vv/vvMainWindow.cxx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17 ======================================================================-====*/
  18
  19 #include <algorithm>
  20 #include <QMessageBox>
  21 #include <QInputDialog>
  22 #include <QTimer>
  23 #include "QTreePushButton.h"
  24
  25 // VV include
  26 #include "vvMainWindow.h"
  27 #include "vvHelpDialog.h"
  28 #include "vvDocumentation.h"
  29 #include "vvProgressDialog.h"
  30 #include "vvQDicomSeriesSelector.h"
  31 #include "vvSlicerManager.h"
  32 #include "clitkImageCommon.h"
  33 #include "vvSlicer.h"
  34 #include "vvInteractorStyleNavigator.h"
  35 #include "vvImageWriter.h"
  36 #include "vvSegmentationDialog.h"
  37 #include "vvSurfaceViewerDialog.h"
  38 #include "vvDeformationDialog.h"
  39 #include "vvImageWarp.h"
  40 #include "vvUtils.h"
  41 #include "vvMaximumIntensityProjection.h"
  42 #include "vvMidPosition.h"
  43 #include "vvMesh.h"
  44 #include "vvStructSelector.h"
  45 #include "vvMeshReader.h"
  46 #include "vvConstants.h"
  47
  48 #ifdef CLITK_VV_USE_BDCM
  49 #include <bdcmDicomFilesSelectorDialog.h>
  50 #endif
  51
  52 // ITK include
  53 #include "itkImage.h"
  54 #include "itkImageFileReader.h"
  55 #include "itkByteSwapper.h"
  56 #include "itkCommand.h"
  57 #include "itkNumericSeriesFileNames.h"
  58
  59 // VTK include
  60 #include "vtkImageData.h"
  61 #include "vtkImageActor.h"
  62 #include "vtkCornerAnnotation.h"
  63 #include "vtkRenderWindow.h"
  64 #include "vtkRenderWindowInteractor.h"
  65 #include "vtkRenderer.h"
  66 #include "vtkRendererCollection.h"
  67 #include "vtkWindowToImageFilter.h"
  68 #include "vtkBMPWriter.h"
  69 #include "vtkTIFFWriter.h"
  70 #include "vtkPNMWriter.h"
  71 #include "vtkPNGWriter.h"
  72 #include "vtkJPEGWriter.h"
  73
  74 // Standard includes
  75 #include <iostream>
  76
  77 #define COLUMN_TREE 0
  78 #define COLUMN_UL_VIEW 1
  79 #define COLUMN_UR_VIEW 2
  80 #define COLUMN_DL_VIEW 3
  81 #define COLUMN_DR_VIEW 4
  82 #define COLUMN_CLOSE_IMAGE 5
  83 #define COLUMN_RELOAD_IMAGE 6
  84 #define COLUMN_IMAGE_NAME 7
  85
  86 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.hdr *.vox *.his *.xdr)"
  87
  88 /*Data Tree values
  89   0,Qt::UserRole full filename
  90   1,Qt::CheckStateRole checkbutton UL View
  91   1,Qt::UserRole overlay, fusion or vector
  92   2,Qt::CheckStateRole checkbutton UR View
  93   3,Qt::CheckStateRole checkbutton DL View
  94   4,Qt::CheckStateRole checkbutton DR View
  95   5,0  short filename
  96   5,Qt::UserRole mSlicerManager id*/
  97
  98 //------------------------------------------------------------------------------
  99 vvMainWindow::vvMainWindow():vvMainWindowBase()
 100 {
 101   setupUi(this); // this sets up the GUI
 102
 103   mInputPathName = "";
 104   mMenuTools = menuTools;
 105   mContextMenu = &contextMenu;
 106   mMenuExperimentalTools = menuExperimental;
 107   mMainWidget = this;
 108   mCurrentTime = -1;
 109
 110   //Init the contextMenu
 111   this->setContextMenuPolicy(Qt::CustomContextMenu);
 112   contextActions.resize(0);
 113   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 114                                   tr("O&pen new Image"));
 115   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 116   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 117   contextActions.push_back(actionOpen_new_image);
 118   contextMenu.addSeparator();
 119
 120   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 121                                tr("Close Current Image"));
 122   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 123   contextActions.push_back(actionClose_Image);
 124
 125   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 126                                 tr("Reload Current Image"));
 127   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 128   contextActions.push_back(actionReload_image);
 129
 130   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 131                               tr("Save Current Image"));
 132   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 133   contextActions.push_back(actionSave_image);
 134
 135   contextMenu.addSeparator();
 136
 137   // QAction* actionCrop_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/crop.png")),
 138   //                                                   tr("Crop Current Image"));
 139   // connect(actionCrop_image,SIGNAL(triggered()),this,SLOT(CropImage()));
 140   // contextActions.push_back(actionCrop_image);
 141
 142   QAction* actionSplit_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/cut.png")),
 143                                tr("Split Current Image"));
 144   connect(actionSplit_image,SIGNAL(triggered()),this,SLOT(SplitImage()));
 145   contextActions.push_back(actionSplit_image);
 146
 147   contextMenu.addSeparator();
 148
 149   contextMenu.addAction(actionAdd_VF_to_current_Image);
 150   contextActions.push_back(actionAdd_VF_to_current_Image);
 151
 152   QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 153       tr("Add overlay image to current image"));
 154   contextMenu.addAction(actionAdd_Overlay_to_current_Image);
 155   contextActions.push_back(actionAdd_Overlay_to_current_Image);
 156
 157   connect(actionAdd_Overlay_to_current_Image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 158
 159   contextMenu.addAction(actionAdd_fusion_image);
 160   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 161   contextActions.push_back(actionAdd_fusion_image);
 162
 163   // TRIAL DS
 164   /*
 165   QMenu * m = new QMenu(menubar);
 166   m->setTitle("TOTO");
 167   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 168   contextMenu.addMenu(m);
 169   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 170                      tr("BIDON"));
 171   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 172                      tr("BIDON2"));
 173   m->addAction(a);
 174   m->addAction(b);
 175   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 176   */
 177
 178   //init the DataTree
 179   mSlicerManagers.resize(0);
 180
 181   QStringList header;
 182   header.append("");
 183   header.append("TL");
 184   header.append("TR");
 185   header.append("BL");
 186   header.append("BR");
 187   header.append("");
 188   header.append("");
 189   header.append("Name");
 190
 191   DataTree->setHeaderLabels(header);
 192   DataTree->resizeColumnToContents(COLUMN_TREE);
 193   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 194   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 195   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 196   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 197   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 198   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 199   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 200
 201   viewMode = 1;
 202   documentation = new vvDocumentation();
 203   help_dialog = new vvHelpDialog();
 204   dicomSeriesSelector = new vvDicomSeriesSelector();
 205
 206   inverseButton->setEnabled(0);
 207   actionAdd_Overlay_to_current_Image->setEnabled(0);
 208   actionSave_As->setEnabled(0);
 209   actionAdd_VF_to_current_Image->setEnabled(0);
 210   actionAdd_fusion_image->setEnabled(0);
 211
 212   //init the sliders
 213   verticalSliders.push_back(NOVerticalSlider);
 214   verticalSliders.push_back(NEVerticalSlider);
 215   verticalSliders.push_back(SOVerticalSlider);
 216   verticalSliders.push_back(SEVerticalSlider);
 217
 218   for (int i =0; i < 4; i++)
 219     verticalSliders[i]->hide();
 220
 221   horizontalSliders.push_back(NOHorizontalSlider);
 222   horizontalSliders.push_back(NEHorizontalSlider);
 223   horizontalSliders.push_back(SOHorizontalSlider);
 224   horizontalSliders.push_back(SEHorizontalSlider);
 225
 226   for (int i =0; i < 4; i++)
 227     horizontalSliders[i]->hide();
 228
 229
 230   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 231   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 232   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 233   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 234
 235   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 236   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 237   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 238   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 239
 240   //connect everything
 241   connect(actionMaximum_Intensity_Projection,SIGNAL(triggered()),this,SLOT(ComputeMIP()));
 242   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 243   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 244   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 245   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 246   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 247   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 248   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 249   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 250   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 251   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 252   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 253   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 254   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 255   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 256   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 257
 258   ///////////////////////////////////////////////
 259   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 260   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 261   ///////////////////////////////////////////////
 262
 263   actionNorth_East_Window->setEnabled(0);
 264   actionNorth_West_Window->setEnabled(0);
 265   actionSouth_East_Window->setEnabled(0);
 266   actionSouth_West_Window->setEnabled(0);
 267
 268   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 269   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 270   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 271   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 272
 273   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 274   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 275           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 276
 277   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 278   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 279   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 280   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 281   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 282   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 283
 284
 285   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 286
 287   connect(linkPanel,SIGNAL(addLink(QString,QString)),this,SLOT(AddLink(QString,QString)));
 288   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 289   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int)),this,SLOT(SetVFProperty(int,int,int,int)));
 290   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int)),this,SLOT(SetOverlayProperty(int)));
 291   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,double,double)),
 292           this,SLOT(SetFusionProperty(int,int,double,double)));
 293   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 294
 295   playMode = 0;//pause
 296   mFrameRate = 10;
 297   playButton->setEnabled(0);
 298   frameRateLabel->setEnabled(0);
 299   frameRateSpinBox->setEnabled(0);
 300   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 301   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 302
 303   goToCursorPushButton->setEnabled(0);
 304   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 305
 306   NOViewWidget->hide();
 307   NEViewWidget->hide();
 308   SOViewWidget->hide();
 309   SEViewWidget->hide();
 310
 311   //Recently opened files
 312   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 313   if ( !recent_files.empty() ) {
 314     QMenu * rmenu = new QMenu("Recently opened files...");
 315     rmenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 316     menuFile->insertMenu(actionOpen_Image_With_Time,rmenu);
 317     for (std::list<std::string>::iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 318       QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")),
 319                                    (*i).c_str(),this);
 320       rmenu->addAction(current);
 321       connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 322     }
 323   }
 324
 325   // Adding all new tools (insertion in the menu)
 326   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 327
 328   if (!CLITK_EXPERIMENTAL)
 329     menuExperimental->menuAction()->setVisible(false);
 330 }
 331 //------------------------------------------------------------------------------
 332
 333
 334 //------------------------------------------------------------------------------
 335 void vvMainWindow::ComputeMIP()
 336 {
 337   vvMaximumIntensityProjection mip;
 338   vvSlicerManager* selected_slicer = mSlicerManagers[GetSlicerIndexFromItem(DataTree->selectedItems()[0])];
 339   QFileInfo info(selected_slicer->GetFileName().c_str());
 340   mip.Compute(selected_slicer);
 341   if (!mip.error)
 342     AddImage(mip.GetOutput(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_mip.mhd");
 343 }
 344 //------------------------------------------------------------------------------
 345
 346
 347 //------------------------------------------------------------------------------
 348 void vvMainWindow::ComputeMidPosition()
 349 {
 350   bool ok;
 351   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 352   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 353                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 354   if (ok) {
 355     vvMidPosition midp;
 356     midp.slicer_manager = mSlicerManagers[index];
 357     midp.reference_image_index = ref;
 358     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 359     midp.Update();
 360     if (midp.error)
 361       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 362     else {
 363       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 364       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 365     }
 366     QApplication::restoreOverrideCursor();
 367   }
 368 }
 369 //------------------------------------------------------------------------------
 370
 371
 372 //------------------------------------------------------------------------------
 373 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 374 {
 375   QTreeWidgetItem *item = new QTreeWidgetItem();
