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 QTabWidget * vvMainWindow::GetTab()
 545 {
 546   return tabWidget;
 547 }
 548 //------------------------------------------------------------------------------
 549
 550
 551 //------------------------------------------------------------------------------
 552 void vvMainWindow::MergeImages()
 553 {
 554   QString Extensions = EXTENSIONS;
 555   Extensions += ";;All Files (*)";
 556   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 557   if (files.isEmpty())
 558     return;
 559   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 560   std::vector<std::string> vector;
 561
 562   unsigned int currentDim = 0;
 563   std::vector<double> currentSpacing;
 564   std::vector<int> currentSize;
 565   std::vector<double> currentOrigin;
 566
 567   for (int i = 0; i < files.size(); i++) {
 568     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 569                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 570     reader->SetFileName(files[i].toStdString().c_str());
 571     reader->ReadImageInformation();
 572     if (reader)        {
 573       //NOViewWidget->hide();
 574       //NEViewWidget->hide();
 575       //SOViewWidget->hide();
 576       //SEViewWidget->hide();
 577       if (i == 0)
 578         currentDim = reader->GetNumberOfDimensions();
 579       bool IsOk = true;
 580       for (unsigned int j = 0; j < currentDim; j++) {
 581         if (i == 0) {
 582           if (j == 0) {
 583             currentSpacing.resize(currentDim);
 584             currentSize.resize(currentDim);
 585             currentOrigin.resize(currentDim);
 586           }
 587           currentOrigin[j] = reader->GetOrigin(j);
 588           currentSpacing[j] = reader->GetSpacing(j);
 589           currentSize[j] = reader->GetDimensions(j);
 590         } else if (currentDim != reader->GetNumberOfDimensions()
 591                    || currentSpacing[j] != reader->GetSpacing(j)
 592                    || currentSize[j] != (int)reader->GetDimensions(j)
 593                    || currentOrigin[j] != reader->GetOrigin(j)) {
 594           QString error = "Cannot read file (too different from others ";
 595           error += files[i].toStdString().c_str();
 596           QMessageBox::information(this,tr("Reading problem"),error);
 597           IsOk = false;
 598           break;
 599         }
 600       }
 601       if (IsOk)
 602         vector.push_back(files[i].toStdString());
 603     }
 604   }
 605   if (vector.size() > 0)
 606     LoadImages(vector, MERGED);
 607 }
 608 //------------------------------------------------------------------------------
 609
 610
 611 //------------------------------------------------------------------------------
 612 void vvMainWindow::MergeImagesWithTime()
 613 {
 614   QString Extensions = EXTENSIONS;
 615   Extensions += ";;All Files (*)";
 616   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 617   if (files.isEmpty())
 618     return;
 619   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 620   std::vector<std::string> vector;
 621
 622   unsigned int currentDim = 0;
 623   std::vector<double> currentSpacing;
 624   std::vector<int> currentSize;
 625   std::vector<double> currentOrigin;
 626
 627   for (int i = 0; i < files.size(); i++) {
 628     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 629                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 630     if (reader) {
 631       reader->SetFileName(files[i].toStdString().c_str());
 632       reader->ReadImageInformation();
 633       if (i == 0)
 634         currentDim = reader->GetNumberOfDimensions();
 635       bool IsOk = true;
 636       for (unsigned int j = 0; j < currentDim; j++) {
 637         if (i == 0) {
 638           if (j == 0) {
 639             currentSpacing.resize(currentDim);
 640             currentSize.resize(currentDim);
 641             currentOrigin.resize(currentDim);
 642           }
 643           currentOrigin[j] = reader->GetOrigin(j);
 644           currentSpacing[j] = reader->GetSpacing(j);
 645           currentSize[j] = reader->GetDimensions(j);
 646         } else if (currentDim != reader->GetNumberOfDimensions()
 647                    || currentSpacing[j] != reader->GetSpacing(j)
 648                    || currentSize[j] != (int)reader->GetDimensions(j)
 649                    || currentOrigin[j] != reader->GetOrigin(j)) {
 650           QString error = "Cannot read file (too different from others ";
 651           error += files[i].toStdString().c_str();
 652           QMessageBox::information(this,tr("Reading problem"),error);
 653           IsOk = false;
 654           break;
 655         }
 656       }
 657       if (IsOk)
 658         vector.push_back(files[i].toStdString());
 659     } else {
 660       QString error = "Cannot read file info for ";
 661       error += files[i].toStdString().c_str();
 662       error += "\n";
 663       error += "Maybe you're trying to open an image in an unsupported format?\n";
 664       QMessageBox::information(this,tr("Reading problem"),error);
 665     }
 666   }
 667   sort(vector.begin(),vector.end());
 668   if (vector.size() > 1)
 669     LoadImages(vector, MERGEDWITHTIME);
 670   else
 671     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.");
 672 }
 673 //------------------------------------------------------------------------------
 674
 675
 676 //------------------------------------------------------------------------------
 677 void vvMainWindow::OpenDicom()
 678 {
 679   std::vector<std::string> files;
 680
 681 #ifdef CLITK_VV_USE_BDCM
 682   bool r = bdcm::OpenDicomFilesSelectorDialog(files,
 683            "DicomFilesSelectorDialog test",
 684            0,0,800,800,1);
 685
 686   if (r) {
 687     std::cout << "$$$$ main : user clicked 'OK' $$$$"<<std::endl;
 688     std::cout << "$$$$ selected files : "<<std::endl;
 689     std::vector<std::string>::iterator i;
 690     for (i=files.begin(); i!=files.end(); ++i) {
 691       std::cout << *i << std::endl;
 692     }
 693     std::cout << "$$$$ "<<std::endl;
 694
 695     LoadImages(files,DICOM);
 696   } else {
 697     std::cout << "$$$$ main : user clicked 'CANCEL' $$$$"<<std::endl;
 698   }
 699 #else
 700   std::cout << "dicomSeriesSelector " << std::endl;
 701   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 702     files = *(dicomSeriesSelector->GetFilenames());
 703     LoadImages(files,DICOM);
 704   }
 705 #endif
 706
 707 }
 708 //------------------------------------------------------------------------------
 709
 710 //------------------------------------------------------------------------------
 711 void vvMainWindow::OpenImages()
 712 {
 713   QString Extensions = EXTENSIONS;
 714   Extensions += ";;All Files (*)";
 715
 716   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 717   if (files.isEmpty())
 718     return;
 719   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 720   std::vector<std::string> vector;
 721   for (int i = 0; i < files.size(); i++)
 722     vector.push_back(files[i].toStdString());
 723   LoadImages(vector, IMAGE);
 724 }
 725 //------------------------------------------------------------------------------
 726 void vvMainWindow::OpenRecentImage()
 727 {
 728   QAction * caller = qobject_cast<QAction*>(sender());
 729   std::vector<std::string> images;
 730   images.push_back(caller->text().toStdString());
 731   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 732   LoadImages(images,IMAGE);
 733 }
 734 //------------------------------------------------------------------------------
 735
 736
 737 //------------------------------------------------------------------------------
 738 void vvMainWindow::OpenImageWithTime()
 739 {
 740   QString Extensions = EXTENSIONS;
 741   Extensions += ";;All Files (*)";
 742
 743   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 744   if (files.isEmpty())
 745     return;
 746   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 747   std::vector<std::string> vector;
 748   for (int i = 0; i < files.size(); i++) {
 749     vector.push_back(files[i].toStdString());
 750   }
 751   LoadImages(vector, IMAGEWITHTIME);
 752 }
 753 //------------------------------------------------------------------------------
 754
 755
 756 //------------------------------------------------------------------------------
 757 void vvMainWindow::LoadImages(std::vector<std::string> files, LoadedImageType filetype)
 758 {
 759   //Separate the way to open images and dicoms
 760   int fileSize;
 761   if (filetype == IMAGE || filetype == IMAGEWITHTIME)
 762     fileSize = files.size();
 763   else
 764     fileSize = 1;
 765
 766   //Only add to the list of recently opened files when a single file is opened,
 767   //to avoid polluting the list of recently opened files
 768   if (files.size() == 1) {
 769     QFileInfo finfo=tr(files[0].c_str());
 770     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 771   }
 772   //init the progress events
 773   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 774   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 775   qApp->processEvents();
 776
 777   int numberofsuccesulreads=0;
 778   //open images as 1 or multiples
 779   for (int i = 0; i < fileSize; i++) {
 780
 781     progress.Update("Opening " + files[i]);
 782     progress.SetProgress(i,fileSize);
 783     qApp->processEvents();
 784
 785     //read the image and put it in mSlicerManagers
 786     vvSlicerManager* imageManager = new vvSlicerManager(4);
 787     qApp->processEvents();
 788
 789     bool SetImageSucceed=false;
 790
 791     // Change filename if an image with the same already exist
 792     //    DD(files[i]);
 793     int number=0;
 794     for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
 795       vvSlicerManager * v = mSlicerManagers[l];
 796       //      DD(v->GetBaseFileName());
 797       // DD(v->GetFileName());
 798       if (v->GetBaseFileName() ==
 799           vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(files[i]))) {
 800         number = std::max(number, v->GetBaseFileNameNumber()+1);
 801       }
 802     }
 803
 804
 805     if (filetype == IMAGE || filetype == IMAGEWITHTIME)
 806       SetImageSucceed = imageManager->SetImage(files[i],filetype, number);
 807     else {
 808       SetImageSucceed = imageManager->SetImages(files,filetype, number);
 809     }
 810     if (SetImageSucceed == false) {
 811       QApplication::restoreOverrideCursor();
 812       QString error = "Cannot open file \n";
 813       error += imageManager->GetLastError().c_str();
 814       QMessageBox::information(this,tr("Reading problem"),error);
 815       delete imageManager;
 816     } else {
 817       mSlicerManagers.push_back(imageManager);
 818
 819       //create an item in the tree with good settings
 820       QTreeWidgetItem *item = new QTreeWidgetItem();
 821       item->setData(0,Qt::UserRole,files[i].c_str());
 822       QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 823       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 824       qApp->processEvents();
 825
 826       //Create the buttons for reload and close
 827       qApp->processEvents();
 828       QTreePushButton* cButton = new QTreePushButton;
 829       cButton->setItem(item);
 830       cButton->setColumn(COLUMN_CLOSE_IMAGE);
 831       cButton->setToolTip(tr("close image"));
 832       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 833       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 834               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 835
 836       QTreePushButton* rButton = new QTreePushButton;
 837       rButton->setItem(item);
 838       rButton->setColumn(COLUMN_RELOAD_IMAGE);
 839       rButton->setToolTip(tr("reload image"));
 840       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 841       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 842               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 843
 844       DataTree->addTopLevelItem(item);
