vv/vvMainWindow.cxx

   1 /*=========================================================================
   2
   3   Program:   vv
   4   Module:    $RCSfile: vvMainWindow.cxx,v $
   5   Language:  C++
   6   Date:      $Date: 2010/02/09 10:28:07 $
   7   Version:   $Revision: 1.10 $
   8   Author :   Pierre Seroul (pierre.seroul@gmail.com)
   9
  10   Copyright (C) 200COLUMN_IMAGE_NAME
  11   Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
  12   CREATIS-LRMN http://www.creatis.insa-lyon.fr
  13
  14   This program is free software: you can redistribute it and/or modify
  15   it under the terms of the GNU General Public License as published by
  16   the Free Software Foundation, version 3 of the License.
  17
  18   This program is distributed in the hope that it will be useful,
  19   but WITHOUT ANY WARRANTY; without even the implied warranty of
  20   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  21   GNU General Public License for more details.
  22
  23   You should have received a copy of the GNU General Public License
  24   along with this program.  If not, see <http://www.gnu.org/licenses/>.
  25
  26   =========================================================================*/
  27
  28 // QT include
  29 #include <algorithm>
  30 #include <QMessageBox>
  31 #include <QInputDialog>
  32 #include <QTimer>
  33 #include "QTreePushButton.h"
  34
  35 // VV include
  36 #include "vvMainWindow.h"
  37 #include "vvHelpDialog.h"
  38 #include "vvDocumentation.h"
  39 #include "vvProgressDialog.h"
  40 #include "vvQDicomSeriesSelector.h"
  41 #include "vvSlicerManager.h"
  42 #include "clitkImageCommon.h"
  43 #include "vvSlicer.h"
  44 #include "vvInteractorStyleNavigator.h"
  45 #include "vvImageWriter.h"
  46 #include "vvResamplerDialog.h"
  47 #include "vvSegmentationDialog.h"
  48 #include "vvSurfaceViewerDialog.h"
  49 #include "vvDeformationDialog.h"
  50 #include "vvImageWarp.h"
  51 #include "vvUtils.h"
  52 #include "vvMaximumIntensityProjection.h"
  53 #include "vvMidPosition.h"
  54 #include "vvMesh.h"
  55 #include "vvStructSelector.h"
  56 #include "vvMeshReader.h"
  57 #include "vvCropDialog.h"
  58 #include "vvConstants.h"
  59 #ifdef CLITK_VV_USE_BDCM
  60 #include <bdcmDicomFilesSelectorDialog.h>
  61 #endif
  62
  63 // ITK include
  64 #include "itkImage.h"
  65 #include "itkImageFileReader.h"
  66 #include "itkByteSwapper.h"
  67 #include "itkCommand.h"
  68 #include "itkNumericSeriesFileNames.h"
  69
  70 // VTK include
  71 #include "vtkImageData.h"
  72 #include "vtkImageActor.h"
  73 #include "vtkCornerAnnotation.h"
  74 #include "vtkRenderWindow.h"
  75 #include "vtkRenderWindowInteractor.h"
  76 #include "vtkRenderer.h"
  77 #include "vtkRendererCollection.h"
  78 #include "vtkWindowToImageFilter.h"
  79 #include "vtkBMPWriter.h"
  80 #include "vtkTIFFWriter.h"
  81 #include "vtkPNMWriter.h"
  82 #include "vtkPNGWriter.h"
  83 #include "vtkJPEGWriter.h"
  84
  85 // Standard includes
  86 #include <iostream>
  87
  88 #define COLUMN_TREE 0
  89 #define COLUMN_UL_VIEW 1
  90 #define COLUMN_UR_VIEW 2
  91 #define COLUMN_DL_VIEW 3
  92 #define COLUMN_DR_VIEW 4
  93 #define COLUMN_CLOSE_IMAGE 5
  94 #define COLUMN_RELOAD_IMAGE 6
  95 #define COLUMN_IMAGE_NAME 7
  96
  97 /*Data Tree values
  98   0,Qt::UserRole full filename
  99   1,Qt::CheckStateRole checkbutton UL View
 100   1,Qt::UserRole overlay, fusion or vector
 101   2,Qt::CheckStateRole checkbutton UR View
 102   3,Qt::CheckStateRole checkbutton DL View
 103   4,Qt::CheckStateRole checkbutton DR View
 104   5,0  short filename
 105   5,Qt::UserRole mSlicerManager id*/
 106
 107 //------------------------------------------------------------------------------
 108 vvMainWindow::vvMainWindow() {
 109   setupUi(this); // this sets up the GUI
 110
 111   mInputPathName = "";
 112   mCurrentToolInfo = 0;
 113
 114   //Init the contextMenu
 115   this->setContextMenuPolicy(Qt::CustomContextMenu);
 116   contextActions.resize(0);
 117   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/fileopen.png")),
 118                                                         tr("O&pen new Image"));
 119   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 120   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 121   contextActions.push_back(actionOpen_new_image);
 122   contextMenu.addSeparator();
 123
 124   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")),
 125                                                      tr("Close Current Image"));
 126   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 127   contextActions.push_back(actionClose_Image);
 128
 129   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")),
 130                                                       tr("Reload Current Image"));
 131   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 132   contextActions.push_back(actionReload_image);
 133
 134   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/filesave.png")),
 135                                                     tr("Save Current Image"));
 136   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 137   contextActions.push_back(actionSave_image);
 138
 139   contextMenu.addSeparator();
 140
 141   QAction* actionCrop_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/crop.png")),
 142                                                     tr("Crop Current Image"));
 143   connect(actionCrop_image,SIGNAL(triggered()),this,SLOT(CropImage()));
 144   contextActions.push_back(actionCrop_image);
 145
 146   QAction* actionSplit_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/cut.png")),
 147                                                      tr("Split Current Image"));
 148   connect(actionSplit_image,SIGNAL(triggered()),this,SLOT(SplitImage()));
 149   contextActions.push_back(actionSplit_image);
 150
 151   contextMenu.addSeparator();
 152
 153   contextMenu.addAction(actionAdd_VF_to_current_Image);
 154   contextActions.push_back(actionAdd_VF_to_current_Image);
 155
 156   QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/GPSup.png")),
 157                                                                        tr("Add overlay image to current image"));
 158   contextMenu.addAction(actionAdd_Overlay_to_current_Image);
 159   contextActions.push_back(actionAdd_Overlay_to_current_Image);
 160
 161   connect(actionAdd_Overlay_to_current_Image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 162
 163   contextMenu.addAction(actionAdd_fusion_image);
 164   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 165   contextActions.push_back(actionAdd_fusion_image);
 166
 167
 168   //init the DataTree
 169   mSlicerManagers.resize(0);
 170
 171   QStringList header;
 172   header.append("");
 173   header.append("TL");
 174   header.append("TR");
 175   header.append("BL");
 176   header.append("BR");
 177   header.append("");
 178   header.append("");
 179   header.append("Name");
 180
 181   DataTree->setHeaderLabels(header);
 182   DataTree->resizeColumnToContents(COLUMN_TREE);
 183   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 184   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 185   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 186   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 187   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 188   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 189   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 190
 191   viewMode = 1;
 192   documentation = new vvDocumentation();
 193   help_dialog = new vvHelpDialog();
 194   dicomSeriesSelector = new vvDicomSeriesSelector();
 195
 196   inverseButton->setEnabled(0);
 197   actionAdd_Overlay_to_current_Image->setEnabled(0);
 198   actionSave_As->setEnabled(0);
 199   actionAdd_VF_to_current_Image->setEnabled(0);
 200   actionAdd_fusion_image->setEnabled(0);
 201
 202   //init the sliders
 203   verticalSliders.push_back(NOVerticalSlider);
 204   verticalSliders.push_back(NEVerticalSlider);
 205   verticalSliders.push_back(SOVerticalSlider);
 206   verticalSliders.push_back(SEVerticalSlider);
 207
 208   for (int i =0; i < 4; i++)
 209     verticalSliders[i]->hide();
 210
 211   horizontalSliders.push_back(NOHorizontalSlider);
 212   horizontalSliders.push_back(NEHorizontalSlider);
 213   horizontalSliders.push_back(SOHorizontalSlider);
 214   horizontalSliders.push_back(SEHorizontalSlider);
 215
 216   for (int i =0; i < 4; i++)
 217     horizontalSliders[i]->hide();
 218
 219
 220   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 221   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 222   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 223   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 224
 225   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 226   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 227   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 228   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 229
 230   //connect everything
 231   connect(actionMaximum_Intensity_Projection,SIGNAL(triggered()),this,SLOT(ComputeMIP()));
 232   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 233   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 234   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 235   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 236   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 237   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 238   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 239   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 240   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 241   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 242   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 243   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 244   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 245   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 246   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 247
 248   ///////////////////////////////////////////////
 249   contextMenu.addAction(actionResampler);
 250   connect(actionResampler,SIGNAL(triggered()),this,SLOT(ResampleCurrentImage()));
 251   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 252   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 253   ///////////////////////////////////////////////
 254
 255   actionNorth_East_Window->setEnabled(0);
 256   actionNorth_West_Window->setEnabled(0);
 257   actionSouth_East_Window->setEnabled(0);
 258   actionSouth_West_Window->setEnabled(0);
 259
 260   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 261   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 262   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 263   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 264
 265   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 266   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 267           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 268
 269   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 270   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 271   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 272   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 273   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 274   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 275
 276
 277   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 278
 279   connect(linkPanel,SIGNAL(addLink(QString,QString)),this,SLOT(AddLink(QString,QString)));
 280   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 281   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int)),this,SLOT(SetVFProperty(int,int,int)));
 282   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int)),this,SLOT(SetOverlayProperty(int)));
 283   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,double,double)),
 284           this,SLOT(SetFusionProperty(int,int,double,double)));
