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://www.centreleonberard.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 "vvMidPosition.h"
  42 #include "vvMesh.h"
  43 #include "vvStructSelector.h"
  44 #include "vvMeshReader.h"
  45 #include "clitkConfiguration.h"
  46
  47 // ITK include
  48 #include <itkImage.h>
  49 #include <itkImageFileReader.h>
  50 #include <itkByteSwapper.h>
  51 #include <itkCommand.h>
  52 #include <itkNumericSeriesFileNames.h>
  53
  54 // VTK include
  55 #include <vtkImageData.h>
  56 #include <vtkImageActor.h>
  57 #include <vtkCornerAnnotation.h>
  58 #include <vtkRenderWindow.h>
  59 #include <vtkRenderWindowInteractor.h>
  60 #include <vtkRenderer.h>
  61 #include <vtkRendererCollection.h>
  62 #include <vtkWindowToImageFilter.h>
  63 #include <vtkBMPWriter.h>
  64 #include <vtkTIFFWriter.h>
  65 #include <vtkPNMWriter.h>
  66 #include <vtkPNGWriter.h>
  67 #include <vtkJPEGWriter.h>
  68 #include <vtkFFMPEGWriter.h>
  69 #ifdef VTK_USE_MPEG2_ENCODER
  70   #include <vtkMPEG2Writer.h>
  71 #endif
  72 #include <vtkMatrix4x4.h>
  73 #include <vtkTransform.h>
  74
  75 // Standard includes
  76 #include <iostream>
  77 #include <sstream>
  78 #include <iomanip>
  79
  80 #define COLUMN_TREE 0
  81 #define COLUMN_UL_VIEW 1
  82 #define COLUMN_UR_VIEW 2
  83 #define COLUMN_DL_VIEW 3
  84 #define COLUMN_DR_VIEW 4
  85 #define COLUMN_CLOSE_IMAGE 5
  86 #define COLUMN_RELOAD_IMAGE 6
  87 #define COLUMN_IMAGE_NAME 7
  88
  89 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN )"
  90
  91 /*Data Tree values
  92   0,Qt::UserRole full filename
  93   1,Qt::CheckStateRole checkbutton UL View
  94   1,Qt::UserRole overlay, fusion or vector
  95   2,Qt::CheckStateRole checkbutton UR View
  96   3,Qt::CheckStateRole checkbutton DL View
  97   4,Qt::CheckStateRole checkbutton DR View
  98   5,0  short filename
  99   5,Qt::UserRole mSlicerManager id*/
 100
 101 //------------------------------------------------------------------------------
 102 vvMainWindow::vvMainWindow():vvMainWindowBase()
 103 {
 104   setupUi(this); // this sets up the GUI
 105
 106   mInputPathName = "";
 107   mMenuTools = menuTools;
 108   //  mMenuSegmentation = menuSegmentation;
 109   mContextMenu = &contextMenu;
 110   mMenuExperimentalTools = menuExperimental;
 111   mMainWidget = this;
 112   mCurrentTime = -1;
 113   mCurrentSelectedImageId = "";
 114   mCurrentPickedImageId = "";
 115   mCurrentPickedImageIndex = 0;
 116
 117   //Init the contextMenu
 118   this->setContextMenuPolicy(Qt::CustomContextMenu);
 119   contextActions.resize(0);
 120   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 121                                   tr("O&pen new Image"));
 122   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 123   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 124   contextActions.push_back(actionOpen_new_image);
 125   contextMenu.addSeparator();
 126
 127   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 128                                tr("Close Current Image"));
 129   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 130   contextActions.push_back(actionClose_Image);
 131
 132   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 133                                 tr("Reload Current Image"));
 134   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 135   contextActions.push_back(actionReload_image);
 136
 137   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 138                               tr("Save Current Image"));
 139   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 140   contextActions.push_back(actionSave_image);
 141
 142   contextMenu.addSeparator();
 143
 144   contextMenu.addAction(actionAdd_VF_to_current_Image);
 145   contextActions.push_back(actionAdd_VF_to_current_Image);
 146
 147   QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 148       tr("Add overlay image to current image"));
 149   contextMenu.addAction(actionAdd_Overlay_to_current_Image);
 150   contextActions.push_back(actionAdd_Overlay_to_current_Image);
 151
 152   connect(actionAdd_Overlay_to_current_Image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 153
 154   contextMenu.addAction(actionAdd_fusion_image);
 155   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 156   contextActions.push_back(actionAdd_fusion_image);
 157
 158   // TRIAL DS
 159   /*
 160   QMenu * m = new QMenu(menubar);
 161   m->setTitle("TOTO");
 162   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 163   contextMenu.addMenu(m);
 164   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 165                      tr("BIDON"));
 166   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 167                      tr("BIDON2"));
 168   m->addAction(a);
 169   m->addAction(b);
 170   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 171   */
 172
 173   //init the DataTree
 174   mSlicerManagers.resize(0);
 175
 176   QStringList header;
 177   header.append("");
 178   header.append("TL");
 179   header.append("TR");
 180   header.append("BL");
 181   header.append("BR");
 182   header.append("");
 183   header.append("");
 184   header.append("Name");
 185
 186   DataTree->setHeaderLabels(header);
 187   DataTree->resizeColumnToContents(COLUMN_TREE);
 188   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 189   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 190   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 191   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 192   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 193   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 194   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 195
 196   viewMode = 1;
 197   documentation = new vvDocumentation();
 198   help_dialog = new vvHelpDialog();
 199   dicomSeriesSelector = new vvDicomSeriesSelector();
 200
 201   inverseButton->setEnabled(0);
 202   actionAdd_Overlay_to_current_Image->setEnabled(0);
 203   actionSave_As->setEnabled(0);
 204   actionAdd_VF_to_current_Image->setEnabled(0);
 205   actionAdd_fusion_image->setEnabled(0);
 206
 207   //init the sliders
 208   verticalSliders.push_back(NOVerticalSlider);
 209   verticalSliders.push_back(NEVerticalSlider);
 210   verticalSliders.push_back(SOVerticalSlider);
 211   verticalSliders.push_back(SEVerticalSlider);
 212
 213   for (int i =0; i < 4; i++)
 214     verticalSliders[i]->hide();
 215
 216   horizontalSliders.push_back(NOHorizontalSlider);
 217   horizontalSliders.push_back(NEHorizontalSlider);
 218   horizontalSliders.push_back(SOHorizontalSlider);
 219   horizontalSliders.push_back(SEHorizontalSlider);
 220
 221   for (int i =0; i < 4; i++)
 222     horizontalSliders[i]->hide();
 223
 224
 225   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 226   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 227   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 228   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 229
 230   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 231   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 232   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 233   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 234
 235   //connect everything
 236   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 237   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 238   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 239   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 240   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 241   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 242   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 243   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 244   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 245   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 246   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 247   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 248   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 249   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 250   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 251   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 252
 253   ///////////////////////////////////////////////
 254   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 255   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 256   ///////////////////////////////////////////////
 257
 258   actionNorth_East_Window->setEnabled(0);
 259   actionNorth_West_Window->setEnabled(0);
 260   actionSouth_East_Window->setEnabled(0);
 261   actionSouth_West_Window->setEnabled(0);
 262
 263   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 264   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 265   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 266   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 267
 268   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 269   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 270           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 271
 272   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 273   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 274   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 275   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 276   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 277   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 278   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 279
 280
 281   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 282
 283   connect(linkPanel,SIGNAL(addLink(QString,QString)),this,SLOT(AddLink(QString,QString)));
 284   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 285   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 286   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int)),this,SLOT(SetOverlayProperty(int)));
 287   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,double,double)),
 288           this,SLOT(SetFusionProperty(int,int,double,double)));
 289   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 290
 291   playMode = 0;//pause
 292   mFrameRate = 10;
 293   playButton->setEnabled(0);
 294   frameRateLabel->setEnabled(0);
 295   frameRateSpinBox->setEnabled(0);
 296   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 297   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 298
 299   goToCursorPushButton->setEnabled(0);
 300   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 301
 302   NOViewWidget->hide();
 303   NEViewWidget->hide();
 304   SOViewWidget->hide();
 305   SEViewWidget->hide();
 306
 307   //Recently opened files
 308   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 309   if ( !recent_files.empty() ) {
 310     QMenu * rmenu = new QMenu("Recently opened files...");
 311     rmenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 312     menuFile->insertMenu(actionOpen_Image_With_Time,rmenu);
 313     menuFile->insertSeparator(actionOpen_Image_With_Time);
 314     for (std::list<std::string>::iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 315       QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")),
 316                                    (*i).c_str(),this);
 317       rmenu->addAction(current);
 318       connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 319     }
 320   }
 321
 322   // Adding all new tools (insertion in the menu)
 323   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 324
 325   if (!CLITK_EXPERIMENTAL)
 326     menuExperimental->menuAction()->setVisible(false);
 327
 328
 329   QTimer * timerMemory = new QTimer(this);
 330   //timerMemory->setInterval(5);
 331   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 332   timerMemory->start(2000);
 333
 334 }
 335 //------------------------------------------------------------------------------
 336
 337
 338 //------------------------------------------------------------------------------
 339 void vvMainWindow::UpdateMemoryUsage()
 340 {
 341   //  clitk::PrintMemory(true);
 342   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 343   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 344 }
 345 //------------------------------------------------------------------------------
 346
 347
 348 //------------------------------------------------------------------------------
 349 void vvMainWindow::ComputeMidPosition()
 350 {
 351   bool ok;
 352   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 353   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 354                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 355   if (ok) {
 356     vvMidPosition midp;
 357     midp.slicer_manager = mSlicerManagers[index];
 358     midp.reference_image_index = ref;
 359     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 360     midp.Update();
 361     if (midp.error)
 362       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 363     else {
 364       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 365       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 366     }
 367     QApplication::restoreOverrideCursor();
 368   }
 369 }
 370 //------------------------------------------------------------------------------
 371
 372
 373 //------------------------------------------------------------------------------
 374 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 375 {
 376   QTreeWidgetItem *item = new QTreeWidgetItem();
 377   item->setData(0,Qt::UserRole,"filename.vtk");
 378   item->setData(1,Qt::UserRole,tr("contour"));
 379   QBrush brush;
 380   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 381   brush.setStyle(Qt::SolidPattern);
 382   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 383   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 384
 385   for (int j = 1; j <= 4; j++)
 386     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 387
 388   QTreePushButton* cButton = new QTreePushButton;
 389   cButton->setItem(item);
 390   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 391   cButton->setToolTip(tr("close image"));
 392   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 393   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 394           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 395
 396   QTreePushButton* rButton = new QTreePushButton;
 397   rButton->setItem(item);
 398   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 399   rButton->setToolTip(tr("reload image"));
 400   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 401   rButton->setEnabled(false);
 402   //Not implemented
 403   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 404   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 405