 845       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 846       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 847
 848       //set the id of the image
 849       QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 850       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 851       mSlicerManagers.back()->SetId(id.toStdString());
 852
 853       linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 854
 855       connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 856               this,SLOT(CurrentImageChanged(std::string)));
 857       connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 858               this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 859       connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 860               this, SLOT(VectorChanged(int,double,double,double, double)));
 861       connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 862               this, SLOT(OverlayChanged(int,double,double)));
 863       connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 864               this, SLOT(FusionChanged(int,double)));
 865       connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
 866               this,SLOT(WindowsChanged(int, int, int)));
 867       connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
 868               this,SLOT(WindowLevelChanged(double, double, int, int)));
 869       connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 870               this,SLOT(UpdateSlice(int,int)));
 871       connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 872               this,SLOT(UpdateTSlice(int, int)));
 873       connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 874               this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 875       connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 876               this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 877       connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 878               this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 879       connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 880       InitSlicers();
 881       numberofsuccesulreads++;
 882     }
 883   }
 884   if (numberofsuccesulreads) {
 885     NOViewWidget->show();
 886     NEViewWidget->show();
 887     SOViewWidget->show();
 888     SEViewWidget->show();
 889     UpdateTree();
 890     InitDisplay();
 891     ShowLastImage();
 892   }
 893   QApplication::restoreOverrideCursor();
 894
 895   // Try to guess default WindowLevel
 896   double range[2];
 897   mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 898   // DD(range[0]);
 899   //   DD(range[1]);
 900   if ((range[0] == 0) && (range[1] == 1)) {
 901     presetComboBox->setCurrentIndex(5);// binary
 902   } else {
 903     // TODO
 904   }
 905 }
 906 //------------------------------------------------------------------------------
 907
 908 //------------------------------------------------------------------------------
 909 void vvMainWindow::UpdateTree()
 910 {
 911   DataTree->resizeColumnToContents(COLUMN_TREE);
 912   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 913   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 914   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 915   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 916   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 917   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 918   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 919 }
 920 //------------------------------------------------------------------------------
 921
 922 //------------------------------------------------------------------------------
 923 void vvMainWindow::CurrentImageChanged(std::string id)
 924 {
 925   //  DD("CurrentImageChanged");
 926   int selected = 0;
 927   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 928     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 929       selected = i;
 930     } else {
 931       DataTree->topLevelItem(i)->setSelected(0);
 932     }
 933     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 934       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 935
 936   }
 937   DataTree->topLevelItem(selected)->setSelected(1);
 938   //  DD(mSlicerManagers[selected]->GetFileName());
 939   emit SelectedImageHasChanged(mSlicerManagers[selected]);
 940 }
 941 //------------------------------------------------------------------------------
 942
 943 //------------------------------------------------------------------------------
 944 void vvMainWindow::ImageInfoChanged()
 945 {
 946   contextActions[7]->setEnabled(1);
 947   contextActions[6]->setEnabled(1);
 948   actionSave_As->setEnabled(1);
 949   actionAdd_VF_to_current_Image->setEnabled(1);
 950   actionAdd_fusion_image->setEnabled(1);
 951   actionNorth_East_Window->setEnabled(1);
 952   actionNorth_West_Window->setEnabled(1);
 953   actionSouth_East_Window->setEnabled(1);
 954   actionSouth_West_Window->setEnabled(1);
 955   inverseButton->setEnabled(1);
 956
 957   goToCursorPushButton->setEnabled(1);
 958
 959   if (DataTree->selectedItems().size()) {
 960     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 961
 962     colorMapComboBox->setEnabled(1);
 963     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
 964       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
 965           DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion") {
 966         colorMapComboBox->setEnabled(0);
 967         break;
 968       }
 969     }
 970
 971     std::vector<double> origin;
 972     std::vector<double> inputSpacing;
 973     std::vector<int> inputSize;
 974     std::vector<double> sizeMM;
 975     int dimension=0;
 976     QString pixelType;
 977     QString inputSizeInBytes;
 978     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
 979
 980     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1) {
 981       playButton->setEnabled(1);
 982       frameRateLabel->setEnabled(1);
 983       frameRateSpinBox->setEnabled(1);
 984     } else {
 985       playButton->setEnabled(0);
 986       frameRateLabel->setEnabled(0);
 987       frameRateSpinBox->setEnabled(0);
 988     }
 989
 990     //read image header
 991     int NPixel = 1;
 992
 993     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
 994       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
 995       dimension = imageSelected->GetNumberOfDimensions();
 996       origin.resize(dimension);
 997       inputSpacing.resize(dimension);
 998       inputSize.resize(dimension);
 999       sizeMM.resize(dimension);
1000       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
1001       for (int i = 0; i < dimension; i++) {
1002         origin[i] = imageSelected->GetOrigin()[i];
1003         inputSpacing[i] = imageSelected->GetSpacing()[i];
1004         inputSize[i] = imageSelected->GetSize()[i];
1005         sizeMM[i] = inputSize[i]*inputSpacing[i];
1006         NPixel *= inputSize[i];
1007       }
1008       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1009     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1010       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1011       dimension = imageSelected->GetNumberOfDimensions();
1012       origin.resize(dimension);
1013       inputSpacing.resize(dimension);
1014       inputSize.resize(dimension);
1015       sizeMM.resize(dimension);
1016       pixelType = mSlicerManagers[index]->GetVF()->GetScalarTypeAsString().c_str();
1017       for (int i = 0; i < dimension; i++) {
1018         origin[i] = imageSelected->GetOrigin()[i];
1019         inputSpacing[i] = imageSelected->GetSpacing()[i];
1020         inputSize[i] = imageSelected->GetSize()[i];
1021         sizeMM[i] = inputSize[i]*inputSpacing[i];
1022         NPixel *= inputSize[i];
1023       }
1024       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1025     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1026       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1027       dimension = imageSelected->GetNumberOfDimensions();
1028       origin.resize(dimension);
1029       inputSpacing.resize(dimension);
1030       inputSize.resize(dimension);
1031       sizeMM.resize(dimension);
1032       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
1033       for (int i = 0; i < dimension; i++) {
1034         origin[i] = imageSelected->GetOrigin()[i];
1035         inputSpacing[i] = imageSelected->GetSpacing()[i];
1036         inputSize[i] = imageSelected->GetSize()[i];
1037         sizeMM[i] = inputSize[i]*inputSpacing[i];
1038         NPixel *= inputSize[i];
1039       }
1040       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1041     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1042       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1043       dimension = imageSelected->GetNumberOfDimensions();
1044       origin.resize(dimension);
1045       inputSpacing.resize(dimension);
1046       inputSize.resize(dimension);
1047       sizeMM.resize(dimension);
1048       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
1049       for (int i = 0; i < dimension; i++) {
1050         origin[i] = imageSelected->GetOrigin()[i];
1051         inputSpacing[i] = imageSelected->GetSpacing()[i];
1052         inputSize[i] = imageSelected->GetSize()[i];
1053         sizeMM[i] = inputSize[i]*inputSpacing[i];
1054         NPixel *= inputSize[i];
1055       }
1056       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1057     }
1058
1059     QString dim = QString::number(dimension) + " (";
1060     dim += pixelType + ")";
1061
1062     infoPanel->setFileName(image);
1063     infoPanel->setDimension(dim);
1064     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1065     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1066     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1067     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1068     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1069
1070     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1071                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1072     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1073     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1074
1075     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1076     for (int i = 0; i < 4; i++) {
1077       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1078         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1079         break;
1080       }
1081     }
1082     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1083     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1084     // DD(mSlicerManagers[index]->GetColorMap());
1085     // DD(mSlicerManagers[index]->GetPreset());
1086     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1087     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1088
1089     infoPanel->setFileName(image);
1090     infoPanel->setDimension(dim);
1091     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1092     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1093     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1094     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1095     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1096
1097     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1098                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1099     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1100     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1101
1102     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1103     for (int i = 0; i < 4; i++) {
1104       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1105         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1106         break;
1107       }
1108     }
1109     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1110     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1111     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1112     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1113