 285   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 286
 287   playMode = 0;//pause
 288   mFrameRate = 10;
 289   playButton->setEnabled(0);
 290   frameRateLabel->setEnabled(0);
 291   frameRateSpinBox->setEnabled(0);
 292   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 293   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 294
 295   goToCursorPushButton->setEnabled(0);
 296   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 297
 298   NOViewWidget->hide();
 299   NEViewWidget->hide();
 300   SOViewWidget->hide();
 301   SEViewWidget->hide();
 302
 303   //Recently opened files
 304   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 305   if ( !recent_files.empty() )
 306     {
 307       QMenu * rmenu = new QMenu("Recently opened files...");
 308       rmenu->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/open.png")));
 309       menuFile->insertMenu(actionOpen_Image_With_Time,rmenu);
 310       for (std::list<std::string>::iterator i = recent_files.begin();i!=recent_files.end();i++)
 311         {
 312           QAction* current=new QAction(QIcon(QString::fromUtf8(":/new/prefix1/icons/open.png")),
 313                                        (*i).c_str(),this);
 314           rmenu->addAction(current);
 315           connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 316         }
 317     }
 318
 319   // Adding all new tools (insertion in the menu)
 320   vvToolManager::GetInstance()->Initialize(this);
 321 }
 322 //------------------------------------------------------------------------------
 323
 324
 325 //------------------------------------------------------------------------------
 326 void vvMainWindow::ComputeMIP()
 327 {
 328   vvMaximumIntensityProjection mip;
 329   vvSlicerManager* selected_slicer = mSlicerManagers[GetSlicerIndexFromItem(DataTree->selectedItems()[0])];
 330   QFileInfo info(selected_slicer->GetFileName().c_str());
 331   mip.Compute(selected_slicer);
 332   AddImage(mip.GetOutput(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_mip.mhd");
 333 }
 334 //------------------------------------------------------------------------------
 335
 336
 337 //------------------------------------------------------------------------------
 338 void vvMainWindow::ComputeMidPosition()
 339 {
 340   bool ok;
 341   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 342   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 343                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 344   if (ok)
 345     {
 346       vvMidPosition midp;
 347       midp.slicer_manager = mSlicerManagers[index];
 348       midp.reference_image_index = ref;
 349       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 350       midp.Update();
 351       if (midp.error)
 352         QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 353       else
 354         {
 355           QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 356           AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 357         }
 358       QApplication::restoreOverrideCursor();
 359     }
 360 }
 361
 362 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 363 {
 364   QTreeWidgetItem *item = new QTreeWidgetItem();
 365   item->setData(0,Qt::UserRole,"filename.vtk");
 366   item->setData(1,Qt::UserRole,tr("contour"));
 367   QBrush brush;
 368   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 369   brush.setStyle(Qt::SolidPattern);
 370   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 371   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 372
 373   for (int j = 1; j <= 4; j++)
 374     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 375
 376   QTreePushButton* cButton = new QTreePushButton;
 377   cButton->setItem(item);
 378   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 379   cButton->setToolTip(tr("close image"));
 380   cButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")));
 381   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 382           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 383
 384   QTreePushButton* rButton = new QTreePushButton;
 385   rButton->setItem(item);
 386   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 387   rButton->setToolTip(tr("reload image"));
 388   rButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")));
 389   rButton->setEnabled(false);
 390   //Not implemented
 391   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 392   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 393
 394   DataTree->topLevelItem(image_index)->setExpanded(1);
 395   DataTree->topLevelItem(image_index)->addChild(item);
 396   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 397   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 398   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 399   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 400
 401   UpdateTree();
 402   mSlicerManagers[image_index]->AddContour(contour,propagation);
 403   mSlicerManagers[image_index]->Render();
 404 }
 405
 406 //------------------------------------------------------------------------------
 407 void vvMainWindow::OpenVTKContour()
 408 {
 409   if (mSlicerManagers.size() > 0)
 410     {
 411       QString Extensions = "Images ( *.vtk)";
 412       Extensions += ";;All Files (*)";
 413       QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 414       if (file.isNull())
 415         return;
 416       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 417       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 418       vvMeshReader reader;
 419       reader.SetModeToVTK();
 420       reader.SetFilename(file.toStdString());
 421       reader.Update();
 422       AddContour(index,reader.GetOutput()[0],false);
 423       QApplication::restoreOverrideCursor();
 424     }
 425 }
 426 //------------------------------------------------------------------------------
 427 void vvMainWindow::OpenDCStructContour()
 428 {
 429   if (mSlicerManagers.size() > 0)
 430     {
 431       QString Extensions = "Dicom Files ( *.dcm)";
 432       Extensions += ";;All Files (*)";
 433       QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 434       if (file.isNull())
 435         return;
 436       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 437       vvMeshReader reader;
 438       reader.SetFilename(file.toStdString());
 439       vvStructSelector selector;
 440       selector.SetStructures(reader.GetROINames());
 441       if (!mSlicerManagers[index]->GetVF().IsNull())
 442         selector.EnablePropagationCheckBox();
 443       if (selector.exec())
 444         {
 445           QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 446           reader.SetSelectedItems(selector.getSelectedItems());
 447           reader.SetImage(mSlicerManagers[index]->GetImage());
 448           if (selector.PropagationEnabled())
 449             reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 450           reader.Update();
 451           std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 452           for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 453                i!=contours.end();i++)
 454             AddContour(index,*i,selector.PropagationEnabled());
 455           QApplication::restoreOverrideCursor();
 456         }
 457     }
 458 }
 459
 460 //------------------------------------------------------------------------------
 461 void vvMainWindow::ComputeDeformableRegistration()
 462 {
 463   if (mSlicerManagers.size() > 0)
 464     {
 465       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 466       vvDeformationDialog dialog(index,mSlicerManagers);
 467       if (dialog.exec())
 468         {
 469           std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 470           AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 471           WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 472         }
 473       else
 474         std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 475     }
 476   else QMessageBox::information(this, "Need to open image","You must open an image first.");
 477 }
 478
 479 //------------------------------------------------------------------------------
 480 void vvMainWindow::WarpImage()
 481 {
 482   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 483   if (!mSlicerManagers[index]->GetVF().IsNull())
 484     {
 485       bool ok;
 486       int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 487                                          mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 488       if (ok)
 489         {
 490           WarpImage(mSlicerManagers[index],ref);
 491         }
 492     }
 493   else
 494     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 495 }
 496
 497 //------------------------------------------------------------------------------
 498 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 499 {
 500   if (!selected_slicer->GetVF().IsNull())
 501     {
 502       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 503       QFileInfo info(selected_slicer->GetFileName().c_str());
 504       vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 505                        reference_phase,this);
 506       if (warp.ComputeWarpedImage())
 507         {
 508           AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 509           AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 510           AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 511           QApplication::restoreOverrideCursor();
 512         }
 513       else
 514         {
 515           QApplication::restoreOverrideCursor();
 516           QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 517         }
 518     }
 519   else
 520     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 521 }
 522
 523 //------------------------------------------------------------------------------
 524 vvMainWindow::~vvMainWindow() {
 525   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
 526     {
 527       if (mSlicerManagers[i] != NULL)
 528         delete mSlicerManagers[i];
 529     }
 530 }
 531 //------------------------------------------------------------------------------
 532
 533 //------------------------------------------------------------------------------
 534 void vvMainWindow::MergeImages() {
 535   QString Extensions = "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.hdr *.vox)";
 536   Extensions += ";;All Files (*)";
 537   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 538   if (files.isEmpty())
 539     return;
 540   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 541   std::vector<std::string> vector;
 542
 543   unsigned int currentDim = 0;
 544   std::vector<double> currentSpacing;
 545   std::vector<int> currentSize;
 546   std::vector<double> currentOrigin;
 547
 548   for (int i = 0; i < files.size(); i++)
 549     {
 550       itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 551                                                                             files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 552       reader->SetFileName(files[i].toStdString().c_str());
 553       reader->ReadImageInformation();
 554       if (reader)  NOViewWidget->hide();
 555       NEViewWidget->hide();
 556       SOViewWidget->hide();
 557       SEViewWidget->hide();
 558       {
 559         if (i == 0)
 560           currentDim = reader->GetNumberOfDimensions();
 561         bool IsOk = true;
 562         for (unsigned int j = 0;j < currentDim; j++)
 563           {
 564             if (i == 0)
 565               {
 566                 if (j == 0)
 567                   {
 568                     currentSpacing.resize(currentDim);
 569                     currentSize.resize(currentDim);
 570                     currentOrigin.resize(currentDim);
 571                   }
 572                 currentOrigin[j] = reader->GetOrigin(j);