 376   item->setData(0,Qt::UserRole,"filename.vtk");
 377   item->setData(1,Qt::UserRole,tr("contour"));
 378   QBrush brush;
 379   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 380   brush.setStyle(Qt::SolidPattern);
 381   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 382   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 383
 384   for (int j = 1; j <= 4; j++)
 385     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 386
 387   QTreePushButton* cButton = new QTreePushButton;
 388   cButton->setItem(item);
 389   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 390   cButton->setToolTip(tr("close image"));
 391   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 392   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 393           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 394
 395   QTreePushButton* rButton = new QTreePushButton;
 396   rButton->setItem(item);
 397   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 398   rButton->setToolTip(tr("reload image"));
 399   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 400   rButton->setEnabled(false);
 401   //Not implemented
 402   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 403   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 404
 405   DataTree->topLevelItem(image_index)->setExpanded(1);
 406   DataTree->topLevelItem(image_index)->addChild(item);
 407   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 408   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 409   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 410   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 411
 412   UpdateTree();
 413   mSlicerManagers[image_index]->AddContour(contour,propagation);
 414   mSlicerManagers[image_index]->Render();
 415 }
 416 //------------------------------------------------------------------------------
 417
 418
 419 //------------------------------------------------------------------------------
 420 void vvMainWindow::OpenVTKContour()
 421 {
 422   if (mSlicerManagers.size() > 0) {
 423     QString Extensions = "Images ( *.vtk *.obj)";
 424     Extensions += ";;All Files (*)";
 425     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 426     if (file.isNull())
 427       return;
 428     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 429     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 430     vvMeshReader reader;
 431     reader.SetImage(mSlicerManagers[index]->GetImage());
 432     reader.SetModeToVTK();
 433     reader.SetFilename(file.toStdString());
 434     reader.Update();
 435     AddContour(index,reader.GetOutput()[0],false);
 436     QApplication::restoreOverrideCursor();
 437   }
 438 }
 439 //------------------------------------------------------------------------------
 440
 441
 442 //------------------------------------------------------------------------------
 443 void vvMainWindow::OpenDCStructContour()
 444 {
 445   if (mSlicerManagers.size() > 0) {
 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       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 460       reader.SetSelectedItems(selector.getSelectedItems());
 461       reader.SetImage(mSlicerManagers[index]->GetImage());
 462       if (selector.PropagationEnabled())
 463         reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 464       reader.Update();
 465       std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 466       for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 467            i!=contours.end(); i++)
 468         AddContour(index,*i,selector.PropagationEnabled());
 469       QApplication::restoreOverrideCursor();
 470     }
 471   }
 472 }
 473 //------------------------------------------------------------------------------
 474
 475
 476 //------------------------------------------------------------------------------
 477 void vvMainWindow::ComputeDeformableRegistration()
 478 {
 479   if (mSlicerManagers.size() > 0) {
 480     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 481     vvDeformationDialog dialog(index,mSlicerManagers);
 482     if (dialog.exec()) {
 483       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 484       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 485       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 486     } else
 487       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 488   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 489 }
 490 //------------------------------------------------------------------------------
 491
 492
 493 //------------------------------------------------------------------------------
 494 void vvMainWindow::WarpImage()
 495 {
 496   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 497   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 498     bool ok;
 499     int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 500                                        mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 501     if (ok) {
 502       WarpImage(mSlicerManagers[index],ref);
 503     }
 504   } else
 505     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 506 }
 507 //------------------------------------------------------------------------------
 508
 509
 510 //------------------------------------------------------------------------------
 511 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 512 {
 513   if (!selected_slicer->GetVF().IsNull()) {
 514     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 515     QFileInfo info(selected_slicer->GetFileName().c_str());
 516     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 517                      reference_phase,this);
 518     if (warp.ComputeWarpedImage()) {
 519       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 520       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 521       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 522       QApplication::restoreOverrideCursor();
 523     } else {
 524       QApplication::restoreOverrideCursor();
 525       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 526     }
 527   } else
 528     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 529 }
 530 //------------------------------------------------------------------------------
 531
 532
 533 //------------------------------------------------------------------------------
 534 vvMainWindow::~vvMainWindow()
 535 {
 536   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 537     if (mSlicerManagers[i] != NULL)
 538       delete mSlicerManagers[i];
 539   }
 540 }
 541 //------------------------------------------------------------------------------
 542
 543
 544 //------------------------------------------------------------------------------
 545 void vvMainWindow::MergeImages()
 546 {
 547   QString Extensions = EXTENSIONS;
 548   Extensions += ";;All Files (*)";
 549   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 550   if (files.isEmpty())
 551     return;
 552   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 553   std::vector<std::string> vector;
 554
 555   unsigned int currentDim = 0;
 556   std::vector<double> currentSpacing;
 557   std::vector<int> currentSize;
 558   std::vector<double> currentOrigin;
 559
 560   for (int i = 0; i < files.size(); i++) {
 561     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 562                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 563     reader->SetFileName(files[i].toStdString().c_str());
 564     reader->ReadImageInformation();
 565     if (reader)        {
 566       //NOViewWidget->hide();
 567       //NEViewWidget->hide();
 568       //SOViewWidget->hide();
 569       //SEViewWidget->hide();
 570       if (i == 0)
 571         currentDim = reader->GetNumberOfDimensions();
 572       bool IsOk = true;
 573       for (unsigned int j = 0; j < currentDim; j++) {
 574         if (i == 0) {
 575           if (j == 0) {
 576             currentSpacing.resize(currentDim);
 577             currentSize.resize(currentDim);
 578             currentOrigin.resize(currentDim);
 579           }
 580           currentOrigin[j] = reader->GetOrigin(j);
 581           currentSpacing[j] = reader->GetSpacing(j);
 582           currentSize[j] = reader->GetDimensions(j);
 583         } else if (currentDim != reader->GetNumberOfDimensions()
 584                    || currentSpacing[j] != reader->GetSpacing(j)
 585                    || currentSize[j] != (int)reader->GetDimensions(j)
 586                    || currentOrigin[j] != reader->GetOrigin(j)) {
 587           QString error = "Cannot read file (too different from others ";
 588           error += files[i].toStdString().c_str();
 589           QMessageBox::information(this,tr("Reading problem"),error);
 590           IsOk = false;
 591           break;
 592         }
 593       }
 594       if (IsOk)
 595         vector.push_back(files[i].toStdString());
 596     }
 597   }
 598   if (vector.size() > 0)
 599     LoadImages(vector, MERGED);
 600 }
 601 //------------------------------------------------------------------------------
 602
 603
 604 //------------------------------------------------------------------------------
 605 void vvMainWindow::MergeImagesWithTime()
 606 {
 607   QString Extensions = EXTENSIONS;
 608   Extensions += ";;All Files (*)";
 609   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 610   if (files.isEmpty())
 611     return;
 612   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 613   std::vector<std::string> vector;
 614
 615   unsigned int currentDim = 0;
 616   std::vector<double> currentSpacing;
 617   std::vector<int> currentSize;
 618   std::vector<double> currentOrigin;
 619
 620   for (int i = 0; i < files.size(); i++) {
 621     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 622                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 623     if (reader) {
 624       reader->SetFileName(files[i].toStdString().c_str());
 625       reader->ReadImageInformation();
 626       if (i == 0)
 627         currentDim = reader->GetNumberOfDimensions();
 628       bool IsOk = true;
 629       for (unsigned int j = 0; j < currentDim; j++) {
 630         if (i == 0) {
 631           if (j == 0) {
 632             currentSpacing.resize(currentDim);
 633             currentSize.resize(currentDim);
 634             currentOrigin.resize(currentDim);
 635           }
 636           currentOrigin[j] = reader->GetOrigin(j);
 637           currentSpacing[j] = reader->GetSpacing(j);
 638           currentSize[j] = reader->GetDimensions(j);
 639         } else if (currentDim != reader->GetNumberOfDimensions()
 640                    || currentSpacing[j] != reader->GetSpacing(j)
 641                    || currentSize[j] != (int)reader->GetDimensions(j)
 642                    || currentOrigin[j] != reader->GetOrigin(j)) {
 643           QString error = "Cannot read file (too different from others ";
 644           error += files[i].toStdString().c_str();
 645           QMessageBox::information(this,tr("Reading problem"),error);
 646           IsOk = false;
 647           break;
 648         }
 649       }
 650       if (IsOk)
 651         vector.push_back(files[i].toStdString());
 652     } else {
 653       QString error = "Cannot read file info for ";
 654       error += files[i].toStdString().c_str();
 655       error += "\n";
 656       error += "Maybe you're trying to open an image in an unsupported format?\n";
 657       QMessageBox::information(this,tr("Reading problem"),error);
 658     }
 659   }
 660   sort(vector.begin(),vector.end());
 661   if (vector.size() > 1)
 662     LoadImages(vector, MERGEDWITHTIME);
 663   else
 664     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.");
 665 }
 666 //------------------------------------------------------------------------------
 667
 668
 669 //------------------------------------------------------------------------------
 670 void vvMainWindow::OpenDicom()
 671 {
 672   std::vector<std::string> files;
 673
 674 #ifdef CLITK_VV_USE_BDCM
 675   bool r = bdcm::OpenDicomFilesSelectorDialog(files,
 676            "DicomFilesSelectorDialog test",
 677            0,0,800,800,1);
 678
 679   if (r) {
 680     std::cout << "$$$$ main : user clicked 'OK' $$$$"<<std::endl;
 681     std::cout << "$$$$ selected files : "<<std::endl;
 682     std::vector<std::string>::iterator i;
 683     for (i=files.begin(); i!=files.end(); ++i) {
 684       std::cout << *i << std::endl;
 685     }
 686     std::cout << "$$$$ "<<std::endl;
 687
 688     LoadImages(files,DICOM);
 689   } else {
 690     std::cout << "$$$$ main : user clicked 'CANCEL' $$$$"<<std::endl;
 691   }
 692 #else
 693   std::cout << "dicomSeriesSelector " << std::endl;
 694   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 695     files = *(dicomSeriesSelector->GetFilenames());
 696     LoadImages(files,DICOM);
 697   }
 698 #endif
 699
 700 }
 701 //------------------------------------------------------------------------------
 702
 703 //------------------------------------------------------------------------------
 704 void vvMainWindow::OpenImages()
 705 {
 706   QString Extensions = EXTENSIONS;
 707   Extensions += ";;All Files (*)";
 708
 709   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 710   if (files.isEmpty())
 711     return;
 712   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 713   std::vector<std::string> vector;
 714   for (int i = 0; i < files.size(); i++)
 715     vector.push_back(files[i].toStdString());
 716   LoadImages(vector, IMAGE);
 717 }
 718 //------------------------------------------------------------------------------
 719 void vvMainWindow::OpenRecentImage()
 720 {
 721   QAction * caller = qobject_cast<QAction*>(sender());
 722   std::vector<std::string> images;
 723   images.push_back(caller->text().toStdString());
 724   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 725   LoadImages(images,IMAGE);
 726 }
 727 //------------------------------------------------------------------------------
 728
 729
 730 //------------------------------------------------------------------------------
 731 void vvMainWindow::OpenImageWithTime()
 732 {
 733   QString Extensions = EXTENSIONS;
 734   Extensions += ";;All Files (*)";
 735
 736   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 737   if (files.isEmpty())
 738     return;
 739   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 740   std::vector<std::string> vector;
 741   for (int i = 0; i < files.size(); i++) {
 742     vector.push_back(files[i].toStdString());
 743   }
 744   LoadImages(vector, IMAGEWITHTIME);