1114     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1115       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1116       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1117                                   mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1118                                   mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1119     } else {
1120       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1121       overlayPanel->getVFProperty(-1,-1,-1);
1122     }
1123     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1124       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1125       overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1126     } else {
1127       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1128       overlayPanel->getOverlayProperty(-1);
1129     }
1130     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1131       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1132       overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1133                                       mSlicerManagers[index]->GetFusionColorMap(),
1134                                       mSlicerManagers[index]->GetFusionWindow(),
1135                                       mSlicerManagers[index]->GetFusionLevel());
1136     } else {
1137       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1138       overlayPanel->getFusionProperty(-1, -1,-1,-1);
1139     }
1140   }
1141 }
1142 //------------------------------------------------------------------------------
1143
1144 //------------------------------------------------------------------------------
1145 void vvMainWindow::ShowDocumentation()
1146 {
1147   documentation->show();
1148 }
1149 //------------------------------------------------------------------------------
1150 void vvMainWindow::ShowHelpDialog()
1151 {
1152   help_dialog->show();
1153 }
1154 //------------------------------------------------------------------------------
1155
1156 //------------------------------------------------------------------------------
1157 void vvMainWindow::ChangeViewMode()
1158 {
1159   QListIterator<int> it0(splitter_3->sizes());
1160   QListIterator<int> it1(splitter_3->sizes());
1161   int max0 = 0;
1162   int max1 = 1;
1163   while (it0.hasNext()) {
1164     max0 += it0.next();
1165   }
1166   while (it1.hasNext()) {
1167     max1 += it1.next();
1168   }
1169   QList<int> size0;
1170   QList<int> size1;
1171   if (viewMode == 1) {
1172     viewMode = 0;
1173     size0.push_back(max0);
1174     size0.push_back(0);
1175     size1.push_back(max1);
1176     size1.push_back(0);
1177     splitter_3->setSizes(size0);
1178     OSplitter->setSizes(size1);
1179     DataTree->setColumnHidden(2,1);
1180     DataTree->setColumnHidden(3,1);
1181     DataTree->setColumnHidden(4,1);
1182   } else {
1183     viewMode = 1;
1184     size0.push_back(int(max0/2));
1185     size0.push_back(int(max0/2));
1186     size1.push_back(int(max1/2));
1187     size1.push_back(int(max1/2));
1188     splitter_3->setSizes(size0);
1189     OSplitter->setSizes(size1);
1190     DataTree->setColumnHidden(2,0);
1191     DataTree->setColumnHidden(3,0);
1192     DataTree->setColumnHidden(4,0);
1193   }
1194 }
1195 //------------------------------------------------------------------------------
1196
1197 //------------------------------------------------------------------------------
1198 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1199 {
1200   QString result = "";// QString::number(size);
1201   //result += " bytes (";
1202   if (size > 1000000000) {
1203     size /= 1000000000;
1204     result += QString::number(size);
1205     result += "Gb";//)";
1206   } else if (size > 1000000) {
1207     size /= 1000000;
1208     result += QString::number(size);
1209     result += "Mb";//)";
1210   } else if (size > 1000) {
1211     size /= 1000;
1212     result += QString::number(size);
1213     result += "kb";//)";
1214   }
1215   return result;
1216 }
1217 //------------------------------------------------------------------------------
1218
1219 //------------------------------------------------------------------------------
1220 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1221 {
1222   QString result;
1223   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1224     if (i != 0)
1225       result += " ";
1226     result += QString::number(vectorDouble[i]);
1227   }
1228   return result;
1229 }
1230 //------------------------------------------------------------------------------
1231
1232 //------------------------------------------------------------------------------
1233 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1234 {
1235   QString result;
1236   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1237     if (i != 0)
1238       result += " ";
1239     result += QString::number(vectorInt[i]);
1240   }
1241   return result;
1242 }
1243 //------------------------------------------------------------------------------
1244
1245 //------------------------------------------------------------------------------
1246 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1247 {
1248   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1249   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1250     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1251       return i;
1252   }
1253   return -1;
1254 }
1255 //------------------------------------------------------------------------------
1256
1257 //------------------------------------------------------------------------------
1258 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1259 {
1260   QString id = sm->GetId().c_str();
1261   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1262     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1263       return DataTree->topLevelItem(i);
1264   }
1265   return NULL;
1266 }
1267 //------------------------------------------------------------------------------
1268
1269 //------------------------------------------------------------------------------
1270 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clicked_item, int column)
1271 {
1272   int index = GetSlicerIndexFromItem(clicked_item);
1273   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1274     return;
1275   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1276     //Trick to avoid redoing twice the job for a key (sr)
1277     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()-> GetInteractor()->SetKeySym("Crap");
1278
1279     QTreeWidgetItem* current_row=DataTree->topLevelItem(i);
1280     if (DataTree->topLevelItem(index) == current_row) {
1281       vvSlicer* clicked_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1282       if (current_row == clicked_item) {
1283         //If we just activated a slicer
1284         if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1285           mSlicerManagers[i]->UpdateSlicer(column-1,clicked_item->data(column,Qt::CheckStateRole).toInt());
1286           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1287           DisplaySliders(i,column-1);
1288           std::map<std::string,int> overlay_counts;
1289           for (int child = 0; child < current_row->childCount(); child++) {
1290             std::string overlay_type =
1291               current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1292             overlay_counts[overlay_type]++;
1293             current_row->child(child)->setData(column,Qt::CheckStateRole,
1294                                                current_row->data(column,Qt::CheckStateRole));
1295             clicked_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,true);
1296           }
1297         } else { //We don't allow simply desactivating a slicer
1298           clicked_item->setData(column,Qt::CheckStateRole,2);
1299           return;
1300         }
1301       }
1302       //if we clicked on the vector(or overlay) and not the image
1303       else {
1304         if (clicked_item->data(column,Qt::CheckStateRole).toInt()) {
1305           current_row->setData(column,Qt::CheckStateRole,2);
1306           mSlicerManagers[i]->UpdateSlicer(column-1,2);
1307           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1308           DisplaySliders(i,column-1);
1309         }
1310         int vis = clicked_item->data(column,Qt::CheckStateRole).toInt();
1311         std::string overlay_type = clicked_item->data(1,Qt::UserRole).toString().toStdString();
1312         int overlay_index=0;
1313         for (int child = 0; child < current_row->childCount(); child++) {
1314           if (current_row->child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1315             overlay_index++;
1316           if (current_row->child(child) == clicked_item) break;
1317         }
1318         clicked_slicer->SetActorVisibility(
1319           clicked_item->data(1,Qt::UserRole).toString().toStdString(), overlay_index-1,vis);
1320       }
1321     } else if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1322       current_row->setData(column,Qt::CheckStateRole,0);
1323       mSlicerManagers[i]->UpdateSlicer(column-1,0);
1324       std::map<std::string,int> overlay_counts;
1325       for (int child = 0; child < current_row->childCount(); child++) {
1326         std::string overlay_type =
1327           current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1328         overlay_counts[overlay_type]++;
1329         current_row->child(child)->setData(column,Qt::CheckStateRole,0);
1330         vvSlicer * current_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1331         current_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,false);
1332       }
1333     }
1334     //mSlicerManagers[i]->SetColorMap(-1);
1335     mSlicerManagers[i]->SetColorMap();
1336   }
1337   mSlicerManagers[index]->GetSlicer(column-1)->Render();
1338 }
1339 //------------------------------------------------------------------------------
1340
1341 void vvMainWindow::InitSlicers()
1342 {
1343   if (mSlicerManagers.size()) {
1344     mSlicerManagers.back()->GenerateDefaultLookupTable();
1345
1346     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1347     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1348     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1349     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1350   }
1351 }
1352
1353 //------------------------------------------------------------------------------
1354 void vvMainWindow::InitDisplay()
1355 {
1356   if (mSlicerManagers.size()) {
1357     //BE CAREFUL : this is absolutely necessary to set the interactor style
1358     //in order to have the same style instanciation for all SlicerManagers in
1359     // a same window
1360     for (int j = 0; j < 4; j++) {
1361       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1362       style->SetAutoAdjustCameraClippingRange(1);
1363       bool AlreadySelected = false;
1364       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1365         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1366
1367         //select the image only if previous are not selected
1368         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1369           mSlicerManagers[i]->UpdateSlicer(j,1);
1370           AlreadySelected = true;
1371         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1372           if (DataTree->selectedItems().size() == 0)
1373             DataTree->topLevelItem(i)->setSelected(1);
1374           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1375           mSlicerManagers[i]->UpdateSlicer(j,1);
1376           DisplaySliders(i,j);
1377         } else {
1378           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1379           mSlicerManagers[i]->UpdateSlicer(j,0);
1380         }
1381       }
1382       style->Delete();
1383     }
1384   }
1385 }
1386 //------------------------------------------------------------------------------
1387
1388 //------------------------------------------------------------------------------