 573                 currentSpacing[j] = reader->GetSpacing(j);
 574                 currentSize[j] = reader->GetDimensions(j);
 575               }
 576             else if (currentDim != reader->GetNumberOfDimensions()
 577                      || currentSpacing[j] != reader->GetSpacing(j)
 578                      || currentSize[j] != (int)reader->GetDimensions(j)
 579                      || currentOrigin[j] != reader->GetOrigin(j))
 580               {
 581                 QString error = "Cannot read file (too different from others ";
 582                 error += files[i].toStdString().c_str();
 583                 QMessageBox::information(this,tr("Reading problem"),error);
 584                 IsOk = false;
 585                 break;
 586               }
 587           }
 588         if (IsOk)
 589           vector.push_back(files[i].toStdString());
 590       }
 591     }
 592   if (vector.size() > 0)
 593     LoadImages(vector, MERGED);
 594 }
 595 //------------------------------------------------------------------------------
 596
 597 //------------------------------------------------------------------------------
 598 void vvMainWindow::MergeImagesWithTime() {
 599   QString Extensions = "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.hdr *.vox)";
 600   Extensions += ";;All Files (*)";
 601   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 602   if (files.isEmpty())
 603     return;
 604   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 605   std::vector<std::string> vector;
 606
 607   unsigned int currentDim = 0;
 608   std::vector<double> currentSpacing;
 609   std::vector<int> currentSize;
 610   std::vector<double> currentOrigin;
 611
 612   for (int i = 0; i < files.size(); i++)
 613     {
 614       itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 615                                                                             files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 616       if (reader)
 617         {
 618           reader->SetFileName(files[i].toStdString().c_str());
 619           reader->ReadImageInformation();
 620           if (i == 0)
 621             currentDim = reader->GetNumberOfDimensions();
 622           bool IsOk = true;
 623           for (unsigned int j = 0;j < currentDim; j++)
 624             {
 625               if (i == 0)
 626                 {
 627                   if (j == 0)
 628                     {
 629                       currentSpacing.resize(currentDim);
 630                       currentSize.resize(currentDim);
 631                       currentOrigin.resize(currentDim);
 632                     }
 633                   currentOrigin[j] = reader->GetOrigin(j);
 634                   currentSpacing[j] = reader->GetSpacing(j);
 635                   currentSize[j] = reader->GetDimensions(j);
 636                 }
 637               else if (currentDim != reader->GetNumberOfDimensions()
 638                        || currentSpacing[j] != reader->GetSpacing(j)
 639                        || currentSize[j] != (int)reader->GetDimensions(j)
 640                        || currentOrigin[j] != reader->GetOrigin(j))
 641                 {
 642                   QString error = "Cannot read file (too different from others ";
 643                   error += files[i].toStdString().c_str();
 644                   QMessageBox::information(this,tr("Reading problem"),error);
 645                   IsOk = false;
 646                   break;
 647                 }
 648             }
 649           if (IsOk)
 650             vector.push_back(files[i].toStdString());
 651         }
 652       else
 653         {
 654           QString error = "Cannot read file info for ";
 655           error += files[i].toStdString().c_str();
 656           error += "\n";
 657           error += "Maybe you're trying to open an image in an unsupported format?\n";
 658           QMessageBox::information(this,tr("Reading problem"),error);
 659         }
 660     }
 661   sort(vector.begin(),vector.end());
 662   if (vector.size() > 1)
 663     LoadImages(vector, MERGEDWITHTIME);
 664   else
 665     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.");
 666 }
 667 //------------------------------------------------------------------------------
 668
 669 //------------------------------------------------------------------------------
 670 void vvMainWindow::OpenDicom() {
 671   std::vector<std::string> files;
 672
 673 #ifdef CLITK_VV_USE_BDCM
 674   bool r = bdcm::OpenDicomFilesSelectorDialog(files,
 675                                               "DicomFilesSelectorDialog test",
 676                                               0,0,800,800,1);
 677
 678   if (r) {
 679     std::cout << "$$$$ main : user clicked 'OK' $$$$"<<std::endl;
 680     std::cout << "$$$$ selected files : "<<std::endl;
 681     std::vector<std::string>::iterator i;
 682     for (i=files.begin();i!=files.end();++i) {
 683       std::cout << *i << std::endl;
 684     }
 685     std::cout << "$$$$ "<<std::endl;
 686
 687     LoadImages(files,DICOM);
 688   }
 689   else {
 690     std::cout << "$$$$ main : user clicked 'CANCEL' $$$$"<<std::endl;
 691   }
 692 #else
 693   std::cout << "dicomSeriesSelector " << std::endl;
 694   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 695     files = *(dicomSeriesSelector->GetFilenames());
 696     LoadImages(files,DICOM);
 697   }
 698 #endif
 699
 700 }
 701 //------------------------------------------------------------------------------
 702
 703 //------------------------------------------------------------------------------
 704 void vvMainWindow::OpenImages() {
 705   QString Extensions = "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.hdr *.vox)";
 706   Extensions += ";;All Files (*)";
 707
 708   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 709   if (files.isEmpty())
 710     return;
 711   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 712   std::vector<std::string> vector;
 713   for (int i = 0; i < files.size(); i++)
 714     vector.push_back(files[i].toStdString());
 715   LoadImages(vector, IMAGE);
 716 }
 717 //------------------------------------------------------------------------------
 718 void vvMainWindow::OpenRecentImage()
 719 {
 720   QAction * caller = qobject_cast<QAction*>(sender());
 721   std::vector<std::string> images;
 722   images.push_back(caller->text().toStdString());
 723   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 724   LoadImages(images,IMAGE);
 725 }
 726
 727 //------------------------------------------------------------------------------
 728 void vvMainWindow::OpenImageWithTime() {
 729   QString Extensions = "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.hdr *.vox)";
 730   Extensions += ";;All Files (*)";
 731
 732   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 733   if (files.isEmpty())
 734     return;
 735   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 736   std::vector<std::string> vector;
 737   for (int i = 0; i < files.size(); i++)
 738     {
 739       vector.push_back(files[i].toStdString());
 740     }
 741   LoadImages(vector, IMAGEWITHTIME);
 742 }
 743 //------------------------------------------------------------------------------
 744
 745 //------------------------------------------------------------------------------
 746 void vvMainWindow::LoadImages(std::vector<std::string> files, LoadedImageType filetype) {
 747   //Separate the way to open images and dicoms
 748   int fileSize;
 749   if (filetype == IMAGE || filetype == IMAGEWITHTIME)
 750     fileSize = files.size();
 751   else
 752     fileSize = 1;
 753
 754   //Only add to the list of recently opened files when a single file is opened,
 755   //to avoid polluting the list of recently opened files
 756   if (files.size() == 1)
 757     {
 758       QFileInfo finfo=tr(files[0].c_str());
 759       AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 760     }
 761   //init the progress events
 762   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 763   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 764   qApp->processEvents();
 765
 766   int numberofsuccesulreads=0;
 767   //open images as 1 or multiples
 768   for (int i = 0; i < fileSize; i++) {
 769
 770     progress.Update("Opening " + files[i]);
 771     progress.SetProgress(i,fileSize);
 772     qApp->processEvents();
 773
 774     //read the image and put it in mSlicerManagers
 775     vvSlicerManager* imageManager = new vvSlicerManager(4);
 776     qApp->processEvents();
 777
 778     bool SetImageSucceed=false;
 779
 780     if (filetype == IMAGE || filetype == IMAGEWITHTIME)
 781       SetImageSucceed = imageManager->SetImage(files[i],filetype);
 782     else
 783       {
 784         SetImageSucceed = imageManager->SetImages(files,filetype);
 785       }
 786     if (SetImageSucceed == false)
 787       {
 788         QApplication::restoreOverrideCursor();
 789         QString error = "Cannot open file \n";
 790         error += imageManager->GetLastError().c_str();
 791         QMessageBox::information(this,tr("Reading problem"),error);
 792         delete imageManager;
 793       }
 794     else
 795       {
 796         mSlicerManagers.push_back(imageManager);
 797
 798         //create an item in the tree with good settings
 799         QTreeWidgetItem *item = new QTreeWidgetItem();
 800         item->setData(0,Qt::UserRole,files[i].c_str());
 801         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 802         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 803         qApp->processEvents();
 804
 805         //Create the buttons for reload and close
 806         qApp->processEvents();
 807         QTreePushButton* cButton = new QTreePushButton;
 808         cButton->setItem(item);
 809         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 810         cButton->setToolTip(tr("close image"));
 811         cButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")));
 812         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 813                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 814
 815         QTreePushButton* rButton = new QTreePushButton;
 816         rButton->setItem(item);
 817         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 818         rButton->setToolTip(tr("reload image"));
 819         rButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")));
 820         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 821                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 822
 823         DataTree->addTopLevelItem(item);
 824         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 825         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 826
 827         //set the id of the image
 828         QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 829         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 830         mSlicerManagers.back()->SetId(id.toStdString());
 831
 832         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 833
 834         connect(mSlicerManagers.back(),SIGNAL(currentImageChanged(std::string)),
 835                 this,SLOT(CurrentImageChanged(std::string)));
 836         connect(mSlicerManagers.back(),SIGNAL(
 837                                               UpdatePosition(int, double, double, double, double, double, double, double)),this,
 838                 SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 839         connect(mSlicerManagers.back(),SIGNAL(UpdateVector(int, double, double, double, double)),
 840                 this, SLOT(VectorChanged(int,double,double,double, double)));
 841         connect(mSlicerManagers.back(),SIGNAL(UpdateOverlay(int, double, double)),
 842                 this, SLOT(OverlayChanged(int,double,double)));
 843         connect(mSlicerManagers.back(),SIGNAL(UpdateFusion(int, double)),