 745 }
 746 //------------------------------------------------------------------------------
 747
 748
 749 //------------------------------------------------------------------------------
 750 void vvMainWindow::LoadImages(std::vector<std::string> files, LoadedImageType filetype)
 751 {
 752   //Separate the way to open images and dicoms
 753   int fileSize;
 754   if (filetype == IMAGE || filetype == IMAGEWITHTIME)
 755     fileSize = files.size();
 756   else
 757     fileSize = 1;
 758
 759   //Only add to the list of recently opened files when a single file is opened,
 760   //to avoid polluting the list of recently opened files
 761   if (files.size() == 1) {
 762     QFileInfo finfo=tr(files[0].c_str());
 763     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 764   }
 765   //init the progress events
 766   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 767   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 768   qApp->processEvents();
 769
 770   int numberofsuccesulreads=0;
 771   //open images as 1 or multiples
 772   for (int i = 0; i < fileSize; i++) {
 773
 774     progress.Update("Opening " + files[i]);
 775     progress.SetProgress(i,fileSize);
 776     qApp->processEvents();
 777
 778     //read the image and put it in mSlicerManagers
 779     vvSlicerManager* imageManager = new vvSlicerManager(4);
 780     qApp->processEvents();
 781
 782     bool SetImageSucceed=false;
 783
 784     // Change filename if an image with the same already exist
 785     //    DD(files[i]);
 786     int number=0;
 787     for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
 788       vvSlicerManager * v = mSlicerManagers[l];
 789       //      DD(v->GetBaseFileName());
 790       // DD(v->GetFileName());
 791       if (v->GetBaseFileName() ==
 792           vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(files[i]))) {
 793         number = std::max(number, v->GetBaseFileNameNumber()+1);
 794       }
 795     }
 796
 797
 798     if (filetype == IMAGE || filetype == IMAGEWITHTIME)
 799       SetImageSucceed = imageManager->SetImage(files[i],filetype, number);
 800     else {
 801       SetImageSucceed = imageManager->SetImages(files,filetype, number);
 802     }
 803     if (SetImageSucceed == false) {
 804       QApplication::restoreOverrideCursor();
 805       QString error = "Cannot open file \n";
 806       error += imageManager->GetLastError().c_str();
 807       QMessageBox::information(this,tr("Reading problem"),error);
 808       delete imageManager;
 809     } else {
 810       mSlicerManagers.push_back(imageManager);
 811
 812       //create an item in the tree with good settings
 813       QTreeWidgetItem *item = new QTreeWidgetItem();
 814       item->setData(0,Qt::UserRole,files[i].c_str());
 815       QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 816       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 817       qApp->processEvents();
 818
 819       //Create the buttons for reload and close
 820       qApp->processEvents();
 821       QTreePushButton* cButton = new QTreePushButton;
 822       cButton->setItem(item);
 823       cButton->setColumn(COLUMN_CLOSE_IMAGE);
 824       cButton->setToolTip(tr("close image"));
 825       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 826       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 827               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 828
 829       QTreePushButton* rButton = new QTreePushButton;
 830       rButton->setItem(item);
 831       rButton->setColumn(COLUMN_RELOAD_IMAGE);
 832       rButton->setToolTip(tr("reload image"));
 833       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 834       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 835               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 836
 837       DataTree->addTopLevelItem(item);
 838       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 839       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 840
 841       //set the id of the image
 842       QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 843       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 844       mSlicerManagers.back()->SetId(id.toStdString());
 845
 846       linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 847
 848       connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 849               this,SLOT(CurrentImageChanged(std::string)));
 850       connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 851               this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 852       connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 853               this, SLOT(VectorChanged(int,double,double,double, double)));
 854       connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 855               this, SLOT(OverlayChanged(int,double,double)));
 856       connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 857               this, SLOT(FusionChanged(int,double)));
 858       connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
 859               this,SLOT(WindowsChanged(int, int, int)));
 860       connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
 861               this,SLOT(WindowLevelChanged(double, double, int, int)));
 862       connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 863               this,SLOT(UpdateSlice(int,int)));
 864       connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 865               this,SLOT(UpdateTSlice(int, int)));
 866       connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 867               this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 868       connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 869               this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 870       connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 871               this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 872       connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 873       InitSlicers();
 874       numberofsuccesulreads++;
 875     }
 876   }
 877   if (numberofsuccesulreads) {
 878     NOViewWidget->show();
 879     NEViewWidget->show();
 880     SOViewWidget->show();
 881     SEViewWidget->show();
 882     UpdateTree();
 883     InitDisplay();
 884     ShowLastImage();
 885   }
 886   QApplication::restoreOverrideCursor();
 887
 888   // Try to guess default WindowLevel
 889   double range[2];
 890   mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 891   // DD(range[0]);
 892   //   DD(range[1]);
 893   if ((range[0] == 0) && (range[1] == 1)) {
 894     presetComboBox->setCurrentIndex(5);// binary
 895   } else {
 896     // TODO
 897   }
 898 }
 899 //------------------------------------------------------------------------------
 900
 901 //------------------------------------------------------------------------------
 902 void vvMainWindow::UpdateTree()
 903 {
 904   DataTree->resizeColumnToContents(COLUMN_TREE);
 905   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 906   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 907   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 908   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 909   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 910   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 911   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 912 }
 913 //------------------------------------------------------------------------------
 914
 915 //------------------------------------------------------------------------------
 916 void vvMainWindow::CurrentImageChanged(std::string id)
 917 {
 918   int selected = 0;
 919   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 920     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 921       selected = i;
 922     } else {
 923       DataTree->topLevelItem(i)->setSelected(0);
 924     }
 925     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 926       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 927
 928   }
 929   DataTree->topLevelItem(selected)->setSelected(1);
 930 }
 931 //------------------------------------------------------------------------------
 932
 933 //------------------------------------------------------------------------------
 934 void vvMainWindow::ImageInfoChanged()
 935 {
 936   contextActions[7]->setEnabled(1);
 937   contextActions[6]->setEnabled(1);
 938   actionSave_As->setEnabled(1);
 939   actionAdd_VF_to_current_Image->setEnabled(1);
 940   actionAdd_fusion_image->setEnabled(1);
 941   actionNorth_East_Window->setEnabled(1);
 942   actionNorth_West_Window->setEnabled(1);
 943   actionSouth_East_Window->setEnabled(1);
 944   actionSouth_West_Window->setEnabled(1);
 945   inverseButton->setEnabled(1);
 946
 947   goToCursorPushButton->setEnabled(1);
 948
 949   if (DataTree->selectedItems().size()) {
 950     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 951
 952     colorMapComboBox->setEnabled(1);
 953     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
 954       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
 955           DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion") {
 956         colorMapComboBox->setEnabled(0);
 957         break;
 958       }
 959     }
 960
 961     std::vector<double> origin;
 962     std::vector<double> inputSpacing;
 963     std::vector<int> inputSize;
 964     std::vector<double> sizeMM;
 965     int dimension=0;
 966     QString pixelType;
 967     QString inputSizeInBytes;
 968     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
 969
 970     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1) {
 971       playButton->setEnabled(1);
 972       frameRateLabel->setEnabled(1);
 973       frameRateSpinBox->setEnabled(1);
 974     } else {
 975       playButton->setEnabled(0);
 976       frameRateLabel->setEnabled(0);
 977       frameRateSpinBox->setEnabled(0);
 978     }
 979
 980     //read image header
 981     int NPixel = 1;
 982
 983     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
 984       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
 985       dimension = imageSelected->GetNumberOfDimensions();
 986       origin.resize(dimension);
 987       inputSpacing.resize(dimension);
 988       inputSize.resize(dimension);
 989       sizeMM.resize(dimension);
 990       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
 991       for (int i = 0; i < dimension; i++) {
 992         origin[i] = imageSelected->GetOrigin()[i];
 993         inputSpacing[i] = imageSelected->GetSpacing()[i];
 994         inputSize[i] = imageSelected->GetSize()[i];
 995         sizeMM[i] = inputSize[i]*inputSpacing[i];
 996         NPixel *= inputSize[i];
 997       }
 998       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
 999     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1000       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1001       dimension = imageSelected->GetNumberOfDimensions();
1002       origin.resize(dimension);
1003       inputSpacing.resize(dimension);
1004       inputSize.resize(dimension);
1005       sizeMM.resize(dimension);
1006       pixelType = mSlicerManagers[index]->GetVF()->GetScalarTypeAsString().c_str();
1007       for (int i = 0; i < dimension; i++) {
1008         origin[i] = imageSelected->GetOrigin()[i];
1009         inputSpacing[i] = imageSelected->GetSpacing()[i];
1010         inputSize[i] = imageSelected->GetSize()[i];
1011         sizeMM[i] = inputSize[i]*inputSpacing[i];
1012         NPixel *= inputSize[i];
1013       }
1014       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1015     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1016       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1017       dimension = imageSelected->GetNumberOfDimensions();
1018       origin.resize(dimension);
1019       inputSpacing.resize(dimension);
1020       inputSize.resize(dimension);
1021       sizeMM.resize(dimension);
1022       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
1023       for (int i = 0; i < dimension; i++) {
1024         origin[i] = imageSelected->GetOrigin()[i];
1025         inputSpacing[i] = imageSelected->GetSpacing()[i];
1026         inputSize[i] = imageSelected->GetSize()[i];
1027         sizeMM[i] = inputSize[i]*inputSpacing[i];
1028         NPixel *= inputSize[i];
1029       }
1030       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1031     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1032       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1033       dimension = imageSelected->GetNumberOfDimensions();
1034       origin.resize(dimension);
1035       inputSpacing.resize(dimension);
1036       inputSize.resize(dimension);
1037       sizeMM.resize(dimension);
1038       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
1039       for (int i = 0; i < dimension; i++) {
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
1049     QString dim = QString::number(dimension) + " (";
1050     dim += pixelType + ")";
1051
1052     infoPanel->setFileName(image);
1053     infoPanel->setDimension(dim);
1054     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1055     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1056     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1057     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1058     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1059
1060     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1061                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1062     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1063     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1064
1065     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1066     for (int i = 0; i < 4; i++) {
1067       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1068         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1069         break;
1070       }
1071     }
1072     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1073     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1074     // DD(mSlicerManagers[index]->GetColorMap());
1075     // DD(mSlicerManagers[index]->GetPreset());
1076     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1077     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1078
1079     infoPanel->setFileName(image);
1080     infoPanel->setDimension(dim);