 406   DataTree->topLevelItem(image_index)->setExpanded(1);
 407   DataTree->topLevelItem(image_index)->addChild(item);
 408   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 409   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 410   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 411   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 412
 413   UpdateTree();
 414   mSlicerManagers[image_index]->AddContour(contour,propagation);
 415   mSlicerManagers[image_index]->Render();
 416 }
 417 //------------------------------------------------------------------------------
 418
 419
 420 //------------------------------------------------------------------------------
 421 void vvMainWindow::OpenVTKContour()
 422 {
 423   if (mSlicerManagers.size() > 0) {
 424     QString Extensions = "Images ( *.vtk *.obj)";
 425     Extensions += ";;All Files (*)";
 426     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 427     if (file.isNull())
 428       return;
 429     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 430     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 431     vvMeshReader reader;
 432     reader.SetImage(mSlicerManagers[index]->GetImage());
 433     reader.SetModeToVTK();
 434     reader.SetFilename(file.toStdString());
 435     reader.Update();
 436     AddContour(index,reader.GetOutput()[0],false);
 437     QApplication::restoreOverrideCursor();
 438   }
 439 }
 440 //------------------------------------------------------------------------------
 441
 442
 443 //------------------------------------------------------------------------------
 444 void vvMainWindow::OpenDCStructContour()
 445 {
 446   if (mSlicerManagers.size() > 0) {
 447     QString Extensions = "Dicom Files ( *.dcm RS*)";
 448     Extensions += ";;All Files (*)";
 449     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 450     if (file.isNull())
 451       return;
 452     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 453     vvMeshReader reader;
 454     reader.SetFilename(file.toStdString());
 455     vvStructSelector selector;
 456     selector.SetStructures(reader.GetROINames());
 457     if (!mSlicerManagers[index]->GetVF().IsNull())
 458       selector.EnablePropagationCheckBox();
 459     if (selector.exec()) {
 460       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 461       reader.SetSelectedItems(selector.getSelectedItems());
 462       reader.SetImage(mSlicerManagers[index]->GetImage());
 463       if (selector.PropagationEnabled())
 464         reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 465       reader.Update();
 466       std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 467       for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 468            i!=contours.end(); i++)
 469         AddContour(index,*i,selector.PropagationEnabled());
 470       QApplication::restoreOverrideCursor();
 471     }
 472   }
 473 }
 474 //------------------------------------------------------------------------------
 475
 476
 477 //------------------------------------------------------------------------------
 478 void vvMainWindow::ComputeDeformableRegistration()
 479 {
 480   if (mSlicerManagers.size() > 0) {
 481     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 482     vvDeformationDialog dialog(index,mSlicerManagers);
 483     if (dialog.exec()) {
 484       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 485       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 486       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 487     } else
 488       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 489   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 490 }
 491 //------------------------------------------------------------------------------
 492
 493
 494 //------------------------------------------------------------------------------
 495 void vvMainWindow::WarpImage()
 496 {
 497   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 498   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 499     bool ok;
 500     int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 501                                        mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 502     if (ok) {
 503       WarpImage(mSlicerManagers[index],ref);
 504     }
 505   } else
 506     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 507 }
 508 //------------------------------------------------------------------------------
 509
 510
 511 //------------------------------------------------------------------------------
 512 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 513 {
 514   if (!selected_slicer->GetVF().IsNull()) {
 515     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 516     QFileInfo info(selected_slicer->GetFileName().c_str());
 517     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 518                      reference_phase,this);
 519     if (warp.ComputeWarpedImage()) {
 520       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 521       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 522       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 523       QApplication::restoreOverrideCursor();
 524     } else {
 525       QApplication::restoreOverrideCursor();
 526       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 527     }
 528   } else
 529     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 530 }
 531 //------------------------------------------------------------------------------
 532
 533
 534 //------------------------------------------------------------------------------
 535 vvMainWindow::~vvMainWindow()
 536 {
 537   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 538     if (mSlicerManagers[i] != NULL)
 539       delete mSlicerManagers[i];
 540   }
 541 }
 542 //------------------------------------------------------------------------------
 543
 544 //------------------------------------------------------------------------------
 545 QTabWidget * vvMainWindow::GetTab()
 546 {
 547   return tabWidget;
 548 }
 549 //------------------------------------------------------------------------------
 550
 551
 552 //------------------------------------------------------------------------------
 553 void vvMainWindow::MergeImages()
 554 {
 555   QString Extensions = EXTENSIONS;
 556   Extensions += ";;All Files (*)";
 557   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 558   if (files.isEmpty())
 559     return;
 560   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 561   std::vector<std::string> vector;
 562
 563   unsigned int currentDim = 0;
 564   std::vector<double> currentSpacing;
 565   std::vector<int> currentSize;
 566   std::vector<double> currentOrigin;
 567
 568   for (int i = 0; i < files.size(); i++) {
 569     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 570                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 571     reader->SetFileName(files[i].toStdString().c_str());
 572     reader->ReadImageInformation();
 573     if (reader)        {
 574       //NOViewWidget->hide();
 575       //NEViewWidget->hide();
 576       //SOViewWidget->hide();
 577       //SEViewWidget->hide();
 578       if (i == 0)
 579         currentDim = reader->GetNumberOfDimensions();
 580       bool IsOk = true;
 581       for (unsigned int j = 0; j < currentDim; j++) {
 582         if (i == 0) {
 583           if (j == 0) {
 584             currentSpacing.resize(currentDim);
 585             currentSize.resize(currentDim);
 586             currentOrigin.resize(currentDim);
 587           }
 588           currentOrigin[j] = reader->GetOrigin(j);
 589           currentSpacing[j] = reader->GetSpacing(j);
 590           currentSize[j] = reader->GetDimensions(j);
 591         } else if (currentDim != reader->GetNumberOfDimensions()
 592                    || currentSpacing[j] != reader->GetSpacing(j)
 593                    || currentSize[j] != (int)reader->GetDimensions(j)
 594                    || currentOrigin[j] != reader->GetOrigin(j)) {
 595           QString error = "Cannot read file (too different from others ";
 596           error += files[i].toStdString().c_str();
 597           QMessageBox::information(this,tr("Reading problem"),error);
 598           IsOk = false;
 599           break;
 600         }
 601       }
 602       if (IsOk)
 603         vector.push_back(files[i].toStdString());
 604     }
 605   }
 606   if (vector.size() > 0)
 607     LoadImages(vector, vvImageReader::MERGED);
 608 }
 609 //------------------------------------------------------------------------------
 610
 611 //------------------------------------------------------------------------------
 612 void vvMainWindow::SliceImages()
 613 {
 614   QString Extensions = EXTENSIONS;
 615   Extensions += ";;All Files (*)";
 616
 617   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 618   if (files.isEmpty())
 619     return;
 620   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 621   std::vector<std::string> vector;
 622   for (int i = 0; i < files.size(); i++)
 623     vector.push_back(files[i].toStdString());
 624   LoadImages(vector, vvImageReader::SLICED);
 625 }
 626 //------------------------------------------------------------------------------
 627
 628 //------------------------------------------------------------------------------
 629 void vvMainWindow::MergeImagesWithTime()
 630 {
 631   QString Extensions = EXTENSIONS;
 632   Extensions += ";;All Files (*)";
 633   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 634   if (files.isEmpty())
 635     return;
 636   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 637   std::vector<std::string> vector;
 638
 639   unsigned int currentDim = 0;
 640   std::vector<double> currentSpacing;
 641   std::vector<int> currentSize;
 642   std::vector<double> currentOrigin;
 643
 644   for (int i = 0; i < files.size(); i++) {
 645     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 646                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 647     if (reader) {
 648       reader->SetFileName(files[i].toStdString().c_str());
 649       reader->ReadImageInformation();
 650       if (i == 0)
 651         currentDim = reader->GetNumberOfDimensions();
 652       bool IsOk = true;
 653       for (unsigned int j = 0; j < currentDim; j++) {
 654         if (i == 0) {
 655           if (j == 0) {
 656             currentSpacing.resize(currentDim);
 657             currentSize.resize(currentDim);
 658             currentOrigin.resize(currentDim);
 659           }
 660           currentOrigin[j] = reader->GetOrigin(j);
 661           currentSpacing[j] = reader->GetSpacing(j);
 662           currentSize[j] = reader->GetDimensions(j);
 663         } else if (currentDim != reader->GetNumberOfDimensions()
 664                    || currentSpacing[j] != reader->GetSpacing(j)
 665                    || currentSize[j] != (int)reader->GetDimensions(j)
 666                    || currentOrigin[j] != reader->GetOrigin(j)) {
 667           QString error = "Cannot read file (too different from others ";
 668           error += files[i].toStdString().c_str();
 669           QMessageBox::information(this,tr("Reading problem"),error);
 670           IsOk = false;
 671           break;
 672         }
 673       }
 674       if (IsOk)
 675         vector.push_back(files[i].toStdString());
 676     } else {
 677       QString error = "Cannot read file info for ";
 678       error += files[i].toStdString().c_str();
 679       error += "\n";
 680       error += "Maybe you're trying to open an image in an unsupported format?\n";
 681       QMessageBox::information(this,tr("Reading problem"),error);
 682     }
 683   }
 684   sort(vector.begin(),vector.end());
 685   if (vector.size() > 1)
 686     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 687   else
 688     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.");
 689 }
 690 //------------------------------------------------------------------------------
 691
 692
 693 //------------------------------------------------------------------------------
 694 void vvMainWindow::OpenDicom()
 695 {
 696   std::vector<std::string> files;
 697
 698   std::cout << "dicomSeriesSelector " << std::endl;
 699   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 700     files = *(dicomSeriesSelector->GetFilenames());
 701     LoadImages(files, vvImageReader::DICOM);
 702   }
 703 }
 704 //------------------------------------------------------------------------------
 705
 706 //------------------------------------------------------------------------------
 707 void vvMainWindow::OpenImages()
 708 {
 709   QString Extensions = EXTENSIONS;
 710   Extensions += ";;All Files (*)";
 711
 712   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 713   if (files.isEmpty())
 714     return;
 715   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 716   std::vector<std::string> vector;
 717   for (int i = 0; i < files.size(); i++)
 718     vector.push_back(files[i].toStdString());
 719   LoadImages(vector, vvImageReader::IMAGE);
 720 }
 721 //------------------------------------------------------------------------------
 722 void vvMainWindow::OpenRecentImage()
 723 {
 724   QAction * caller = qobject_cast<QAction*>(sender());
 725   std::vector<std::string> images;
 726   images.push_back(caller->text().toStdString());
 727   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 728   LoadImages(images, vvImageReader::IMAGE);
 729 }
 730 //------------------------------------------------------------------------------
 731
 732
 733 //------------------------------------------------------------------------------
 734 void vvMainWindow::OpenImageWithTime()
 735 {
 736   QString Extensions = EXTENSIONS;
 737   Extensions += ";;All Files (*)";
 738
 739   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 740   if (files.isEmpty())
 741     return;
 742   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 743   std::vector<std::string> vector;
 744   for (int i = 0; i < files.size(); i++) {
 745     vector.push_back(files[i].toStdString());
 746   }
 747   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 748 }
 749 //------------------------------------------------------------------------------
 750
 751
 752 //------------------------------------------------------------------------------
 753 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 754 {
 755   //Separate the way to open images and dicoms
 756   int fileSize;
 757   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 758     fileSize = files.size();