 844                 this, SLOT(FusionChanged(int,double)));
 845         connect(mSlicerManagers.back(),SIGNAL(UpdateWindows(int, int, int)),
 846                 this,SLOT(WindowsChanged(int, int, int)));
 847         connect(mSlicerManagers.back(),SIGNAL(WindowLevelChanged(double, double,int, int)),
 848                 this,SLOT(WindowLevelChanged(double, double, int, int)));
 849         connect(mSlicerManagers.back(),SIGNAL(UpdateSlice(int,int)),
 850                 this,SLOT(UpdateSlice(int,int)));
 851         connect(mSlicerManagers.back(),SIGNAL(UpdateTSlice(int, int)),
 852                 this,SLOT(UpdateTSlice(int, int)));
 853         connect(mSlicerManagers.back(),SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 854                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 855         connect(mSlicerManagers.back(),SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 856                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 857         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 858         InitSlicers();
 859         numberofsuccesulreads++;
 860       }
 861   }
 862   if (numberofsuccesulreads)
 863     {
 864       NOViewWidget->show();
 865       NEViewWidget->show();
 866       SOViewWidget->show();
 867       SEViewWidget->show();
 868       UpdateTree();
 869       InitDisplay();
 870       ShowLastImage();
 871     }
 872   QApplication::restoreOverrideCursor();
 873
 874
 875   // vvToolManager::GetInstance()->UpdateEnabledTool();
 876   // emit SlicerManagersHasChanged();
 877 }
 878 //------------------------------------------------------------------------------
 879
 880 //------------------------------------------------------------------------------
 881 void vvMainWindow::UpdateTree() {
 882   DataTree->resizeColumnToContents(COLUMN_TREE);
 883   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 884   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 885   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 886   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 887   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 888   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 889   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 890 }
 891 //------------------------------------------------------------------------------
 892
 893 //------------------------------------------------------------------------------
 894 void vvMainWindow::CurrentImageChanged(std::string id) {
 895   int selected = 0;
 896   for (int i = 0; i < DataTree->topLevelItemCount(); i++)
 897     {
 898       if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id)
 899         {
 900           selected = i;
 901         }
 902       else
 903         {
 904           DataTree->topLevelItem(i)->setSelected(0);
 905         }
 906       for (int child = 0; child < DataTree->topLevelItem(i)->childCount();child++)
 907         DataTree->topLevelItem(i)->child(child)->setSelected(0);
 908
 909     }
 910   DataTree->topLevelItem(selected)->setSelected(1);
 911 }
 912 //------------------------------------------------------------------------------
 913
 914 //------------------------------------------------------------------------------
 915 void vvMainWindow::ImageInfoChanged() {
 916   contextActions[7]->setEnabled(1);
 917   contextActions[6]->setEnabled(1);
 918   actionSave_As->setEnabled(1);
 919   actionAdd_VF_to_current_Image->setEnabled(1);
 920   actionAdd_fusion_image->setEnabled(1);
 921   actionNorth_East_Window->setEnabled(1);
 922   actionNorth_West_Window->setEnabled(1);
 923   actionSouth_East_Window->setEnabled(1);
 924   actionSouth_West_Window->setEnabled(1);
 925   inverseButton->setEnabled(1);
 926
 927   goToCursorPushButton->setEnabled(1);
 928
 929   if (DataTree->selectedItems().size()) {
 930     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 931
 932     colorMapComboBox->setEnabled(1);
 933     for (int i = 0; i < DataTree->topLevelItem(index)->childCount();i++)
 934       {
 935         if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
 936             DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion")
 937           {
 938             colorMapComboBox->setEnabled(0);
 939             break;
 940           }
 941       }
 942
 943     std::vector<double> origin;
 944     std::vector<double> inputSpacing;
 945     std::vector<int> inputSize;
 946     std::vector<double> sizeMM;
 947     int dimension=0;
 948     QString pixelType;
 949     QString inputSizeInBytes;
 950     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
 951
 952     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1)
 953       {
 954         playButton->setEnabled(1);
 955         frameRateLabel->setEnabled(1);
 956         frameRateSpinBox->setEnabled(1);
 957       }
 958     else
 959       {
 960         playButton->setEnabled(0);
 961         frameRateLabel->setEnabled(0);
 962         frameRateSpinBox->setEnabled(0);
 963       }
 964
 965     //read image header
 966     int NPixel = 1;
 967
 968     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0])
 969       {
 970         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
 971         dimension = imageSelected->GetNumberOfDimensions();
 972         origin.resize(dimension);
 973         inputSpacing.resize(dimension);
 974         inputSize.resize(dimension);
 975         sizeMM.resize(dimension);
 976         pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
 977         for (int i = 0;i < dimension;i++)
 978           {
 979             origin[i] = imageSelected->GetOrigin()[i];
 980             inputSpacing[i] = imageSelected->GetSpacing()[i];
 981             inputSize[i] = imageSelected->GetSize()[i];
 982             sizeMM[i] = inputSize[i]*inputSpacing[i];
 983             NPixel *= inputSize[i];
 984           }
 985         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
 986       }
 987     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector")
 988       {
 989         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
 990         dimension = imageSelected->GetNumberOfDimensions();
 991         origin.resize(dimension);
 992         inputSpacing.resize(dimension);
 993         inputSize.resize(dimension);
 994         sizeMM.resize(dimension);
 995         pixelType = mSlicerManagers[index]->GetVF()->GetScalarTypeAsString().c_str();
 996         for (int i = 0;i < dimension;i++)
 997           {
 998             origin[i] = imageSelected->GetOrigin()[i];
 999             inputSpacing[i] = imageSelected->GetSpacing()[i];
1000             inputSize[i] = imageSelected->GetSize()[i];
1001             sizeMM[i] = inputSize[i]*inputSpacing[i];
1002             NPixel *= inputSize[i];
1003           }
1004         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1005       }
1006     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay")
1007       {
1008         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1009         dimension = imageSelected->GetNumberOfDimensions();
1010         origin.resize(dimension);
1011         inputSpacing.resize(dimension);
1012         inputSize.resize(dimension);
1013         sizeMM.resize(dimension);
1014         pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
1015         for (int i = 0;i < dimension;i++)
1016           {
1017             origin[i] = imageSelected->GetOrigin()[i];
1018             inputSpacing[i] = imageSelected->GetSpacing()[i];
1019             inputSize[i] = imageSelected->GetSize()[i];
1020             sizeMM[i] = inputSize[i]*inputSpacing[i];
1021             NPixel *= inputSize[i];
1022           }
1023         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1024       }
1025     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion")
1026       {
1027         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1028         dimension = imageSelected->GetNumberOfDimensions();
1029         origin.resize(dimension);
1030         inputSpacing.resize(dimension);
1031         inputSize.resize(dimension);
1032         sizeMM.resize(dimension);
1033         pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
1034         for (int i = 0;i < dimension;i++)
1035           {
1036             origin[i] = imageSelected->GetOrigin()[i];
1037             inputSpacing[i] = imageSelected->GetSpacing()[i];
1038             inputSize[i] = imageSelected->GetSize()[i];
1039             sizeMM[i] = inputSize[i]*inputSpacing[i];
1040             NPixel *= inputSize[i];
1041           }
1042         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1043       }
1044
1045     QString dim = QString::number(dimension) + " (";
1046     dim += pixelType + ")";
1047
1048     infoPanel->setFileName(image);
1049     infoPanel->setDimension(dim);
1050     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1051     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1052     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1053     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1054     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1055
1056     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1057                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1058     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1059     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1060
1061     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1062     for (int i = 0; i < 4;i++)
1063       {
1064         if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3)
1065           {
1066             mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1067             break;
1068           }
1069       }
1070     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1071     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1072     DD(mSlicerManagers[index]->GetColorMap());
1073     DD(mSlicerManagers[index]->GetPreset());
1074     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1075     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1076
1077         infoPanel->setFileName(image);
1078         infoPanel->setDimension(dim);
1079         infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1080         infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1081         infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1082         infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1083         infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1084
1085         landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1086                                             mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1087         landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1088         landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1089
1090         overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1091         for (int i = 0; i < 4;i++)
1092         {
1093             if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3)
1094             {
1095                 mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1096                 break;
1097             }
1098         }
1099         windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1100         levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1101         presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1102         colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1103
1104         if (mSlicerManagers[index]->GetSlicer(0)->GetVF())
1105         {
1106             overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1107             overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1108                                         mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1109                                         mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1110         }
1111         else