1081     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1082     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1083     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1084     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1085     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1086
1087     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1088                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1089     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1090     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1091
1092     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1093     for (int i = 0; i < 4; i++) {
1094       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1095         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1096         break;
1097       }
1098     }
1099     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1100     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1101     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1102     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1103
1104     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1105       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1106       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1107                                   mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1108                                   mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1109     } else {
1110       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1111       overlayPanel->getVFProperty(-1,-1,-1);
1112     }
1113     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1114       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1115       overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1116     } else {
1117       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1118       overlayPanel->getOverlayProperty(-1);
1119     }
1120     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1121       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1122       overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1123                                       mSlicerManagers[index]->GetFusionColorMap(),
1124                                       mSlicerManagers[index]->GetFusionWindow(),
1125                                       mSlicerManagers[index]->GetFusionLevel());
1126     } else {
1127       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1128       overlayPanel->getFusionProperty(-1, -1,-1,-1);
1129     }
1130   }
1131 }
1132 //------------------------------------------------------------------------------
1133
1134 //------------------------------------------------------------------------------
1135 void vvMainWindow::ShowDocumentation()
1136 {
1137   documentation->show();
1138 }
1139 //------------------------------------------------------------------------------
1140 void vvMainWindow::ShowHelpDialog()
1141 {
1142   help_dialog->show();
1143 }
1144 //------------------------------------------------------------------------------
1145
1146 //------------------------------------------------------------------------------
1147 void vvMainWindow::ChangeViewMode()
1148 {
1149   QListIterator<int> it0(splitter_3->sizes());
1150   QListIterator<int> it1(splitter_3->sizes());
1151   int max0 = 0;
1152   int max1 = 1;
1153   while (it0.hasNext()) {
1154     max0 += it0.next();
1155   }
1156   while (it1.hasNext()) {
1157     max1 += it1.next();
1158   }
1159   QList<int> size0;
1160   QList<int> size1;
1161   if (viewMode == 1) {
1162     viewMode = 0;
1163     size0.push_back(max0);
1164     size0.push_back(0);
1165     size1.push_back(max1);
1166     size1.push_back(0);
1167     splitter_3->setSizes(size0);
1168     OSplitter->setSizes(size1);
1169     DataTree->setColumnHidden(2,1);
1170     DataTree->setColumnHidden(3,1);
1171     DataTree->setColumnHidden(4,1);
1172   } else {
1173     viewMode = 1;
1174     size0.push_back(int(max0/2));
1175     size0.push_back(int(max0/2));
1176     size1.push_back(int(max1/2));
1177     size1.push_back(int(max1/2));
1178     splitter_3->setSizes(size0);
1179     OSplitter->setSizes(size1);
1180     DataTree->setColumnHidden(2,0);
1181     DataTree->setColumnHidden(3,0);
1182     DataTree->setColumnHidden(4,0);
1183   }
1184 }
1185 //------------------------------------------------------------------------------
1186
1187 //------------------------------------------------------------------------------
1188 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1189 {
1190   QString result = "";// QString::number(size);
1191   //result += " bytes (";
1192   if (size > 1000000000) {
1193     size /= 1000000000;
1194     result += QString::number(size);
1195     result += "Gb";//)";
1196   } else if (size > 1000000) {
1197     size /= 1000000;
1198     result += QString::number(size);
1199     result += "Mb";//)";
1200   } else if (size > 1000) {
1201     size /= 1000;
1202     result += QString::number(size);
1203     result += "kb";//)";
1204   }
1205   return result;
1206 }
1207 //------------------------------------------------------------------------------
1208
1209 //------------------------------------------------------------------------------
1210 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1211 {
1212   QString result;
1213   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1214     if (i != 0)
1215       result += " ";
1216     result += QString::number(vectorDouble[i]);
1217   }
1218   return result;
1219 }
1220 //------------------------------------------------------------------------------
1221
1222 //------------------------------------------------------------------------------
1223 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1224 {
1225   QString result;
1226   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1227     if (i != 0)
1228       result += " ";
1229     result += QString::number(vectorInt[i]);
1230   }
1231   return result;
1232 }
1233 //------------------------------------------------------------------------------
1234
1235 //------------------------------------------------------------------------------
1236 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1237 {
1238   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1239   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1240     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1241       return i;
1242   }
1243   return -1;
1244 }
1245 //------------------------------------------------------------------------------
1246
1247 //------------------------------------------------------------------------------
1248 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1249 {
1250   QString id = sm->GetId().c_str();
1251   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1252     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1253       return DataTree->topLevelItem(i);
1254   }
1255   return NULL;
1256 }
1257 //------------------------------------------------------------------------------
1258
1259 //------------------------------------------------------------------------------
1260 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clicked_item, int column)
1261 {
1262   int index = GetSlicerIndexFromItem(clicked_item);
1263   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1264     return;
1265   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1266     //Trick to avoid redoing twice the job for a key (sr)
1267     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()-> GetInteractor()->SetKeySym("Crap");
1268
1269     QTreeWidgetItem* current_row=DataTree->topLevelItem(i);
1270     if (DataTree->topLevelItem(index) == current_row) {
1271       vvSlicer* clicked_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1272       if (current_row == clicked_item) {
1273         //If we just activated a slicer
1274         if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1275           mSlicerManagers[i]->UpdateSlicer(column-1,clicked_item->data(column,Qt::CheckStateRole).toInt());
1276           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1277           DisplaySliders(i,column-1);
1278           std::map<std::string,int> overlay_counts;
1279           for (int child = 0; child < current_row->childCount(); child++) {
1280             std::string overlay_type =
1281               current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1282             overlay_counts[overlay_type]++;
1283             current_row->child(child)->setData(column,Qt::CheckStateRole,
1284                                                current_row->data(column,Qt::CheckStateRole));
1285             clicked_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,true);
1286           }
1287         } else { //We don't allow simply desactivating a slicer
1288           clicked_item->setData(column,Qt::CheckStateRole,2);
1289           return;
1290         }
1291       }
1292       //if we clicked on the vector(or overlay) and not the image
1293       else {
1294         if (clicked_item->data(column,Qt::CheckStateRole).toInt()) {
1295           current_row->setData(column,Qt::CheckStateRole,2);
1296           mSlicerManagers[i]->UpdateSlicer(column-1,2);
1297           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1298           DisplaySliders(i,column-1);
1299         }
1300         int vis = clicked_item->data(column,Qt::CheckStateRole).toInt();
1301         std::string overlay_type = clicked_item->data(1,Qt::UserRole).toString().toStdString();
1302         int overlay_index=0;
1303         for (int child = 0; child < current_row->childCount(); child++) {
1304           if (current_row->child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1305             overlay_index++;
1306           if (current_row->child(child) == clicked_item) break;
1307         }
1308         clicked_slicer->SetActorVisibility(
1309           clicked_item->data(1,Qt::UserRole).toString().toStdString(), overlay_index-1,vis);
1310       }
1311     } else if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1312       current_row->setData(column,Qt::CheckStateRole,0);
1313       mSlicerManagers[i]->UpdateSlicer(column-1,0);
1314       std::map<std::string,int> overlay_counts;
1315       for (int child = 0; child < current_row->childCount(); child++) {
1316         std::string overlay_type =
1317           current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1318         overlay_counts[overlay_type]++;
1319         current_row->child(child)->setData(column,Qt::CheckStateRole,0);
1320         vvSlicer * current_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1321         current_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,false);
1322       }
1323     }
1324     //mSlicerManagers[i]->SetColorMap(-1);
1325     mSlicerManagers[i]->SetColorMap();
1326   }
1327   mSlicerManagers[index]->GetSlicer(column-1)->Render();
1328 }
1329 //------------------------------------------------------------------------------
1330
1331 void vvMainWindow::InitSlicers()
1332 {
1333   if (mSlicerManagers.size()) {
1334     mSlicerManagers.back()->GenerateDefaultLookupTable();
1335
1336     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1337     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1338     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1339     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1340   }
1341 }
1342
1343 //------------------------------------------------------------------------------
1344 void vvMainWindow::InitDisplay()
1345 {
1346   if (mSlicerManagers.size()) {
1347     //BE CAREFUL : this is absolutely necessary to set the interactor style
1348     //in order to have the same style instanciation for all SlicerManagers in
1349     // a same window
1350     for (int j = 0; j < 4; j++) {
1351       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1352       style->SetAutoAdjustCameraClippingRange(1);
1353       bool AlreadySelected = false;
1354       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1355         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1356
1357         //select the image only if previous are not selected
1358         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1359           mSlicerManagers[i]->UpdateSlicer(j,1);
1360           AlreadySelected = true;
1361         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1362           if (DataTree->selectedItems().size() == 0)
1363             DataTree->topLevelItem(i)->setSelected(1);
1364           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1365           mSlicerManagers[i]->UpdateSlicer(j,1);
1366           DisplaySliders(i,j);
1367         } else {
1368           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1369           mSlicerManagers[i]->UpdateSlicer(j,0);
1370         }
1371       }
1372       style->Delete();
1373     }
1374   }
1375 }
1376 //------------------------------------------------------------------------------
1377
1378 //------------------------------------------------------------------------------
1379 void vvMainWindow::DisplaySliders(int slicer, int window)
1380 {
1381   int range[2];
1382   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1383   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1384
1385   int tRange[2];
1386   tRange[0] = 0;
1387   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1388   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1389   bool showHorizontal = false;
1390   bool showVertical = false;
1391   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1392       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1393           && mSlicerManagers[slicer]->GetType() != IMAGEWITHTIME
1394           && mSlicerManagers[slicer]->GetType() != MERGEDWITHTIME))
1395     showVertical = true;
1396   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1397       || mSlicerManagers[slicer]->GetType() == IMAGEWITHTIME
1398       || mSlicerManagers[slicer]->GetType() == MERGEDWITHTIME)
1399     showHorizontal = true;
1400
1401   if (showVertical)
1402     verticalSliders[window]->show();
1403   else
1404     verticalSliders[window]->hide();
1405   verticalSliders[window]->setRange(range[0],range[1]);
1406   verticalSliders[window]->setValue(position);
1407
1408   if (showHorizontal)
1409     horizontalSliders[window]->show();
1410   else
1411     horizontalSliders[window]->hide();
1412   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1413   horizontalSliders[window]->setValue(tPosition);
1414 }
1415 //------------------------------------------------------------------------------
1416
1417 //------------------------------------------------------------------------------
