = new QMenu("Recently opened files...");
 311       rmenu->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/open.png")));
 312       menuFile->insertMenu(actionOpen_Image_With_Time,rmenu);
 313       for (std::list<std::string>::iterator i = recent_files.begin();i!=recent_files.end();i++)
 314         {
 315           QAction* current=new QAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/open.png")),
 316                                        (*i).c_str(),this);
 317           rmenu->addAction(current);
 318           connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 319         }
 320     }
 321
 322   // Adding all new tools (insertion in the menu)
 323   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 324
 325   if (!CLITK_EXPERIMENTAL)
 326       menuExperimental->menuAction()->setVisible(false);
 327 }
 328 //------------------------------------------------------------------------------
 329
 330
 331 //------------------------------------------------------------------------------
 332 void vvMainWindow::ComputeMIP()
 333 {
 334   vvMaximumIntensityProjection mip;
 335   vvSlicerManager* selected_slicer = mSlicerManagers[GetSlicerIndexFromItem(DataTree->selectedItems()[0])];
 336   QFileInfo info(selected_slicer->GetFileName().c_str());
 337   mip.Compute(selected_slicer);
 338   AddImage(mip.GetOutput(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_mip.mhd");
 339 }
 340 //------------------------------------------------------------------------------
 341
 342
 343 //------------------------------------------------------------------------------
 344 void vvMainWindow::ComputeMidPosition()
 345 {
 346   bool ok;
 347   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 348   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 349                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 350   if (ok)
 351     {
 352       vvMidPosition midp;
 353       midp.slicer_manager = mSlicerManagers[index];
 354       midp.reference_image_index = ref;
 355       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 356       midp.Update();
 357       if (midp.error)
 358         QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 359       else
 360         {
 361           QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 362           AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 363         }
 364       QApplication::restoreOverrideCursor();
 365     }
 366 }
 367 //------------------------------------------------------------------------------
 368
 369
 370 //------------------------------------------------------------------------------
 371 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 372 {
 373   QTreeWidgetItem *item = new QTreeWidgetItem();
 374   item->setData(0,Qt::UserRole,"filename.vtk");
 375   item->setData(1,Qt::UserRole,tr("contour"));
 376   QBrush brush;
 377   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 378   brush.setStyle(Qt::SolidPattern);
 379   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 380   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 381
 382   for (int j = 1; j <= 4; j++)
 383     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 384
 385   QTreePushButton* cButton = new QTreePushButton;
 386   cButton->setItem(item);
 387   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 388   cButton->setToolTip(tr("close image"));
 389   cButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")));
 390   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 391           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 392
 393   QTreePushButton* rButton = new QTreePushButton;
 394   rButton->setItem(item);
 395   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 396   rButton->setToolTip(tr("reload image"));
 397   rButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")));
 398   rButton->setEnabled(false);
 399   //Not implemented
 400   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 401   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 402
 403   DataTree->topLevelItem(image_index)->setExpanded(1);
 404   DataTree->topLevelItem(image_index)->addChild(item);
 405   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 406   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 407   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 408   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 409
 410   UpdateTree();
 411   mSlicerManagers[image_index]->AddContour(contour,propagation);
 412   mSlicerManagers[image_index]->Render();
 413 }
 414 //------------------------------------------------------------------------------
 415
 416
 417 //------------------------------------------------------------------------------
 418 void vvMainWindow::OpenVTKContour()
 419 {
 420   if (mSlicerManagers.size() > 0)
 421     {
 422       QString Extensions = "Images ( *.vtk; *.obj)";
 423       Extensions += ";;All Files (*)";
 424       QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 425       if (file.isNull())
 426         return;
 427       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 428       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 429       vvMeshReader reader;
 430       reader.SetImage(mSlicerManagers[index]->GetImage());
 431       reader.SetModeToVTK();
 432       reader.SetFilename(file.toStdString());
 433       reader.Update();
 434       AddContour(index,reader.GetOutput()[0],false);
 435       QApplication::restoreOverrideCursor();
 436     }
 437 }
 438 //------------------------------------------------------------------------------
 439
 440
 441 //------------------------------------------------------------------------------
 442 void vvMainWindow::OpenDCStructContour()
 443 {
 444   if (mSlicerManagers.size() > 0)
 445     {
 446       QString Extensions = "Dicom Files ( *.dcm; RS*)";
 447       Extensions += ";;All Files (*)";
 448       QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 449       if (file.isNull())
 450         return;
 451       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 452       vvMeshReader reader;
 453       reader.SetFilename(file.toStdString());
 454       vvStructSelector selector;
 455       selector.SetStructures(reader.GetROINames());
 456       if (!mSlicerManagers[index]->GetVF().IsNull())
 457         selector.EnablePropagationCheckBox();
 458       if (selector.exec())
 459         {
 460           QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 461           reader.SetSelectedItems(selector.getSelectedItems());
 462           reader.SetImage(mSlicerManagers[index]->GetImage());
 463           if (selector.PropagationEnabled())
 464             reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 465           reader.Update();
 466           std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 467           for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 468                i!=contours.end();i++)
 469             AddContour(index,*i,selector.PropagationEnabled());
 470           QApplication::restoreOverrideCursor();
 471         }
 472     }
 473 }
 474 //------------------------------------------------------------------------------
 475
 476
 477 //------------------------------------------------------------------------------
 478 void vvMainWindow::ComputeDeformableRegistration()
 479 {
 480   if (mSlicerManagers.size() > 0)
 481     {
 482       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 483       vvDeformationDialog dialog(index,mSlicerManagers);
 484       if (dialog.exec())
 485         {
 486           std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 487           AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 488           WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 489         }
 490       else
 491         std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 492     }
 493   else QMessageBox::information(this, "Need to open image","You must open an image first.");
 494 }
 495 //------------------------------------------------------------------------------
 496
 497
 498 //------------------------------------------------------------------------------
 499 void vvMainWindow::WarpImage()
 500 {
 501   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 502   if (!mSlicerManagers[index]->GetVF().IsNull())
 503     {
 504       bool ok;
 505       int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 506                                          mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 507       if (ok)
 508         {
 509           WarpImage(mSlicerManagers[index],ref);
 510         }
 511     }
 512   else
 513     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 514 }
 515 //------------------------------------------------------------------------------
 516
 517
 518 //------------------------------------------------------------------------------
 519 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 520 {
 521   if (!selected_slicer->GetVF().IsNull())
 522     {
 523       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 524       QFileInfo info(selected_slicer->GetFileName().c_str());
 525       vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 526                        reference_phase,this);
 527       if (warp.ComputeWarpedImage())
 528         {
 529           AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 530           AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 531           AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 532           QApplication::restoreOverrideCursor();
 533         }
 534       else
 535         {
 536           QApplication::restoreOverrideCursor();
 537           QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 538         }
 539     }
 540   else
 541     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 542 }
 543 //------------------------------------------------------------------------------
 544
 545
 546 //------------------------------------------------------------------------------
 547 vvMainWindow::~vvMainWindow() {
 548   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
 549     {
 550       if (mSlicerManagers[i] != NULL)
 551         delete mSlicerManagers[i];
 552     }
 553 }
 554 //------------------------------------------------------------------------------
 555
 556
 557 //------------------------------------------------------------------------------
 558 void vvMainWindow::MergeImages() {
 559   QString Extensions = EXTENSIONS;
 560   Extensions += ";;All Files (*)";
 561   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 562   if (files.isEmpty())
 563     return;
 564   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 565   std::vector<std::string> vector;
 566
 567   unsigned int currentDim = 0;
 568   std::vector<double> currentSpacing;
 569   std::vector<int> currentSize;
 570   std::vector<double> currentOrigin;
 571
 572   for (int i = 0; i < files.size(); i++)
 573     {
 574       itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 575               files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 576       reader->SetFileName(files[i].toStdString().c_str());
 577       reader->ReadImageInformation();
 578       if (reader)        {
 579           //NOViewWidget->hide();
 580           //NEViewWidget->hide();
 581           //SOViewWidget->hide();
 582           //SEViewWidget->hide();
 583           if (i == 0)
 584               currentDim = reader->GetNumberOfDimensions();
 585           bool IsOk = true;
 586           for (unsigned int j = 0;j < currentDim; j++)
 587           {
 588               if (i == 0)
 589               {
 590                   if (j == 0)
 591                   {
 592                       currentSpacing.resize(currentDim);
 593                       currentSize.resize(currentDim);
 594                       currentOrigin.resize(currentDim);
 595                   }
 596                   currentOrigin[j] = reader->GetOrigin(j);
 597                   currentSpacing[j] = reader->GetSpacing(j);
 598                   currentSize[j] = reader->GetDimensions(j);
 599               }
 600               else if (currentDim != reader->GetNumberOfDimensions()
 601                       || currentSpacing[j] != reader->GetSpacing(j)
 602                       || currentSize[j] != (int)reader->GetDimensions(j)
 603                       || currentOrigin[j] != reader->GetOrigin(j))
 604               {
 605                   QString error = "Cannot read file (too different from others ";
 606                   error += files[i].toStdString().c_str();
 607                   QMessageBox::information(this,tr("Reading problem"),error);
 608                   IsOk = false;
 609                   break;
 610               }
 611           }
 612           if (IsOk)
 613               vector.push_back(files[i].toStdString());
 614       }
 615     }
 616   if (vector.size() > 0)
 617     LoadImages(vector, MERGED);
 618 }
 619 //------------------------------------------------------------------------------
 620
 621
 622 //------------------------------------------------------------------------------
 623 void vvMainWindow::MergeImagesWithTime() {
 624   QString Extensions = EXTENSIONS;
 625   Extensions += ";;All Files (*)";
 626   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 627   if (files.isEmpty())
 628     return;
 629   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 630   std::vector<std::string> vector;
 631
 632   unsigned int currentDim = 0;
 633   std::vector<double> currentSpacing;