1112         {
1113             overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1114             overlayPanel->getVFProperty(-1,-1,-1);
1115         }
1116         if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1117         {
1118             overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1119             overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1120         }
1121         else
1122         {
1123             overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1124             overlayPanel->getOverlayProperty(-1);
1125         }
1126         if (mSlicerManagers[index]->GetSlicer(0)->GetFusion())
1127         {
1128             overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1129             overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1130                                             mSlicerManagers[index]->GetFusionColorMap(),
1131                                             mSlicerManagers[index]->GetFusionWindow(),
1132                                             mSlicerManagers[index]->GetFusionLevel());
1133         }
1134         else
1135         {
1136             overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1137             overlayPanel->getFusionProperty(-1, -1,-1,-1);
1138         }
1139     }
1140 }
1141 //------------------------------------------------------------------------------
1142
1143 //------------------------------------------------------------------------------
1144 void vvMainWindow::ShowDocumentation() {
1145   documentation->show();
1146 }
1147 //------------------------------------------------------------------------------
1148 void vvMainWindow::ShowHelpDialog() {
1149   help_dialog->show();
1150 }
1151 //------------------------------------------------------------------------------
1152
1153 //------------------------------------------------------------------------------
1154 void vvMainWindow::ChangeViewMode() {
1155   QListIterator<int> it0(splitter_3->sizes());
1156   QListIterator<int> it1(splitter_3->sizes());
1157   int max0 = 0;
1158   int max1 = 1;
1159   while (it0.hasNext())
1160     {
1161       max0 += it0.next();
1162     }
1163   while (it1.hasNext())
1164     {
1165       max1 += it1.next();
1166     }
1167   QList<int> size0;
1168   QList<int> size1;
1169   if (viewMode == 1)
1170     {
1171       viewMode = 0;
1172       size0.push_back(max0);
1173       size0.push_back(0);
1174       size1.push_back(max1);
1175       size1.push_back(0);
1176       splitter_3->setSizes(size0);
1177       OSplitter->setSizes(size1);
1178       DataTree->setColumnHidden(2,1);
1179       DataTree->setColumnHidden(3,1);
1180       DataTree->setColumnHidden(4,1);
1181     }
1182   else
1183     {
1184       viewMode = 1;
1185       size0.push_back(int(max0/2));
1186       size0.push_back(int(max0/2));
1187       size1.push_back(int(max1/2));
1188       size1.push_back(int(max1/2));
1189       splitter_3->setSizes(size0);
1190       OSplitter->setSizes(size1);
1191       DataTree->setColumnHidden(2,0);
1192       DataTree->setColumnHidden(3,0);
1193       DataTree->setColumnHidden(4,0);
1194     }
1195 }
1196 //------------------------------------------------------------------------------
1197
1198 //------------------------------------------------------------------------------
1199 QString vvMainWindow::GetSizeInBytes(unsigned long size) {
1200   QString result = "";// QString::number(size);
1201   //result += " bytes (";
1202   if (size > 1000000000)
1203     {
1204       size /= 1000000000;
1205       result += QString::number(size);
1206       result += "Gb";//)";
1207     }
1208   else if (size > 1000000)
1209     {
1210       size /= 1000000;
1211       result += QString::number(size);
1212       result += "Mb";//)";
1213     }
1214   else if (size > 1000)
1215     {
1216       size /= 1000;
1217       result += QString::number(size);
1218       result += "kb";//)";
1219     }
1220   return result;
1221 }
1222 //------------------------------------------------------------------------------
1223
1224 //------------------------------------------------------------------------------
1225 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble) {
1226   QString result;
1227   for (unsigned int i= 0; i < vectorDouble.size(); i++)
1228     {
1229       if (i != 0)
1230         result += " ";
1231       result += QString::number(vectorDouble[i]);
1232     }
1233   return result;
1234 }
1235 //------------------------------------------------------------------------------
1236
1237 //------------------------------------------------------------------------------
1238 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt) {
1239   QString result;
1240   for (unsigned int i= 0; i < vectorInt.size(); i++)
1241     {
1242       if (i != 0)
1243         result += " ";
1244       result += QString::number(vectorInt[i]);
1245     }
1246   return result;
1247 }
1248 //------------------------------------------------------------------------------
1249
1250 //------------------------------------------------------------------------------
1251 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item) {
1252   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1253   for (int i = 0; i < DataTree->topLevelItemCount(); i++)
1254     {
1255       if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1256         return i;
1257     }
1258   return -1;
1259 }
1260 //------------------------------------------------------------------------------
1261
1262 //------------------------------------------------------------------------------
1263 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clicked_item, int column) {
1264   int index = GetSlicerIndexFromItem(clicked_item);
1265   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1266     return;
1267   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
1268     {
1269       QTreeWidgetItem* current_row=DataTree->topLevelItem(i);
1270       if (DataTree->topLevelItem(index) == current_row)
1271         {
1272           vvSlicer* clicked_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1273           if (current_row == clicked_item)
1274             {
1275               //If we just activated a slicer
1276               if (current_row->data(column,Qt::CheckStateRole).toInt() > 0)
1277                 {
1278                   mSlicerManagers[i]->UpdateSlicer(column-1,clicked_item->data(column,Qt::CheckStateRole).toInt());
1279                   mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1280                   DisplaySliders(i,column-1);
1281                   std::map<std::string,int> overlay_counts;
1282                   for (int child = 0; child < current_row->childCount(); child++)
1283                     {
1284                       std::string overlay_type =
1285                         current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1286                       overlay_counts[overlay_type]++;
1287                       current_row->child(child)->setData(column,Qt::CheckStateRole,
1288                                                          current_row->data(column,Qt::CheckStateRole));
1289                       clicked_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,true);
1290                     }
1291                 }
1292               else //We don't allow simply desactivating a slicer
1293                 {
1294                   clicked_item->setData(column,Qt::CheckStateRole,2);
1295                   return;
1296                 }
1297             }
1298           //if we clicked on the vector(or overlay) and not the image
1299           else
1300             {
1301               if (clicked_item->data(column,Qt::CheckStateRole).toInt())
1302                 {
1303                   current_row->setData(column,Qt::CheckStateRole,2);
1304                   mSlicerManagers[i]->UpdateSlicer(column-1,2);
1305                   mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1306                   DisplaySliders(i,column-1);
1307                 }
1308               int vis = clicked_item->data(column,Qt::CheckStateRole).toInt();
1309               std::string overlay_type = clicked_item->data(1,Qt::UserRole).toString().toStdString();
1310               int overlay_index=0;
1311               for (int child = 0; child < current_row->childCount(); child++)
1312                 {
1313                   if (current_row->child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1314                     overlay_index++;
1315                   if (current_row->child(child) == clicked_item) break;
1316                 }
1317               clicked_slicer->SetActorVisibility(
1318                                                  clicked_item->data(1,Qt::UserRole).toString().toStdString(), overlay_index-1,vis);
1319             }
1320         }
1321       else if (current_row->data(column,Qt::CheckStateRole).toInt() > 0)
1322         {
1323           current_row->setData(column,Qt::CheckStateRole,0);
1324           mSlicerManagers[i]->UpdateSlicer(column-1,0);
1325           std::map<std::string,int> overlay_counts;
1326           for (int child = 0; child < current_row->childCount(); child++)
1327             {
1328               std::string overlay_type =
1329                 current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1330               overlay_counts[overlay_type]++;
1331               current_row->child(child)->setData(column,Qt::CheckStateRole,0);
1332               vvSlicer * current_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1333               current_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,false);
1334             }
1335         }
1336       //mSlicerManagers[i]->SetColorMap(-1);
1337       mSlicerManagers[i]->SetColorMap();
1338     }
1339   mSlicerManagers[index]->GetSlicer(column-1)->Render();
1340 }
1341 //------------------------------------------------------------------------------
1342
1343 void vvMainWindow::InitSlicers()
1344 {
1345   if (mSlicerManagers.size())
1346     {
1347       mSlicerManagers.back()->GenerateDefaultLookupTable();
1348
1349       mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1350       mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1351       mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1352       mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1353     }
1354 }
1355
1356 //------------------------------------------------------------------------------
1357 void vvMainWindow::InitDisplay() {
1358   if (mSlicerManagers.size())
1359     {
1360       //BE CAREFUL : this is absolutely necessary to set the interactor style
1361       //in order to have the same style instanciation for all SlicerManagers in
1362       // a same window
1363       for (int j = 0; j < 4; j++)
1364         {
1365           vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1366           style->SetAutoAdjustCameraClippingRange(1);
1367           bool AlreadySelected = false;
1368           for (int i = 0; i < DataTree->topLevelItemCount(); i++)
1369             {
1370               mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1371
1372               //select the image only if previous are not selected
1373               if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1)
1374                 {
1375                   mSlicerManagers[i]->UpdateSlicer(j,1);
1376                   AlreadySelected = true;
1377                 }
1378               else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected)
1379                 {
1380                   if (DataTree->selectedItems().size() == 0)
1381                     DataTree->topLevelItem(i)->setSelected(1);
1382                   DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1383                   mSlicerManagers[i]->UpdateSlicer(j,1);
1384                   DisplaySliders(i,j);
1385                 }