1389 void vvMainWindow::DisplaySliders(int slicer, int window)
1390 {
1391   int range[2];
1392   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1393   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1394
1395   int tRange[2];
1396   tRange[0] = 0;
1397   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1398   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1399   bool showHorizontal = false;
1400   bool showVertical = false;
1401   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1402       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1403           && mSlicerManagers[slicer]->GetType() != IMAGEWITHTIME
1404           && mSlicerManagers[slicer]->GetType() != MERGEDWITHTIME))
1405     showVertical = true;
1406   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1407       || mSlicerManagers[slicer]->GetType() == IMAGEWITHTIME
1408       || mSlicerManagers[slicer]->GetType() == MERGEDWITHTIME)
1409     showHorizontal = true;
1410
1411   if (showVertical)
1412     verticalSliders[window]->show();
1413   else
1414     verticalSliders[window]->hide();
1415   verticalSliders[window]->setRange(range[0],range[1]);
1416   verticalSliders[window]->setValue(position);
1417
1418   if (showHorizontal)
1419     horizontalSliders[window]->show();
1420   else
1421     horizontalSliders[window]->hide();
1422   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1423   horizontalSliders[window]->setValue(tPosition);
1424 }
1425 //------------------------------------------------------------------------------
1426
1427 //------------------------------------------------------------------------------
1428 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1429 {
1430   int index = GetSlicerIndexFromItem(item);
1431
1432   if (DataTree->topLevelItem(index) != item) {
1433     QString warning = "Do you really want to close the overlay : ";
1434     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1435     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1436                        warning, 0, this);
1437     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1438     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1439     if (msgBox.exec() == QMessageBox::AcceptRole) {
1440       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1441       int overlay_index=0;
1442       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1443         if (DataTree->topLevelItem(index)->\
1444             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1445           overlay_index++;
1446         if (DataTree->topLevelItem(index)->child(child) == item) break;
1447       }
1448       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1449       mSlicerManagers[index]->SetColorMap(0);
1450       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1451       mSlicerManagers[index]->Render();
1452     }
1453   } else if (DataTree->topLevelItemCount() <= 1) {
1454     QString warning = "Do you really want to close the image : ";
1455     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1456     warning += "\nThis is the last image, you're about to close vv !!!";
1457     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1458                        warning, 0, this);
1459     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1460     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1461     if (msgBox.exec() == QMessageBox::AcceptRole) {
1462       this->close();
1463     }
1464   } else {
1465     QString warning = "Do you really want to close the image : ";
1466     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1467     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1468                        warning, 0, this);
1469     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1470     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1471     if (msgBox.exec() == QMessageBox::AcceptRole) {
1472
1473       // Tell tools that we close an image
1474       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1475
1476       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1477       DataTree->takeTopLevelItem(index);
1478       for (int i = 0; i < index; i++) {
1479         Manageriter++;
1480       }
1481       linkPanel->removeImage(index);
1482       mSlicerManagers[index]->RemoveActors();
1483       delete mSlicerManagers[index];
1484       mSlicerManagers.erase(Manageriter);
1485
1486       //
1487       InitDisplay();
1488     }
1489   }
1490 }
1491 //------------------------------------------------------------------------------
1492
1493 //------------------------------------------------------------------------------
1494 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1495 {
1496   // int index = GetSlicerIndexFromItem(item);
1497   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1498   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1499   //     mSlicerManagers[index]->ReloadVF();
1500   //   else
1501   //     mSlicerManagers[index]->Reload();
1502
1503   //   QApplication::restoreOverrideCursor();
1504   int index = GetSlicerIndexFromItem(item);
1505   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1506   QString role=item->data(1,Qt::UserRole).toString();
1507   if ( role == "vector")
1508     mSlicerManagers[index]->ReloadVF();
1509   else if (role == "overlay")
1510     mSlicerManagers[index]->ReloadOverlay();
1511   else if (role == "fusion")
1512     mSlicerManagers[index]->ReloadFusion();
1513   else
1514     mSlicerManagers[index]->Reload();
1515
1516   // Update view and info
1517   ImageInfoChanged();
1518   mSlicerManagers[index]->Render();
1519   QApplication::restoreOverrideCursor();
1520 }
1521 //------------------------------------------------------------------------------
1522
1523 // void vvMainWindow::CropImage()
1524 // {
1525 //   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1526 //   vvCropDialog crop(mSlicerManagers,index);
1527 //   if(crop.exec())
1528 //     AddImage(crop.GetOutput(),"cropped.mhd");
1529 // }
1530
1531 //------------------------------------------------------------------------------
1532 void vvMainWindow::SplitImage()
1533 {
1534   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1535   int dim = mSlicerManagers[index]->GetDimension();
1536   QString warning = "Do you really want to split the ";
1537   warning += QString::number(dim) + "D image ";
1538   warning += DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString() + " into ";
1539   warning += QString::number(mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetSize()[dim-1]) + " ";
1540   warning += QString::number(dim-1) + "D images.";
1541   QMessageBox msgBox(QMessageBox::Warning, tr("Split Image"),
1542                      warning, 0, this);
1543   msgBox.addButton(tr("Split"), QMessageBox::AcceptRole);
1544   msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1545   if (msgBox.exec() == QMessageBox::AcceptRole) {
1546     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1547     if (dim > 2) {
1548       std::string filename = DataTree->selectedItems()[0]->data(0,Qt::UserRole).toString().toStdString();
1549       int numberOfSlice = mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetSize()[dim-1];
1550       std::string path = itksys::SystemTools::GetFilenamePath(
1551                            filename);
1552       path += "/";
1553       path += DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString().toStdString();
1554       path += "%03d";
1555       path += itksys::SystemTools::GetFilenameLastExtension(
1556                 filename).c_str();
1557
1558       typedef itk::NumericSeriesFileNames NameGeneratorType;
1559       NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
1560       nameGenerator->SetSeriesFormat(path.c_str());
1561       nameGenerator->SetStartIndex(0);
1562       nameGenerator->SetEndIndex(numberOfSlice-1);
1563       nameGenerator->SetIncrementIndex(1);
1564
1565       for (int i = 0; i < numberOfSlice; i++) {
1566         vvSlicerManager* imageManager = new vvSlicerManager(4);
1567         imageManager->SetExtractedImage(nameGenerator->GetFileNames()[i],
1568                                         mSlicerManagers[index]->GetSlicer(0)->GetImage(), i);
1569         mSlicerManagers.push_back(imageManager);
1570
1571         //create an item in the tree with good settings
1572         QTreeWidgetItem *item = new QTreeWidgetItem();
1573         item->setData(0,Qt::UserRole,nameGenerator->GetFileNames()[i].c_str());
1574         std::string fileI = itksys::SystemTools::GetFilenameWithoutLastExtension(
1575                               nameGenerator->GetFileNames()[i]).c_str();
1576         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileI.c_str());
1577         for (int j = 1; j <= 4; j++) {
1578           for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1579             DataTree->topLevelItem(i)->setData(j,Qt::CheckStateRole,0);
1580           }
1581           item->setData(j,Qt::CheckStateRole,2);
1582         }
1583
1584         //Create the buttons for reload and close
1585         QTreePushButton* cButton = new QTreePushButton;
1586         cButton->setItem(item);
1587         cButton->setColumn(COLUMN_CLOSE_IMAGE);
1588         cButton->setToolTip(tr("close image"));
1589         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1590         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1591                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1592
1593         QTreePushButton* rButton = new QTreePushButton;
1594         rButton->setItem(item);
1595         rButton->setColumn(COLUMN_RELOAD_IMAGE);
1596         rButton->setToolTip(tr("reload image"));
1597         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1598         rButton->setEnabled(false);
1599         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1600                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1601
1602         DataTree->addTopLevelItem(item);
1603         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1604         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1605
1606         //set the id of the image
1607         QString id = nameGenerator->GetFileNames()[i].c_str() + QString::number(mSlicerManagers.size()-1);
1608         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1609         mSlicerManagers.back()->SetId(id.toStdString());
1610         linkPanel->addImage(fileI, id.toStdString());
1611         connect(mSlicerManagers.back(),SIGNAL(currentImageChanged(std::string)),
1612                 this,SLOT(CurrentImageChanged(std::string)));
1613         connect(mSlicerManagers.back(),SIGNAL(
1614                   UpdatePosition(int, double, double, double, double, double, double, double)),this,
1615                 SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
1616         connect(mSlicerManagers.back(),SIGNAL(UpdateVector(int, double, double, double, double)),
1617                 this, SLOT(VectorChanged(int,double,double,double, double)));
1618         connect(mSlicerManagers.back(),SIGNAL(UpdateOverlay(int, double, double)),
1619                 this, SLOT(OverlayChanged(int,double,double)));
1620         connect(mSlicerManagers.back(),SIGNAL(UpdateFusion(int, double)),
1621                 this, SLOT(FusionChanged(int,double)));
1622         connect(mSlicerManagers.back(),SIGNAL(UpdateWindows(int, int, int)),
1623                 this,SLOT(WindowsChanged(int, int, int)));
1624         connect(mSlicerManagers.back(),SIGNAL(WindowLevelChanged(double, double,int, int)),
1625                 this,SLOT(WindowLevelChanged(double, double, int, int)));
1626         connect(mSlicerManagers.back(),SIGNAL(UpdateSlice(int,int)),
1627                 this,SLOT(UpdateSlice(int,int)));
1628         connect(mSlicerManagers.back(),SIGNAL(UpdateTSlice(int, int)),
1629                 this,SLOT(UpdateTSlice(int, int)));
1630         connect(mSlicerManagers.back(),SIGNAL(UpdateSliceRange(int,int,int,int,int)),
1631                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