 634   std::vector<int> currentSize;
 635   std::vector<double> currentOrigin;
 636
 637   for (int i = 0; i < files.size(); i++)
 638     {
 639       itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 640                                                                             files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 641       if (reader)
 642         {
 643           reader->SetFileName(files[i].toStdString().c_str());
 644           reader->ReadImageInformation();
 645           if (i == 0)
 646             currentDim = reader->GetNumberOfDimensions();
 647           bool IsOk = true;
 648           for (unsigned int j = 0;j < currentDim; j++)
 649             {
 650               if (i == 0)
 651                 {
 652                   if (j == 0)
 653                     {
 654                       currentSpacing.resize(currentDim);
 655                       currentSize.resize(currentDim);
 656                       currentOrigin.resize(currentDim);
 657                     }
 658                   currentOrigin[j] = reader->GetOrigin(j);
 659                   currentSpacing[j] = reader->GetSpacing(j);
 660                   currentSize[j] = reader->GetDimensions(j);
 661                 }
 662               else if (currentDim != reader->GetNumberOfDimensions()
 663                        || currentSpacing[j] != reader->GetSpacing(j)
 664                        || currentSize[j] != (int)reader->GetDimensions(j)
 665                        || currentOrigin[j] != reader->GetOrigin(j))
 666                 {
 667                   QString error = "Cannot read file (too different from others ";
 668                   error += files[i].toStdString().c_str();
 669                   QMessageBox::information(this,tr("Reading problem"),error);
 670                   IsOk = false;
 671                   break;
 672                 }
 673             }
 674           if (IsOk)
 675             vector.push_back(files[i].toStdString());
 676         }
 677       else
 678         {
 679           QString error = "Cannot read file info for ";
 680           error += files[i].toStdString().c_str();
 681           error += "\n";
 682           error += "Maybe you're trying to open an image in an unsupported format?\n";
 683           QMessageBox::information(this,tr("Reading problem"),error);
 684         }
 685     }
 686   sort(vector.begin(),vector.end());
 687   if (vector.size() > 1)
 688     LoadImages(vector, MERGEDWITHTIME);
 689   else
 690     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.");
 691 }
 692 //------------------------------------------------------------------------------
 693
 694
 695 //------------------------------------------------------------------------------
 696 void vvMainWindow::OpenDicom() {
 697   std::vector<std::string> files;
 698
 699 #ifdef CLITK_VV_USE_BDCM
 700   bool r = bdcm::OpenDicomFilesSelectorDialog(files,
 701                                               "DicomFilesSelectorDialog test",
 702                                               0,0,800,800,1);
 703
 704   if (r) {
 705     std::cout << "$$$$ main : user clicked 'OK' $$$$"<<std::endl;
 706     std::cout << "$$$$ selected files : "<<std::endl;
 707     std::vector<std::string>::iterator i;
 708     for (i=files.begin();i!=files.end();++i) {
 709       std::cout << *i << std::endl;
 710     }
 711     std::cout << "$$$$ "<<std::endl;
 712
 713     LoadImages(files,DICOM);
 714   }
 715   else {
 716     std::cout << "$$$$ main : user clicked 'CANCEL' $$$$"<<std::endl;
 717   }
 718 #else
 719   std::cout << "dicomSeriesSelector " << std::endl;
 720   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 721     files = *(dicomSeriesSelector->GetFilenames());
 722     LoadImages(files,DICOM);
 723   }
 724 #endif
 725
 726 }
 727 //------------------------------------------------------------------------------
 728
 729 //------------------------------------------------------------------------------
 730 void vvMainWindow::OpenImages() {
 731   QString Extensions = EXTENSIONS;
 732   Extensions += ";;All Files (*)";
 733
 734   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 735   if (files.isEmpty())
 736     return;
 737   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 738   std::vector<std::string> vector;
 739   for (int i = 0; i < files.size(); i++)
 740     vector.push_back(files[i].toStdString());
 741   LoadImages(vector, IMAGE);
 742 }
 743 //------------------------------------------------------------------------------
 744 void vvMainWindow::OpenRecentImage()
 745 {
 746   QAction * caller = qobject_cast<QAction*>(sender());
 747   std::vector<std::string> images;
 748   images.push_back(caller->text().toStdString());
 749   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 750   LoadImages(images,IMAGE);
 751 }
 752
 753 //------------------------------------------------------------------------------
 754 void vvMainWindow::OpenImageWithTime() {
 755   QString Extensions = EXTENSIONS;
 756   Extensions += ";;All Files (*)";
 757
 758   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 759   if (files.isEmpty())
 760     return;
 761   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 762   std::vector<std::string> vector;
 763   for (int i = 0; i < files.size(); i++)
 764     {
 765       vector.push_back(files[i].toStdString());
 766     }
 767   LoadImages(vector, IMAGEWITHTIME);
 768 }
 769 //------------------------------------------------------------------------------
 770
 771 //------------------------------------------------------------------------------
 772 void vvMainWindow::LoadImages(std::vector<std::string> files, LoadedImageType filetype) {
 773   //Separate the way to open images and dicoms
 774   int fileSize;
 775   if (filetype == IMAGE || filetype == IMAGEWITHTIME)
 776     fileSize = files.size();
 777   else
 778     fileSize = 1;
 779
 780   //Only add to the list of recently opened files when a single file is opened,
 781   //to avoid polluting the list of recently opened files
 782   if (files.size() == 1)
 783     {
 784       QFileInfo finfo=tr(files[0].c_str());
 785       AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 786     }
 787   //init the progress events
 788   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 789   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 790   qApp->processEvents();
 791
 792   int numberofsuccesulreads=0;
 793   //open images as 1 or multiples
 794   for (int i = 0; i < fileSize; i++) {
 795
 796     progress.Update("Opening " + files[i]);
 797     progress.SetProgress(i,fileSize);
 798     qApp->processEvents();
 799
 800     //read the image and put it in mSlicerManagers
 801     vvSlicerManager* imageManager = new vvSlicerManager(4);
 802     qApp->processEvents();
 803
 804     bool SetImageSucceed=false;
 805
 806     if (filetype == IMAGE || filetype == IMAGEWITHTIME)
 807       SetImageSucceed = imageManager->SetImage(files[i],filetype);
 808     else
 809       {
 810         SetImageSucceed = imageManager->SetImages(files,filetype);
 811       }
 812     if (SetImageSucceed == false)
 813       {
 814         QApplication::restoreOverrideCursor();
 815         QString error = "Cannot open file \n";
 816         error += imageManager->GetLastError().c_str();
 817         QMessageBox::information(this,tr("Reading problem"),error);
 818         delete imageManager;
 819       }
 820     else
 821       {
 822         mSlicerManagers.push_back(imageManager);
 823
 824         //create an item in the tree with good settings
 825         QTreeWidgetItem *item = new QTreeWidgetItem();
 826         item->setData(0,Qt::UserRole,files[i].c_str());
 827         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 828         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 829         qApp->processEvents();
 830
 831         //Create the buttons for reload and close
 832         qApp->processEvents();
 833         QTreePushButton* cButton = new QTreePushButton;
 834         cButton->setItem(item);
 835         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 836         cButton->setToolTip(tr("close image"));
 837         cButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")));
 838         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 839                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 840
 841         QTreePushButton* rButton = new QTreePushButton;
 842         rButton->setItem(item);
 843         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 844         rButton->setToolTip(tr("reload image"));
 845         rButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")));
 846         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 847                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 848
 849         DataTree->addTopLevelItem(item);
 850         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 851         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 852
 853         //set the id of the image
 854         QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 855         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 856         mSlicerManagers.back()->SetId(id.toStdString());
 857
 858         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 859
 860         connect(mSlicerManagers.back(),SIGNAL(currentImageChanged(std::string)),
 861                 this,SLOT(CurrentImageChanged(std::string)));
 862         connect(mSlicerManagers.back(),SIGNAL(
 863                                               UpdatePosition(int, double, double, double, double, double, double, double)),this,
 864                 SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 865         connect(mSlicerManagers.back(),SIGNAL(UpdateVector(int, double, double, double, double)),
 866                 this, SLOT(VectorChanged(int,double,double,double, double)));
 867         connect(mSlicerManagers.back(),SIGNAL(UpdateOverlay(int, double, double)),
 868                 this, SLOT(OverlayChanged(int,double,double)));
 869         connect(mSlicerManagers.back(),SIGNAL(UpdateFusion(int, double)),
 870                 this, SLOT(FusionChanged(int,double)));
 871         connect(mSlicerManagers.back(),SIGNAL(UpdateWindows(int, int, int)),
 872                 this,SLOT(WindowsChanged(int, int, int)));
 873         connect(mSlicerManagers.back(),SIGNAL(WindowLevelChanged(double, double,int, int)),
 874                 this,SLOT(WindowLevelChanged(double, double, int, int)));
 875         connect(mSlicerManagers.back(),SIGNAL(UpdateSlice(int,int)),
 876                 this,SLOT(UpdateSlice(int,int)));
 877         connect(mSlicerManagers.back(),SIGNAL(UpdateTSlice(int, int)),
 878                 this,SLOT(UpdateTSlice(int, int)));
 879         connect(mSlicerManagers.back(),SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 880                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 881         connect(mSlicerManagers.back(),SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 882                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 883         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 884         InitSlicers();
 885         numberofsuccesulreads++;
 886       }
 887   }
 888   if (numberofsuccesulreads)
 889     {
 890       NOViewWidget->show();
 891       NEViewWidget->show();
 892       SOViewWidget->show();
 893       SEViewWidget->show();
 894       UpdateTree();
 895       InitDisplay();
 896       ShowLastImage();
 897     }
 898   QApplication::restoreOverrideCursor();
 899
 900 }
 901 //------------------------------------------------------------------------------
 902
 903 //------------------------------------------------------------------------------
 904 void vvMainWindow::UpdateTree() {
 905   DataTree->resizeColumnToContents(COLUMN_TREE);
 906   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 907   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 908   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 909   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 910   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 911   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 912   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 913 }
 914 //------------------------------------------------------------------------------
 915
 916 //------------------------------------------------------------------------------
 917 void vvMainWindow::CurrentImageChanged(std::string id) {
 918   int selected = 0;
 919   for (int i = 0; i < DataTree->topLevelItemCount(); i++)
 920     {
 921       if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id)
 922         {
 923           selected = i;
 924         }
 925       else
 926         {
 927           DataTree->topLevelItem(i)->setSelected(0);
 928         }
 929       for (int child = 0; child < DataTree->topLevelItem(i)->childCount();child++)
 930         DataTree->topLevelItem(i)->child(child)->setSelected(0);
 931
 932     }
 933   DataTree->topLevelItem(selected)->setSelected(1);
 934 }
 935 //------------------------------------------------------------------------------
 936
 937 //------------------------------------------------------------------------------
 938 void vvMainWindow::ImageInfoChanged() {
 939   contextActions[7]->setEnabled(1);
 940   contextActions[6]->setEnabled(1);
 941   actionSave_As->setEnabled(1);
 942   actionAdd_VF_to_current_Image->setEnabled(1);
 943   actionAdd_fusion_image->setEnabled(1);
 944   actionNorth_East_Window->setEnabled(1);