1386               else
1387                 {
1388                   DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1389                   mSlicerManagers[i]->UpdateSlicer(j,0);
1390                 }
1391             }
1392           style->Delete();
1393         }
1394     }
1395 }
1396 //------------------------------------------------------------------------------
1397
1398 //------------------------------------------------------------------------------
1399 void vvMainWindow::DisplaySliders(int slicer, int window) {
1400   int range[2];
1401   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1402   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1403
1404   int tRange[2];
1405   tRange[0] = 0;
1406   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1407   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1408   bool showHorizontal = false;
1409   bool showVertical = false;
1410   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1411       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1412           && mSlicerManagers[slicer]->GetType() != IMAGEWITHTIME
1413           && mSlicerManagers[slicer]->GetType() != MERGEDWITHTIME))
1414     showVertical = true;
1415   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1416       || mSlicerManagers[slicer]->GetType() == IMAGEWITHTIME
1417       || mSlicerManagers[slicer]->GetType() == MERGEDWITHTIME)
1418     showHorizontal = true;
1419
1420   if (showVertical)
1421     verticalSliders[window]->show();
1422   else
1423     verticalSliders[window]->hide();
1424   verticalSliders[window]->setRange(range[0],range[1]);
1425   verticalSliders[window]->setValue(position);
1426
1427   if (showHorizontal)
1428     horizontalSliders[window]->show();
1429   else
1430     horizontalSliders[window]->hide();
1431   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1432   horizontalSliders[window]->setValue(tPosition);
1433 }
1434 //------------------------------------------------------------------------------
1435
1436 //------------------------------------------------------------------------------
1437 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column) {
1438   int index = GetSlicerIndexFromItem(item);
1439
1440   if (DataTree->topLevelItem(index) != item)
1441     {
1442       QString warning = "Do you really want to close the overlay : ";
1443       warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1444       QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1445                          warning, 0, this);
1446       msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1447       msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1448       if (msgBox.exec() == QMessageBox::AcceptRole)
1449         {
1450           std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1451           int overlay_index=0;
1452           for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1453             {
1454               if (DataTree->topLevelItem(index)->\
1455                   child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1456                 overlay_index++;
1457               if (DataTree->topLevelItem(index)->child(child) == item) break;
1458             }
1459           mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1460           mSlicerManagers[index]->SetColorMap(0);
1461           DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1462           mSlicerManagers[index]->Render();
1463         }
1464     }
1465   else if (DataTree->topLevelItemCount() <= 1)
1466     {
1467       QString warning = "Do you really want to close the image : ";
1468       warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1469       warning += "\nThis is the last image, you're about to close vv !!!";
1470       QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1471                          warning, 0, this);
1472       msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1473       msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1474       if (msgBox.exec() == QMessageBox::AcceptRole)
1475         {
1476           this->close();
1477         }
1478     }
1479   else
1480     {
1481       QString warning = "Do you really want to close the image : ";
1482       warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1483       QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1484                          warning, 0, this);
1485       msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1486       msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1487       if (msgBox.exec() == QMessageBox::AcceptRole)
1488         {
1489           std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1490           DataTree->takeTopLevelItem(index);
1491           for (int i = 0; i < index; i++)
1492             {
1493               Manageriter++;
1494             }
1495           linkPanel->removeImage(index);
1496           mSlicerManagers[index]->RemoveActors();
1497           delete mSlicerManagers[index];
1498           mSlicerManagers.erase(Manageriter);
1499           InitDisplay();
1500         }
1501     }
1502
1503   // vvToolManager::GetInstance()->UpdateEnabledTool();
1504   // emit SlicerManagersHasChanged();
1505 }
1506 //------------------------------------------------------------------------------
1507
1508 //------------------------------------------------------------------------------
1509 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column) {
1510   // int index = GetSlicerIndexFromItem(item);
1511 //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1512 //   if (item->data(1,Qt::UserRole).toString() == "vector")
1513 //     mSlicerManagers[index]->ReloadVF();
1514 //   else
1515 //     mSlicerManagers[index]->Reload();
1516
1517 //   QApplication::restoreOverrideCursor();
1518   int index = GetSlicerIndexFromItem(item);
1519   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1520   QString role=item->data(1,Qt::UserRole).toString();
1521   if ( role == "vector")
1522     mSlicerManagers[index]->ReloadVF();
1523   else if (role == "overlay")
1524     mSlicerManagers[index]->ReloadOverlay();
1525   else if (role == "fusion")
1526     mSlicerManagers[index]->ReloadFusion();
1527   else
1528     mSlicerManagers[index]->Reload();
1529   QApplication::restoreOverrideCursor();
1530 }
1531 //------------------------------------------------------------------------------
1532
1533 void vvMainWindow::CropImage()
1534 {
1535   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1536   vvCropDialog crop(mSlicerManagers,index);
1537   if(crop.exec())
1538     AddImage(crop.GetOutput(),"cropped.mhd");
1539 }
1540
1541 //------------------------------------------------------------------------------
1542 void vvMainWindow::SplitImage() {
1543   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1544   int dim = mSlicerManagers[index]->GetDimension();
1545   QString warning = "Do you really want to split the ";
1546   warning += QString::number(dim) + "D image ";
1547   warning += DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString() + " into ";
1548   warning += QString::number(mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetSize()[dim-1]) + " ";
1549   warning += QString::number(dim-1) + "D images.";
1550   QMessageBox msgBox(QMessageBox::Warning, tr("Split Image"),
1551                      warning, 0, this);
1552   msgBox.addButton(tr("Split"), QMessageBox::AcceptRole);
1553   msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1554   if (msgBox.exec() == QMessageBox::AcceptRole)
1555     {
1556       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1557       if (dim > 2)
1558         {
1559           std::string filename = DataTree->selectedItems()[0]->data(0,Qt::UserRole).toString().toStdString();
1560           int numberOfSlice = mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetSize()[dim-1];
1561           std::string path = itksys::SystemTools::GetFilenamePath(
1562                                                                   filename);
1563           path += "/";
1564           path += DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString().toStdString();
1565           path += "%03d";
1566           path += itksys::SystemTools::GetFilenameLastExtension(
1567                                                                 filename).c_str();
1568
1569           typedef itk::NumericSeriesFileNames NameGeneratorType;
1570           NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
1571           nameGenerator->SetSeriesFormat(path.c_str());
1572           nameGenerator->SetStartIndex(0);
1573           nameGenerator->SetEndIndex(numberOfSlice-1);
1574           nameGenerator->SetIncrementIndex(1);
1575
1576           for (int i = 0; i < numberOfSlice; i++)
1577             {
1578               vvSlicerManager* imageManager = new vvSlicerManager(4);
1579               imageManager->SetExtractedImage(nameGenerator->GetFileNames()[i],
1580                                               mSlicerManagers[index]->GetSlicer(0)->GetImage(), i);
1581               mSlicerManagers.push_back(imageManager);
1582
1583               //create an item in the tree with good settings
1584               QTreeWidgetItem *item = new QTreeWidgetItem();
1585               item->setData(0,Qt::UserRole,nameGenerator->GetFileNames()[i].c_str());
1586               std::string fileI = itksys::SystemTools::GetFilenameWithoutLastExtension(
1587                                                                                        nameGenerator->GetFileNames()[i]).c_str();
1588               item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileI.c_str());
1589               for (int j = 1; j <= 4; j++)
1590                 {
1591                   for (int i = 0; i < DataTree->topLevelItemCount(); i++)
1592                     {
1593                       DataTree->topLevelItem(i)->setData(j,Qt::CheckStateRole,0);
1594                     }
1595                   item->setData(j,Qt::CheckStateRole,2);
1596                 }
1597
1598               //Create the buttons for reload and close
1599               QTreePushButton* cButton = new QTreePushButton;
1600               cButton->setItem(item);
1601               cButton->setColumn(COLUMN_CLOSE_IMAGE);
1602               cButton->setToolTip(tr("close image"));
1603               cButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")));
1604               connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1605                       this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1606
1607               QTreePushButton* rButton = new QTreePushButton;
1608               rButton->setItem(item);
1609               rButton->setColumn(COLUMN_RELOAD_IMAGE);
1610               rButton->setToolTip(tr("reload image"));
1611               rButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")));
1612               rButton->setEnabled(false);
1613               connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1614                       this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1615
1616               DataTree->addTopLevelItem(item);
1617               DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1618               DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1619
1620               //set the id of the image
1621               QString id = nameGenerator->GetFileNames()[i].c_str() + QString::number(mSlicerManagers.size()-1);
1622               item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1623               mSlicerManagers.back()->SetId(id.toStdString());
1624               linkPanel->addImage(fileI, id.toStdString());
1625               connect(mSlicerManagers.back(),SIGNAL(currentImageChanged(std::string)),
1626                       this,SLOT(CurrentImageChanged(std::string)));
1627               connect(mSlicerManagers.back(),SIGNAL(