1418 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1419 {
1420   int index = GetSlicerIndexFromItem(item);
1421
1422   if (DataTree->topLevelItem(index) != item) {
1423     QString warning = "Do you really want to close the overlay : ";
1424     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1425     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1426                        warning, 0, this);
1427     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1428     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1429     if (msgBox.exec() == QMessageBox::AcceptRole) {
1430       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1431       int overlay_index=0;
1432       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1433         if (DataTree->topLevelItem(index)->\
1434             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1435           overlay_index++;
1436         if (DataTree->topLevelItem(index)->child(child) == item) break;
1437       }
1438       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1439       mSlicerManagers[index]->SetColorMap(0);
1440       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1441       mSlicerManagers[index]->Render();
1442     }
1443   } else if (DataTree->topLevelItemCount() <= 1) {
1444     QString warning = "Do you really want to close the image : ";
1445     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1446     warning += "\nThis is the last image, you're about to close vv !!!";
1447     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1448                        warning, 0, this);
1449     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1450     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1451     if (msgBox.exec() == QMessageBox::AcceptRole) {
1452       this->close();
1453     }
1454   } else {
1455     QString warning = "Do you really want to close the image : ";
1456     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1457     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1458                        warning, 0, this);
1459     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1460     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1461     if (msgBox.exec() == QMessageBox::AcceptRole) {
1462
1463       // Tell tools that we close an image
1464       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1465
1466       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1467       DataTree->takeTopLevelItem(index);
1468       for (int i = 0; i < index; i++) {
1469         Manageriter++;
1470       }
1471       linkPanel->removeImage(index);
1472       mSlicerManagers[index]->RemoveActors();
1473       delete mSlicerManagers[index];
1474       mSlicerManagers.erase(Manageriter);
1475
1476       //
1477       InitDisplay();
1478     }
1479   }
1480 }
1481 //------------------------------------------------------------------------------
1482
1483 //------------------------------------------------------------------------------
1484 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1485 {
1486   // int index = GetSlicerIndexFromItem(item);
1487   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1488   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1489   //     mSlicerManagers[index]->ReloadVF();
1490   //   else
1491   //     mSlicerManagers[index]->Reload();
1492
1493   //   QApplication::restoreOverrideCursor();
1494   int index = GetSlicerIndexFromItem(item);
1495   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1496   QString role=item->data(1,Qt::UserRole).toString();
1497   if ( role == "vector")
1498     mSlicerManagers[index]->ReloadVF();
1499   else if (role == "overlay")
1500     mSlicerManagers[index]->ReloadOverlay();
1501   else if (role == "fusion")
1502     mSlicerManagers[index]->ReloadFusion();
1503   else
1504     mSlicerManagers[index]->Reload();
1505
1506   // Update view and info
1507   ImageInfoChanged();
1508   mSlicerManagers[index]->Render();
1509   QApplication::restoreOverrideCursor();
1510 }
1511 //------------------------------------------------------------------------------
1512
1513 // void vvMainWindow::CropImage()
1514 // {
1515 //   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1516 //   vvCropDialog crop(mSlicerManagers,index);
1517 //   if(crop.exec())
1518 //     AddImage(crop.GetOutput(),"cropped.mhd");
1519 // }
1520
1521 //------------------------------------------------------------------------------
1522 void vvMainWindow::SplitImage()
1523 {
1524   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1525   int dim = mSlicerManagers[index]->GetDimension();
1526   QString warning = "Do you really want to split the ";
1527   warning += QString::number(dim) + "D image ";
1528   warning += DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString() + " into ";
1529   warning += QString::number(mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetSize()[dim-1]) + " ";
1530   warning += QString::number(dim-1) + "D images.";
1531   QMessageBox msgBox(QMessageBox::Warning, tr("Split Image"),
1532                      warning, 0, this);
1533   msgBox.addButton(tr("Split"), QMessageBox::AcceptRole);
1534   msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1535   if (msgBox.exec() == QMessageBox::AcceptRole) {
1536     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1537     if (dim > 2) {
1538       std::string filename = DataTree->selectedItems()[0]->data(0,Qt::UserRole).toString().toStdString();
1539       int numberOfSlice = mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetSize()[dim-1];
1540       std::string path = itksys::SystemTools::GetFilenamePath(
1541                            filename);
1542       path += "/";
1543       path += DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString().toStdString();
1544       path += "%03d";
1545       path += itksys::SystemTools::GetFilenameLastExtension(
1546                 filename).c_str();
1547
1548       typedef itk::NumericSeriesFileNames NameGeneratorType;
1549       NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
1550       nameGenerator->SetSeriesFormat(path.c_str());
1551       nameGenerator->SetStartIndex(0);
1552       nameGenerator->SetEndIndex(numberOfSlice-1);
1553       nameGenerator->SetIncrementIndex(1);
1554
1555       for (int i = 0; i < numberOfSlice; i++) {
1556         vvSlicerManager* imageManager = new vvSlicerManager(4);
1557         imageManager->SetExtractedImage(nameGenerator->GetFileNames()[i],
1558                                         mSlicerManagers[index]->GetSlicer(0)->GetImage(), i);
1559         mSlicerManagers.push_back(imageManager);
1560
1561         //create an item in the tree with good settings
1562         QTreeWidgetItem *item = new QTreeWidgetItem();
1563         item->setData(0,Qt::UserRole,nameGenerator->GetFileNames()[i].c_str());
1564         std::string fileI = itksys::SystemTools::GetFilenameWithoutLastExtension(
1565                               nameGenerator->GetFileNames()[i]).c_str();
1566         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileI.c_str());
1567         for (int j = 1; j <= 4; j++) {
1568           for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1569             DataTree->topLevelItem(i)->setData(j,Qt::CheckStateRole,0);
1570           }
1571           item->setData(j,Qt::CheckStateRole,2);
1572         }
1573
1574         //Create the buttons for reload and close
1575         QTreePushButton* cButton = new QTreePushButton;
1576         cButton->setItem(item);
1577         cButton->setColumn(COLUMN_CLOSE_IMAGE);
1578         cButton->setToolTip(tr("close image"));
1579         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1580         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1581                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1582
1583         QTreePushButton* rButton = new QTreePushButton;
1584         rButton->setItem(item);
1585         rButton->setColumn(COLUMN_RELOAD_IMAGE);
1586         rButton->setToolTip(tr("reload image"));
1587         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1588         rButton->setEnabled(false);
1589         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1590                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1591
1592         DataTree->addTopLevelItem(item);
1593         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1594         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1595
1596         //set the id of the image
1597         QString id = nameGenerator->GetFileNames()[i].c_str() + QString::number(mSlicerManagers.size()-1);
1598         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1599         mSlicerManagers.back()->SetId(id.toStdString());
1600         linkPanel->addImage(fileI, id.toStdString());
1601         connect(mSlicerManagers.back(),SIGNAL(currentImageChanged(std::string)),
1602                 this,SLOT(CurrentImageChanged(std::string)));
1603         connect(mSlicerManagers.back(),SIGNAL(
1604                   UpdatePosition(int, double, double, double, double, double, double, double)),this,
1605                 SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
1606         connect(mSlicerManagers.back(),SIGNAL(UpdateVector(int, double, double, double, double)),
1607                 this, SLOT(VectorChanged(int,double,double,double, double)));
1608         connect(mSlicerManagers.back(),SIGNAL(UpdateOverlay(int, double, double)),
1609                 this, SLOT(OverlayChanged(int,double,double)));
1610         connect(mSlicerManagers.back(),SIGNAL(UpdateFusion(int, double)),
1611                 this, SLOT(FusionChanged(int,double)));
1612         connect(mSlicerManagers.back(),SIGNAL(UpdateWindows(int, int, int)),
1613                 this,SLOT(WindowsChanged(int, int, int)));
1614         connect(mSlicerManagers.back(),SIGNAL(WindowLevelChanged(double, double,int, int)),
1615                 this,SLOT(WindowLevelChanged(double, double, int, int)));
1616         connect(mSlicerManagers.back(),SIGNAL(UpdateSlice(int,int)),
1617                 this,SLOT(UpdateSlice(int,int)));
1618         connect(mSlicerManagers.back(),SIGNAL(UpdateTSlice(int, int)),
1619                 this,SLOT(UpdateTSlice(int, int)));
1620         connect(mSlicerManagers.back(),SIGNAL(UpdateSliceRange(int,int,int,int,int)),
1621                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
1622         connect(mSlicerManagers.back(),SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
1623                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
1624         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
1625         UpdateTree();
1626         qApp->processEvents();
1627         InitSlicers();
1628         InitDisplay();
1629         qApp->processEvents();
1630       }
1631       QApplication::restoreOverrideCursor();
1632     } else {
1633       QApplication::restoreOverrideCursor();
1634       QString error = "Cannot split file (dimensions must be greater than 2) ";
1635       QMessageBox::information(this,tr("Splitting problem"),error);
1636     }
1637   }
1638 }
1639 //------------------------------------------------------------------------------
1640
1641 //------------------------------------------------------------------------------
1642 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1643 {
1644   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1645 }
1646 //------------------------------------------------------------------------------
1647
1648 //------------------------------------------------------------------------------
1649 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1650 {
1651   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1652 }
1653 //------------------------------------------------------------------------------
1654
1655 //------------------------------------------------------------------------------
1656 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1657 {
1658   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1659 }
1660 //------------------------------------------------------------------------------
1661
1662 //------------------------------------------------------------------------------
1663 void vvMainWindow::FusionChanged(int visibility, double value)
1664 {
1665   overlayPanel->getCurrentFusionInfo(visibility,value);
1666 }
1667 //------------------------------------------------------------------------------
1668
1669 //------------------------------------------------------------------------------
1670 void vvMainWindow::WindowsChanged(int window, int view, int slice)
1671 {
1672   infoPanel->setViews(window, view, slice);
1673 }
1674 //------------------------------------------------------------------------------
1675
1676 //------------------------------------------------------------------------------
1677 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap)
1678 {
1679   windowSpinBox->setValue(window);
1680   levelSpinBox->setValue(level);
1681   colorMapComboBox->setCurrentIndex(colormap);
1682   presetComboBox->setCurrentIndex(preset);
1683 }
1684 //------------------------------------------------------------------------------
1685
1686 //------------------------------------------------------------------------------
1687 void vvMainWindow::WindowLevelEdited()
1688 {
1689   presetComboBox->setCurrentIndex(6);
1690   UpdateWindowLevel();
1691 }
1692 //------------------------------------------------------------------------------
1693
1694 //------------------------------------------------------------------------------
1695 void vvMainWindow::UpdateWindowLevel()
1696 {
1697   if (DataTree->selectedItems().size()) {
1698     if (presetComboBox->currentIndex() == 7) //For ventilation
1699       colorMapComboBox->setCurrentIndex(5);
1700     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1701     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1702     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1703     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1704     mSlicerManagers[index]->Render();
1705   }
1706 }
1707 //------------------------------------------------------------------------------
1708
1709 //------------------------------------------------------------------------------
1710 void vvMainWindow::UpdateColorMap()
1711 {
1712   if (DataTree->selectedItems().size()) {
1713     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1714     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1715     mSlicerManagers[index]->Render();