 945   actionNorth_West_Window->setEnabled(1);
 946   actionSouth_East_Window->setEnabled(1);
 947   actionSouth_West_Window->setEnabled(1);
 948   inverseButton->setEnabled(1);
 949
 950   goToCursorPushButton->setEnabled(1);
 951
 952   if (DataTree->selectedItems().size()) {
 953     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 954
 955     colorMapComboBox->setEnabled(1);
 956     for (int i = 0; i < DataTree->topLevelItem(index)->childCount();i++)
 957       {
 958         if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
 959             DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion")
 960           {
 961             colorMapComboBox->setEnabled(0);
 962             break;
 963           }
 964       }
 965
 966     std::vector<double> origin;
 967     std::vector<double> inputSpacing;
 968     std::vector<int> inputSize;
 969     std::vector<double> sizeMM;
 970     int dimension=0;
 971     QString pixelType;
 972     QString inputSizeInBytes;
 973     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
 974
 975     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1)
 976       {
 977         playButton->setEnabled(1);
 978         frameRateLabel->setEnabled(1);
 979         frameRateSpinBox->setEnabled(1);
 980       }
 981     else
 982       {
 983         playButton->setEnabled(0);
 984         frameRateLabel->setEnabled(0);
 985         frameRateSpinBox->setEnabled(0);
 986       }
 987
 988     //read image header
 989     int NPixel = 1;
 990
 991     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0])
 992       {
 993         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
 994         dimension = imageSelected->GetNumberOfDimensions();
 995         origin.resize(dimension);
 996         inputSpacing.resize(dimension);
 997         inputSize.resize(dimension);
 998         sizeMM.resize(dimension);
 999         pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
1000         for (int i = 0;i < dimension;i++)
1001           {
1002             origin[i] = imageSelected->GetOrigin()[i];
1003             inputSpacing[i] = imageSelected->GetSpacing()[i];
1004             inputSize[i] = imageSelected->GetSize()[i];
1005             sizeMM[i] = inputSize[i]*inputSpacing[i];
1006             NPixel *= inputSize[i];
1007           }
1008         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1009       }
1010     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector")
1011       {
1012         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1013         dimension = imageSelected->GetNumberOfDimensions();
1014         origin.resize(dimension);
1015         inputSpacing.resize(dimension);
1016         inputSize.resize(dimension);
1017         sizeMM.resize(dimension);
1018         pixelType = mSlicerManagers[index]->GetVF()->GetScalarTypeAsString().c_str();
1019         for (int i = 0;i < dimension;i++)
1020           {
1021             origin[i] = imageSelected->GetOrigin()[i];
1022             inputSpacing[i] = imageSelected->GetSpacing()[i];
1023             inputSize[i] = imageSelected->GetSize()[i];
1024             sizeMM[i] = inputSize[i]*inputSpacing[i];
1025             NPixel *= inputSize[i];
1026           }
1027         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1028       }
1029     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay")
1030       {
1031         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1032         dimension = imageSelected->GetNumberOfDimensions();
1033         origin.resize(dimension);
1034         inputSpacing.resize(dimension);
1035         inputSize.resize(dimension);
1036         sizeMM.resize(dimension);
1037         pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
1038         for (int i = 0;i < dimension;i++)
1039           {
1040             origin[i] = imageSelected->GetOrigin()[i];
1041             inputSpacing[i] = imageSelected->GetSpacing()[i];
1042             inputSize[i] = imageSelected->GetSize()[i];
1043             sizeMM[i] = inputSize[i]*inputSpacing[i];
1044             NPixel *= inputSize[i];
1045           }
1046         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1047       }
1048     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion")
1049       {
1050         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1051         dimension = imageSelected->GetNumberOfDimensions();
1052         origin.resize(dimension);
1053         inputSpacing.resize(dimension);
1054         inputSize.resize(dimension);
1055         sizeMM.resize(dimension);
1056         pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
1057         for (int i = 0;i < dimension;i++)
1058           {
1059             origin[i] = imageSelected->GetOrigin()[i];
1060             inputSpacing[i] = imageSelected->GetSpacing()[i];
1061             inputSize[i] = imageSelected->GetSize()[i];
1062             sizeMM[i] = inputSize[i]*inputSpacing[i];
1063             NPixel *= inputSize[i];
1064           }
1065         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1066       }
1067
1068     QString dim = QString::number(dimension) + " (";
1069     dim += pixelType + ")";
1070
1071     infoPanel->setFileName(image);
1072     infoPanel->setDimension(dim);
1073     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1074     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1075     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1076     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1077     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1078
1079     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1080                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1081     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1082     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1083
1084     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1085     for (int i = 0; i < 4;i++)
1086       {
1087         if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3)
1088           {
1089             mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1090             break;
1091           }
1092       }
1093     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1094     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1095     // DD(mSlicerManagers[index]->GetColorMap());
1096     // DD(mSlicerManagers[index]->GetPreset());
1097     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1098     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1099
1100     infoPanel->setFileName(image);
1101     infoPanel->setDimension(dim);
1102     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1103     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1104     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1105     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1106     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1107
1108     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1109                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1110     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1111     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1112
1113     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1114     for (int i = 0; i < 4;i++)
1115       {
1116         if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3)
1117           {
1118             mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1119             break;
1120           }
1121       }
1122     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1123     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1124     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1125     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1126
1127     if (mSlicerManagers[index]->GetSlicer(0)->GetVF())
1128       {
1129         overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1130         overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1131                                     mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1132                                     mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1133       }
1134     else
1135       {
1136         overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1137         overlayPanel->getVFProperty(-1,-1,-1);
1138       }
1139     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1140       {
1141         overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1142         overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1143       }
1144     else
1145       {
1146         overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1147         overlayPanel->getOverlayProperty(-1);
1148       }
1149     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion())
1150       {
1151         overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1152         overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1153                                         mSlicerManagers[index]->GetFusionColorMap(),
1154                                         mSlicerManagers[index]->GetFusionWindow(),
1155                                         mSlicerManagers[index]->GetFusionLevel());
1156       }
1157     else
1158       {
1159         overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1160         overlayPanel->getFusionProperty(-1, -1,-1,-1);
1161       }
1162   }
1163 }
1164 //------------------------------------------------------------------------------
1165
1166 //------------------------------------------------------------------------------
1167 void vvMainWindow::ShowDocumentation() {
1168   documentation->show();
1169 }
1170 //------------------------------------------------------------------------------
1171 void vvMainWindow::ShowHelpDialog() {
1172   help_dialog->show();
1173 }
1174 //------------------------------------------------------------------------------
1175
1176 //------------------------------------------------------------------------------
1177 void vvMainWindow::ChangeViewMode() {
1178   QListIterator<int> it0(splitter_3->sizes());
1179   QListIterator<int> it1(splitter_3->sizes());
1180   int max0 = 0;
1181   int max1 = 1;
1182   while (it0.hasNext())
1183     {
1184       max0 += it0.next();
1185     }
1186   while (it1.hasNext())
1187     {
1188       max1 += it1.next();
1189     }
1190   QList<int> size0;
1191   QList<int> size1;
1192   if (viewMode == 1)
1193     {
1194       viewMode = 0;
1195       size0.push_back(max0);
1196       size0.push_back(0);
1197       size1.push_back(max1);
1198       size1.push_back(0);
1199       splitter_3->setSizes(size0);
1200       OSplitter->setSizes(size1);
1201       DataTree->setColumnHidden(2,1);
1202       DataTree->setColumnHidden(3,1);
1203       DataTree->setColumnHidden(4,1);
1204     }
1205   else
1206     {
1207       viewMode = 1;
1208       size0.push_back(int(max0/2));
1209       size0.push_back(int(max0/2));
1210       size1.push_back(int(max1/2));
1211       size1.push_back(int(max1/2));
1212       splitter_3->setSizes(size0);
1213       OSplitter->setSizes(size1);
1214       DataTree->setColumnHidden(2,0);
1215       DataTree->setColumnHidden(3,0);
1216       DataTree->setColumnHidden(4,0);
1217     }
1218 }
1219 //------------------------------------------------------------------------------
1220
1221 //------------------------------------------------------------------------------
1222 QString vvMainWindow::GetSizeInBytes(unsigned long size) {
1223   QString result = "";// QString::number(size);
1224   //result += " bytes (";
1225   if (size > 1000000000)
1226     {
1227       size /= 1000000000;
1228       result += QString::number(size);
1229       result += "Gb";//)";
1230     }
1231   else if (size > 1000000)
1232     {
1233       size /= 1000000;
1234       result += QString::number(size);
1235       result += "Mb";//)";
1236     }
1237   else if (size > 1000)
1238     {
1239       size /= 1000;
1240       result += QString::number(size);
1241       result += "kb";//)";
1242     }
1243   return result;
1244 }
1245 //------------------------------------------------------------------------------
1246
1247 //------------------------------------------------------------------------------
1248 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble) {
1249   QString result;
1250   for (unsigned int i= 0; i < vectorDouble.size(); i++)
1251     {
1252       if (i != 0)
1253         result += " ";
1254       result += QString::number(vectorDouble[i]);
1255     }
1256   return result;
1257 }
1258 //------------------------------------------------------------------------------
1259
1260 //------------------------------------------------------------------------------
1261 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt) {
1262   QString result;
1263   for (unsigned int i= 0; i < vectorInt.size(); i++)
1264     {
1265       if (i != 0)
1266         result += " ";
1267       result += QString::number(vectorInt[i]);
1268     }
1269   return result;
1270 }
1271 //------------------------------------------------------------------------------
1272
1273 //------------------------------------------------------------------------------
1274 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item) {
1275   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1276   for (int i = 0; i < DataTree->topLevelItemCount(); i++)
1277     {
1278       if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1279         return i;
1280     }
1281   return -1;
1282 }
1283 //------------------------------------------------------------------------------
1284