1632         connect(mSlicerManagers.back(),SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
1633                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
1634         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
1635         UpdateTree();
1636         qApp->processEvents();
1637         InitSlicers();
1638         InitDisplay();
1639         qApp->processEvents();
1640       }
1641       QApplication::restoreOverrideCursor();
1642     } else {
1643       QApplication::restoreOverrideCursor();
1644       QString error = "Cannot split file (dimensions must be greater than 2) ";
1645       QMessageBox::information(this,tr("Splitting problem"),error);
1646     }
1647   }
1648 }
1649 //------------------------------------------------------------------------------
1650
1651 //------------------------------------------------------------------------------
1652 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1653 {
1654   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1655 }
1656 //------------------------------------------------------------------------------
1657
1658 //------------------------------------------------------------------------------
1659 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1660 {
1661   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1662 }
1663 //------------------------------------------------------------------------------
1664
1665 //------------------------------------------------------------------------------
1666 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1667 {
1668   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1669 }
1670 //------------------------------------------------------------------------------
1671
1672 //------------------------------------------------------------------------------
1673 void vvMainWindow::FusionChanged(int visibility, double value)
1674 {
1675   overlayPanel->getCurrentFusionInfo(visibility,value);
1676 }
1677 //------------------------------------------------------------------------------
1678
1679 //------------------------------------------------------------------------------
1680 void vvMainWindow::WindowsChanged(int window, int view, int slice)
1681 {
1682   infoPanel->setViews(window, view, slice);
1683 }
1684 //------------------------------------------------------------------------------
1685
1686 //------------------------------------------------------------------------------
1687 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap)
1688 {
1689   windowSpinBox->setValue(window);
1690   levelSpinBox->setValue(level);
1691   colorMapComboBox->setCurrentIndex(colormap);
1692   presetComboBox->setCurrentIndex(preset);
1693 }
1694 //------------------------------------------------------------------------------
1695
1696 //------------------------------------------------------------------------------
1697 void vvMainWindow::WindowLevelEdited()
1698 {
1699   presetComboBox->setCurrentIndex(6);
1700   UpdateWindowLevel();
1701 }
1702 //------------------------------------------------------------------------------
1703
1704 //------------------------------------------------------------------------------
1705 void vvMainWindow::UpdateWindowLevel()
1706 {
1707   if (DataTree->selectedItems().size()) {
1708     if (presetComboBox->currentIndex() == 7) //For ventilation
1709       colorMapComboBox->setCurrentIndex(5);
1710     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1711     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1712     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1713     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1714     mSlicerManagers[index]->Render();
1715   }
1716 }
1717 //------------------------------------------------------------------------------
1718
1719 //------------------------------------------------------------------------------
1720 void vvMainWindow::UpdateColorMap()
1721 {
1722   if (DataTree->selectedItems().size()) {
1723     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1724     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1725     mSlicerManagers[index]->Render();
1726   }
1727 }
1728 //------------------------------------------------------------------------------
1729 void vvMainWindow::SwitchWindowLevel()
1730 {
1731   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1732   int window = mSlicerManagers[index]->GetColorWindow();
1733   presetComboBox->setCurrentIndex(6);
1734   windowSpinBox->setValue(-window);
1735   UpdateWindowLevel();
1736 }
1737 //------------------------------------------------------------------------------
1738
1739 //------------------------------------------------------------------------------
1740 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1741 {
1742   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1743     if (mSlicerManagers[i]->GetId() == id) {
1744       //mSlicerManagers[i]->SetTSlice(temps);
1745       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1746       mSlicerManagers[i]->UpdateViews(0,slicer);
1747       break;
1748     }
1749   }
1750 }
1751 //------------------------------------------------------------------------------
1752
1753 //------------------------------------------------------------------------------
1754 void vvMainWindow::ShowContextMenu(QPoint point)
1755 {
1756   if (!DataTree->selectedItems().size()) {
1757     contextActions[1]->setEnabled(0);
1758     contextActions[2]->setEnabled(0);
1759     contextActions[3]->setEnabled(0);
1760     contextActions[4]->setEnabled(0);
1761     contextActions[5]->setEnabled(0);
1762     contextActions[6]->setEnabled(0);
1763     contextActions[7]->setEnabled(0);
1764   } else {
1765     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1766     contextActions[1]->setEnabled(1);
1767     contextActions[2]->setEnabled(
1768       DataTree->itemWidget(DataTree->selectedItems()[0],
1769                            COLUMN_RELOAD_IMAGE)->isEnabled());
1770     contextActions[3]->setEnabled(1);
1771     contextActions[5]->setEnabled(1);
1772     contextActions[6]->setEnabled(1);
1773     contextActions[7]->setEnabled(1);
1774
1775     if (mSlicerManagers[index]->GetDimension() < 3)
1776       contextActions[4]->setEnabled(0);
1777     else
1778       contextActions[4]->setEnabled(1);
1779   }
1780   contextMenu.exec(QCursor::pos());
1781 }
1782 //------------------------------------------------------------------------------
1783
1784 //------------------------------------------------------------------------------
1785 void vvMainWindow::CloseImage()
1786 {
1787   CloseImage(DataTree->selectedItems()[0],0);
1788 }
1789 //------------------------------------------------------------------------------
1790
1791 //------------------------------------------------------------------------------
1792 void vvMainWindow::ReloadImage()
1793 {
1794   ReloadImage(DataTree->selectedItems()[0],0);
1795 }
1796 //------------------------------------------------------------------------------
1797
1798 //------------------------------------------------------------------------------
1799 void vvMainWindow::SelectOverlayImage()
1800 {
1801   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1802
1803   //check if one overlay image is added
1804   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1805     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1806       QString error = "Cannot add more than one compared image\n";
1807       error += "Please remove first ";
1808       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1809       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1810       return;
1811     }
1812
1813   QString Extensions = EXTENSIONS;
1814   Extensions += ";;All Files (*)";
1815   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1816   if (!file.isEmpty())
1817     AddOverlayImage(index,file);
1818 }
1819 //------------------------------------------------------------------------------
1820
1821 //------------------------------------------------------------------------------
1822 void vvMainWindow::AddOverlayImage(int index, QString file)
1823 {
1824
1825   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1826   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1827                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1828   reader->SetFileName(file.toStdString().c_str());
1829   reader->ReadImageInformation();
1830   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1831   int dimension = reader->GetNumberOfDimensions();
1832   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1833   vvProgressDialog progress("Opening " + file.toStdString());
1834   qApp->processEvents();
1835
1836   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1837   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component)) {
1838     //create an item in the tree with good settings
1839     QTreeWidgetItem *item = new QTreeWidgetItem();
1840     item->setData(0,Qt::UserRole,file.toStdString().c_str());
1841     item->setData(1,Qt::UserRole,tr("overlay"));
1842     item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
1843     qApp->processEvents();
1844
1845     for (int j = 1; j <= 4; j++) {
1846       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1847       mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("overlay",0,
1848           DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1849     }
1850
1851     //Create the buttons for reload and close
1852     qApp->processEvents();
1853     QTreePushButton* cButton = new QTreePushButton;
1854     cButton->setItem(item);
1855     cButton->setColumn(COLUMN_CLOSE_IMAGE);
1856     cButton->setToolTip(tr("close image"));
1857     cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1858     connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1859             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1860
1861     QTreePushButton* rButton = new QTreePushButton;
1862     rButton->setItem(item);
1863     rButton->setColumn(COLUMN_RELOAD_IMAGE);
1864     rButton->setToolTip(tr("reload image"));
1865     rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1866     connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1867             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1868
1869     DataTree->topLevelItem(index)->setExpanded(1);
1870     DataTree->topLevelItem(index)->addChild(item);
1871     DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1872     DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1873
1874     //set the id of the image
1875     QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1876     item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1877     UpdateTree();
1878     qApp->processEvents();
1879     ImageInfoChanged();
1880     QApplication::restoreOverrideCursor();
1881   } else {
1882     QApplication::restoreOverrideCursor();
1883     QString error = "Cannot import the new image.\n";
1884     error += mSlicerManagers[index]->GetLastError().c_str();
1885     QMessageBox::information(this,tr("Problem reading image !"),error);
1886   }
1887 }
1888
1889 void vvMainWindow::AddFusionImage()
1890 {
1891   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1892
1893   //check if one fusion image is added
1894   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1895     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
1896       QString error = "Cannot add more than one fusion image\n";
1897       error += "Please remove first ";
1898       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1899       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1900       return;
1901     }
1902
1903   QString Extensions = EXTENSIONS;
1904   Extensions += ";;All Files (*)";
1905   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1906   if (!file.isEmpty()) {
1907     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1908     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1909                                          file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1910     reader->SetFileName(file.toStdString().c_str());