1716   }
1717 }
1718 //------------------------------------------------------------------------------
1719 void vvMainWindow::SwitchWindowLevel()
1720 {
1721   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1722   int window = mSlicerManagers[index]->GetColorWindow();
1723   presetComboBox->setCurrentIndex(6);
1724   windowSpinBox->setValue(-window);
1725   UpdateWindowLevel();
1726 }
1727 //------------------------------------------------------------------------------
1728
1729 //------------------------------------------------------------------------------
1730 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1731 {
1732   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1733     if (mSlicerManagers[i]->GetId() == id) {
1734       //mSlicerManagers[i]->SetTSlice(temps);
1735       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1736       mSlicerManagers[i]->UpdateViews(0,slicer);
1737       break;
1738     }
1739   }
1740 }
1741 //------------------------------------------------------------------------------
1742
1743 //------------------------------------------------------------------------------
1744 void vvMainWindow::ShowContextMenu(QPoint point)
1745 {
1746   if (!DataTree->selectedItems().size()) {
1747     contextActions[1]->setEnabled(0);
1748     contextActions[2]->setEnabled(0);
1749     contextActions[3]->setEnabled(0);
1750     contextActions[4]->setEnabled(0);
1751     contextActions[5]->setEnabled(0);
1752     contextActions[6]->setEnabled(0);
1753     contextActions[7]->setEnabled(0);
1754   } else {
1755     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1756     contextActions[1]->setEnabled(1);
1757     contextActions[2]->setEnabled(
1758       DataTree->itemWidget(DataTree->selectedItems()[0],
1759                            COLUMN_RELOAD_IMAGE)->isEnabled());
1760     contextActions[3]->setEnabled(1);
1761     contextActions[5]->setEnabled(1);
1762     contextActions[6]->setEnabled(1);
1763     contextActions[7]->setEnabled(1);
1764
1765     if (mSlicerManagers[index]->GetDimension() < 3)
1766       contextActions[4]->setEnabled(0);
1767     else
1768       contextActions[4]->setEnabled(1);
1769   }
1770   contextMenu.exec(QCursor::pos());
1771 }
1772 //------------------------------------------------------------------------------
1773
1774 //------------------------------------------------------------------------------
1775 void vvMainWindow::CloseImage()
1776 {
1777   CloseImage(DataTree->selectedItems()[0],0);
1778 }
1779 //------------------------------------------------------------------------------
1780
1781 //------------------------------------------------------------------------------
1782 void vvMainWindow::ReloadImage()
1783 {
1784   ReloadImage(DataTree->selectedItems()[0],0);
1785 }
1786 //------------------------------------------------------------------------------
1787
1788 //------------------------------------------------------------------------------
1789 void vvMainWindow::SelectOverlayImage()
1790 {
1791   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1792
1793   //check if one overlay image is added
1794   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1795     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1796       QString error = "Cannot add more than one compared image\n";
1797       error += "Please remove first ";
1798       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1799       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1800       return;
1801     }
1802
1803   QString Extensions = EXTENSIONS;
1804   Extensions += ";;All Files (*)";
1805   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1806   if (!file.isEmpty())
1807     AddOverlayImage(index,file);
1808 }
1809 //------------------------------------------------------------------------------
1810
1811 //------------------------------------------------------------------------------
1812 void vvMainWindow::AddOverlayImage(int index, QString file)
1813 {
1814
1815   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1816   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1817                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1818   reader->SetFileName(file.toStdString().c_str());
1819   reader->ReadImageInformation();
1820   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1821   int dimension = reader->GetNumberOfDimensions();
1822   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1823   vvProgressDialog progress("Opening " + file.toStdString());
1824   qApp->processEvents();
1825
1826   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1827   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component)) {
1828     //create an item in the tree with good settings
1829     QTreeWidgetItem *item = new QTreeWidgetItem();
1830     item->setData(0,Qt::UserRole,file.toStdString().c_str());
1831     item->setData(1,Qt::UserRole,tr("overlay"));
1832     item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
1833     qApp->processEvents();
1834
1835     for (int j = 1; j <= 4; j++) {
1836       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1837       mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("overlay",0,
1838           DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1839     }
1840
1841     //Create the buttons for reload and close
1842     qApp->processEvents();
1843     QTreePushButton* cButton = new QTreePushButton;
1844     cButton->setItem(item);
1845     cButton->setColumn(COLUMN_CLOSE_IMAGE);
1846     cButton->setToolTip(tr("close image"));
1847     cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1848     connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1849             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1850
1851     QTreePushButton* rButton = new QTreePushButton;
1852     rButton->setItem(item);
1853     rButton->setColumn(COLUMN_RELOAD_IMAGE);
1854     rButton->setToolTip(tr("reload image"));
1855     rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1856     connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1857             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1858
1859     DataTree->topLevelItem(index)->setExpanded(1);
1860     DataTree->topLevelItem(index)->addChild(item);
1861     DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1862     DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1863
1864     //set the id of the image
1865     QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1866     item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1867     UpdateTree();
1868     qApp->processEvents();
1869     ImageInfoChanged();
1870     QApplication::restoreOverrideCursor();
1871   } else {
1872     QApplication::restoreOverrideCursor();
1873     QString error = "Cannot import the new image.\n";
1874     error += mSlicerManagers[index]->GetLastError().c_str();
1875     QMessageBox::information(this,tr("Problem reading image !"),error);
1876   }
1877 }
1878
1879 void vvMainWindow::AddFusionImage()
1880 {
1881   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1882
1883   //check if one fusion image is added
1884   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1885     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
1886       QString error = "Cannot add more than one fusion image\n";
1887       error += "Please remove first ";
1888       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1889       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1890       return;
1891     }
1892
1893   QString Extensions = EXTENSIONS;
1894   Extensions += ";;All Files (*)";
1895   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1896   if (!file.isEmpty()) {
1897     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1898     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1899                                          file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1900     reader->SetFileName(file.toStdString().c_str());
1901     reader->ReadImageInformation();
1902     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1903     if (reader) {
1904       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1905       vvProgressDialog progress("Opening fusion");
1906       qApp->processEvents();
1907
1908       std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1909       if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1910                                             reader->GetNumberOfDimensions(), component)) {
1911         //create an item in the tree with good settings
1912         QTreeWidgetItem *item = new QTreeWidgetItem();
1913         item->setData(0,Qt::UserRole,file.toStdString().c_str());
1914         item->setData(1,Qt::UserRole,tr("fusion"));
1915         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
1916         qApp->processEvents();
1917
1918         for (int j = 1; j <= 4; j++) {
1919           item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1920           mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("fusion",0,
1921               DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1922         }
1923
1924         //Create the buttons for reload and close
1925         qApp->processEvents();
1926         QTreePushButton* cButton = new QTreePushButton;
1927         cButton->setItem(item);
1928         cButton->setColumn(COLUMN_CLOSE_IMAGE);
1929         cButton->setToolTip(tr("close image"));
1930         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1931         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1932                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1933
1934         QTreePushButton* rButton = new QTreePushButton;
1935         rButton->setItem(item);
1936         rButton->setColumn(COLUMN_RELOAD_IMAGE);
1937         rButton->setToolTip(tr("reload image"));
1938         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1939         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1940                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1941
1942         DataTree->topLevelItem(index)->setExpanded(1);
1943         DataTree->topLevelItem(index)->addChild(item);
1944         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1945         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1946
1947         //set the id of the image
1948         QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1949         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1950         UpdateTree();
1951         qApp->processEvents();
1952         ImageInfoChanged();
1953         QApplication::restoreOverrideCursor();
1954       } else {
1955         QApplication::restoreOverrideCursor();
1956         QString error = "Cannot import the new image.\n";
1957         error += mSlicerManagers[index]->GetLastError().c_str();
1958         QMessageBox::information(this,tr("Problem reading image !"),error);
1959       }
1960     } else {
1961       QString error = "Cannot import the new image.\n";
1962       QMessageBox::information(this,tr("Problem reading image !"),error);
1963     }
1964   }
1965 }
1966 //------------------------------------------------------------------------------
1967
1968
1969 //------------------------------------------------------------------------------
1970 void vvMainWindow::OpenField()
1971 {
1972   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1973   //check if a vector field has already been added
1974   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1975     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
1976       QString error = "Cannot add more than one vector field\n";
1977       error += "Please remove first ";
1978       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1979       QMessageBox::information(this,tr("Problem adding vector field!"),error);
1980       return;
1981     }
1982
1983   QString Extensions = "Images ( *.mhd)";
1984   Extensions += ";;Images ( *.vf)";
1985   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
1986   if (!file.isEmpty())
1987     AddField(file,index);
1988 }
1989 //------------------------------------------------------------------------------
1990
1991
1992 //------------------------------------------------------------------------------
1993 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
1994 {
1995   //create an item in the tree with good settings
1996   QTreeWidgetItem *item = new QTreeWidgetItem();
1997   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
1998   item->setData(1,Qt::UserRole,tr("vector"));
1999   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename);
2000   qApp->processEvents();
2001
2002   for (int j = 1; j <= 4; j++) {
2003     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2004     mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("vector",0,
2005         DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
2006   }
2007
2008   //Create the buttons for reload and close
2009   qApp->processEvents();
2010   QTreePushButton* cButton = new QTreePushButton;
2011   cButton->setItem(item);
2012   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2013   cButton->setToolTip(tr("close vector field"));
2014   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2015   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2016           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2017
2018   QTreePushButton* rButton = new QTreePushButton;
2019   rButton->setItem(item);
2020   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2021   rButton->setToolTip(tr("reload vector field"));
2022   rButton->setEnabled(from_disk);
2023   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2024   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2025           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2026
2027   DataTree->topLevelItem(index)->setExpanded(1);
2028   DataTree->topLevelItem(index)->addChild(item);
2029   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2030   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2031
2032   //set the id of the image
2033   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2034   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2035   UpdateTree();
2036   qApp->processEvents();
2037   ImageInfoChanged();
2038   QApplication::restoreOverrideCursor();
2039 }
2040 //------------------------------------------------------------------------------
2041
2042
2043 //------------------------------------------------------------------------------