1285 //------------------------------------------------------------------------------
1286 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clicked_item, int column) {
1287   int index = GetSlicerIndexFromItem(clicked_item);
1288   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1289     return;
1290   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
1291     {
1292       QTreeWidgetItem* current_row=DataTree->topLevelItem(i);
1293       if (DataTree->topLevelItem(index) == current_row)
1294         {
1295           vvSlicer* clicked_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1296           if (current_row == clicked_item)
1297             {
1298               //If we just activated a slicer
1299               if (current_row->data(column,Qt::CheckStateRole).toInt() > 0)
1300                 {
1301                   mSlicerManagers[i]->UpdateSlicer(column-1,clicked_item->data(column,Qt::CheckStateRole).toInt());
1302                   mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1303                   DisplaySliders(i,column-1);
1304                   std::map<std::string,int> overlay_counts;
1305                   for (int child = 0; child < current_row->childCount(); child++)
1306                     {
1307                       std::string overlay_type =
1308                         current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1309                       overlay_counts[overlay_type]++;
1310                       current_row->child(child)->setData(column,Qt::CheckStateRole,
1311                                                          current_row->data(column,Qt::CheckStateRole));
1312                       clicked_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,true);
1313                     }
1314                 }
1315               else //We don't allow simply desactivating a slicer
1316                 {
1317                   clicked_item->setData(column,Qt::CheckStateRole,2);
1318                   return;
1319                 }
1320             }
1321           //if we clicked on the vector(or overlay) and not the image
1322           else
1323             {
1324               if (clicked_item->data(column,Qt::CheckStateRole).toInt())
1325                 {
1326                   current_row->setData(column,Qt::CheckStateRole,2);
1327                   mSlicerManagers[i]->UpdateSlicer(column-1,2);
1328                   mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1329                   DisplaySliders(i,column-1);
1330                 }
1331               int vis = clicked_item->data(column,Qt::CheckStateRole).toInt();
1332               std::string overlay_type = clicked_item->data(1,Qt::UserRole).toString().toStdString();
1333               int overlay_index=0;
1334               for (int child = 0; child < current_row->childCount(); child++)
1335                 {
1336                   if (current_row->child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1337                     overlay_index++;
1338                   if (current_row->child(child) == clicked_item) break;
1339                 }
1340               clicked_slicer->SetActorVisibility(
1341                                                  clicked_item->data(1,Qt::UserRole).toString().toStdString(), overlay_index-1,vis);
1342             }
1343         }
1344       else if (current_row->data(column,Qt::CheckStateRole).toInt() > 0)
1345         {
1346           current_row->setData(column,Qt::CheckStateRole,0);
1347           mSlicerManagers[i]->UpdateSlicer(column-1,0);
1348           std::map<std::string,int> overlay_counts;
1349           for (int child = 0; child < current_row->childCount(); child++)
1350             {
1351               std::string overlay_type =
1352                 current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1353               overlay_counts[overlay_type]++;
1354               current_row->child(child)->setData(column,Qt::CheckStateRole,0);
1355               vvSlicer * current_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1356               current_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,false);
1357             }
1358         }
1359       //mSlicerManagers[i]->SetColorMap(-1);
1360       mSlicerManagers[i]->SetColorMap();
1361     }
1362   mSlicerManagers[index]->GetSlicer(column-1)->Render();
1363 }
1364 //------------------------------------------------------------------------------
1365
1366 void vvMainWindow::InitSlicers()
1367 {
1368   if (mSlicerManagers.size())
1369     {
1370       mSlicerManagers.back()->GenerateDefaultLookupTable();
1371
1372       mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1373       mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1374       mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1375       mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1376     }
1377 }
1378
1379 //------------------------------------------------------------------------------
1380 void vvMainWindow::InitDisplay() {
1381   if (mSlicerManagers.size())
1382     {
1383       //BE CAREFUL : this is absolutely necessary to set the interactor style
1384       //in order to have the same style instanciation for all SlicerManagers in
1385       // a same window
1386       for (int j = 0; j < 4; j++)
1387         {
1388           vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1389           style->SetAutoAdjustCameraClippingRange(1);
1390           bool AlreadySelected = false;
1391           for (int i = 0; i < DataTree->topLevelItemCount(); i++)
1392             {
1393               mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1394
1395               //select the image only if previous are not selected
1396               if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1)
1397                 {
1398                   mSlicerManagers[i]->UpdateSlicer(j,1);
1399                   AlreadySelected = true;
1400                 }
1401               else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected)
1402                 {
1403                   if (DataTree->selectedItems().size() == 0)
1404                     DataTree->topLevelItem(i)->setSelected(1);
1405                   DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1406                   mSlicerManagers[i]->UpdateSlicer(j,1);
1407                   DisplaySliders(i,j);
1408                 }
1409               else
1410                 {
1411                   DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1412                   mSlicerManagers[i]->UpdateSlicer(j,0);
1413                 }
1414             }
1415           style->Delete();
1416         }
1417     }
1418 }
1419 //------------------------------------------------------------------------------
1420
1421 //------------------------------------------------------------------------------
1422 void vvMainWindow::DisplaySliders(int slicer, int window) {
1423   int range[2];
1424   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1425   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1426
1427   int tRange[2];
1428   tRange[0] = 0;
1429   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1430   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1431   bool showHorizontal = false;
1432   bool showVertical = false;
1433   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1434       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1435           && mSlicerManagers[slicer]->GetType() != IMAGEWITHTIME
1436           && mSlicerManagers[slicer]->GetType() != MERGEDWITHTIME))
1437     showVertical = true;
1438   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1439       || mSlicerManagers[slicer]->GetType() == IMAGEWITHTIME
1440       || mSlicerManagers[slicer]->GetType() == MERGEDWITHTIME)
1441     showHorizontal = true;
1442
1443   if (showVertical)
1444     verticalSliders[window]->show();
1445   else
1446     verticalSliders[window]->hide();
1447   verticalSliders[window]->setRange(range[0],range[1]);
1448   verticalSliders[window]->setValue(position);
1449
1450   if (showHorizontal)
1451     horizontalSliders[window]->show();
1452   else
1453     horizontalSliders[window]->hide();
1454   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1455   horizontalSliders[window]->setValue(tPosition);
1456 }
1457 //------------------------------------------------------------------------------
1458
1459 //------------------------------------------------------------------------------
1460 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column) {
1461   int index = GetSlicerIndexFromItem(item);
1462
1463   if (DataTree->topLevelItem(index) != item)
1464     {
1465       QString warning = "Do you really want to close the overlay : ";
1466       warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1467       QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1468                          warning, 0, this);
1469       msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1470       msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1471       if (msgBox.exec() == QMessageBox::AcceptRole)
1472         {
1473           std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1474           int overlay_index=0;
1475           for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1476             {
1477               if (DataTree->topLevelItem(index)->\
1478                   child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1479                 overlay_index++;
1480               if (DataTree->topLevelItem(index)->child(child) == item) break;
1481             }
1482           mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1483           mSlicerManagers[index]->SetColorMap(0);
1484           DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1485           mSlicerManagers[index]->Render();
1486         }
1487     }
1488   else if (DataTree->topLevelItemCount() <= 1)
1489     {
1490       QString warning = "Do you really want to close the image : ";
1491       warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1492       warning += "\nThis is the last image, you're about to close vv !!!";
1493       QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1494                          warning, 0, this);
1495       msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1496       msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1497       if (msgBox.exec() == QMessageBox::AcceptRole)
1498         {
1499           this->close();
1500         }
1501     }
1502   else
1503     {
1504       QString warning = "Do you really want to close the image : ";
1505       warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1506       QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1507                          warning, 0, this);
1508       msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1509       msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1510       if (msgBox.exec() == QMessageBox::AcceptRole)
1511         {
1512
1513           // Tell tools that we close an image
1514           emit AnImageIsBeingClosed(mSlicerManagers[index]);
1515
1516           std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1517           DataTree->takeTopLevelItem(index);
1518           for (int i = 0; i < index; i++)
1519             {
1520               Manageriter++;
1521             }
1522           linkPanel->removeImage(index);
1523           mSlicerManagers[index]->RemoveActors();
1524           delete mSlicerManagers[index];
1525           mSlicerManagers.erase(Manageriter);
1526
1527           //
1528           InitDisplay();
1529         }
1530     }
1531 }
1532 //------------------------------------------------------------------------------
1533
1534 //------------------------------------------------------------------------------
1535 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column) {
1536   // int index = GetSlicerIndexFromItem(item);
1537   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1538   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1539   //     mSlicerManagers[index]->ReloadVF();
1540   //   else
1541   //     mSlicerManagers[index]->Reload();
1542
1543   //   QApplication::restoreOverrideCursor();
1544   int index = GetSlicerIndexFromItem(item);
1545   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1546   QString role=item->data(1,Qt::UserRole).toString();
1547   if ( role == "vector")
1548     mSlicerManagers[index]->ReloadVF();
1549   else if (role == "overlay")
1550     mSlicerManagers[index]->ReloadOverlay();
1551   else if (role == "fusion")
1552     mSlicerManagers[index]->ReloadFusion();
1553   else
1554     mSlicerManagers[index]->Reload();
1555   QApplication::restoreOverrideCursor();
1556 }
1557 //------------------------------------------------------------------------------
1558
1559 // void vvMainWindow::CropImage()
1560 // {
1561 //   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1562 //   vvCropDialog crop(mSlicerManagers,index);
1563 //   if(crop.exec())
1564 //     AddImage(crop.GetOutput(),"cropped.mhd");
1565 // }
1566
1567 //------------------------------------------------------------------------------
1568 void vvMainWindow::SplitImage() {
1569   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1570   int dim = mSlicerManagers[index]->GetDimension();
1571   QString warning = "Do you really want to split the ";
1572   warning += QString::number(dim) + "D image ";
1573   warning += DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString() + " into ";
1574   warning += QString::number(mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetSize()[dim-1]) + " ";