 759   else
 760     fileSize = 1;
 761
 762   // For SLICED, we need the number of slices (ndim and #slices)
 763   std::vector<unsigned int> nSlices;
 764   nSlices.resize(files.size());
 765   std::fill(nSlices.begin(), nSlices.end(), 1);
 766   if (filetype == vvImageReader::SLICED) {
 767     for (int i = 0; i < fileSize; i++) {
 768       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 769       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 770       if (!header) {
 771         nSlices[i] = 0;
 772         QString error = "Cannot open file \n";
 773         error += files[i].c_str();
 774         QMessageBox::information(this,tr("Reading problem"),error);
 775         return;
 776       }
 777       if (header->GetNumberOfDimensions() < 3) {
 778         nSlices[i] = 0;
 779         QString error = "Dimension problem. Cannot slice \n";
 780         error += files[i].c_str();
 781         QMessageBox::information(this,tr("Reading problem"),error);
 782         return;
 783       }
 784       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 785     }
 786   }
 787
 788   //Only add to the list of recently opened files when a single file is opened,
 789   //to avoid polluting the list of recently opened files
 790   if (files.size() == 1) {
 791     QFileInfo finfo=tr(files[0].c_str());
 792     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 793   }
 794   //init the progress events
 795   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 796   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 797   qApp->processEvents();
 798
 799   int numberofsuccesulreads=0;
 800   //open images as 1 or multiples
 801   for (int i = 0; i < fileSize; i++) {
 802
 803     progress.SetText("Opening " + files[i]);
 804     progress.SetProgress(i,fileSize);
 805     qApp->processEvents();
 806
 807     for (unsigned int j = 0; j < nSlices[i]; j++) {
 808       //read the image and put it in mSlicerManagers
 809       vvSlicerManager* imageManager = new vvSlicerManager(4);
 810       qApp->processEvents();
 811
 812       bool SetImageSucceed=false;
 813
 814       // Change filename if an image with the same already exist
 815       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 816
 817       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED)
 818         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 819       else {
 820         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 821       }
 822       if (!SetImageSucceed) {
 823         QApplication::restoreOverrideCursor();
 824         QString error = "Cannot open file \n";
 825         error += imageManager->GetLastError().c_str();
 826         QMessageBox::information(this,tr("Reading problem"),error);
 827         delete imageManager;
 828       } else {
 829         mSlicerManagers.push_back(imageManager);
 830
 831         //create an item in the tree with good settings
 832         QTreeWidgetItem *item = new QTreeWidgetItem();
 833         item->setData(0,Qt::UserRole,files[i].c_str());
 834         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 835         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 836         item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
 837         qApp->processEvents();
 838
 839         //Create the buttons for reload and close
 840         qApp->processEvents();
 841         QTreePushButton* cButton = new QTreePushButton;
 842         cButton->setItem(item);
 843         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 844         cButton->setToolTip(tr("close image"));
 845         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 846         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 847                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 848
 849         QTreePushButton* rButton = new QTreePushButton;
 850         rButton->setItem(item);
 851         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 852         rButton->setToolTip(tr("reload image"));
 853         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 854         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 855                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 856
 857         DataTree->addTopLevelItem(item);
 858         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 859         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 860
 861         //set the id of the image
 862         QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 863         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 864         mSlicerManagers.back()->SetId(id.toStdString());
 865
 866         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 867
 868         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 869                 this,SLOT(CurrentImageChanged(std::string)));
 870         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 871                 this, SLOT(CurrentPickedImageChanged(std::string)));
 872         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 873                 this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 874         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 875                 this, SLOT(VectorChanged(int,double,double,double, double)));
 876         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 877                 this, SLOT(OverlayChanged(int,double,double)));
 878         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 879                 this, SLOT(FusionChanged(int,double)));
 880         connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
 881                 this,SLOT(WindowsChanged(int, int, int)));
 882         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
 883                 this,SLOT(WindowLevelChanged(double, double, int, int)));
 884         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 885                 this,SLOT(UpdateSlice(int,int)));
 886         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 887                 this,SLOT(UpdateTSlice(int, int)));
 888         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 889                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 890         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 891                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 892         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 893                 this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 894         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 895                 this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 896         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 897         InitSlicers();
 898         numberofsuccesulreads++;
 899       }
 900     }
 901   }
 902   if (numberofsuccesulreads) {
 903     NOViewWidget->show();
 904     NEViewWidget->show();
 905     SOViewWidget->show();
 906     SEViewWidget->show();
 907     UpdateTree();
 908     InitDisplay();
 909     ShowLastImage();
 910
 911     // Try to guess default WindowLevel
 912     double range[2];
 913     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 914     if ((range[0] == 0) && (range[1] == 1)) {
 915       presetComboBox->setCurrentIndex(5);// binary
 916     } else {
 917       // TODO
 918     }
 919   }
 920   QApplication::restoreOverrideCursor();
 921 }
 922 //------------------------------------------------------------------------------
 923
 924 //------------------------------------------------------------------------------
 925 void vvMainWindow::UpdateTree()
 926 {
 927   DataTree->resizeColumnToContents(COLUMN_TREE);
 928   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 929   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 930   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 931   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 932   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 933   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 934   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 935 }
 936 //------------------------------------------------------------------------------
 937
 938 //------------------------------------------------------------------------------
 939 void vvMainWindow::CurrentImageChanged(std::string id)
 940 {
 941   if (id == mCurrentSelectedImageId) return; // Do nothing
 942   int selected = 0;
 943   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 944     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 945       selected = i;
 946     } else {
 947       DataTree->topLevelItem(i)->setSelected(0);
 948     }
 949     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 950       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 951
 952   }
 953   DataTree->topLevelItem(selected)->setSelected(1);
 954   mCurrentSelectedImageId = id;
 955   emit SelectedImageHasChanged(mSlicerManagers[selected]);
 956 }
 957 //------------------------------------------------------------------------------
 958
 959 //------------------------------------------------------------------------------
 960 void vvMainWindow::CurrentPickedImageChanged(std::string id)
 961 {
 962   if (id == mCurrentPickedImageId) return; // Do nothing
 963   int selected = 0;
 964   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 965     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 966       selected = i;
 967     } else {
 968       DataTree->topLevelItem(i)->setSelected(0);
 969     }
 970     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 971       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 972
 973   }
 974   DataTree->topLevelItem(selected)->setSelected(1);
 975   mCurrentPickedImageId = id;
 976   mCurrentPickedImageIndex = selected;
 977 }
 978 //------------------------------------------------------------------------------
 979
 980 //------------------------------------------------------------------------------
 981 void vvMainWindow::ImageInfoChanged()
 982 {
 983   contextActions[6]->setEnabled(1);
 984   contextActions[5]->setEnabled(1);
 985   actionSave_As->setEnabled(1);
 986   actionAdd_VF_to_current_Image->setEnabled(1);
 987   actionAdd_fusion_image->setEnabled(1);
 988   actionNorth_East_Window->setEnabled(1);
 989   actionNorth_West_Window->setEnabled(1);
 990   actionSouth_East_Window->setEnabled(1);
 991   actionSouth_West_Window->setEnabled(1);
 992   inverseButton->setEnabled(1);
 993
 994   goToCursorPushButton->setEnabled(1);
 995
 996   if (DataTree->selectedItems().size()) {
 997     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 998
 999     colorMapComboBox->setEnabled(1);
1000     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1001       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1002           DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion") {
1003         colorMapComboBox->setEnabled(0);
1004         break;
1005       }
1006     }
1007
1008     std::vector<double> origin;
1009     std::vector<double> inputSpacing;
1010     std::vector<int> inputSize;
1011     std::vector<double> sizeMM;
1012     vtkSmartPointer<vtkMatrix4x4> transformation;
1013     int dimension=0;
1014     QString pixelType;
1015     QString inputSizeInBytes;
1016     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1017
1018     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1) {
1019       playButton->setEnabled(1);
1020       frameRateLabel->setEnabled(1);
1021       frameRateSpinBox->setEnabled(1);
1022     } else {
1023       playButton->setEnabled(0);
1024       frameRateLabel->setEnabled(0);
1025       frameRateSpinBox->setEnabled(0);
1026     }
1027
1028     //read image header
1029     int NPixel = 1;
1030
1031     vvImage::Pointer imageSelected;
1032     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1033       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1034       dimension = imageSelected->GetNumberOfDimensions();
1035       origin.resize(dimension);
1036       inputSpacing.resize(dimension);
1037       inputSize.resize(dimension);
1038       sizeMM.resize(dimension);
1039       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1040       for (int i = 0; i < dimension; i++) {
1041         origin[i] = imageSelected->GetOrigin()[i];
1042         inputSpacing[i] = imageSelected->GetSpacing()[i];
1043         inputSize[i] = imageSelected->GetSize()[i];
1044         sizeMM[i] = inputSize[i]*inputSpacing[i];
1045         NPixel *= inputSize[i];
1046       }
1047       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1048     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1049       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1050       dimension = imageSelected->GetNumberOfDimensions();
1051       origin.resize(dimension);
1052       inputSpacing.resize(dimension);
1053       inputSize.resize(dimension);
1054       sizeMM.resize(dimension);
1055       pixelType = mSlicerManagers[index]->GetVF()->GetScalarTypeAsITKString().c_str();
1056       for (int i = 0; i < dimension; i++) {
1057         origin[i] = imageSelected->GetOrigin()[i];
1058         inputSpacing[i] = imageSelected->GetSpacing()[i];
1059         inputSize[i] = imageSelected->GetSize()[i];
1060         sizeMM[i] = inputSize[i]*inputSpacing[i];
1061         NPixel *= inputSize[i];
1062       }
1063       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1064     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1065       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1066       dimension = imageSelected->GetNumberOfDimensions();
1067       origin.resize(dimension);
1068       inputSpacing.resize(dimension);
1069       inputSize.resize(dimension);
1070       sizeMM.resize(dimension);
1071       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1072       for (int i = 0; i < dimension; i++) {
1073         origin[i] = imageSelected->GetOrigin()[i];
1074         inputSpacing[i] = imageSelected->GetSpacing()[i];
1075         inputSize[i] = imageSelected->GetSize()[i];
1076         sizeMM[i] = inputSize[i]*inputSpacing[i];
1077         NPixel *= inputSize[i];
1078       }
1079       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1080     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1081       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1082       dimension = imageSelected->GetNumberOfDimensions();
1083       origin.resize(dimension);
1084       inputSpacing.resize(dimension);
1085       inputSize.resize(dimension);
1086       sizeMM.resize(dimension);
1087       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1088       for (int i = 0; i < dimension; i++) {