1628                                                     UpdatePosition(int, double, double, double, double, double, double, double)),this,
1629                       SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
1630               connect(mSlicerManagers.back(),SIGNAL(UpdateVector(int, double, double, double, double)),
1631                       this, SLOT(VectorChanged(int,double,double,double, double)));
1632               connect(mSlicerManagers.back(),SIGNAL(UpdateOverlay(int, double, double)),
1633                       this, SLOT(OverlayChanged(int,double,double)));
1634               connect(mSlicerManagers.back(),SIGNAL(UpdateFusion(int, double)),
1635                       this, SLOT(FusionChanged(int,double)));
1636               connect(mSlicerManagers.back(),SIGNAL(UpdateWindows(int, int, int)),
1637                       this,SLOT(WindowsChanged(int, int, int)));
1638               connect(mSlicerManagers.back(),SIGNAL(WindowLevelChanged(double, double,int, int)),
1639                       this,SLOT(WindowLevelChanged(double, double, int, int)));
1640               connect(mSlicerManagers.back(),SIGNAL(UpdateSlice(int,int)),
1641                       this,SLOT(UpdateSlice(int,int)));
1642               connect(mSlicerManagers.back(),SIGNAL(UpdateTSlice(int, int)),
1643                       this,SLOT(UpdateTSlice(int, int)));
1644               connect(mSlicerManagers.back(),SIGNAL(UpdateSliceRange(int,int,int,int,int)),
1645                       this,SLOT(UpdateSliceRange(int,int,int,int,int)));
1646               connect(mSlicerManagers.back(),SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
1647                       this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
1648               connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
1649               UpdateTree();
1650               qApp->processEvents();
1651               InitSlicers();
1652               InitDisplay();
1653               qApp->processEvents();
1654             }
1655           QApplication::restoreOverrideCursor();
1656         }
1657       else
1658         {
1659           QApplication::restoreOverrideCursor();
1660           QString error = "Cannot split file (dimensions must be greater than 2) ";
1661           QMessageBox::information(this,tr("Splitting problem"),error);
1662         }
1663     }
1664 }
1665 //------------------------------------------------------------------------------
1666
1667 //------------------------------------------------------------------------------
1668 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value) {
1669   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1670 }
1671 //------------------------------------------------------------------------------
1672
1673 //------------------------------------------------------------------------------
1674 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value) {
1675   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1676 }
1677 //------------------------------------------------------------------------------
1678
1679 //------------------------------------------------------------------------------
1680 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef) {
1681   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1682 }
1683 //------------------------------------------------------------------------------
1684
1685 //------------------------------------------------------------------------------
1686 void vvMainWindow::FusionChanged(int visibility, double value) {
1687   overlayPanel->getCurrentFusionInfo(visibility,value);
1688 }
1689 //------------------------------------------------------------------------------
1690
1691 //------------------------------------------------------------------------------
1692 void vvMainWindow::WindowsChanged(int window, int view, int slice) {
1693   infoPanel->setViews(window, view, slice);
1694 }
1695 //------------------------------------------------------------------------------
1696
1697 //------------------------------------------------------------------------------
1698 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap) {
1699   windowSpinBox->setValue(window);
1700   levelSpinBox->setValue(level);
1701   colorMapComboBox->setCurrentIndex(colormap);
1702   presetComboBox->setCurrentIndex(preset);
1703 }
1704 //------------------------------------------------------------------------------
1705
1706 //------------------------------------------------------------------------------
1707 void vvMainWindow::WindowLevelEdited() {
1708   presetComboBox->setCurrentIndex(6);
1709   UpdateWindowLevel();
1710 }
1711 //------------------------------------------------------------------------------
1712
1713 //------------------------------------------------------------------------------
1714 void vvMainWindow::UpdateWindowLevel() {
1715   if (DataTree->selectedItems().size())
1716     {
1717       if (presetComboBox->currentIndex() == 7) //For ventilation
1718         colorMapComboBox->setCurrentIndex(5);
1719       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1720       mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1721       mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1722       mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1723       mSlicerManagers[index]->Render();
1724     }
1725 }
1726 //------------------------------------------------------------------------------
1727
1728 //------------------------------------------------------------------------------
1729 void vvMainWindow::UpdateColorMap() {
1730   if (DataTree->selectedItems().size())
1731     {
1732       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1733       mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1734       mSlicerManagers[index]->Render();
1735     }
1736 }
1737 //------------------------------------------------------------------------------
1738 void vvMainWindow::SwitchWindowLevel() {
1739   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1740   int window = mSlicerManagers[index]->GetColorWindow();
1741   presetComboBox->setCurrentIndex(6);
1742   windowSpinBox->setValue(-window);
1743   UpdateWindowLevel();
1744 }
1745 //------------------------------------------------------------------------------
1746
1747 //------------------------------------------------------------------------------
1748 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps) {
1749   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
1750     {
1751       if (mSlicerManagers[i]->GetId() == id)
1752         {
1753           //mSlicerManagers[i]->SetTSlice(temps);
1754           mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1755           mSlicerManagers[i]->UpdateViews(0,slicer);
1756           break;
1757         }
1758     }
1759 }
1760 //------------------------------------------------------------------------------
1761
1762 //------------------------------------------------------------------------------
1763 void vvMainWindow::ShowContextMenu(QPoint point) {
1764   if (!DataTree->selectedItems().size())
1765     {
1766       contextActions[1]->setEnabled(0);
1767       contextActions[2]->setEnabled(0);
1768       contextActions[3]->setEnabled(0);
1769       contextActions[4]->setEnabled(0);
1770       contextActions[5]->setEnabled(0);
1771       contextActions[6]->setEnabled(0);
1772       contextActions[7]->setEnabled(0);
1773     }
1774   else
1775     {
1776       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1777       contextActions[1]->setEnabled(1);
1778       contextActions[2]->setEnabled(
1779                                     DataTree->itemWidget(DataTree->selectedItems()[0],
1780                                                          COLUMN_RELOAD_IMAGE)->isEnabled());
1781       contextActions[3]->setEnabled(1);
1782       contextActions[5]->setEnabled(1);
1783       contextActions[6]->setEnabled(1);
1784       contextActions[7]->setEnabled(1);
1785
1786       if (mSlicerManagers[index]->GetDimension() < 3)
1787         contextActions[4]->setEnabled(0);
1788       else
1789         contextActions[4]->setEnabled(1);
1790     }
1791   contextMenu.exec(QCursor::pos());
1792 }
1793 //------------------------------------------------------------------------------
1794
1795 //------------------------------------------------------------------------------
1796 void vvMainWindow::CloseImage() {
1797   CloseImage(DataTree->selectedItems()[0],0);
1798 }
1799 //------------------------------------------------------------------------------
1800
1801 //------------------------------------------------------------------------------
1802 void vvMainWindow::ReloadImage() {
1803   ReloadImage(DataTree->selectedItems()[0],0);
1804 }
1805 //------------------------------------------------------------------------------
1806
1807 //------------------------------------------------------------------------------
1808 void vvMainWindow::SelectOverlayImage() {
1809   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1810
1811   //check if one overlay image is added
1812   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1813     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay")
1814       {
1815         QString error = "Cannot add more than one compared image\n";
1816         error += "Please remove first ";
1817         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1818         QMessageBox::information(this,tr("Problem adding compared image !"),error);
1819         return;
1820       }
1821
1822   QString Extensions = "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.hdr *.vox)";
1823   Extensions += ";;All Files (*)";
1824   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1825   if (!file.isEmpty())
1826     AddOverlayImage(index,file);
1827 }
1828 //------------------------------------------------------------------------------
1829
1830 //------------------------------------------------------------------------------
1831 void vvMainWindow::AddOverlayImage(int index, QString file) {
1832   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1833   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1834                                                                         file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1835   reader->SetFileName(file.toStdString().c_str());
1836   reader->ReadImageInformation();
1837   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1838   int dimension = reader->GetNumberOfDimensions();
1839   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1840   vvProgressDialog progress("Opening " + file.toStdString());
1841   qApp->processEvents();
1842
1843   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1844   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component))
1845     {
1846       //create an item in the tree with good settings
1847       QTreeWidgetItem *item = new QTreeWidgetItem();
1848       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1849       item->setData(1,Qt::UserRole,tr("overlay"));
1850       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
1851       qApp->processEvents();
1852
1853       for (int j = 1; j <= 4; j++)
1854         {
1855           item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1856           mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("overlay",0,
1857                                                                      DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1858         }
1859
1860       //Create the buttons for reload and close
1861       qApp->processEvents();
1862       QTreePushButton* cButton = new QTreePushButton;
1863       cButton->setItem(item);
1864       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1865       cButton->setToolTip(tr("close image"));
1866       cButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")));