1911     reader->ReadImageInformation();
1912     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1913     if (reader) {
1914       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1915       vvProgressDialog progress("Opening fusion");
1916       qApp->processEvents();
1917
1918       std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1919       if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1920                                             reader->GetNumberOfDimensions(), component)) {
1921         //create an item in the tree with good settings
1922         QTreeWidgetItem *item = new QTreeWidgetItem();
1923         item->setData(0,Qt::UserRole,file.toStdString().c_str());
1924         item->setData(1,Qt::UserRole,tr("fusion"));
1925         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
1926         qApp->processEvents();
1927
1928         for (int j = 1; j <= 4; j++) {
1929           item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1930           mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("fusion",0,
1931               DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1932         }
1933
1934         //Create the buttons for reload and close
1935         qApp->processEvents();
1936         QTreePushButton* cButton = new QTreePushButton;
1937         cButton->setItem(item);
1938         cButton->setColumn(COLUMN_CLOSE_IMAGE);
1939         cButton->setToolTip(tr("close image"));
1940         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1941         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1942                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1943
1944         QTreePushButton* rButton = new QTreePushButton;
1945         rButton->setItem(item);
1946         rButton->setColumn(COLUMN_RELOAD_IMAGE);
1947         rButton->setToolTip(tr("reload image"));
1948         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1949         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1950                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1951
1952         DataTree->topLevelItem(index)->setExpanded(1);
1953         DataTree->topLevelItem(index)->addChild(item);
1954         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1955         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1956
1957         //set the id of the image
1958         QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1959         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1960         UpdateTree();
1961         qApp->processEvents();
1962         ImageInfoChanged();
1963         QApplication::restoreOverrideCursor();
1964       } else {
1965         QApplication::restoreOverrideCursor();
1966         QString error = "Cannot import the new image.\n";
1967         error += mSlicerManagers[index]->GetLastError().c_str();
1968         QMessageBox::information(this,tr("Problem reading image !"),error);
1969       }
1970     } else {
1971       QString error = "Cannot import the new image.\n";
1972       QMessageBox::information(this,tr("Problem reading image !"),error);
1973     }
1974   }
1975 }
1976 //------------------------------------------------------------------------------
1977
1978
1979 //------------------------------------------------------------------------------
1980 void vvMainWindow::OpenField()
1981 {
1982   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1983   //check if a vector field has already been added
1984   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1985     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
1986       QString error = "Cannot add more than one vector field\n";
1987       error += "Please remove first ";
1988       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1989       QMessageBox::information(this,tr("Problem adding vector field!"),error);
1990       return;
1991     }
1992
1993   QString Extensions = "Images ( *.mhd)";
1994   Extensions += ";;Images ( *.vf)";
1995   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
1996   if (!file.isEmpty())
1997     AddField(file,index);
1998 }
1999 //------------------------------------------------------------------------------
2000
2001
2002 //------------------------------------------------------------------------------
2003 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2004 {
2005   //create an item in the tree with good settings
2006   QTreeWidgetItem *item = new QTreeWidgetItem();
2007   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2008   item->setData(1,Qt::UserRole,tr("vector"));
2009   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename);
2010   qApp->processEvents();
2011
2012   for (int j = 1; j <= 4; j++) {
2013     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2014     mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("vector",0,
2015         DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
2016   }
2017
2018   //Create the buttons for reload and close
2019   qApp->processEvents();
2020   QTreePushButton* cButton = new QTreePushButton;
2021   cButton->setItem(item);
2022   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2023   cButton->setToolTip(tr("close vector field"));
2024   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2025   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2026           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2027
2028   QTreePushButton* rButton = new QTreePushButton;
2029   rButton->setItem(item);
2030   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2031   rButton->setToolTip(tr("reload vector field"));
2032   rButton->setEnabled(from_disk);
2033   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2034   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2035           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2036
2037   DataTree->topLevelItem(index)->setExpanded(1);
2038   DataTree->topLevelItem(index)->addChild(item);
2039   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2040   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2041
2042   //set the id of the image
2043   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2044   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2045   UpdateTree();
2046   qApp->processEvents();
2047   ImageInfoChanged();
2048   QApplication::restoreOverrideCursor();
2049 }
2050 //------------------------------------------------------------------------------
2051
2052
2053 //------------------------------------------------------------------------------
2054 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2055 {
2056   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2057   vvSlicerManager* imageManager = mSlicerManagers[index];
2058   if (imageManager->SetVF(vf,file.toStdString())) {
2059     AddFieldEntry(file,index,false);
2060   } else {
2061     QString error = "Cannot import the vector field for this image.\n";
2062     error += imageManager->GetLastError().c_str();
2063     QMessageBox::information(this,tr("Problem reading VF !"),error);
2064   }
2065   QApplication::restoreOverrideCursor();
2066 }
2067 //------------------------------------------------------------------------------
2068
2069
2070 //------------------------------------------------------------------------------
2071 void vvMainWindow::AddField(QString file,int index)
2072 {
2073   if (QFile::exists(file)) {
2074     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2075
2076     //init the progress events
2077     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2078     vvProgressDialog progress("Opening " + file.toStdString());
2079     qApp->processEvents();
2080
2081     //read the vector and put it in the current mSlicerManager
2082     vvSlicerManager* imageManager = mSlicerManagers[index];
2083     qApp->processEvents();
2084
2085     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2086     if (imageManager->SetVF(file.toStdString())) {
2087       imageManager->Render();
2088       AddFieldEntry(file,index,true);
2089     } else {
2090       QApplication::restoreOverrideCursor();
2091       QString error = "Cannot import the vector field for this image.\n";
2092       error += imageManager->GetLastError().c_str();
2093       QMessageBox::information(this,tr("Problem reading VF !"),error);
2094     }
2095   } else
2096     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2097
2098 }
2099 //------------------------------------------------------------------------------
2100
2101
2102 //------------------------------------------------------------------------------
2103 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width)
2104 {
2105   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2106   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2107     for (int i = 0; i < 4; i++) {
2108       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2109       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2110       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2111       if (log > 0)
2112         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2113       else
2114         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2115     }
2116   }
2117 }
2118 //------------------------------------------------------------------------------
2119
2120
2121 //------------------------------------------------------------------------------
2122 void vvMainWindow::SetOverlayProperty(int color)
2123 {
2124   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2125   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2126     mSlicerManagers[index]->SetOverlayColor(color);
2127     mSlicerManagers[index]->SetColorMap(0);
2128     mSlicerManagers[index]->Render();
2129   }
2130 }
2131 //------------------------------------------------------------------------------
2132
2133 //------------------------------------------------------------------------------
2134 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level)
2135 {
2136   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2137   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2138     mSlicerManagers[index]->SetFusionOpacity(opacity);
2139     mSlicerManagers[index]->SetFusionColorMap(colormap);
2140     mSlicerManagers[index]->SetFusionWindow(window);
2141     mSlicerManagers[index]->SetFusionLevel(level);
2142     mSlicerManagers[index]->SetColorMap(0);
2143     mSlicerManagers[index]->Render();
2144   }
2145 }
2146 //------------------------------------------------------------------------------
2147
2148 //------------------------------------------------------------------------------
2149 void vvMainWindow::SaveAs()
2150 {
2151   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2152     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2153     return;
2154   }
2155
2156   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2157   int dimension = mSlicerManagers[index]->GetDimension();
2158   QStringList OutputListeFormat;
2159   OutputListeFormat.clear();
2160   if (dimension == 1) {
2161     OutputListeFormat.push_back(".mhd");
2162   }
2163   if (dimension == 2) {
2164     OutputListeFormat.push_back(".bmp");
2165     OutputListeFormat.push_back(".png");
2166     OutputListeFormat.push_back(".jpeg");
2167     OutputListeFormat.push_back(".tif");
2168     OutputListeFormat.push_back(".mhd");
2169     OutputListeFormat.push_back(".hdr");
2170     OutputListeFormat.push_back(".vox");
2171   } else if (dimension == 3) {
2172     OutputListeFormat.push_back(".mhd");
2173     OutputListeFormat.push_back(".hdr");
2174     OutputListeFormat.push_back(".vox");
2175   } else if (dimension == 4) {
2176     OutputListeFormat.push_back(".mhd");
2177   }
2178   QString Extensions = "AllFiles(*.*)";
2179   for (int i = 0; i < OutputListeFormat.count(); i++) {
2180     Extensions += ";;Images ( *";
2181     Extensions += OutputListeFormat[i];
2182     Extensions += ")";
2183   }
2184   QString fileName = QFileDialog::getSaveFileName(this,