1089         origin[i] = imageSelected->GetOrigin()[i];
1090         inputSpacing[i] = imageSelected->GetSpacing()[i];
1091         inputSize[i] = imageSelected->GetSize()[i];
1092         sizeMM[i] = inputSize[i]*inputSpacing[i];
1093         NPixel *= inputSize[i];
1094       }
1095       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1096     }
1097
1098     QString dim = QString::number(dimension) + " (";
1099     dim += pixelType + ")";
1100
1101     infoPanel->setFileName(image);
1102     infoPanel->setDimension(dim);
1103     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1104     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1105     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1106     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1107     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1108     transformation = imageSelected->GetTransform()->GetMatrix();
1109     infoPanel->setTransformation(Get4x4MatrixDoubleAsString(transformation));
1110
1111     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1112                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1113     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1114     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1115
1116     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1117     for (int i = 0; i < 4; i++) {
1118       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1119         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1120         break;
1121       }
1122     }
1123     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1124     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1125     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1126     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1127
1128     infoPanel->setFileName(image);
1129     infoPanel->setDimension(dim);
1130     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1131     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1132     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1133     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1134     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1135
1136     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1137                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1138     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1139     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1140
1141     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1142     for (int i = 0; i < 4; i++) {
1143       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1144         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1145         break;
1146       }
1147     }
1148     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1149     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1150     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1151     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1152
1153     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1154       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1155       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1156                                   mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1157                                   mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1158     } else {
1159       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1160       overlayPanel->getVFProperty(-1,-1,-1);
1161     }
1162     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1163       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1164       overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1165     } else {
1166       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1167       overlayPanel->getOverlayProperty(-1);
1168     }
1169     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1170       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1171       overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1172                                       mSlicerManagers[index]->GetFusionColorMap(),
1173                                       mSlicerManagers[index]->GetFusionWindow(),
1174                                       mSlicerManagers[index]->GetFusionLevel());
1175     } else {
1176       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1177       overlayPanel->getFusionProperty(-1, -1,-1,-1);
1178     }
1179   }
1180 }
1181 //------------------------------------------------------------------------------
1182
1183 //------------------------------------------------------------------------------
1184 void vvMainWindow::ShowDocumentation()
1185 {
1186   documentation->show();
1187 }
1188 //------------------------------------------------------------------------------
1189 void vvMainWindow::ShowHelpDialog()
1190 {
1191   help_dialog->show();
1192 }
1193 //------------------------------------------------------------------------------
1194
1195 //------------------------------------------------------------------------------
1196 void vvMainWindow::ChangeViewMode()
1197 {
1198   QListIterator<int> it0(splitter_3->sizes());
1199   QListIterator<int> it1(splitter_3->sizes());
1200   int max0 = 0;
1201   int max1 = 1;
1202   while (it0.hasNext()) {
1203     max0 += it0.next();
1204   }
1205   while (it1.hasNext()) {
1206     max1 += it1.next();
1207   }
1208   QList<int> size0;
1209   QList<int> size1;
1210   if (viewMode == 1) {
1211     viewMode = 0;
1212     size0.push_back(max0);
1213     size0.push_back(0);
1214     size1.push_back(max1);
1215     size1.push_back(0);
1216     splitter_3->setSizes(size0);
1217     OSplitter->setSizes(size1);
1218     DataTree->setColumnHidden(2,1);
1219     DataTree->setColumnHidden(3,1);
1220     DataTree->setColumnHidden(4,1);
1221   } else {
1222     viewMode = 1;
1223     size0.push_back(int(max0/2));
1224     size0.push_back(int(max0/2));
1225     size1.push_back(int(max1/2));
1226     size1.push_back(int(max1/2));
1227     splitter_3->setSizes(size0);
1228     OSplitter->setSizes(size1);
1229     DataTree->setColumnHidden(2,0);
1230     DataTree->setColumnHidden(3,0);
1231     DataTree->setColumnHidden(4,0);
1232   }
1233 }
1234 //------------------------------------------------------------------------------
1235
1236 //------------------------------------------------------------------------------
1237 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1238 {
1239   QString result = "";// QString::number(size);
1240   //result += " bytes (";
1241   if (size > 1000000000) {
1242     size /= 1000000000;
1243     result += QString::number(size);
1244     result += "Gb";//)";
1245   } else if (size > 1000000) {
1246     size /= 1000000;
1247     result += QString::number(size);
1248     result += "Mb";//)";
1249   } else if (size > 1000) {
1250     size /= 1000;
1251     result += QString::number(size);
1252     result += "kb";//)";
1253   }
1254   return result;
1255 }
1256 //------------------------------------------------------------------------------
1257
1258 //------------------------------------------------------------------------------
1259 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix)
1260 {
1261   std::ostringstream strmatrix;
1262
1263   for (unsigned int i = 0; i < 4; i++) {
1264     for (unsigned int j = 0; j < 4; j++) {
1265       strmatrix.flags(ios::showpos);
1266       strmatrix.width(10);
1267       strmatrix.precision(3);
1268       strmatrix.setf(ios::fixed,ios::floatfield);
1269       strmatrix.fill(' ');
1270       strmatrix << std::left << matrix->GetElement(i, j);
1271       //strmatrix.width(10);
1272       strmatrix << " ";
1273     }
1274     strmatrix << std::endl;
1275   }
1276   QString result = strmatrix.str().c_str();
1277   return result;
1278 }
1279 //------------------------------------------------------------------------------
1280
1281 //------------------------------------------------------------------------------
1282 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1283 {
1284   QString result;
1285   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1286     if (i != 0)
1287       result += " ";
1288     result += QString::number(vectorDouble[i]);
1289   }
1290   return result;
1291 }
1292 //------------------------------------------------------------------------------
1293
1294 //------------------------------------------------------------------------------
1295 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1296 {
1297   QString result;
1298   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1299     if (i != 0)
1300       result += " ";
1301     result += QString::number(vectorInt[i]);
1302   }
1303   return result;
1304 }
1305 //------------------------------------------------------------------------------
1306
1307 //------------------------------------------------------------------------------
1308 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1309 {
1310   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1311   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1312     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1313       return i;
1314   }
1315   return -1;
1316 }
1317 //------------------------------------------------------------------------------
1318
1319 //------------------------------------------------------------------------------
1320 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1321 {
1322   QString id = sm->GetId().c_str();
1323   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1324     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1325       return DataTree->topLevelItem(i);
1326   }
1327   return NULL;
1328 }
1329 //------------------------------------------------------------------------------
1330
1331 //------------------------------------------------------------------------------
1332 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clicked_item, int column)
1333 {
1334   int index = GetSlicerIndexFromItem(clicked_item);
1335   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1336     return;
1337   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1338     //Trick to avoid redoing twice the job for a key (sr)
1339     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()-> GetInteractor()->SetKeySym("Crap");
1340
1341     QTreeWidgetItem* current_row=DataTree->topLevelItem(i);
1342     if (DataTree->topLevelItem(index) == current_row) {
1343       vvSlicer* clicked_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1344       if (current_row == clicked_item) {
1345         //If we just activated a slicer
1346         if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1347           mSlicerManagers[i]->UpdateSlicer(column-1,clicked_item->data(column,Qt::CheckStateRole).toInt());
1348           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1349           DisplaySliders(i,column-1);
1350           std::map<std::string,int> overlay_counts;
1351           for (int child = 0; child < current_row->childCount(); child++) {
1352             std::string overlay_type =
1353               current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1354             overlay_counts[overlay_type]++;
1355             current_row->child(child)->setData(column,Qt::CheckStateRole,
1356                                                current_row->data(column,Qt::CheckStateRole));
1357             clicked_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,true);
1358           }
1359         } else { //We don't allow simply desactivating a slicer
1360           clicked_item->setData(column,Qt::CheckStateRole,2);
1361           return;
1362         }
1363       }
1364       //if we clicked on the vector(or overlay) and not the image
1365       else {
1366         if (clicked_item->data(column,Qt::CheckStateRole).toInt()) {
1367           current_row->setData(column,Qt::CheckStateRole,2);
1368           mSlicerManagers[i]->UpdateSlicer(column-1,2);
1369           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1370           DisplaySliders(i,column-1);
1371         }
1372         int vis = clicked_item->data(column,Qt::CheckStateRole).toInt();
1373         std::string overlay_type = clicked_item->data(1,Qt::UserRole).toString().toStdString();
1374         int overlay_index=0;
1375         for (int child = 0; child < current_row->childCount(); child++) {
1376           if (current_row->child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1377             overlay_index++;
1378           if (current_row->child(child) == clicked_item) break;
1379         }
1380         clicked_slicer->SetActorVisibility(
1381           clicked_item->data(1,Qt::UserRole).toString().toStdString(), overlay_index-1,vis);
1382       }
1383     } else if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1384       current_row->setData(column,Qt::CheckStateRole,0);
1385       mSlicerManagers[i]->UpdateSlicer(column-1,0);
1386       std::map<std::string,int> overlay_counts;
1387       for (int child = 0; child < current_row->childCount(); child++) {
1388         std::string overlay_type =
1389           current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1390         overlay_counts[overlay_type]++;
1391         current_row->child(child)->setData(column,Qt::CheckStateRole,0);
1392         vvSlicer * current_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1393         current_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,false);
1394       }
1395     }
1396     //mSlicerManagers[i]->SetColorMap(-1);
1397     mSlicerManagers[i]->SetColorMap();
1398   }
1399   mSlicerManagers[index]->GetSlicer(column-1)->Render();
1400 }
1401 //------------------------------------------------------------------------------
1402
1403 void vvMainWindow::InitSlicers()
1404 {
1405   if (mSlicerManagers.size()) {
1406     mSlicerManagers.back()->GenerateDefaultLookupTable();
1407
1408     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1409     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1410     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1411     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1412   }
1413 }
1414
1415 //------------------------------------------------------------------------------
1416 void vvMainWindow::InitDisplay()
1417 {
1418   if (mSlicerManagers.size()) {
1419     //BE CAREFUL : this is absolutely necessary to set the interactor style
1420     //in order to have the same style instanciation for all SlicerManagers in
1421     // a same window
1422     for (int j = 0; j < 4; j++) {
1423       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1424       style->SetAutoAdjustCameraClippingRange(1);