1575   warning += QString::number(dim-1) + "D images.";
1576   QMessageBox msgBox(QMessageBox::Warning, tr("Split Image"),
1577                      warning, 0, this);
1578   msgBox.addButton(tr("Split"), QMessageBox::AcceptRole);
1579   msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1580   if (msgBox.exec() == QMessageBox::AcceptRole)
1581     {
1582       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1583       if (dim > 2)
1584         {
1585           std::string filename = DataTree->selectedItems()[0]->data(0,Qt::UserRole).toString().toStdString();
1586           int numberOfSlice = mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetSize()[dim-1];
1587           std::string path = itksys::SystemTools::GetFilenamePath(
1588                                                                   filename);
1589           path += "/";
1590           path += DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString().toStdString();
1591           path += "%03d";
1592           path += itksys::SystemTools::GetFilenameLastExtension(
1593                                                                 filename).c_str();
1594
1595           typedef itk::NumericSeriesFileNames NameGeneratorType;
1596           NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
1597           nameGenerator->SetSeriesFormat(path.c_str());
1598           nameGenerator->SetStartIndex(0);
1599           nameGenerator->SetEndIndex(numberOfSlice-1);
1600           nameGenerator->SetIncrementIndex(1);
1601
1602           for (int i = 0; i < numberOfSlice; i++)
1603             {
1604               vvSlicerManager* imageManager = new vvSlicerManager(4);
1605               imageManager->SetExtractedImage(nameGenerator->GetFileNames()[i],
1606                                               mSlicerManagers[index]->GetSlicer(0)->GetImage(), i);
1607               mSlicerManagers.push_back(imageManager);
1608
1609               //create an item in the tree with good settings
1610               QTreeWidgetItem *item = new QTreeWidgetItem();
1611               item->setData(0,Qt::UserRole,nameGenerator->GetFileNames()[i].c_str());
1612               std::string fileI = itksys::SystemTools::GetFilenameWithoutLastExtension(
1613                                                                                        nameGenerator->GetFileNames()[i]).c_str();
1614               item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileI.c_str());
1615               for (int j = 1; j <= 4; j++)
1616                 {
1617                   for (int i = 0; i < DataTree->topLevelItemCount(); i++)
1618                     {
1619                       DataTree->topLevelItem(i)->setData(j,Qt::CheckStateRole,0);
1620                     }
1621                   item->setData(j,Qt::CheckStateRole,2);
1622                 }
1623
1624               //Create the buttons for reload and close
1625               QTreePushButton* cButton = new QTreePushButton;
1626               cButton->setItem(item);
1627               cButton->setColumn(COLUMN_CLOSE_IMAGE);
1628               cButton->setToolTip(tr("close image"));
1629               cButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")));
1630               connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1631                       this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1632
1633               QTreePushButton* rButton = new QTreePushButton;
1634               rButton->setItem(item);
1635               rButton->setColumn(COLUMN_RELOAD_IMAGE);
1636               rButton->setToolTip(tr("reload image"));
1637               rButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")));
1638               rButton->setEnabled(false);
1639               connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1640                       this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1641
1642               DataTree->addTopLevelItem(item);
1643               DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1644               DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1645
1646               //set the id of the image
1647               QString id = nameGenerator->GetFileNames()[i].c_str() + QString::number(mSlicerManagers.size()-1);
1648               item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1649               mSlicerManagers.back()->SetId(id.toStdString());
1650               linkPanel->addImage(fileI, id.toStdString());
1651               connect(mSlicerManagers.back(),SIGNAL(currentImageChanged(std::string)),
1652                       this,SLOT(CurrentImageChanged(std::string)));
1653               connect(mSlicerManagers.back(),SIGNAL(
1654                                                     UpdatePosition(int, double, double, double, double, double, double, double)),this,
1655                       SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
1656               connect(mSlicerManagers.back(),SIGNAL(UpdateVector(int, double, double, double, double)),
1657                       this, SLOT(VectorChanged(int,double,double,double, double)));
1658               connect(mSlicerManagers.back(),SIGNAL(UpdateOverlay(int, double, double)),
1659                       this, SLOT(OverlayChanged(int,double,double)));
1660               connect(mSlicerManagers.back(),SIGNAL(UpdateFusion(int, double)),
1661                       this, SLOT(FusionChanged(int,double)));
1662               connect(mSlicerManagers.back(),SIGNAL(UpdateWindows(int, int, int)),
1663                       this,SLOT(WindowsChanged(int, int, int)));
1664               connect(mSlicerManagers.back(),SIGNAL(WindowLevelChanged(double, double,int, int)),
1665                       this,SLOT(WindowLevelChanged(double, double, int, int)));
1666               connect(mSlicerManagers.back(),SIGNAL(UpdateSlice(int,int)),
1667                       this,SLOT(UpdateSlice(int,int)));
1668               connect(mSlicerManagers.back(),SIGNAL(UpdateTSlice(int, int)),
1669                       this,SLOT(UpdateTSlice(int, int)));
1670               connect(mSlicerManagers.back(),SIGNAL(UpdateSliceRange(int,int,int,int,int)),
1671                       this,SLOT(UpdateSliceRange(int,int,int,int,int)));
1672               connect(mSlicerManagers.back(),SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
1673                       this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
1674               connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
1675               UpdateTree();
1676               qApp->processEvents();
1677               InitSlicers();
1678               InitDisplay();
1679               qApp->processEvents();
1680             }
1681           QApplication::restoreOverrideCursor();
1682         }
1683       else
1684         {
1685           QApplication::restoreOverrideCursor();
1686           QString error = "Cannot split file (dimensions must be greater than 2) ";
1687           QMessageBox::information(this,tr("Splitting problem"),error);
1688         }
1689     }
1690 }
1691 //------------------------------------------------------------------------------
1692
1693 //------------------------------------------------------------------------------
1694 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value) {
1695   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1696 }
1697 //------------------------------------------------------------------------------
1698
1699 //------------------------------------------------------------------------------
1700 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value) {
1701   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1702 }
1703 //------------------------------------------------------------------------------
1704
1705 //------------------------------------------------------------------------------
1706 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef) {
1707   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1708 }
1709 //------------------------------------------------------------------------------
1710
1711 //------------------------------------------------------------------------------
1712 void vvMainWindow::FusionChanged(int visibility, double value) {
1713   overlayPanel->getCurrentFusionInfo(visibility,value);
1714 }
1715 //------------------------------------------------------------------------------
1716
1717 //------------------------------------------------------------------------------
1718 void vvMainWindow::WindowsChanged(int window, int view, int slice) {
1719   infoPanel->setViews(window, view, slice);
1720 }
1721 //------------------------------------------------------------------------------
1722
1723 //------------------------------------------------------------------------------
1724 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap) {
1725   windowSpinBox->setValue(window);
1726   levelSpinBox->setValue(level);
1727   colorMapComboBox->setCurrentIndex(colormap);
1728   presetComboBox->setCurrentIndex(preset);
1729 }
1730 //------------------------------------------------------------------------------
1731
1732 //------------------------------------------------------------------------------
1733 void vvMainWindow::WindowLevelEdited() {
1734   presetComboBox->setCurrentIndex(6);
1735   UpdateWindowLevel();
1736 }
1737 //------------------------------------------------------------------------------
1738
1739 //------------------------------------------------------------------------------
1740 void vvMainWindow::UpdateWindowLevel() {
1741   if (DataTree->selectedItems().size())
1742     {
1743       if (presetComboBox->currentIndex() == 7) //For ventilation
1744         colorMapComboBox->setCurrentIndex(5);
1745       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1746       mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1747       mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1748       mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1749       mSlicerManagers[index]->Render();
1750     }
1751 }
1752 //------------------------------------------------------------------------------
1753
1754 //------------------------------------------------------------------------------
1755 void vvMainWindow::UpdateColorMap() {
1756   if (DataTree->selectedItems().size())
1757     {
1758       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1759       mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1760       mSlicerManagers[index]->Render();
1761     }
1762 }
1763 //------------------------------------------------------------------------------
1764 void vvMainWindow::SwitchWindowLevel() {
1765   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1766   int window = mSlicerManagers[index]->GetColorWindow();
1767   presetComboBox->setCurrentIndex(6);
1768   windowSpinBox->setValue(-window);
1769   UpdateWindowLevel();
1770 }
1771 //------------------------------------------------------------------------------
1772
1773 //------------------------------------------------------------------------------
1774 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps) {
1775   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
1776     {
1777       if (mSlicerManagers[i]->GetId() == id)
1778         {
1779           //mSlicerManagers[i]->SetTSlice(temps);
1780           mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1781           mSlicerManagers[i]->UpdateViews(0,slicer);
1782           break;
1783         }
1784     }
1785 }
1786 //------------------------------------------------------------------------------
1787
1788 //------------------------------------------------------------------------------
1789 void vvMainWindow::ShowContextMenu(QPoint point) {
1790   if (!DataTree->selectedItems().size())
1791     {
1792       contextActions[1]->setEnabled(0);
1793       contextActions[2]->setEnabled(0);
1794       contextActions[3]->setEnabled(0);
1795       contextActions[4]->setEnabled(0);
1796       contextActions[5]->setEnabled(0);
1797       contextActions[6]->setEnabled(0);
1798       contextActions[7]->setEnabled(0);
1799     }
1800   else
1801     {
1802       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1803       contextActions[1]->setEnabled(1);
1804       contextActions[2]->setEnabled(
1805                                     DataTree->itemWidget(DataTree->selectedItems()[0],
1806                                                          COLUMN_RELOAD_IMAGE)->isEnabled());
1807       contextActions[3]->setEnabled(1);
1808       contextActions[5]->setEnabled(1);
1809       contextActions[6]->setEnabled(1);
1810       contextActions[7]->setEnabled(1);
1811
1812       if (mSlicerManagers[index]->GetDimension() < 3)
1813         contextActions[4]->setEnabled(0);
1814       else
1815         contextActions[4]->setEnabled(1);
1816     }
1817   contextMenu.exec(QCursor::pos());
1818 }
1819 //------------------------------------------------------------------------------
1820
1821 //------------------------------------------------------------------------------
1822 void vvMainWindow::CloseImage() {
1823   CloseImage(DataTree->selectedItems()[0],0);
1824 }
1825 //------------------------------------------------------------------------------
1826
1827 //------------------------------------------------------------------------------
1828 void vvMainWindow::ReloadImage() {
1829   ReloadImage(DataTree->selectedItems()[0],0);
1830 }
1831 //------------------------------------------------------------------------------
1832
1833 //------------------------------------------------------------------------------