2044 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2045 {
2046   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2047   vvSlicerManager* imageManager = mSlicerManagers[index];
2048   if (imageManager->SetVF(vf,file.toStdString())) {
2049     AddFieldEntry(file,index,false);
2050   } else {
2051     QString error = "Cannot import the vector field for this image.\n";
2052     error += imageManager->GetLastError().c_str();
2053     QMessageBox::information(this,tr("Problem reading VF !"),error);
2054   }
2055   QApplication::restoreOverrideCursor();
2056 }
2057 //------------------------------------------------------------------------------
2058
2059
2060 //------------------------------------------------------------------------------
2061 void vvMainWindow::AddField(QString file,int index)
2062 {
2063   if (QFile::exists(file)) {
2064     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2065
2066     //init the progress events
2067     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2068     vvProgressDialog progress("Opening " + file.toStdString());
2069     qApp->processEvents();
2070
2071     //read the vector and put it in the current mSlicerManager
2072     vvSlicerManager* imageManager = mSlicerManagers[index];
2073     qApp->processEvents();
2074
2075     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2076     if (imageManager->SetVF(file.toStdString())) {
2077       imageManager->Render();
2078       AddFieldEntry(file,index,true);
2079     } else {
2080       QApplication::restoreOverrideCursor();
2081       QString error = "Cannot import the vector field for this image.\n";
2082       error += imageManager->GetLastError().c_str();
2083       QMessageBox::information(this,tr("Problem reading VF !"),error);
2084     }
2085   } else
2086     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2087
2088 }
2089 //------------------------------------------------------------------------------
2090
2091
2092 //------------------------------------------------------------------------------
2093 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width)
2094 {
2095   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2096   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2097     for (int i = 0; i < 4; i++) {
2098       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2099       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2100       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2101       if (log > 0)
2102         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2103       else
2104         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2105     }
2106   }
2107 }
2108 //------------------------------------------------------------------------------
2109
2110
2111 //------------------------------------------------------------------------------
2112 void vvMainWindow::SetOverlayProperty(int color)
2113 {
2114   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2115   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2116     mSlicerManagers[index]->SetOverlayColor(color);
2117     mSlicerManagers[index]->SetColorMap(0);
2118     mSlicerManagers[index]->Render();
2119   }
2120 }
2121 //------------------------------------------------------------------------------
2122
2123 //------------------------------------------------------------------------------
2124 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level)
2125 {
2126   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2127   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2128     mSlicerManagers[index]->SetFusionOpacity(opacity);
2129     mSlicerManagers[index]->SetFusionColorMap(colormap);
2130     mSlicerManagers[index]->SetFusionWindow(window);
2131     mSlicerManagers[index]->SetFusionLevel(level);
2132     mSlicerManagers[index]->SetColorMap(0);
2133     mSlicerManagers[index]->Render();
2134   }
2135 }
2136 //------------------------------------------------------------------------------
2137
2138 //------------------------------------------------------------------------------
2139 void vvMainWindow::SaveAs()
2140 {
2141   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2142     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2143     return;
2144   }
2145
2146   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2147   int dimension = mSlicerManagers[index]->GetDimension();
2148   QStringList OutputListeFormat;
2149   OutputListeFormat.clear();
2150   if (dimension == 1) {
2151     OutputListeFormat.push_back(".mhd");
2152   }
2153   if (dimension == 2) {
2154     OutputListeFormat.push_back(".bmp");
2155     OutputListeFormat.push_back(".png");
2156     OutputListeFormat.push_back(".jpeg");
2157     OutputListeFormat.push_back(".tif");
2158     OutputListeFormat.push_back(".mhd");
2159     OutputListeFormat.push_back(".hdr");
2160     OutputListeFormat.push_back(".vox");
2161   } else if (dimension == 3) {
2162     OutputListeFormat.push_back(".mhd");
2163     OutputListeFormat.push_back(".hdr");
2164     OutputListeFormat.push_back(".vox");
2165   } else if (dimension == 4) {
2166     OutputListeFormat.push_back(".mhd");
2167   }
2168   QString Extensions = "AllFiles(*.*)";
2169   for (int i = 0; i < OutputListeFormat.count(); i++) {
2170     Extensions += ";;Images ( *";
2171     Extensions += OutputListeFormat[i];
2172     Extensions += ")";
2173   }
2174   QString fileName = QFileDialog::getSaveFileName(this,
2175                      tr("Save As"),
2176                      mSlicerManagers[index]->GetFileName().c_str(),
2177                      Extensions);
2178   if (!fileName.isEmpty()) {
2179     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2180     if (OutputListeFormat.contains(
2181           fileformat.c_str())) {
2182       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2183       std::string action = "Saving";
2184       vvProgressDialog progress("Saving "+fileName.toStdString());
2185       qApp->processEvents();
2186       vvImageWriter *writer = new vvImageWriter;
2187       writer->SetOutputFileName(fileName.toStdString());
2188       writer->SetInput(mSlicerManagers[index]->GetImage());
2189       writer->Update();
2190       QApplication::restoreOverrideCursor();
2191       if (writer->GetLastError().size()) {
2192         QString error = "Saving did not succeed\n";
2193         error += writer->GetLastError().c_str();
2194         QMessageBox::information(this,tr("Saving Problem"),error);
2195         SaveAs();
2196       }
2197     } else {
2198       QString error = fileformat.c_str();
2199       if (error.isEmpty())
2200         error += "no file format specified !";
2201       else
2202         error += " format unknown !!!\n";
2203       QMessageBox::information(this,tr("Saving Problem"),error);
2204       SaveAs();
2205     }
2206   }
2207 }
2208 //------------------------------------------------------------------------------
2209
2210
2211 //------------------------------------------------------------------------------
2212 void vvMainWindow::AddLink(QString image1,QString image2)
2213 {
2214   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2215     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2216       mSlicerManagers[i]->AddLink(image2.toStdString());
2217     }
2218     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2219       mSlicerManagers[i]->AddLink(image1.toStdString());
2220     }
2221   }
2222 }
2223 //------------------------------------------------------------------------------
2224
2225
2226 //------------------------------------------------------------------------------
2227 void vvMainWindow::RemoveLink(QString image1,QString image2)
2228 {
2229   // DD("vvMainWindow:RemoveLink");
2230   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2231     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2232       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2233     }
2234     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2235       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2236     }
2237   }
2238 }
2239 //------------------------------------------------------------------------------
2240
2241 //------------------------------------------------------------------------------
2242 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2243 {
2244   int index = 0;
2245   while(sm != mSlicerManagers[index])
2246     index++;
2247   index = (index+offset) % mSlicerManagers.size();
2248
2249   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2250   //CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2251   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2252   DisplayChanged(item,slicer+1);
2253 }
2254 //------------------------------------------------------------------------------
2255
2256 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2257 {
2258   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2259     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2260       for (int j = 0; j < 4; j++) {
2261         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2262         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2263         //UpdateTSlice(j,value);
2264       }
2265       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2266       break;
2267     }
2268   }
2269 }
2270 //------------------------------------------------------------------------------
2271
2272
2273 //------------------------------------------------------------------------------
2274 void vvMainWindow::NOHorizontalSliderMoved()
2275 {
2276   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2277   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2278 //  mCurrentTime = NOHorizontalSlider->value();
2279 }
2280 //------------------------------------------------------------------------------
2281
2282
2283 //------------------------------------------------------------------------------
2284 void vvMainWindow::NEHorizontalSliderMoved()
2285 {
2286   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2287   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2288 //  mCurrentTime = NEHorizontalSlider->value();
2289 }
2290 //------------------------------------------------------------------------------
2291
2292
2293 //------------------------------------------------------------------------------
2294 void vvMainWindow::SOHorizontalSliderMoved()
2295 {
2296   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2297   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2298   // mCurrentTime = SOHorizontalSlider->value();
2299 }
2300 //------------------------------------------------------------------------------
2301
2302
2303 //------------------------------------------------------------------------------
2304 void vvMainWindow::SEHorizontalSliderMoved()
2305 {
2306   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2307   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2308   // mCurrentTime = SEHorizontalSlider->value();
2309 }
2310 //------------------------------------------------------------------------------
2311
2312 //------------------------------------------------------------------------------
2313 void vvMainWindow::NOVerticalSliderChanged()
2314 {
2315   static int value=-1;
2316   if (value == NOVerticalSlider->value()) return;
2317   else value = NOVerticalSlider->value();
2318   //  int value = NOVerticalSlider->value();
2319   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2320     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2321       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2322         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2323         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2324         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2325         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2326       }
2327       break;
2328     }
2329   }
2330 }
2331 //------------------------------------------------------------------------------
2332
2333
2334 //------------------------------------------------------------------------------
2335 void vvMainWindow::NEVerticalSliderChanged()
2336 {
2337   static int value=-1;
2338   if (value == NEVerticalSlider->value()) return;
2339   else value = NEVerticalSlider->value();
2340   //  int value = NEVerticalSlider->value();
2341   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2342     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2343       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2344         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2345         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2346         mSlicerManagers[i]->UpdateSlice(1);
2347         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2348       }
2349       break;
2350     }
2351   }
2352 }
2353 //------------------------------------------------------------------------------
2354
2355
2356 //------------------------------------------------------------------------------
2357 void vvMainWindow::SOVerticalSliderChanged()
2358 {
2359   // DD("SOVerticalSliderChanged");
2360   static int value=-1;
2361   // DD(value);
2362 //   DD(SOVerticalSlider->value());
2363   if (value == SOVerticalSlider->value()) return;
2364   else value = SOVerticalSlider->value();
2365   //int value = SOVerticalSlider->value();
2366   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2367     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2368       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2369         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2370         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2371         mSlicerManagers[i]->UpdateSlice(2);
2372         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2373       }
2374       // else { DD("avoid SOVerticalSlider slicer update"); }
2375       break;
2376     }
2377   }
2378 }
2379 //------------------------------------------------------------------------------
2380
2381
2382 //------------------------------------------------------------------------------
2383 void vvMainWindow::SEVerticalSliderChanged()
2384 {
2385   static int value=-1;
2386   if (value == SEVerticalSlider->value()) return;
2387   else value = SEVerticalSlider->value();
2388   // int value = SEVerticalSlider->value();
2389   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2390     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2391       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2392         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2393         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2394         mSlicerManagers[i]->UpdateSlice(3);