1425       bool AlreadySelected = false;
1426       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1427         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1428
1429         //select the image only if previous are not selected
1430         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1431           mSlicerManagers[i]->UpdateSlicer(j,1);
1432           AlreadySelected = true;
1433         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1434           if (DataTree->selectedItems().size() == 0)
1435             DataTree->topLevelItem(i)->setSelected(1);
1436           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1437           mSlicerManagers[i]->UpdateSlicer(j,1);
1438           DisplaySliders(i,j);
1439         } else {
1440           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1441           mSlicerManagers[i]->UpdateSlicer(j,0);
1442         }
1443       }
1444       style->Delete();
1445     }
1446   }
1447 }
1448 //------------------------------------------------------------------------------
1449
1450 //------------------------------------------------------------------------------
1451 void vvMainWindow::DisplaySliders(int slicer, int window)
1452 {
1453   int range[2];
1454   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1455   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1456
1457   int tRange[2];
1458   tRange[0] = 0;
1459   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1460   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1461   bool showHorizontal = false;
1462   bool showVertical = false;
1463   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1464       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1465           && mSlicerManagers[slicer]->GetType() != vvImageReader::IMAGEWITHTIME
1466           && mSlicerManagers[slicer]->GetType() != vvImageReader::MERGEDWITHTIME))
1467     showVertical = true;
1468   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1469       || mSlicerManagers[slicer]->GetType() == vvImageReader::IMAGEWITHTIME
1470       || mSlicerManagers[slicer]->GetType() == vvImageReader::MERGEDWITHTIME)
1471     showHorizontal = true;
1472
1473   if (showVertical)
1474     verticalSliders[window]->show();
1475   else
1476     verticalSliders[window]->hide();
1477   verticalSliders[window]->setRange(range[0],range[1]);
1478   verticalSliders[window]->setValue(position);
1479
1480   if (showHorizontal)
1481     horizontalSliders[window]->show();
1482   else
1483     horizontalSliders[window]->hide();
1484   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1485   horizontalSliders[window]->setValue(tPosition);
1486 }
1487 //------------------------------------------------------------------------------
1488
1489 //------------------------------------------------------------------------------
1490 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1491 {
1492   int index = GetSlicerIndexFromItem(item);
1493
1494   if (DataTree->topLevelItem(index) != item) {
1495     QString warning = "Do you really want to close the overlay : ";
1496     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1497     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1498                        warning, 0, this);
1499     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1500     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1501     if (msgBox.exec() == QMessageBox::AcceptRole) {
1502       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1503       int overlay_index=0;
1504       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1505         if (DataTree->topLevelItem(index)->\
1506             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1507           overlay_index++;
1508         if (DataTree->topLevelItem(index)->child(child) == item) break;
1509       }
1510       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1511       mSlicerManagers[index]->SetColorMap(0);
1512       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1513       mSlicerManagers[index]->Render();
1514     }
1515   } else if (DataTree->topLevelItemCount() <= 1) {
1516     QString warning = "Do you really want to close the image : ";
1517     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1518     warning += "\nThis is the last image, you're about to close vv !!!";
1519     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1520                        warning, 0, this);
1521     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1522     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1523     if (msgBox.exec() == QMessageBox::AcceptRole) {
1524       this->close();
1525     }
1526   } else {
1527     QString warning = "Do you really want to close the image : ";
1528     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1529     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1530                        warning, 0, this);
1531     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1532     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1533     if (msgBox.exec() == QMessageBox::AcceptRole) {
1534
1535       // Tell tools that we close an image
1536       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1537
1538       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1539       DataTree->takeTopLevelItem(index);
1540       for (int i = 0; i < index; i++) {
1541         Manageriter++;
1542       }
1543       linkPanel->removeImage(index);
1544       mSlicerManagers[index]->RemoveActors();
1545       delete mSlicerManagers[index];
1546       mSlicerManagers.erase(Manageriter);
1547
1548       //
1549       InitDisplay();
1550     }
1551   }
1552   ImageInfoChanged();
1553 }
1554 //------------------------------------------------------------------------------
1555
1556 //------------------------------------------------------------------------------
1557 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1558 {
1559   // int index = GetSlicerIndexFromItem(item);
1560   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1561   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1562   //     mSlicerManagers[index]->ReloadVF();
1563   //   else
1564   //     mSlicerManagers[index]->Reload();
1565
1566   //   QApplication::restoreOverrideCursor();
1567   int index = GetSlicerIndexFromItem(item);
1568   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1569   QString role=item->data(1,Qt::UserRole).toString();
1570   if ( role == "vector")
1571     mSlicerManagers[index]->ReloadVF();
1572   else if (role == "overlay")
1573     mSlicerManagers[index]->ReloadOverlay();
1574   else if (role == "fusion")
1575     mSlicerManagers[index]->ReloadFusion();
1576   else
1577     mSlicerManagers[index]->Reload();
1578
1579   // Update view and info
1580   ImageInfoChanged();
1581   mSlicerManagers[index]->Render();
1582   QApplication::restoreOverrideCursor();
1583 }
1584 //------------------------------------------------------------------------------
1585
1586 //------------------------------------------------------------------------------
1587 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1588 {
1589   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1590 }
1591 //------------------------------------------------------------------------------
1592
1593 //------------------------------------------------------------------------------
1594 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1595 {
1596   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1597 }
1598 //------------------------------------------------------------------------------
1599
1600 //------------------------------------------------------------------------------
1601 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1602 {
1603   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1604 }
1605 //------------------------------------------------------------------------------
1606
1607 //------------------------------------------------------------------------------
1608 void vvMainWindow::FusionChanged(int visibility, double value)
1609 {
1610   overlayPanel->getCurrentFusionInfo(visibility,value);
1611 }
1612 //------------------------------------------------------------------------------
1613
1614 //------------------------------------------------------------------------------
1615 void vvMainWindow::WindowsChanged(int window, int view, int slice)
1616 {
1617   infoPanel->setViews(window, view, slice);
1618 }
1619 //------------------------------------------------------------------------------
1620
1621 //------------------------------------------------------------------------------
1622 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap)
1623 {
1624   windowSpinBox->setValue(window);
1625   levelSpinBox->setValue(level);
1626   colorMapComboBox->setCurrentIndex(colormap);
1627   presetComboBox->setCurrentIndex(preset);
1628 }
1629 //------------------------------------------------------------------------------
1630
1631 //------------------------------------------------------------------------------
1632 void vvMainWindow::WindowLevelEdited()
1633 {
1634   presetComboBox->setCurrentIndex(6);
1635   UpdateWindowLevel();
1636 }
1637 //------------------------------------------------------------------------------
1638
1639 //------------------------------------------------------------------------------
1640 void vvMainWindow::UpdateWindowLevel()
1641 {
1642   if (DataTree->selectedItems().size()) {
1643     if (presetComboBox->currentIndex() == 7) //For ventilation
1644       colorMapComboBox->setCurrentIndex(5);
1645     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1646     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1647     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1648     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1649     mSlicerManagers[index]->Render();
1650     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1651     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1652   }
1653 }
1654 //------------------------------------------------------------------------------
1655
1656 //------------------------------------------------------------------------------
1657 void vvMainWindow::UpdateColorMap()
1658 {
1659   if (DataTree->selectedItems().size()) {
1660     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1661     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1662     mSlicerManagers[index]->Render();
1663   }
1664 }
1665 //------------------------------------------------------------------------------
1666 void vvMainWindow::SwitchWindowLevel()
1667 {
1668   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1669   int window = mSlicerManagers[index]->GetColorWindow();
1670   presetComboBox->setCurrentIndex(6);
1671   windowSpinBox->setValue(-window);
1672   UpdateWindowLevel();
1673 }
1674 //------------------------------------------------------------------------------
1675
1676 //------------------------------------------------------------------------------
1677 void vvMainWindow::ApplyWindowLevelToAllImages()
1678 {
1679   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1680     if (mSlicerManagers[i] == NULL)
1681       continue;
1682     mSlicerManagers[i]->SetColorWindow(windowSpinBox->value());
1683     mSlicerManagers[i]->SetColorLevel(levelSpinBox->value());
1684     mSlicerManagers[i]->SetPreset(6);
1685     mSlicerManagers[i]->Render();
1686   }
1687 }
1688 //------------------------------------------------------------------------------
1689
1690 //------------------------------------------------------------------------------
1691 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1692 {
1693   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1694     if (mSlicerManagers[i]->GetId() == id) {
1695       //mSlicerManagers[i]->SetTSlice(temps);
1696       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1697       mSlicerManagers[i]->UpdateViews(0,slicer);
1698       break;
1699     }
1700   }
1701 }
1702 //------------------------------------------------------------------------------
1703
1704 //------------------------------------------------------------------------------
1705 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1706 {
1707   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1708     if (id == mSlicerManagers[i]->GetId()) {
1709       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1710     }
1711   }
1712 }
1713 //------------------------------------------------------------------------------
1714
1715 //------------------------------------------------------------------------------
1716 void vvMainWindow::ShowContextMenu(QPoint point)
1717 {
1718   if (!DataTree->selectedItems().size()) {
1719     contextActions[1]->setEnabled(0);
1720     contextActions[2]->setEnabled(0);
1721     contextActions[3]->setEnabled(0);
1722     contextActions[4]->setEnabled(0);
1723     contextActions[5]->setEnabled(0);
1724     contextActions[6]->setEnabled(0);
1725   } else {
1726     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1727     contextActions[1]->setEnabled(1);
1728     contextActions[2]->setEnabled(
1729       DataTree->itemWidget(DataTree->selectedItems()[0],
1730                            COLUMN_RELOAD_IMAGE)->isEnabled());
1731     contextActions[3]->setEnabled(1);
1732     contextActions[5]->setEnabled(1);
1733     contextActions[6]->setEnabled(1);
1734
1735     if (mSlicerManagers[index]->GetDimension() < 3)
1736       contextActions[4]->setEnabled(0);
1737     else
1738       contextActions[4]->setEnabled(1);
1739   }
1740   contextMenu.exec(QCursor::pos());
1741 }
1742 //------------------------------------------------------------------------------
1743
1744 //------------------------------------------------------------------------------
1745 void vvMainWindow::CloseImage()
1746 {
1747   CloseImage(DataTree->selectedItems()[0],0);
1748 }
1749 //------------------------------------------------------------------------------
1750
1751 //------------------------------------------------------------------------------
1752 void vvMainWindow::ReloadImage()
1753 {
1754   ReloadImage(DataTree->selectedItems()[0],0);
1755 }
1756 //------------------------------------------------------------------------------
1757
1758 //------------------------------------------------------------------------------
1759 void vvMainWindow::SelectOverlayImage()
1760 {
1761   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1762
1763   //check if one overlay image is added
1764   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1765     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1766       QString error = "Cannot add more than one compared image\n";