1834 void vvMainWindow::SelectOverlayImage() {
1835   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1836
1837   //check if one overlay image is added
1838   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1839     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay")
1840       {
1841         QString error = "Cannot add more than one compared image\n";
1842         error += "Please remove first ";
1843         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1844         QMessageBox::information(this,tr("Problem adding compared image !"),error);
1845         return;
1846       }
1847
1848   QString Extensions = EXTENSIONS;
1849   Extensions += ";;All Files (*)";
1850   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1851   if (!file.isEmpty())
1852     AddOverlayImage(index,file);
1853 }
1854 //------------------------------------------------------------------------------
1855
1856 //------------------------------------------------------------------------------
1857 void vvMainWindow::AddOverlayImage(int index, QString file) {
1858   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1859   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1860                                                                         file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1861   reader->SetFileName(file.toStdString().c_str());
1862   reader->ReadImageInformation();
1863   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1864   int dimension = reader->GetNumberOfDimensions();
1865   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1866   vvProgressDialog progress("Opening " + file.toStdString());
1867   qApp->processEvents();
1868
1869   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1870   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component))
1871     {
1872       //create an item in the tree with good settings
1873       QTreeWidgetItem *item = new QTreeWidgetItem();
1874       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1875       item->setData(1,Qt::UserRole,tr("overlay"));
1876       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
1877       qApp->processEvents();
1878
1879       for (int j = 1; j <= 4; j++)
1880         {
1881           item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1882           mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("overlay",0,
1883                                                                      DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1884         }
1885
1886       //Create the buttons for reload and close
1887       qApp->processEvents();
1888       QTreePushButton* cButton = new QTreePushButton;
1889       cButton->setItem(item);
1890       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1891       cButton->setToolTip(tr("close image"));
1892       cButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")));
1893       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1894               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1895
1896       QTreePushButton* rButton = new QTreePushButton;
1897       rButton->setItem(item);
1898       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1899       rButton->setToolTip(tr("reload image"));
1900       rButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")));
1901       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1902               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1903
1904       DataTree->topLevelItem(index)->setExpanded(1);
1905       DataTree->topLevelItem(index)->addChild(item);
1906       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1907       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1908
1909       //set the id of the image
1910       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1911       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1912       UpdateTree();
1913       qApp->processEvents();
1914       ImageInfoChanged();
1915       QApplication::restoreOverrideCursor();
1916     }
1917   else
1918     {
1919       QApplication::restoreOverrideCursor();
1920       QString error = "Cannot import the new image.\n";
1921       error += mSlicerManagers[index]->GetLastError().c_str();
1922       QMessageBox::information(this,tr("Problem reading image !"),error);
1923     }
1924 }
1925
1926 void vvMainWindow::AddFusionImage()
1927 {
1928   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1929
1930   //check if one fusion image is added
1931   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1932     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion")
1933       {
1934         QString error = "Cannot add more than one fusion image\n";
1935         error += "Please remove first ";
1936         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1937         QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1938         return;
1939       }
1940
1941   QString Extensions = EXTENSIONS;
1942   Extensions += ";;All Files (*)";
1943   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1944   if (!file.isEmpty())
1945     {
1946       mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1947       itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1948                                                                             file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1949       reader->SetFileName(file.toStdString().c_str());
1950       reader->ReadImageInformation();
1951       std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1952       if (reader)
1953         {
1954           QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1955           vvProgressDialog progress("Opening fusion");
1956           qApp->processEvents();
1957
1958           std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1959           if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1960                                                 reader->GetNumberOfDimensions(), component))
1961             {
1962               //create an item in the tree with good settings
1963               QTreeWidgetItem *item = new QTreeWidgetItem();
1964               item->setData(0,Qt::UserRole,file.toStdString().c_str());
1965               item->setData(1,Qt::UserRole,tr("fusion"));
1966               item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
1967               qApp->processEvents();
1968
1969               for (int j = 1; j <= 4; j++)
1970                 {
1971                   item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1972                   mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("fusion",0,
1973                                                                              DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1974                 }
1975
1976               //Create the buttons for reload and close
1977               qApp->processEvents();
1978               QTreePushButton* cButton = new QTreePushButton;
1979               cButton->setItem(item);
1980               cButton->setColumn(COLUMN_CLOSE_IMAGE);
1981               cButton->setToolTip(tr("close image"));
1982               cButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")));
1983               connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1984                       this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1985
1986               QTreePushButton* rButton = new QTreePushButton;
1987               rButton->setItem(item);
1988               rButton->setColumn(COLUMN_RELOAD_IMAGE);
1989               rButton->setToolTip(tr("reload image"));
1990               rButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")));
1991               connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1992                       this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1993
1994               DataTree->topLevelItem(index)->setExpanded(1);
1995               DataTree->topLevelItem(index)->addChild(item);
1996               DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1997               DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1998
1999               //set the id of the image
2000               QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2001               item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2002               UpdateTree();
2003               qApp->processEvents();
2004               ImageInfoChanged();
2005               QApplication::restoreOverrideCursor();
2006             }
2007           else
2008             {
2009               QApplication::restoreOverrideCursor();
2010               QString error = "Cannot import the new image.\n";
2011               error += mSlicerManagers[index]->GetLastError().c_str();
2012               QMessageBox::information(this,tr("Problem reading image !"),error);
2013             }
2014         }
2015       else
2016         {
2017           QString error = "Cannot import the new image.\n";
2018           QMessageBox::information(this,tr("Problem reading image !"),error);
2019         }
2020     }
2021 }
2022
2023
2024 void vvMainWindow::OpenField()
2025 {
2026   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2027   //check if a vector field has already been added
2028   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2029     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector")
2030       {
2031         QString error = "Cannot add more than one vector field\n";
2032         error += "Please remove first ";
2033         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2034         QMessageBox::information(this,tr("Problem adding vector field!"),error);
2035         return;
2036       }
2037
2038   QString Extensions = "Images ( *.mhd)";
2039   Extensions += ";;Images ( *.vf)";
2040   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2041   if (!file.isEmpty())
2042     AddField(file,index);
2043 }
2044
2045 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2046 {
2047   //create an item in the tree with good settings
2048   QTreeWidgetItem *item = new QTreeWidgetItem();
2049   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2050   item->setData(1,Qt::UserRole,tr("vector"));
2051   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename);
2052   qApp->processEvents();
2053
2054   for (int j = 1; j <= 4; j++)
2055     {
2056       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2057       mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("vector",0,
2058                                                                  DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
2059     }
2060
2061   //Create the buttons for reload and close
2062   qApp->processEvents();
2063   QTreePushButton* cButton = new QTreePushButton;
2064   cButton->setItem(item);
2065   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2066   cButton->setToolTip(tr("close vector field"));
2067   cButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")));
2068   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2069           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2070
2071   QTreePushButton* rButton = new QTreePushButton;
2072   rButton->setItem(item);
2073   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2074   rButton->setToolTip(tr("reload vector field"));
2075   rButton->setEnabled(from_disk);
2076   rButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")));
2077   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2078           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2079
2080   DataTree->topLevelItem(index)->setExpanded(1);
2081   DataTree->topLevelItem(index)->addChild(item);
2082   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2083   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2084
2085   //set the id of the image
2086   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2087   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2088   UpdateTree();
2089   qApp->processEvents();
2090   ImageInfoChanged();
2091   QApplication::restoreOverrideCursor();
2092 }
2093
2094 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2095 {
2096   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2097   vvSlicerManager* imageManager = mSlicerManagers[index];
2098   if (imageManager->SetVF(vf,file.toStdString()))
2099     {
2100       AddFieldEntry(file,index,false);
2101     }
2102   else
2103     {
2104       QString error = "Cannot import the vector field for this image.\n";
2105       error += imageManager->GetLastError().c_str();
2106       QMessageBox::information(this,tr("Problem reading VF !"),error);
2107     }
2108   QApplication::restoreOverrideCursor();
2109 }
2110
2111 void vvMainWindow::AddField(QString file,int index)
2112 {
2113   if (QFile::exists(file))
2114     {
2115       mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2116
2117       //init the progress events
2118       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2119       vvProgressDialog progress("Opening " + file.toStdString());
2120       qApp->processEvents();
2121
2122       //read the vector and put it in the current mSlicerManager
2123       vvSlicerManager* imageManager = mSlicerManagers[index];
2124       qApp->processEvents();
2125
2126       std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2127       if (imageManager->SetVF(file.toStdString()))
2128         {
2129           imageManager->Render();
2130           AddFieldEntry(file,index,true);
2131         }
2132       else
2133         {
2134           QApplication::restoreOverrideCursor();