2395         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2396       }
2397       break;
2398     }
2399   }
2400 }
2401 //------------------------------------------------------------------------------
2402
2403
2404 //------------------------------------------------------------------------------
2405 void vvMainWindow::UpdateSlice(int slicer, int slice)
2406 {
2407   // DD("vvMainWindow::UpdateSlice");
2408 //   DD(slicer);
2409 //   DD(slice);
2410   if (slicer == 0) {
2411     //    if (slice != NOVerticalSlider->value())
2412     NOVerticalSlider->setValue(slice);
2413   } else {
2414     if (slicer == 1)
2415       NEVerticalSlider->setValue(slice);
2416     else {
2417       if (slicer == 2)
2418         SOVerticalSlider->setValue(slice);
2419       else {
2420         if (slicer == 3)
2421           SEVerticalSlider->setValue(slice);
2422       }
2423     }
2424   }
2425   // DD("vvMainWindow:UpdateSlice END");
2426 }
2427 //------------------------------------------------------------------------------
2428
2429
2430 //------------------------------------------------------------------------------
2431 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2432 {
2433   switch (slicer) {
2434   case 0:
2435     NOHorizontalSlider->setValue(slice);
2436     break;
2437   case 1:
2438     NEHorizontalSlider->setValue(slice);
2439     break;
2440   case 2:
2441     SOHorizontalSlider->setValue(slice);
2442     break;
2443   case 3:
2444     SEHorizontalSlider->setValue(slice);
2445     break;
2446   }
2447 }
2448 //------------------------------------------------------------------------------
2449
2450
2451 //------------------------------------------------------------------------------
2452 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2453 {
2454   int position = int((min+max)/2);
2455   int tPosition = int((tmin+tmax)/2);
2456   if (slicer == 0) {
2457     NOVerticalSlider->setValue(position);
2458     NOVerticalSlider->setRange(min,max);
2459     NOHorizontalSlider->setRange(tmin,tmax);
2460     NOHorizontalSlider->setValue(tPosition);
2461   } else if (slicer == 1) {
2462     NEVerticalSlider->setValue(position);
2463     NEVerticalSlider->setRange(min,max);
2464     NEHorizontalSlider->setRange(tmin,tmax);
2465     NEHorizontalSlider->setValue(tPosition);
2466   } else if (slicer == 2) {
2467     SOVerticalSlider->setValue(position);
2468     SOVerticalSlider->setRange(min,max);
2469     SOHorizontalSlider->setRange(tmin,tmax);
2470     SOHorizontalSlider->setValue(tPosition);
2471   } else if (slicer == 3) {
2472     SEVerticalSlider->setValue(position);
2473     SEVerticalSlider->setRange(min,max);
2474     SEHorizontalSlider->setRange(tmin,tmax);
2475     SEHorizontalSlider->setValue(tPosition);
2476   }
2477 }
2478 //------------------------------------------------------------------------------
2479
2480
2481 //------------------------------------------------------------------------------
2482 void vvMainWindow::SaveNOScreenshot()
2483 {
2484   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2485   w2i->SetInput(NOViewWidget->GetRenderWindow());
2486   w2i->Update();
2487   SaveScreenshot(w2i->GetOutput());
2488   w2i->Delete();
2489 }
2490 //------------------------------------------------------------------------------
2491
2492
2493 //------------------------------------------------------------------------------
2494 void vvMainWindow::SaveNEScreenshot()
2495 {
2496   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2497   w2i->SetInput(NEViewWidget->GetRenderWindow());
2498   w2i->Update();
2499   SaveScreenshot(w2i->GetOutput());
2500   w2i->Delete();
2501 }
2502 //------------------------------------------------------------------------------
2503
2504
2505 //------------------------------------------------------------------------------
2506 void vvMainWindow::SaveSOScreenshot()
2507 {
2508   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2509   w2i->SetInput(SOViewWidget->GetRenderWindow());
2510   w2i->Update();
2511   SaveScreenshot(w2i->GetOutput());
2512   w2i->Delete();
2513 }
2514 //------------------------------------------------------------------------------
2515
2516
2517 //------------------------------------------------------------------------------
2518 void vvMainWindow::SaveSEScreenshot()
2519 {
2520   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2521   w2i->SetInput(SEViewWidget->GetRenderWindow());
2522   w2i->Update();
2523   SaveScreenshot(w2i->GetOutput());
2524   w2i->Delete();
2525 }
2526 //------------------------------------------------------------------------------
2527
2528
2529 //------------------------------------------------------------------------------
2530 void vvMainWindow::SaveScreenshot(vtkImageData* image)
2531 {
2532   QString Extensions = "Images( *.png);;";
2533   Extensions += "Images( *.jpg);;";
2534   Extensions += "Images( *.bmp);;";
2535   Extensions += "Images( *.tif);;";
2536   Extensions += "Images( *.ppm)";
2537   QString fileName = QFileDialog::getSaveFileName(this,
2538                      tr("Save As"),
2539                      itksys::SystemTools::GetFilenamePath(
2540                        mSlicerManagers[0]->GetFileName()).c_str(),
2541                      Extensions);
2542   if (!fileName.isEmpty()) {
2543     const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2544     if (!strcmp(ext, ".bmp")) {
2545       vtkBMPWriter *bmp = vtkBMPWriter::New();
2546       bmp->SetInput(image);
2547       bmp->SetFileName(fileName.toStdString().c_str());
2548       bmp->Write();
2549       bmp->Delete();
2550     } else if (!strcmp(ext, ".tif")) {
2551       vtkTIFFWriter *tif = vtkTIFFWriter::New();
2552       tif->SetInput(image);
2553       tif->SetFileName(fileName.toStdString().c_str());
2554       tif->Write();
2555       tif->Delete();
2556     } else if (!strcmp(ext, ".ppm")) {
2557       vtkPNMWriter *pnm = vtkPNMWriter::New();
2558       pnm->SetInput(image);
2559       pnm->SetFileName(fileName.toStdString().c_str());
2560       pnm->Write();
2561       pnm->Delete();
2562     } else if (!strcmp(ext, ".png")) {
2563       vtkPNGWriter *png = vtkPNGWriter::New();
2564       png->SetInput(image);
2565       png->SetFileName(fileName.toStdString().c_str());
2566       png->Write();
2567       png->Delete();
2568     } else if (!strcmp(ext, ".jpg")) {
2569       vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2570       jpg->SetInput(image);
2571       jpg->SetFileName(fileName.toStdString().c_str());
2572       jpg->Write();
2573       jpg->Delete();
2574     } else {
2575       QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2576     }
2577   }
2578
2579 }
2580 //------------------------------------------------------------------------------
2581
2582
2583 //------------------------------------------------------------------------------
2584 void vvMainWindow::GoToCursor()
2585 {
2586   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2587   for (int column = 1; column < 5; column++) {
2588     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
2589       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2590       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2591         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2592       mSlicerManagers[index]->UpdateViews(1,column-1);
2593       mSlicerManagers[index]->UpdateLinked(column-1);
2594       break;
2595     }
2596   }
2597 }
2598 //------------------------------------------------------------------------------
2599
2600 //------------------------------------------------------------------------------
2601 void vvMainWindow::PlayPause()
2602 {
2603   if (playMode) {
2604     playMode = 0;
2605     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2606     ImageInfoChanged();
2607     return;
2608   } else {
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         has_temporal=true;
2614         break;
2615       }
2616     if (has_temporal) {
2617       playMode = 1;
2618       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2619       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2620     }
2621   }
2622 }
2623 //------------------------------------------------------------------------------
2624
2625 //------------------------------------------------------------------------------
2626 void vvMainWindow::PlayNext()
2627 {
2628   if (playMode && !this->isHidden()) {
2629     int image_number=DataTree->topLevelItemCount();
2630     ///Only play one slicer per SM, and only if the SM is being displayed
2631     for (int i=0; i<image_number; i++)
2632       for (int j=0; j<4; j++)
2633         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2634             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
2635           mSlicerManagers[i]->SetNextTSlice(j);
2636           break;
2637         }
2638     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2639   }
2640 }
2641 //------------------------------------------------------------------------------
2642
2643 void vvMainWindow::ShowLastImage()
2644 {
2645   if (mSlicerManagers.size() > 1) {
2646     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2647     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2648     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2649     DisplayChanged(item,1);
2650   }
2651 }
2652
2653 //------------------------------------------------------------------------------
2654 void vvMainWindow::UpdateRenderWindows()
2655 {
2656   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2657   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2658   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2659   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2660 }
2661 //------------------------------------------------------------------------------
2662
2663 //------------------------------------------------------------------------------
2664 void vvMainWindow::SegmentationOnCurrentImage()
2665 {
2666   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2667
2668   vvSegmentationDialog segmentation;
2669   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2670   segmentation.exec();
2671 }
2672 //------------------------------------------------------------------------------
2673
2674 void vvMainWindow::SurfaceViewerLaunch()
2675 {
2676   vvSurfaceViewerDialog surfaceViewer;
2677   surfaceViewer.exec();
2678 }
2679
2680 //------------------------------------------------------------------------------
2681 void vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2682 {
2683   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
2684   slicer_manager->SetImage(image);
2685   slicer_manager->SetFilename(filename);
2686   mSlicerManagers.push_back(slicer_manager);
2687
2688   //create an item in the tree with good settings
2689   QTreeWidgetItem *item = new QTreeWidgetItem();
2690   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2691   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
2692   qApp->processEvents();
2693
2694   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2695
2696   //Create the buttons for reload and close
2697   qApp->processEvents();
2698   QTreePushButton* cButton = new QTreePushButton;
2699   cButton->setItem(item);
2700   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2701   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2702   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2703           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2704
2705   QTreePushButton* rButton = new QTreePushButton;
2706   rButton->setItem(item);
2707   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2708   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2709   rButton->setEnabled(0);
2710   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2711           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2712
2713   DataTree->addTopLevelItem(item);
2714   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2715   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2716
2717   //set the id of the image
2718   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2719   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2720   mSlicerManagers.back()->SetId(id.toStdString());
2721
2722   linkPanel->addImage(filename, id.toStdString());
2723
2724   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
2725           this, SLOT(CurrentImageChanged(std::string)));
2726   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
2727           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2728   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
2729           this, SLOT(VectorChanged(int,double,double,double, double)));
2730   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
2731           this, SLOT(OverlayChanged(int,double,double)));
2732   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
2733           this, SLOT(FusionChanged(int,double)));
2734   connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
2735           this,SLOT(WindowsChanged(int, int, int)));
2736   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
2737           this,SLOT(WindowLevelChanged(double, double, int, int)));
2738   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
2739           this,SLOT(UpdateSlice(int,int)));
2740   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
2741           this,SLOT(UpdateTSlice(int, int)));
2742   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2743           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2744   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2745           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2746   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
2747           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
2748   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2749   UpdateTree();
2750   qApp->processEvents();
2751   InitSlicers();
2752   ShowLastImage();
2753   InitDisplay();
2754   qApp->processEvents();
2755 }
2756 //------------------------------------------------------------------------------
2757
2758
2759 //------------------------------------------------------------------------------
2760 void vvMainWindow::UpdateCurrentSlicer()
2761 {
2762   int index = -1;
2763   if (DataTree->selectedItems().size() > 0) {
2764     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2765   }
2766   mSlicerManagerCurrentIndex = index;
2767 }
2768 //------------------------------------------------------------------------------
2769