1767       error += "Please remove first ";
1768       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1769       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1770       return;
1771     }
1772
1773   QString Extensions = EXTENSIONS;
1774   Extensions += ";;All Files (*)";
1775   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1776   if (!file.isEmpty())
1777     AddOverlayImage(index,file);
1778 }
1779 //------------------------------------------------------------------------------
1780
1781 //------------------------------------------------------------------------------
1782 void vvMainWindow::AddOverlayImage(int index, QString file)
1783 {
1784
1785   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1786   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1787                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1788   reader->SetFileName(file.toStdString().c_str());
1789   reader->ReadImageInformation();
1790   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1791   int dimension = reader->GetNumberOfDimensions();
1792   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1793   vvProgressDialog progress("Opening " + file.toStdString());
1794   qApp->processEvents();
1795
1796   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1797   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component)) {
1798     //create an item in the tree with good settings
1799     QTreeWidgetItem *item = new QTreeWidgetItem();
1800     item->setData(0,Qt::UserRole,file.toStdString().c_str());
1801     item->setData(1,Qt::UserRole,tr("overlay"));
1802     QFileInfo fileinfo(file); //Do not show the path
1803     item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1804     item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1805     qApp->processEvents();
1806
1807     for (int j = 1; j <= 4; j++) {
1808       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1809       mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("overlay",0,
1810           DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1811     }
1812
1813     //Create the buttons for reload and close
1814     qApp->processEvents();
1815     QTreePushButton* cButton = new QTreePushButton;
1816     cButton->setItem(item);
1817     cButton->setColumn(COLUMN_CLOSE_IMAGE);
1818     cButton->setToolTip(tr("close image"));
1819     cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1820     connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1821             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1822
1823     QTreePushButton* rButton = new QTreePushButton;
1824     rButton->setItem(item);
1825     rButton->setColumn(COLUMN_RELOAD_IMAGE);
1826     rButton->setToolTip(tr("reload image"));
1827     rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1828     connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1829             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1830
1831     DataTree->topLevelItem(index)->setExpanded(1);
1832     DataTree->topLevelItem(index)->addChild(item);
1833     DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1834     DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1835
1836     //set the id of the image
1837     QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1838     item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1839     UpdateTree();
1840     qApp->processEvents();
1841     ImageInfoChanged();
1842     QApplication::restoreOverrideCursor();
1843   } else {
1844     QApplication::restoreOverrideCursor();
1845     QString error = "Cannot import the new image.\n";
1846     error += mSlicerManagers[index]->GetLastError().c_str();
1847     QMessageBox::information(this,tr("Problem reading image !"),error);
1848   }
1849 }
1850 //------------------------------------------------------------------------------
1851
1852
1853 //------------------------------------------------------------------------------
1854 void vvMainWindow::AddROI(int index, QString file)
1855 {
1856   /*
1857   // Get slice manager
1858
1859   // Load image
1860
1861   vvImageReader * mReader = new vvImageReader;
1862   mReader->SetInputFilename(filename.toStdString());
1863   mReader->Update(IMAGE);
1864   if (mReader->GetLastError().size() != 0) {
1865     std::cerr << "Error while reading " << filename.toStdString() << std::endl;
1866     QString error = "Cannot open file \n";
1867     error += mReader->GetLastError().c_str();
1868     QMessageBox::information(this,tr("Reading problem"),error);
1869     delete mReader;
1870     return;
1871   }
1872   vvImage::Pointer roi = mReader->GetOutput();
1873
1874   // Create roi in new tool
1875   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
1876   */
1877 }
1878 //------------------------------------------------------------------------------
1879
1880 //------------------------------------------------------------------------------
1881 void vvMainWindow::SelectFusionImage()
1882 {
1883   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1884
1885   //check if one fusion image is added
1886   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1887     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
1888       QString error = "Cannot add more than one fusion image\n";
1889       error += "Please remove first ";
1890       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1891       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1892       return;
1893     }
1894
1895   QString Extensions = EXTENSIONS;
1896   Extensions += ";;All Files (*)";
1897   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1898   if (!file.isEmpty())
1899     AddFusionImage(index,file);
1900 }
1901 //------------------------------------------------------------------------------
1902
1903 //------------------------------------------------------------------------------
1904 void vvMainWindow::AddFusionImage(int index, QString file)
1905 {
1906   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1907   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1908                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1909   reader->SetFileName(file.toStdString().c_str());
1910   reader->ReadImageInformation();
1911   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1912   if (reader) {
1913     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1914     vvProgressDialog progress("Opening fusion");
1915     qApp->processEvents();
1916
1917     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1918     if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1919                                           reader->GetNumberOfDimensions(), component)) {
1920       //create an item in the tree with good settings
1921       QTreeWidgetItem *item = new QTreeWidgetItem();
1922       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1923       item->setData(1,Qt::UserRole,tr("fusion"));
1924       QFileInfo fileinfo(filename.c_str()); //Do not show the path
1925       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1926       item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1927       qApp->processEvents();
1928
1929       for (int j = 1; j <= 4; j++) {
1930         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1931         mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("fusion",0,
1932             DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1933       }
1934
1935       //Create the buttons for reload and close
1936       qApp->processEvents();
1937       QTreePushButton* cButton = new QTreePushButton;
1938       cButton->setItem(item);
1939       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1940       cButton->setToolTip(tr("close image"));
1941       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1942       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1943               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1944
1945       QTreePushButton* rButton = new QTreePushButton;
1946       rButton->setItem(item);
1947       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1948       rButton->setToolTip(tr("reload image"));
1949       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1950       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1951               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1952
1953       DataTree->topLevelItem(index)->setExpanded(1);
1954       DataTree->topLevelItem(index)->addChild(item);
1955       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1956       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1957
1958       //set the id of the image
1959       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1960       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1961       UpdateTree();
1962       qApp->processEvents();
1963       ImageInfoChanged();
1964       QApplication::restoreOverrideCursor();
1965     } else {
1966       QApplication::restoreOverrideCursor();
1967       QString error = "Cannot import the new image.\n";
1968       error += mSlicerManagers[index]->GetLastError().c_str();
1969       QMessageBox::information(this,tr("Problem reading image !"),error);
1970     }
1971   } else {
1972     QString error = "Cannot import the new image.\n";
1973     QMessageBox::information(this,tr("Problem reading image !"),error);
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   QFileInfo fileinfo(filename); //Do not show the path
2010   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2011   item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
2012   qApp->processEvents();
2013
2014   for (int j = 1; j <= 4; j++) {
2015     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2016     mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("vector",0,
2017         DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
2018   }
2019
2020   //Create the buttons for reload and close
2021   qApp->processEvents();
2022   QTreePushButton* cButton = new QTreePushButton;
2023   cButton->setItem(item);
2024   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2025   cButton->setToolTip(tr("close vector field"));
2026   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2027   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2028           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2029
2030   QTreePushButton* rButton = new QTreePushButton;
2031   rButton->setItem(item);
2032   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2033   rButton->setToolTip(tr("reload vector field"));
2034   rButton->setEnabled(from_disk);
2035   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2036   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2037           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2038
2039   DataTree->topLevelItem(index)->setExpanded(1);
2040   DataTree->topLevelItem(index)->addChild(item);
2041   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2042   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2043
2044   //set the id of the image
2045   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2046   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2047   UpdateTree();
2048   qApp->processEvents();
2049   ImageInfoChanged();
2050   QApplication::restoreOverrideCursor();
2051 }
2052 //------------------------------------------------------------------------------
2053
2054
2055 //------------------------------------------------------------------------------
2056 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2057 {
2058   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2059   vvSlicerManager* imageManager = mSlicerManagers[index];
2060   if (imageManager->SetVF(vf,file.toStdString())) {
2061     AddFieldEntry(file,index,false);
2062   } else {
2063     QString error = "Cannot import the vector field for this image.\n";
2064     error += imageManager->GetLastError().c_str();
2065     QMessageBox::information(this,tr("Problem reading VF !"),error);
2066   }
2067   QApplication::restoreOverrideCursor();
2068 }
2069 //------------------------------------------------------------------------------
2070
2071
2072 //------------------------------------------------------------------------------
2073 void vvMainWindow::AddField(QString file,int index)
2074 {
2075   if (QFile::exists(file)) {
2076     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2077
2078     //init the progress events
2079     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2080     vvProgressDialog progress("Opening " + file.toStdString());
2081     qApp->processEvents();
2082
2083     //read the vector and put it in the current mSlicerManager
2084     vvSlicerManager* imageManager = mSlicerManagers[index];
2085     qApp->processEvents();
2086
2087     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2088     if (imageManager->SetVF(file.toStdString())) {
2089       imageManager->Render();
2090       AddFieldEntry(file,index,true);
2091     } else {
2092       QApplication::restoreOverrideCursor();
2093       QString error = "Cannot import the vector field for this image.\n";
2094       error += imageManager->GetLastError().c_str();
2095       QMessageBox::information(this,tr("Problem reading VF !"),error);
2096     }
2097   } else
2098     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2099
2100 }
2101 //------------------------------------------------------------------------------
2102
2103
2104 //------------------------------------------------------------------------------
2105 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2106 {
2107   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2108   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2109     for (int i = 0; i < 4; i++) {
2110       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2111       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2112       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2113       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2114       if (log > 0)
2115         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2116       else
2117         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2118     }
2119   }
2120 }
2121 //------------------------------------------------------------------------------
2122
2123
2124 //------------------------------------------------------------------------------
2125 void vvMainWindow::SetOverlayProperty(int color)
2126 {
2127   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2128   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2129     mSlicerManagers[index]->SetOverlayColor(color);