2135           QString error = "Cannot import the vector field for this image.\n";
2136           error += imageManager->GetLastError().c_str();
2137           QMessageBox::information(this,tr("Problem reading VF !"),error);
2138         }
2139     }
2140   else
2141     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2142
2143 }
2144 //------------------------------------------------------------------------------
2145
2146 //------------------------------------------------------------------------------
2147 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log) {
2148   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2149   if (mSlicerManagers[index]->GetSlicer(0)->GetVF())
2150     {
2151       for (int i = 0; i < 4; i++)
2152         {
2153           mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2154           mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2155           if (log > 0)
2156             mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2157           else
2158             mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2159         }
2160     }
2161 }
2162 //------------------------------------------------------------------------------
2163
2164 //------------------------------------------------------------------------------
2165 void vvMainWindow::SetOverlayProperty(int color) {
2166   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2167   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
2168     {
2169       mSlicerManagers[index]->SetOverlayColor(color);
2170       mSlicerManagers[index]->SetColorMap(0);
2171       mSlicerManagers[index]->Render();
2172     }
2173 }
2174 //------------------------------------------------------------------------------
2175
2176 //------------------------------------------------------------------------------
2177 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level) {
2178   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2179   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion())
2180     {
2181       mSlicerManagers[index]->SetFusionOpacity(opacity);
2182       mSlicerManagers[index]->SetFusionColorMap(colormap);
2183       mSlicerManagers[index]->SetFusionWindow(window);
2184       mSlicerManagers[index]->SetFusionLevel(level);
2185       mSlicerManagers[index]->SetColorMap(0);
2186       mSlicerManagers[index]->Render();
2187     }
2188 }
2189 //------------------------------------------------------------------------------
2190
2191 //------------------------------------------------------------------------------
2192 void vvMainWindow::SaveAs() {
2193   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector")
2194     {
2195       QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2196       return;
2197     }
2198
2199   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2200   int dimension = mSlicerManagers[index]->GetDimension();
2201   QStringList OutputListeFormat;
2202   OutputListeFormat.clear();
2203   if (dimension == 1)
2204     {
2205       OutputListeFormat.push_back(".mhd");
2206     }
2207   if (dimension == 2)
2208     {
2209       OutputListeFormat.push_back(".bmp");
2210       OutputListeFormat.push_back(".png");
2211       OutputListeFormat.push_back(".jpeg");
2212       OutputListeFormat.push_back(".tif");
2213       OutputListeFormat.push_back(".mhd");
2214       OutputListeFormat.push_back(".hdr");
2215       OutputListeFormat.push_back(".vox");
2216     }
2217   else if (dimension == 3)
2218     {
2219       OutputListeFormat.push_back(".mhd");
2220       OutputListeFormat.push_back(".hdr");
2221       OutputListeFormat.push_back(".vox");
2222     }
2223   else if (dimension == 4)
2224     {
2225       OutputListeFormat.push_back(".mhd");
2226     }
2227   QString Extensions = "AllFiles(*.*)";
2228   for (int i = 0; i < OutputListeFormat.count(); i++)
2229     {
2230       Extensions += ";;Images ( *";
2231       Extensions += OutputListeFormat[i];
2232       Extensions += ")";
2233     }
2234   QString fileName = QFileDialog::getSaveFileName(this,
2235                                                   tr("Save As"),
2236                                                   mSlicerManagers[index]->GetFileName().c_str(),
2237                                                   Extensions);
2238   if (!fileName.isEmpty())
2239     {
2240       std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2241       if (OutputListeFormat.contains(
2242                                      fileformat.c_str()))
2243         {
2244           QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2245           std::string action = "Saving";
2246           vvProgressDialog progress("Saving "+fileName.toStdString());
2247           qApp->processEvents();
2248           vvImageWriter *writer = new vvImageWriter;
2249           writer->SetOutputFileName(fileName.toStdString());
2250           writer->SetInput(mSlicerManagers[index]->GetImage());
2251           writer->Update();
2252           QApplication::restoreOverrideCursor();
2253           if (writer->GetLastError().size())
2254             {
2255               QString error = "Saving did not succeed\n";
2256               error += writer->GetLastError().c_str();
2257               QMessageBox::information(this,tr("Saving Problem"),error);
2258               SaveAs();
2259             }
2260         }
2261       else
2262         {
2263           QString error = fileformat.c_str();
2264           if (error.isEmpty())
2265             error += "no file format specified !";
2266           else
2267             error += " format unknown !!!\n";
2268           QMessageBox::information(this,tr("Saving Problem"),error);
2269           SaveAs();
2270         }
2271     }
2272 }
2273 //------------------------------------------------------------------------------
2274
2275 //------------------------------------------------------------------------------
2276 void vvMainWindow::AddLink(QString image1,QString image2) {
2277   for (unsigned int i = 0; i < mSlicerManagers.size();i++)
2278     {
2279       if (image1.toStdString() == mSlicerManagers[i]->GetId())
2280         {
2281           mSlicerManagers[i]->AddLink(image2.toStdString());
2282         }
2283       if (image2.toStdString() == mSlicerManagers[i]->GetId())
2284         {
2285           mSlicerManagers[i]->AddLink(image1.toStdString());
2286         }
2287     }
2288 }
2289 //------------------------------------------------------------------------------
2290
2291 //------------------------------------------------------------------------------
2292 void vvMainWindow::RemoveLink(QString image1,QString image2) {
2293   for (unsigned int i = 0; i < mSlicerManagers.size();i++)
2294     {
2295       if (image1.toStdString() == mSlicerManagers[i]->GetId())
2296         {
2297           mSlicerManagers[i]->RemoveLink(image2.toStdString());
2298         }
2299       if (image2.toStdString() == mSlicerManagers[i]->GetId())
2300         {
2301           mSlicerManagers[i]->RemoveLink(image1.toStdString());
2302         }
2303     }
2304 }
2305 //------------------------------------------------------------------------------
2306
2307 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2308 {
2309   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2310     {
2311       if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1)
2312         {
2313           for (int j = 0; j < 4; j++)
2314             {
2315               mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2316               //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2317               //UpdateTSlice(j,value);
2318             }
2319           mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2320           break;
2321         }
2322     }
2323 }
2324
2325 //------------------------------------------------------------------------------
2326 void vvMainWindow::NOHorizontalSliderMoved() {
2327   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2328 }
2329 //------------------------------------------------------------------------------
2330
2331 //------------------------------------------------------------------------------
2332 void vvMainWindow::NEHorizontalSliderMoved() {
2333   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2334 }
2335 //------------------------------------------------------------------------------
2336
2337 //------------------------------------------------------------------------------
2338 void vvMainWindow::SOHorizontalSliderMoved() {
2339   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2340 }
2341 //------------------------------------------------------------------------------
2342
2343 //------------------------------------------------------------------------------
2344 void vvMainWindow::SEHorizontalSliderMoved() {
2345   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2346 }
2347 //------------------------------------------------------------------------------
2348
2349 //------------------------------------------------------------------------------
2350 void vvMainWindow::NOVerticalSliderChanged() {
2351   int value = NOVerticalSlider->value();
2352   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2353     {
2354       if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
2355         {
2356           mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2357           mSlicerManagers[i]->UpdateSlice(0); // <-- DS add this. Not too much update ?
2358           break;
2359         }
2360     }
2361 }
2362 //------------------------------------------------------------------------------
2363
2364 //------------------------------------------------------------------------------
2365 void vvMainWindow::NEVerticalSliderChanged() {
2366   int value = NEVerticalSlider->value();
2367   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2368     {
2369       if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1)
2370         {
2371           mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2372           break;
2373         }
2374     }
2375 }
2376 //------------------------------------------------------------------------------
2377
2378 //------------------------------------------------------------------------------
2379 void vvMainWindow::SOVerticalSliderChanged() {
2380   int value = SOVerticalSlider->value();
2381   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2382     {
2383       if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
2384         {
2385           mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2386           break;
2387         }
2388     }
2389 }
2390 //------------------------------------------------------------------------------
2391
2392 //------------------------------------------------------------------------------
2393 void vvMainWindow::SEVerticalSliderChanged() {
2394   int value = SEVerticalSlider->value();
2395   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2396     {
2397       if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1)
2398         {
2399           mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2400           break;
2401         }
2402     }
2403 }
2404 //------------------------------------------------------------------------------
2405
2406 //------------------------------------------------------------------------------
2407 void vvMainWindow::UpdateSlice(int slicer, int slice) {
2408   if (slicer == 0) {
2409     if (slice != NOVerticalSlider->value())
2410       NOVerticalSlider->setValue(slice);
2411   }
2412   else if (slicer == 1)
2413     NEVerticalSlider->setValue(slice);
2414   else if (slicer == 2)
2415     SOVerticalSlider->setValue(slice);
2416   else if (slicer == 3)
2417     SEVerticalSlider->setValue(slice);
2418 }
2419 //------------------------------------------------------------------------------
2420
2421 //------------------------------------------------------------------------------
2422 void vvMainWindow::UpdateTSlice(int slicer, int slice) {
2423   switch (slicer)
2424     {
2425     case 0:
2426       NOHorizontalSlider->setValue(slice);
2427       break;
2428     case 1:
2429       NEHorizontalSlider->setValue(slice);
2430       break;
2431     case 2:
2432       SOHorizontalSlider->setValue(slice);
2433       break;
2434     case 3:
2435       SEHorizontalSlider->setValue(slice);
2436       break;
2437     }
2438 }
2439 //------------------------------------------------------------------------------
2440
2441 //------------------------------------------------------------------------------
2442 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax) {
2443   int position = int((min+max)/2);
2444   int tPosition = int((tmin+tmax)/2);
2445   if (slicer == 0)
2446     {
2447       NOVerticalSlider->setValue(position);
2448       NOVerticalSlider->setRange(min,max);
2449       NOHorizontalSlider->setRange(tmin,tmax);
2450       NOHorizontalSlider->setValue(tPosition);
2451     }
2452   else if (slicer == 1)
2453     {
2454       NEVerticalSlider->setValue(position);
2455       NEVerticalSlider->setRange(min,max);
2456       NEHorizontalSlider->setRange(tmin,tmax);
2457       NEHorizontalSlider->setValue(tPosition);
2458     }
2459   else if (slicer == 2)
2460     {
2461       SOVerticalSlider->setValue(position);
2462       SOVerticalSlider->setRange(min,max);
2463       SOHorizontalSlider->setRange(tmin,tmax);
2464       SOHorizontalSlider->setValue(tPosition);
2465     }
2466   else if (slicer == 3)
2467     {
2468       SEVerticalSlider->setValue(position);
2469       SEVerticalSlider->setRange(min,max);
2470       SEHorizontalSlider->setRange(tmin,tmax);