2185                      tr("Save As"),
2186                      mSlicerManagers[index]->GetFileName().c_str(),
2187                      Extensions);
2188   if (!fileName.isEmpty()) {
2189     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2190     if (OutputListeFormat.contains(
2191           fileformat.c_str())) {
2192       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2193       std::string action = "Saving";
2194       vvProgressDialog progress("Saving "+fileName.toStdString());
2195       qApp->processEvents();
2196       vvImageWriter *writer = new vvImageWriter;
2197       writer->SetOutputFileName(fileName.toStdString());
2198       writer->SetInput(mSlicerManagers[index]->GetImage());
2199       writer->Update();
2200       QApplication::restoreOverrideCursor();
2201       if (writer->GetLastError().size()) {
2202         QString error = "Saving did not succeed\n";
2203         error += writer->GetLastError().c_str();
2204         QMessageBox::information(this,tr("Saving Problem"),error);
2205         SaveAs();
2206       }
2207     } else {
2208       QString error = fileformat.c_str();
2209       if (error.isEmpty())
2210         error += "no file format specified !";
2211       else
2212         error += " format unknown !!!\n";
2213       QMessageBox::information(this,tr("Saving Problem"),error);
2214       SaveAs();
2215     }
2216   }
2217 }
2218 //------------------------------------------------------------------------------
2219
2220
2221 //------------------------------------------------------------------------------
2222 void vvMainWindow::AddLink(QString image1,QString image2)
2223 {
2224   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2225     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2226       mSlicerManagers[i]->AddLink(image2.toStdString());
2227     }
2228     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2229       mSlicerManagers[i]->AddLink(image1.toStdString());
2230     }
2231   }
2232 }
2233 //------------------------------------------------------------------------------
2234
2235
2236 //------------------------------------------------------------------------------
2237 void vvMainWindow::RemoveLink(QString image1,QString image2)
2238 {
2239   // DD("vvMainWindow:RemoveLink");
2240   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2241     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2242       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2243     }
2244     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2245       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2246     }
2247   }
2248 }
2249 //------------------------------------------------------------------------------
2250
2251 //------------------------------------------------------------------------------
2252 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2253 {
2254   int index = 0;
2255   while(sm != mSlicerManagers[index])
2256     index++;
2257   index = (index+offset) % mSlicerManagers.size();
2258
2259   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2260   //CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2261   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2262   DisplayChanged(item,slicer+1);
2263 }
2264 //------------------------------------------------------------------------------
2265
2266 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2267 {
2268   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2269     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2270       for (int j = 0; j < 4; j++) {
2271         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2272         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2273         //UpdateTSlice(j,value);
2274       }
2275       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2276       break;
2277     }
2278   }
2279 }
2280 //------------------------------------------------------------------------------
2281
2282
2283 //------------------------------------------------------------------------------
2284 void vvMainWindow::NOHorizontalSliderMoved()
2285 {
2286   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2287   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2288 //  mCurrentTime = NOHorizontalSlider->value();
2289 }
2290 //------------------------------------------------------------------------------
2291
2292
2293 //------------------------------------------------------------------------------
2294 void vvMainWindow::NEHorizontalSliderMoved()
2295 {
2296   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2297   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2298 //  mCurrentTime = NEHorizontalSlider->value();
2299 }
2300 //------------------------------------------------------------------------------
2301
2302
2303 //------------------------------------------------------------------------------
2304 void vvMainWindow::SOHorizontalSliderMoved()
2305 {
2306   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2307   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2308   // mCurrentTime = SOHorizontalSlider->value();
2309 }
2310 //------------------------------------------------------------------------------
2311
2312
2313 //------------------------------------------------------------------------------
2314 void vvMainWindow::SEHorizontalSliderMoved()
2315 {
2316   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2317   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2318   // mCurrentTime = SEHorizontalSlider->value();
2319 }
2320 //------------------------------------------------------------------------------
2321
2322 //------------------------------------------------------------------------------
2323 void vvMainWindow::NOVerticalSliderChanged()
2324 {
2325   static int value=-1;
2326   if (value == NOVerticalSlider->value()) return;
2327   else value = NOVerticalSlider->value();
2328   //  int value = NOVerticalSlider->value();
2329   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2330     {
2331       if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
2332         {
2333           if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2334             mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2335             mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2336
2337             // If nor Update/Render -> slider not work
2338             // only render = ok navigation, but for contour Update needed but slower ?
2339
2340             mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2341             //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2342           }
2343           break;
2344         }
2345     }
2346 }
2347 //------------------------------------------------------------------------------
2348
2349
2350 //------------------------------------------------------------------------------
2351 void vvMainWindow::NEVerticalSliderChanged()
2352 {
2353   static int value=-1;
2354   if (value == NEVerticalSlider->value()) return;
2355   else value = NEVerticalSlider->value();
2356   //  int value = NEVerticalSlider->value();
2357   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2358     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2359       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2360         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2361         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2362         mSlicerManagers[i]->UpdateSlice(1);
2363         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2364       }
2365       break;
2366     }
2367   }
2368 }
2369 //------------------------------------------------------------------------------
2370
2371
2372 //------------------------------------------------------------------------------
2373 void vvMainWindow::SOVerticalSliderChanged()
2374 {
2375   // DD("SOVerticalSliderChanged");
2376   static int value=-1;
2377   // DD(value);
2378 //   DD(SOVerticalSlider->value());
2379   if (value == SOVerticalSlider->value()) return;
2380   else value = SOVerticalSlider->value();
2381   //int value = SOVerticalSlider->value();
2382   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2383     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2384       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2385         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2386         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2387         mSlicerManagers[i]->UpdateSlice(2);
2388         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2389       }
2390       // else { DD("avoid SOVerticalSlider slicer update"); }
2391       break;
2392     }
2393   }
2394 }
2395 //------------------------------------------------------------------------------
2396
2397
2398 //------------------------------------------------------------------------------
2399 void vvMainWindow::SEVerticalSliderChanged()
2400 {
2401   static int value=-1;
2402   if (value == SEVerticalSlider->value()) return;
2403   else value = SEVerticalSlider->value();
2404   // int value = SEVerticalSlider->value();
2405   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2406     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2407       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2408         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2409         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2410         mSlicerManagers[i]->UpdateSlice(3);
2411         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2412       }
2413       break;
2414     }
2415   }
2416 }
2417 //------------------------------------------------------------------------------
2418
2419
2420 //------------------------------------------------------------------------------
2421 void vvMainWindow::UpdateSlice(int slicer, int slice)
2422 {
2423   // DD("vvMainWindow::UpdateSlice");
2424 //   DD(slicer);
2425 //   DD(slice);
2426   if (slicer == 0) {
2427     //    if (slice != NOVerticalSlider->value())
2428     NOVerticalSlider->setValue(slice);
2429   } else {
2430     if (slicer == 1)
2431       NEVerticalSlider->setValue(slice);
2432     else {
2433       if (slicer == 2)
2434         SOVerticalSlider->setValue(slice);
2435       else {
2436         if (slicer == 3)
2437           SEVerticalSlider->setValue(slice);
2438       }
2439     }
2440   }
2441   // DD("vvMainWindow:UpdateSlice END");
2442 }
2443 //------------------------------------------------------------------------------
2444
2445
2446 //------------------------------------------------------------------------------
2447 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2448 {
2449   switch (slicer) {
2450   case 0:
2451     NOHorizontalSlider->setValue(slice);
2452     break;
2453   case 1:
2454     NEHorizontalSlider->setValue(slice);
2455     break;
2456   case 2:
2457     SOHorizontalSlider->setValue(slice);
2458     break;
2459   case 3:
2460     SEHorizontalSlider->setValue(slice);
2461     break;
2462   }
2463 }
2464 //------------------------------------------------------------------------------
2465
2466
2467 //------------------------------------------------------------------------------
2468 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2469 {
2470   int position = int((min+max)/2);
2471   int tPosition = int((tmin+tmax)/2);
2472   if (slicer == 0) {
2473     NOVerticalSlider->setValue(position);
2474     NOVerticalSlider->setRange(min,max);
2475     NOHorizontalSlider->setRange(tmin,tmax);
2476     NOHorizontalSlider->setValue(tPosition);
2477   } else if (slicer == 1) {
2478     NEVerticalSlider->setValue(position);
2479     NEVerticalSlider->setRange(min,max);
2480     NEHorizontalSlider->setRange(tmin,tmax);
2481     NEHorizontalSlider->setValue(tPosition);
2482   } else if (slicer == 2) {
2483     SOVerticalSlider->setValue(position);
2484     SOVerticalSlider->setRange(min,max);
2485     SOHorizontalSlider->setRange(tmin,tmax);
2486     SOHorizontalSlider->setValue(tPosition);
2487   } else if (slicer == 3) {
2488     SEVerticalSlider->setValue(position);