2130     mSlicerManagers[index]->SetColorMap(0);
2131     mSlicerManagers[index]->Render();
2132   }
2133 }
2134 //------------------------------------------------------------------------------
2135
2136 //------------------------------------------------------------------------------
2137 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level)
2138 {
2139   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2140   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2141     mSlicerManagers[index]->SetFusionOpacity(opacity);
2142     mSlicerManagers[index]->SetFusionColorMap(colormap);
2143     mSlicerManagers[index]->SetFusionWindow(window);
2144     mSlicerManagers[index]->SetFusionLevel(level);
2145     mSlicerManagers[index]->SetColorMap(0);
2146     mSlicerManagers[index]->Render();
2147   }
2148 }
2149 //------------------------------------------------------------------------------
2150
2151 //------------------------------------------------------------------------------
2152 void vvMainWindow::SaveAs()
2153 {
2154   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2155     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2156     return;
2157   }
2158
2159   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2160   int dimension = mSlicerManagers[index]->GetDimension();
2161   QStringList OutputListeFormat;
2162   OutputListeFormat.clear();
2163   if (dimension == 1) {
2164     OutputListeFormat.push_back(".mhd");
2165   }
2166   if (dimension == 2) {
2167     OutputListeFormat.push_back(".bmp");
2168     OutputListeFormat.push_back(".png");
2169     OutputListeFormat.push_back(".jpeg");
2170     OutputListeFormat.push_back(".tif");
2171     OutputListeFormat.push_back(".mhd");
2172     OutputListeFormat.push_back(".hdr");
2173     OutputListeFormat.push_back(".vox");
2174   } else if (dimension == 3) {
2175     OutputListeFormat.push_back(".mhd");
2176     OutputListeFormat.push_back(".hdr");
2177     OutputListeFormat.push_back(".vox");
2178   } else if (dimension == 4) {
2179     OutputListeFormat.push_back(".mhd");
2180   }
2181   QString Extensions = "AllFiles(*.*)";
2182   for (int i = 0; i < OutputListeFormat.count(); i++) {
2183     Extensions += ";;Images ( *";
2184     Extensions += OutputListeFormat[i];
2185     Extensions += ")";
2186   }
2187   QString fileName = QFileDialog::getSaveFileName(this,
2188                      tr("Save As"),
2189                      mSlicerManagers[index]->GetFileName().c_str(),
2190                      Extensions);
2191   if (!fileName.isEmpty()) {
2192     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2193     if (OutputListeFormat.contains(
2194           fileformat.c_str())) {
2195       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2196       std::string action = "Saving";
2197       vvProgressDialog progress("Saving "+fileName.toStdString());
2198       qApp->processEvents();
2199       vvImageWriter::Pointer writer = vvImageWriter::New();
2200       writer->SetOutputFileName(fileName.toStdString());
2201       writer->SetInput(mSlicerManagers[index]->GetImage());
2202       writer->Update();
2203       QApplication::restoreOverrideCursor();
2204       if (writer->GetLastError().size()) {
2205         QString error = "Saving did not succeed\n";
2206         error += writer->GetLastError().c_str();
2207         QMessageBox::information(this,tr("Saving Problem"),error);
2208         SaveAs();
2209       }
2210     } else {
2211       QString error = fileformat.c_str();
2212       if (error.isEmpty())
2213         error += "no file format specified !";
2214       else
2215         error += " format unknown !!!\n";
2216       QMessageBox::information(this,tr("Saving Problem"),error);
2217       SaveAs();
2218     }
2219   }
2220 }
2221 //------------------------------------------------------------------------------
2222
2223
2224 //------------------------------------------------------------------------------
2225 void vvMainWindow::AddLink(QString image1,QString image2)
2226 {
2227   unsigned int sm1 = 0;
2228   unsigned int sm2 = 0;
2229
2230   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2231     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2232       mSlicerManagers[i]->AddLink(image2.toStdString());
2233       sm1 = i;
2234     }
2235     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2236       mSlicerManagers[i]->AddLink(image1.toStdString());
2237       sm2 = i;
2238     }
2239   }
2240
2241   if (linkPanel->isLinkAll())   {
2242     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2243     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2244   }
2245   else {
2246     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2247   }
2248 }
2249
2250 //------------------------------------------------------------------------------
2251
2252
2253 //------------------------------------------------------------------------------
2254 void vvMainWindow::RemoveLink(QString image1,QString image2)
2255 {
2256   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2257     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2258       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2259     }
2260     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2261       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2262     }
2263   }
2264 }
2265 //------------------------------------------------------------------------------
2266
2267 //------------------------------------------------------------------------------
2268 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2269 {
2270   int index = 0;
2271   while(sm != mSlicerManagers[index])
2272     index++;
2273   index = (index+offset) % mSlicerManagers.size();
2274
2275   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2276   //CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2277   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2278   DisplayChanged(item,slicer+1);
2279 }
2280 //------------------------------------------------------------------------------
2281
2282 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2283 {
2284   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2285     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2286       for (int j = 0; j < 4; j++) {
2287         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2288         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2289         //UpdateTSlice(j,value);
2290       }
2291       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2292       break;
2293     }
2294   }
2295 }
2296 //------------------------------------------------------------------------------
2297
2298
2299 //------------------------------------------------------------------------------
2300 void vvMainWindow::NOHorizontalSliderMoved()
2301 {
2302   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2303   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2304 //  mCurrentTime = NOHorizontalSlider->value();
2305 }
2306 //------------------------------------------------------------------------------
2307
2308
2309 //------------------------------------------------------------------------------
2310 void vvMainWindow::NEHorizontalSliderMoved()
2311 {
2312   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2313   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2314 //  mCurrentTime = NEHorizontalSlider->value();
2315 }
2316 //------------------------------------------------------------------------------
2317
2318
2319 //------------------------------------------------------------------------------
2320 void vvMainWindow::SOHorizontalSliderMoved()
2321 {
2322   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2323   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2324   // mCurrentTime = SOHorizontalSlider->value();
2325 }
2326 //------------------------------------------------------------------------------
2327
2328
2329 //------------------------------------------------------------------------------
2330 void vvMainWindow::SEHorizontalSliderMoved()
2331 {
2332   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2333   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2334   // mCurrentTime = SEHorizontalSlider->value();
2335 }
2336 //------------------------------------------------------------------------------
2337
2338 //------------------------------------------------------------------------------
2339 void vvMainWindow::NOVerticalSliderChanged()
2340 {
2341   static int value=-1;
2342   if (value == NOVerticalSlider->value()) return;
2343   else value = NOVerticalSlider->value();
2344   //  int value = NOVerticalSlider->value();
2345   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2346     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2347       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2348         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2349         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2350
2351         // If nor Update/Render -> slider not work
2352         // only render = ok navigation, but for contour Update needed but slower ?
2353
2354         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2355         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2356       }
2357       break;
2358     }
2359   }
2360 }
2361 //------------------------------------------------------------------------------
2362
2363
2364 //------------------------------------------------------------------------------
2365 void vvMainWindow::NEVerticalSliderChanged()
2366 {
2367   static int value=-1;
2368   if (value == NEVerticalSlider->value()) return;
2369   else value = NEVerticalSlider->value();
2370   //  int value = NEVerticalSlider->value();
2371   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2372     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2373       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2374         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2375         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2376         mSlicerManagers[i]->UpdateSlice(1);
2377         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2378       }
2379       break;
2380     }
2381   }
2382 }
2383 //------------------------------------------------------------------------------
2384
2385
2386 //------------------------------------------------------------------------------
2387 void vvMainWindow::SOVerticalSliderChanged()
2388 {
2389   static int value=-1;
2390   if (value == SOVerticalSlider->value()) return;
2391   else value = SOVerticalSlider->value();
2392   //int value = SOVerticalSlider->value();
2393   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2394     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2395       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2396         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2397         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2398         mSlicerManagers[i]->UpdateSlice(2);
2399         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2400       }
2401       // else { DD("avoid SOVerticalSlider slicer update"); }
2402       break;
2403     }
2404   }
2405 }
2406 //------------------------------------------------------------------------------
2407
2408
2409 //------------------------------------------------------------------------------
2410 void vvMainWindow::SEVerticalSliderChanged()
2411 {
2412   static int value=-1;
2413   if (value == SEVerticalSlider->value()) return;
2414   else value = SEVerticalSlider->value();
2415   // int value = SEVerticalSlider->value();
2416   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2417     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2418       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2419         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2420         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2421         mSlicerManagers[i]->UpdateSlice(3);
2422         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2423       }
2424       break;
2425     }
2426   }
2427 }
2428 //------------------------------------------------------------------------------
2429
2430
2431 //------------------------------------------------------------------------------
2432 void vvMainWindow::UpdateSlice(int slicer, int slice)
2433 {
2434   // DD("vvMainWindow::UpdateSlice");
2435 //   DD(slicer);
2436 //   DD(slice);
2437   if (slicer == 0) {
2438     //    if (slice != NOVerticalSlider->value())
2439     NOVerticalSlider->setValue(slice);
2440   } else {
2441     if (slicer == 1)
2442       NEVerticalSlider->setValue(slice);
2443     else {
2444       if (slicer == 2)
2445         SOVerticalSlider->setValue(slice);
2446       else {
2447         if (slicer == 3)
2448           SEVerticalSlider->setValue(slice);
2449       }
2450     }
2451   }
2452   // DD("vvMainWindow:UpdateSlice END");
2453 }
2454 //------------------------------------------------------------------------------
2455
2456
2457 //------------------------------------------------------------------------------
2458 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2459 {
2460   switch (slicer) {
2461   case 0:
2462     NOHorizontalSlider->setValue(slice);
2463     break;
2464   case 1:
2465     NEHorizontalSlider->setValue(slice);
2466     break;
2467   case 2:
2468     SOHorizontalSlider->setValue(slice);
2469     break;
2470   case 3:
2471     SEHorizontalSlider->setValue(slice);
2472     break;
2473   }
2474 }
2475 //------------------------------------------------------------------------------
2476
2477
2478 //------------------------------------------------------------------------------
2479 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2480 {
2481   int position = int((min+max)/2);
2482   int tPosition = int((tmin+tmax)/2);
2483   if (slicer == 0) {
2484     NOVerticalSlider->setValue(position);
2485     NOVerticalSlider->setRange(min,max);
2486     NOHorizontalSlider->setRange(tmin,tmax);
2487     NOHorizontalSlider->setValue(tPosition);
2488   } else if (slicer == 1) {
2489     NEVerticalSlider->setValue(position);
2490     NEVerticalSlider->setRange(min,max);
2491     NEHorizontalSlider->setRange(tmin,tmax);
2492     NEHorizontalSlider->setValue(tPosition);
2493   } else if (slicer == 2) {
2494     SOVerticalSlider->setValue(position);
2495     SOVerticalSlider->setRange(min,max);
2496     SOHorizontalSlider->setRange(tmin,tmax);
2497     SOHorizontalSlider->setValue(tPosition);
2498   } else if (slicer == 3) {
2499     SEVerticalSlider->setValue(position);
2500     SEVerticalSlider->setRange(min,max);
2501     SEHorizontalSlider->setRange(tmin,tmax);