2471       SEHorizontalSlider->setValue(tPosition);
2472     }
2473 }
2474 //------------------------------------------------------------------------------
2475
2476 //------------------------------------------------------------------------------
2477 void vvMainWindow::SaveNOScreenshot() {
2478   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2479   w2i->SetInput(NOViewWidget->GetRenderWindow());
2480   w2i->Update();
2481   SaveScreenshot(w2i->GetOutput());
2482   w2i->Delete();
2483 }
2484 //------------------------------------------------------------------------------
2485
2486 //------------------------------------------------------------------------------
2487 void vvMainWindow::SaveNEScreenshot() {
2488   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2489   w2i->SetInput(NEViewWidget->GetRenderWindow());
2490   w2i->Update();
2491   SaveScreenshot(w2i->GetOutput());
2492   w2i->Delete();
2493 }
2494 //------------------------------------------------------------------------------
2495
2496 //------------------------------------------------------------------------------
2497 void vvMainWindow::SaveSOScreenshot() {
2498   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2499   w2i->SetInput(SOViewWidget->GetRenderWindow());
2500   w2i->Update();
2501   SaveScreenshot(w2i->GetOutput());
2502   w2i->Delete();
2503 }
2504 //------------------------------------------------------------------------------
2505
2506 //------------------------------------------------------------------------------
2507 void vvMainWindow::SaveSEScreenshot() {
2508   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2509   w2i->SetInput(SEViewWidget->GetRenderWindow());
2510   w2i->Update();
2511   SaveScreenshot(w2i->GetOutput());
2512   w2i->Delete();
2513 }
2514 //------------------------------------------------------------------------------
2515
2516 //------------------------------------------------------------------------------
2517 void vvMainWindow::SaveScreenshot(vtkImageData* image) {
2518   QString Extensions = "Images( *.png);;";
2519   Extensions += "Images( *.jpg);;";
2520   Extensions += "Images( *.bmp);;";
2521   Extensions += "Images( *.tif);;";
2522   Extensions += "Images( *.ppm)";
2523   QString fileName = QFileDialog::getSaveFileName(this,
2524                                                   tr("Save As"),
2525                                                   itksys::SystemTools::GetFilenamePath(
2526                                                                                        mSlicerManagers[0]->GetFileName()).c_str(),
2527                                                   Extensions);
2528   if (!fileName.isEmpty())
2529     {
2530       const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2531       if (!strcmp(ext, ".bmp"))
2532         {
2533           vtkBMPWriter *bmp = vtkBMPWriter::New();
2534           bmp->SetInput(image);
2535           bmp->SetFileName(fileName.toStdString().c_str());
2536           bmp->Write();
2537           bmp->Delete();
2538         }
2539       else if (!strcmp(ext, ".tif"))
2540         {
2541           vtkTIFFWriter *tif = vtkTIFFWriter::New();
2542           tif->SetInput(image);
2543           tif->SetFileName(fileName.toStdString().c_str());
2544           tif->Write();
2545           tif->Delete();
2546         }
2547       else if (!strcmp(ext, ".ppm"))
2548         {
2549           vtkPNMWriter *pnm = vtkPNMWriter::New();
2550           pnm->SetInput(image);
2551           pnm->SetFileName(fileName.toStdString().c_str());
2552           pnm->Write();
2553           pnm->Delete();
2554         }
2555       else if (!strcmp(ext, ".png"))
2556         {
2557           vtkPNGWriter *png = vtkPNGWriter::New();
2558           png->SetInput(image);
2559           png->SetFileName(fileName.toStdString().c_str());
2560           png->Write();
2561           png->Delete();
2562         }
2563       else if (!strcmp(ext, ".jpg"))
2564         {
2565           vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2566           jpg->SetInput(image);
2567           jpg->SetFileName(fileName.toStdString().c_str());
2568           jpg->Write();
2569           jpg->Delete();
2570         }
2571       else
2572         {
2573           QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2574         }
2575     }
2576
2577 }
2578 //------------------------------------------------------------------------------
2579
2580 //------------------------------------------------------------------------------
2581 void vvMainWindow::GoToCursor() {
2582   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2583   for (int column = 1; column < 5; column++)
2584     {
2585       if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1)
2586         {
2587           double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2588           mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2589                                                                           cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2590           mSlicerManagers[index]->UpdateViews(1,column-1);
2591           mSlicerManagers[index]->UpdateLinked(column-1);
2592           break;
2593         }
2594     }
2595 }
2596 //------------------------------------------------------------------------------
2597
2598 //------------------------------------------------------------------------------
2599 void vvMainWindow::PlayPause() {
2600   if (playMode)
2601     {
2602       playMode = 0;
2603       playButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/player_play.png")));
2604       ImageInfoChanged();
2605       return;
2606     }
2607   else
2608     {
2609       int image_number=DataTree->topLevelItemCount();
2610       bool has_temporal;
2611       for (int i=0;i<image_number;i++)
2612         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1)
2613           {
2614             has_temporal=true;
2615             break;
2616           }
2617       if (has_temporal)
2618         {
2619           playMode = 1;
2620           playButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/player_pause.png")));
2621           QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2622         }
2623     }
2624 }
2625 //------------------------------------------------------------------------------
2626
2627 //------------------------------------------------------------------------------
2628 void vvMainWindow::PlayNext() {
2629   if (playMode && !this->isHidden())
2630     {
2631       int image_number=DataTree->topLevelItemCount();
2632       ///Only play one slicer per SM, and only if the SM is being displayed
2633       for (int i=0;i<image_number;i++)
2634         for (int j=0;j<4;j++)
2635           if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2636               DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0)
2637             {
2638               mSlicerManagers[i]->SetNextTSlice(j);
2639               break;
2640             }
2641       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2642     }
2643 }
2644 //------------------------------------------------------------------------------
2645
2646 void vvMainWindow::ShowLastImage()
2647 {
2648   if (mSlicerManagers.size() > 1)
2649     {
2650       QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2651       CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2652       item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2653       DisplayChanged(item,1);
2654     }
2655 }
2656
2657 //------------------------------------------------------------------------------
2658 void vvMainWindow::UpdateRenderWindows() {
2659   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2660   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2661   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2662   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2663 }
2664 //------------------------------------------------------------------------------
2665
2666 //------------------------------------------------------------------------------
2667 void vvMainWindow::ResampleCurrentImage() {
2668   vvResamplerDialog resampler;
2669   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2670   resampler.SetSlicerManagers(mSlicerManagers,index);
2671   if (resampler.exec())
2672     AddImage(resampler.GetOutput(),resampler.GetOutputFileName());
2673 }
2674 //------------------------------------------------------------------------------
2675
2676 //------------------------------------------------------------------------------
2677 void vvMainWindow::SegmentationOnCurrentImage() {
2678   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2679
2680   vvSegmentationDialog segmentation;
2681   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2682   segmentation.exec();
2683 }
2684 //------------------------------------------------------------------------------
2685
2686 void vvMainWindow::SurfaceViewerLaunch()
2687 {
2688   vvSurfaceViewerDialog surfaceViewer;
2689   surfaceViewer.exec();
2690 }
2691
2692 //------------------------------------------------------------------------------
2693 void vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2694 {
2695   vvSlicerManager* m = new vvSlicerManager(4);
2696   m->SetImage(image);
2697   m->SetFilename(filename);
2698   AddImage(m);
2699 }
2700
2701 //------------------------------------------------------------------------------
2702 void vvMainWindow::AddImage(vvSlicerManager * slicer_manager) {
2703   mSlicerManagers.push_back(slicer_manager);
2704
2705   std::string filename = slicer_manager->GetFileName();
2706
2707   //create an item in the tree with good settings
2708   QTreeWidgetItem *item = new QTreeWidgetItem();
2709   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2710   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
2711   qApp->processEvents();
2712
2713   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2714
2715   //Create the buttons for reload and close
2716   qApp->processEvents();
2717   QTreePushButton* cButton = new QTreePushButton;
2718   cButton->setItem(item);
2719   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2720   cButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")));
2721   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2722           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2723
2724   QTreePushButton* rButton = new QTreePushButton;
2725   rButton->setItem(item);
2726   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2727   rButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")));
2728   rButton->setEnabled(0);
2729   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2730           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2731
2732   DataTree->addTopLevelItem(item);
2733   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2734   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2735
2736   //set the id of the image
2737   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2738   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2739   mSlicerManagers.back()->SetId(id.toStdString());
2740
2741   linkPanel->addImage(filename, id.toStdString());
2742
2743   connect(mSlicerManagers.back(),SIGNAL(currentImageChanged(std::string)),
2744           this,SLOT(CurrentImageChanged(std::string)));
2745   connect(mSlicerManagers.back(),SIGNAL(
2746                                         UpdatePosition(int, double, double, double, double, double, double, double)),this,
2747           SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2748   connect(mSlicerManagers.back(),SIGNAL(UpdateVector(int, double, double, double, double)),
2749           this, SLOT(VectorChanged(int,double,double,double, double)));
2750   connect(mSlicerManagers.back(),SIGNAL(UpdateOverlay(int, double, double)),
2751           this, SLOT(OverlayChanged(int,double,double)));
2752   connect(mSlicerManagers.back(),SIGNAL(UpdateFusion(int, double)),
2753           this, SLOT(FusionChanged(int,double)));
2754   connect(mSlicerManagers.back(),SIGNAL(UpdateWindows(int, int, int)),
2755           this,SLOT(WindowsChanged(int, int, int)));
2756   connect(mSlicerManagers.back(),SIGNAL(WindowLevelChanged(double, double,int, int)),
2757           this,SLOT(WindowLevelChanged(double, double, int, int)));
2758   connect(mSlicerManagers.back(),SIGNAL(UpdateSlice(int,int)),
2759           this,SLOT(UpdateSlice(int,int)));
2760   connect(mSlicerManagers.back(),SIGNAL(UpdateTSlice(int, int)),
2761           this,SLOT(UpdateTSlice(int, int)));
2762   connect(mSlicerManagers.back(),SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2763           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2764   connect(mSlicerManagers.back(),SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2765           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2766   connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2767   UpdateTree();
2768   qApp->processEvents();
2769   InitSlicers();
2770   ShowLastImage();
2771   InitDisplay();
2772   qApp->processEvents();
2773 }
2774 //------------------------------------------------------------------------------
2775
2776
2777 //------------------------------------------------------------------------------
2778 void vvMainWindow::UpdateCurrentSlicer() {
2779   int index = -1;
2780   if (DataTree->selectedItems().size() > 0) {
2781     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2782   }
2783   mSlicerManagerCurrentIndex = index;
2784 }
2785 //------------------------------------------------------------------------------
2786