2489     SEVerticalSlider->setRange(min,max);
2490     SEHorizontalSlider->setRange(tmin,tmax);
2491     SEHorizontalSlider->setValue(tPosition);
2492   }
2493 }
2494 //------------------------------------------------------------------------------
2495
2496
2497 //------------------------------------------------------------------------------
2498 void vvMainWindow::SaveNOScreenshot()
2499 {
2500   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2501   w2i->SetInput(NOViewWidget->GetRenderWindow());
2502   w2i->Update();
2503   SaveScreenshot(w2i->GetOutput());
2504   w2i->Delete();
2505 }
2506 //------------------------------------------------------------------------------
2507
2508
2509 //------------------------------------------------------------------------------
2510 void vvMainWindow::SaveNEScreenshot()
2511 {
2512   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2513   w2i->SetInput(NEViewWidget->GetRenderWindow());
2514   w2i->Update();
2515   SaveScreenshot(w2i->GetOutput());
2516   w2i->Delete();
2517 }
2518 //------------------------------------------------------------------------------
2519
2520
2521 //------------------------------------------------------------------------------
2522 void vvMainWindow::SaveSOScreenshot()
2523 {
2524   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2525   w2i->SetInput(SOViewWidget->GetRenderWindow());
2526   w2i->Update();
2527   SaveScreenshot(w2i->GetOutput());
2528   w2i->Delete();
2529 }
2530 //------------------------------------------------------------------------------
2531
2532
2533 //------------------------------------------------------------------------------
2534 void vvMainWindow::SaveSEScreenshot()
2535 {
2536   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2537   w2i->SetInput(SEViewWidget->GetRenderWindow());
2538   w2i->Update();
2539   SaveScreenshot(w2i->GetOutput());
2540   w2i->Delete();
2541 }
2542 //------------------------------------------------------------------------------
2543
2544
2545 //------------------------------------------------------------------------------
2546 void vvMainWindow::SaveScreenshot(vtkImageData* image)
2547 {
2548   QString Extensions = "Images( *.png);;";
2549   Extensions += "Images( *.jpg);;";
2550   Extensions += "Images( *.bmp);;";
2551   Extensions += "Images( *.tif);;";
2552   Extensions += "Images( *.ppm)";
2553   QString fileName = QFileDialog::getSaveFileName(this,
2554                      tr("Save As"),
2555                      itksys::SystemTools::GetFilenamePath(
2556                        mSlicerManagers[0]->GetFileName()).c_str(),
2557                      Extensions);
2558   if (!fileName.isEmpty()) {
2559     const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2560     if (!strcmp(ext, ".bmp")) {
2561       vtkBMPWriter *bmp = vtkBMPWriter::New();
2562       bmp->SetInput(image);
2563       bmp->SetFileName(fileName.toStdString().c_str());
2564       bmp->Write();
2565       bmp->Delete();
2566     } else if (!strcmp(ext, ".tif")) {
2567       vtkTIFFWriter *tif = vtkTIFFWriter::New();
2568       tif->SetInput(image);
2569       tif->SetFileName(fileName.toStdString().c_str());
2570       tif->Write();
2571       tif->Delete();
2572     } else if (!strcmp(ext, ".ppm")) {
2573       vtkPNMWriter *pnm = vtkPNMWriter::New();
2574       pnm->SetInput(image);
2575       pnm->SetFileName(fileName.toStdString().c_str());
2576       pnm->Write();
2577       pnm->Delete();
2578     } else if (!strcmp(ext, ".png")) {
2579       vtkPNGWriter *png = vtkPNGWriter::New();
2580       png->SetInput(image);
2581       png->SetFileName(fileName.toStdString().c_str());
2582       png->Write();
2583       png->Delete();
2584     } else if (!strcmp(ext, ".jpg")) {
2585       vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2586       jpg->SetInput(image);
2587       jpg->SetFileName(fileName.toStdString().c_str());
2588       jpg->Write();
2589       jpg->Delete();
2590     } else {
2591       QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2592     }
2593   }
2594
2595 }
2596 //------------------------------------------------------------------------------
2597
2598
2599 //------------------------------------------------------------------------------
2600 void vvMainWindow::GoToCursor()
2601 {
2602   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2603   for (int column = 1; column < 5; column++) {
2604     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
2605       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2606       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2607         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2608       mSlicerManagers[index]->UpdateViews(1,column-1);
2609       mSlicerManagers[index]->UpdateLinked(column-1);
2610       break;
2611     }
2612   }
2613 }
2614 //------------------------------------------------------------------------------
2615
2616 //------------------------------------------------------------------------------
2617 void vvMainWindow::PlayPause()
2618 {
2619   if (playMode) {
2620     playMode = 0;
2621     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2622     ImageInfoChanged();
2623     return;
2624   } else {
2625     int image_number=DataTree->topLevelItemCount();
2626     bool has_temporal;
2627     for (int i=0; i<image_number; i++)
2628       if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1) {
2629         has_temporal=true;
2630         break;
2631       }
2632     if (has_temporal) {
2633       playMode = 1;
2634       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2635       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2636     }
2637   }
2638 }
2639 //------------------------------------------------------------------------------
2640
2641 //------------------------------------------------------------------------------
2642 void vvMainWindow::PlayNext()
2643 {
2644   if (playMode && !this->isHidden()) {
2645     int image_number=DataTree->topLevelItemCount();
2646     ///Only play one slicer per SM, and only if the SM is being displayed
2647     for (int i=0; i<image_number; i++)
2648       for (int j=0; j<4; j++)
2649         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2650             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
2651           mSlicerManagers[i]->SetNextTSlice(j);
2652           break;
2653         }
2654     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2655   }
2656 }
2657 //------------------------------------------------------------------------------
2658
2659 void vvMainWindow::ShowLastImage()
2660 {
2661   if (mSlicerManagers.size() > 1) {
2662     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2663     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2664     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2665     DisplayChanged(item,1);
2666   }
2667 }
2668
2669 //------------------------------------------------------------------------------
2670 void vvMainWindow::UpdateRenderWindows()
2671 {
2672   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2673   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2674   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2675   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2676 }
2677 //------------------------------------------------------------------------------
2678
2679 //------------------------------------------------------------------------------
2680 void vvMainWindow::SegmentationOnCurrentImage()
2681 {
2682   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2683
2684   vvSegmentationDialog segmentation;
2685   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2686   segmentation.exec();
2687 }
2688 //------------------------------------------------------------------------------
2689
2690 void vvMainWindow::SurfaceViewerLaunch()
2691 {
2692   vvSurfaceViewerDialog surfaceViewer;
2693   surfaceViewer.exec();
2694 }
2695
2696 //------------------------------------------------------------------------------
2697 void vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2698 {
2699   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
2700   slicer_manager->SetImage(image);
2701   slicer_manager->SetFilename(filename);
2702   mSlicerManagers.push_back(slicer_manager);
2703
2704   //create an item in the tree with good settings
2705   QTreeWidgetItem *item = new QTreeWidgetItem();
2706   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2707   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
2708   qApp->processEvents();
2709
2710   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2711
2712   //Create the buttons for reload and close
2713   qApp->processEvents();
2714   QTreePushButton* cButton = new QTreePushButton;
2715   cButton->setItem(item);
2716   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2717   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2718   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2719           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2720
2721   QTreePushButton* rButton = new QTreePushButton;
2722   rButton->setItem(item);
2723   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2724   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2725   rButton->setEnabled(0);
2726   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2727           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2728
2729   DataTree->addTopLevelItem(item);
2730   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2731   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2732
2733   //set the id of the image
2734   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2735   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2736   mSlicerManagers.back()->SetId(id.toStdString());
2737
2738   linkPanel->addImage(filename, id.toStdString());
2739
2740   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
2741           this, SLOT(CurrentImageChanged(std::string)));
2742   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
2743           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2744   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
2745           this, SLOT(VectorChanged(int,double,double,double, double)));
2746   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
2747           this, SLOT(OverlayChanged(int,double,double)));
2748   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
2749           this, SLOT(FusionChanged(int,double)));
2750   connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
2751           this,SLOT(WindowsChanged(int, int, int)));
2752   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
2753           this,SLOT(WindowLevelChanged(double, double, int, int)));
2754   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
2755           this,SLOT(UpdateSlice(int,int)));
2756   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
2757           this,SLOT(UpdateTSlice(int, int)));
2758   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2759           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2760   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2761           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2762   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
2763           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
2764   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2765   UpdateTree();
2766   qApp->processEvents();
2767   InitSlicers();
2768   ShowLastImage();
2769   InitDisplay();
2770   qApp->processEvents();
2771 }
2772 //------------------------------------------------------------------------------
2773
2774
2775 //------------------------------------------------------------------------------
2776 void vvMainWindow::UpdateCurrentSlicer()
2777 {
2778   int index = -1;
2779   if (DataTree->selectedItems().size() > 0) {
2780     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2781   }
2782   mSlicerManagerCurrentIndex = index;
2783 }
2784 //------------------------------------------------------------------------------
2785