2502     SEHorizontalSlider->setValue(tPosition);
2503   }
2504 }
2505 //------------------------------------------------------------------------------
2506
2507
2508 //------------------------------------------------------------------------------
2509 void vvMainWindow::SaveNOScreenshot()
2510 {
2511   SaveScreenshot(NOViewWidget);
2512 }
2513 //------------------------------------------------------------------------------
2514
2515
2516 //------------------------------------------------------------------------------
2517 void vvMainWindow::SaveNEScreenshot()
2518 {
2519   SaveScreenshot(NEViewWidget);
2520 }
2521 //------------------------------------------------------------------------------
2522
2523
2524 //------------------------------------------------------------------------------
2525 void vvMainWindow::SaveSOScreenshot()
2526 {
2527   SaveScreenshot(SOViewWidget);
2528 }
2529 //------------------------------------------------------------------------------
2530
2531
2532 //------------------------------------------------------------------------------
2533 void vvMainWindow::SaveSEScreenshot()
2534 {
2535   SaveScreenshot(SEViewWidget);
2536 }
2537 //------------------------------------------------------------------------------
2538
2539
2540 //------------------------------------------------------------------------------
2541 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
2542 {
2543   QString Extensions = "Images( *.png);;";
2544   Extensions += "Images( *.jpg);;";
2545   Extensions += "Images( *.bmp);;";
2546   Extensions += "Images( *.tif);;";
2547   Extensions += "Images( *.ppm)";
2548 #ifdef VTK_USE_FFMPEG_ENCODER
2549   Extensions += "Images( *.avi)";
2550 #endif
2551 #ifdef VTK_USE_MPEG2_ENCODER
2552   Extensions += "Images( *.mpg)";
2553 #endif
2554
2555   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2556   QString fileName = QFileDialog::getSaveFileName(this,
2557                      tr("Save As"),
2558                      itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
2559                      Extensions);
2560
2561   if (!fileName.isEmpty()) {
2562     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2563     w2i->SetInput(widget->GetRenderWindow());
2564     w2i->Update();
2565     vtkImageData *image = w2i->GetOutput();
2566
2567     const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2568     if (!strcmp(ext, ".bmp")) {
2569       vtkBMPWriter *bmp = vtkBMPWriter::New();
2570       bmp->SetInput(image);
2571       bmp->SetFileName(fileName.toStdString().c_str());
2572       bmp->Write();
2573       bmp->Delete();
2574     } else if (!strcmp(ext, ".tif")) {
2575       vtkTIFFWriter *tif = vtkTIFFWriter::New();
2576       tif->SetInput(image);
2577       tif->SetFileName(fileName.toStdString().c_str());
2578       tif->Write();
2579       tif->Delete();
2580     } else if (!strcmp(ext, ".ppm")) {
2581       vtkPNMWriter *pnm = vtkPNMWriter::New();
2582       pnm->SetInput(image);
2583       pnm->SetFileName(fileName.toStdString().c_str());
2584       pnm->Write();
2585       pnm->Delete();
2586     } else if (!strcmp(ext, ".png")) {
2587       vtkPNGWriter *png = vtkPNGWriter::New();
2588       png->SetInput(image);
2589       png->SetFileName(fileName.toStdString().c_str());
2590       png->Write();
2591       png->Delete();
2592     } else if (!strcmp(ext, ".jpg")) {
2593       vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2594       jpg->SetInput(image);
2595       jpg->SetFileName(fileName.toStdString().c_str());
2596       jpg->Write();
2597       jpg->Delete();
2598 #ifdef VTK_USE_FFMPEG_ENCODER
2599     } else if (!strcmp(ext, ".avi")) {
2600       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
2601       mpg->SetInput(image);
2602       mpg->SetFileName(fileName.toStdString().c_str());
2603       mpg->SetQuality(2);
2604       mpg->SetRate(5);
2605       mpg->Start();
2606
2607       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2608       int nSlice = vvImg->GetVTKImages().size();
2609       for(int i=0; i<nSlice; i++)
2610       {
2611         mSlicerManagers[smIndex]->SetNextTSlice(0);
2612         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2613         w2i->SetInput(widget->GetRenderWindow());
2614         w2i->Update();
2615         mpg->SetInput(w2i->GetOutput());
2616         mpg->Write();
2617       }
2618       mpg->End();
2619       mpg->Delete();
2620 #endif
2621 #ifdef VTK_USE_MPEG2_ENCODER
2622     } else if (!strcmp(ext, ".mpg")) {
2623       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
2624       mpg->SetInput(image);
2625       mpg->SetFileName(fileName.toStdString().c_str());
2626       mpg->Start();
2627
2628       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2629       int nSlice = vvImg->GetVTKImages().size();
2630       for(int i=0; i<nSlice; i++)
2631       {
2632         mSlicerManagers[smIndex]->SetNextTSlice(0);
2633         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2634         w2i->SetInput(widget->GetRenderWindow());
2635         w2i->Update();
2636         mpg->SetInput(w2i->GetOutput());
2637         mpg->Write();
2638       }
2639       mpg->End();
2640       mpg->Delete();
2641 #endif
2642     } else {
2643       QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2644     }
2645   }
2646 }
2647 //------------------------------------------------------------------------------
2648
2649
2650 //------------------------------------------------------------------------------
2651 void vvMainWindow::GoToCursor()
2652 {
2653   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2654   for (int column = 1; column < 5; column++) {
2655     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
2656       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2657       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2658         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2659       mSlicerManagers[index]->UpdateViews(1,column-1);
2660       mSlicerManagers[index]->UpdateLinked(column-1);
2661       break;
2662     }
2663   }
2664 }
2665 //------------------------------------------------------------------------------
2666
2667 //------------------------------------------------------------------------------
2668 void vvMainWindow::PlayPause()
2669 {
2670   if (playMode) {
2671     playMode = 0;
2672     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2673     ImageInfoChanged();
2674     return;
2675   } else {
2676     int image_number=DataTree->topLevelItemCount();
2677     bool has_temporal;
2678     for (int i=0; i<image_number; i++)
2679       if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1) {
2680         has_temporal=true;
2681         break;
2682       }
2683     if (has_temporal) {
2684       playMode = 1;
2685       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2686       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2687     }
2688   }
2689 }
2690 //------------------------------------------------------------------------------
2691
2692 //------------------------------------------------------------------------------
2693 void vvMainWindow::PlayNext()
2694 {
2695   if (playMode && !this->isHidden()) {
2696     int image_number=DataTree->topLevelItemCount();
2697     ///Only play one slicer per SM, and only if the SM is being displayed
2698     for (int i=0; i<image_number; i++)
2699       for (int j=0; j<4; j++)
2700         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2701             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
2702           mSlicerManagers[i]->SetNextTSlice(j);
2703           break;
2704         }
2705     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2706   }
2707 }
2708 //------------------------------------------------------------------------------
2709
2710 void vvMainWindow::ShowLastImage()
2711 {
2712   if (mSlicerManagers.size() > 1) {
2713     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2714     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2715     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2716     DisplayChanged(item,1);
2717   }
2718 }
2719
2720 //------------------------------------------------------------------------------
2721 void vvMainWindow::UpdateRenderWindows()
2722 {
2723   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2724   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2725   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2726   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2727 }
2728 //------------------------------------------------------------------------------
2729
2730 //------------------------------------------------------------------------------
2731 void vvMainWindow::SegmentationOnCurrentImage()
2732 {
2733   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2734
2735   vvSegmentationDialog segmentation;
2736   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2737   segmentation.exec();
2738 }
2739 //------------------------------------------------------------------------------
2740
2741 void vvMainWindow::SurfaceViewerLaunch()
2742 {
2743   vvSurfaceViewerDialog surfaceViewer;
2744   surfaceViewer.exec();
2745 }
2746 //------------------------------------------------------------------------------
2747
2748
2749 //------------------------------------------------------------------------------
2750 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
2751 {
2752   int number=0;
2753   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
2754     vvSlicerManager * v = mSlicerManagers[l];
2755     if (v->GetBaseFileName() ==
2756         vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
2757       number = std::max(number, v->GetBaseFileNameNumber()+1);
2758     }
2759   }
2760   return number;
2761 }
2762 //------------------------------------------------------------------------------
2763
2764
2765 //------------------------------------------------------------------------------
2766 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2767 {
2768   // Change filename if another image exist with the same name
2769   int number = GetImageDuplicateFilenameNumber(filename);
2770
2771   // Create new SliceManager
2772   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
2773   slicer_manager->SetImage(image);//, IMAGE, number);
2774   //  filename = filename+"_"+clitk::toString(number);
2775   slicer_manager->SetFilename(filename, number);
2776   mSlicerManagers.push_back(slicer_manager);
2777
2778   //create an item in the tree with good settings
2779   QTreeWidgetItem *item = new QTreeWidgetItem();
2780   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2781   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
2782   qApp->processEvents();
2783
2784   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2785
2786   //Create the buttons for reload and close
2787   qApp->processEvents();
2788   QTreePushButton* cButton = new QTreePushButton;
2789   cButton->setItem(item);
2790   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2791   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2792   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2793           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2794
2795   QTreePushButton* rButton = new QTreePushButton;
2796   rButton->setItem(item);
2797   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2798   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2799   rButton->setEnabled(0);
2800   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2801           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2802
2803   DataTree->addTopLevelItem(item);
2804   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2805   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2806
2807   //set the id of the image
2808   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2809   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2810   mSlicerManagers.back()->SetId(id.toStdString());
2811
2812   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
2813                       , id.toStdString());
2814
2815   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
2816           this, SLOT(CurrentImageChanged(std::string)));
2817   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
2818           this, SLOT(CurrentPickedImageChanged(std::string)));
2819   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
2820           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2821   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
2822           this, SLOT(VectorChanged(int,double,double,double, double)));
2823   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
2824           this, SLOT(OverlayChanged(int,double,double)));
2825   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
2826           this, SLOT(FusionChanged(int,double)));
2827   connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
2828           this,SLOT(WindowsChanged(int, int, int)));
2829   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
2830           this,SLOT(WindowLevelChanged(double, double, int, int)));
2831   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
2832           this,SLOT(UpdateSlice(int,int)));
2833   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
2834           this,SLOT(UpdateTSlice(int, int)));
2835   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2836           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2837   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2838           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2839   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
2840           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
2841   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
2842           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
2843   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2844   UpdateTree();
2845   qApp->processEvents();
2846   InitSlicers();
2847   ShowLastImage();
2848   InitDisplay();
2849   qApp->processEvents();
2850
2851   // End
2852   ImageInfoChanged();
2853   return slicer_manager;
2854 }
2855 //------------------------------------------------------------------------------
2856
2857
2858 //------------------------------------------------------------------------------
2859 void vvMainWindow::UpdateCurrentSlicer()
2860 {
2861   int index = -1;
2862   if (DataTree->selectedItems().size() > 0) {
2863     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2864   }
2865   mSlicerManagerCurrentIndex = index;
2866 }
2867 //------------------------------------------------------------------------------
2868