1867       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1868               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1869
1870       QTreePushButton* rButton = new QTreePushButton;
1871       rButton->setItem(item);
1872       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1873       rButton->setToolTip(tr("reload image"));
1874       rButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")));
1875       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1876               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1877
1878       DataTree->topLevelItem(index)->setExpanded(1);
1879       DataTree->topLevelItem(index)->addChild(item);
1880       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1881       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1882
1883       //set the id of the image
1884       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1885       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1886       UpdateTree();
1887       qApp->processEvents();
1888       ImageInfoChanged();
1889       QApplication::restoreOverrideCursor();
1890     }
1891   else
1892     {
1893       QApplication::restoreOverrideCursor();
1894       QString error = "Cannot import the new image.\n";
1895       error += mSlicerManagers[index]->GetLastError().c_str();
1896       QMessageBox::information(this,tr("Problem reading image !"),error);
1897     }
1898 }
1899
1900 void vvMainWindow::AddFusionImage()
1901 {
1902   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1903
1904   //check if one fusion image is added
1905   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1906     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion")
1907       {
1908         QString error = "Cannot add more than one fusion image\n";
1909         error += "Please remove first ";
1910         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1911         QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1912         return;
1913       }
1914
1915   QString Extensions = "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.hdr *.vox)";
1916   Extensions += ";;All Files (*)";
1917   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1918   if (!file.isEmpty())
1919     {
1920       mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1921       itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1922                                                                             file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1923       reader->SetFileName(file.toStdString().c_str());
1924       reader->ReadImageInformation();
1925       std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1926       if (reader)
1927         {
1928           QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1929           vvProgressDialog progress("Opening fusion");
1930           qApp->processEvents();
1931
1932           std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1933           if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1934                                                 reader->GetNumberOfDimensions(), component))
1935             {
1936               //create an item in the tree with good settings
1937               QTreeWidgetItem *item = new QTreeWidgetItem();
1938               item->setData(0,Qt::UserRole,file.toStdString().c_str());
1939               item->setData(1,Qt::UserRole,tr("fusion"));
1940               item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
1941               qApp->processEvents();
1942
1943               for (int j = 1; j <= 4; j++)
1944                 {
1945                   item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1946                   mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("fusion",0,
1947                                                                              DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1948                 }
1949
1950               //Create the buttons for reload and close
1951               qApp->processEvents();
1952               QTreePushButton* cButton = new QTreePushButton;
1953               cButton->setItem(item);
1954               cButton->setColumn(COLUMN_CLOSE_IMAGE);
1955               cButton->setToolTip(tr("close image"));
1956               cButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")));
1957               connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1958                       this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1959
1960               QTreePushButton* rButton = new QTreePushButton;
1961               rButton->setItem(item);
1962               rButton->setColumn(COLUMN_RELOAD_IMAGE);
1963               rButton->setToolTip(tr("reload image"));
1964               rButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")));
1965               connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1966                       this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1967
1968               DataTree->topLevelItem(index)->setExpanded(1);
1969               DataTree->topLevelItem(index)->addChild(item);
1970               DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1971               DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1972
1973               //set the id of the image
1974               QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1975               item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1976               UpdateTree();
1977               qApp->processEvents();
1978               ImageInfoChanged();
1979               QApplication::restoreOverrideCursor();
1980             }
1981           else
1982             {
1983               QApplication::restoreOverrideCursor();
1984               QString error = "Cannot import the new image.\n";
1985               error += mSlicerManagers[index]->GetLastError().c_str();
1986               QMessageBox::information(this,tr("Problem reading image !"),error);
1987             }
1988         }
1989       else
1990         {
1991           QString error = "Cannot import the new image.\n";
1992           QMessageBox::information(this,tr("Problem reading image !"),error);
1993         }
1994     }
1995 }
1996
1997
1998 void vvMainWindow::OpenField()
1999 {
2000   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2001   //check if a vector field has already been added
2002   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2003     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector")
2004       {
2005         QString error = "Cannot add more than one vector field\n";
2006         error += "Please remove first ";
2007         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2008         QMessageBox::information(this,tr("Problem adding vector field!"),error);
2009         return;
2010       }
2011
2012   QString Extensions = "Images ( *.mhd)";
2013   Extensions += ";;Images ( *.vf)";
2014   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2015   if (!file.isEmpty())
2016     AddField(file,index);
2017 }
2018
2019 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2020 {
2021   //create an item in the tree with good settings
2022   QTreeWidgetItem *item = new QTreeWidgetItem();
2023   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2024   item->setData(1,Qt::UserRole,tr("vector"));
2025   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename);
2026   qApp->processEvents();
2027
2028   for (int j = 1; j <= 4; j++)
2029     {
2030       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2031       mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("vector",0,
2032                                                                  DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
2033     }
2034
2035   //Create the buttons for reload and close
2036   qApp->processEvents();
2037   QTreePushButton* cButton = new QTreePushButton;
2038   cButton->setItem(item);
2039   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2040   cButton->setToolTip(tr("close vector field"));
2041   cButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")));
2042   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2043           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2044
2045   QTreePushButton* rButton = new QTreePushButton;
2046   rButton->setItem(item);
2047   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2048   rButton->setToolTip(tr("reload vector field"));
2049   rButton->setEnabled(from_disk);
2050   rButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")));
2051   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2052           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2053
2054   DataTree->topLevelItem(index)->setExpanded(1);
2055   DataTree->topLevelItem(index)->addChild(item);
2056   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2057   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2058
2059   //set the id of the image
2060   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2061   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2062   UpdateTree();
2063   qApp->processEvents();
2064   ImageInfoChanged();
2065   QApplication::restoreOverrideCursor();
2066 }
2067
2068 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2069 {
2070   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2071   vvSlicerManager* imageManager = mSlicerManagers[index];
2072   if (imageManager->SetVF(vf,file.toStdString()))
2073     {
2074       AddFieldEntry(file,index,false);
2075     }
2076   else
2077     {
2078       QString error = "Cannot import the vector field for this image.\n";
2079       error += imageManager->GetLastError().c_str();
2080       QMessageBox::information(this,tr("Problem reading VF !"),error);
2081     }
2082   QApplication::restoreOverrideCursor();
2083 }
2084
2085 void vvMainWindow::AddField(QString file,int index)
2086 {
2087   if (QFile::exists(file))
2088     {
2089       mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2090
2091       //init the progress events
2092       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2093       vvProgressDialog progress("Opening " + file.toStdString());
2094       qApp->processEvents();
2095
2096       //read the vector and put it in the current mSlicerManager
2097       vvSlicerManager* imageManager = mSlicerManagers[index];
2098       qApp->processEvents();
2099
2100       std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2101       if (imageManager->SetVF(file.toStdString()))
2102         {
2103           imageManager->Render();
2104           AddFieldEntry(file,index,true);
2105         }
2106       else
2107         {
2108           QApplication::restoreOverrideCursor();
2109           QString error = "Cannot import the vector field for this image.\n";
2110           error += imageManager->GetLastError().c_str();
2111           QMessageBox::information(this,tr("Problem reading VF !"),error);
2112         }
2113     }
2114   else
2115     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2116
2117 }
2118 //------------------------------------------------------------------------------
2119
2120 //------------------------------------------------------------------------------
2121 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log) {
2122   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2123   if (mSlicerManagers[index]->GetSlicer(0)->GetVF())
2124     {
2125       for (int i = 0; i < 4; i++)
2126         {
2127           mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2128           mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2129           if (log > 0)
2130             mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2131           else
2132             mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2133         }
2134     }
2135 }
2136 //------------------------------------------------------------------------------
2137
2138 //------------------------------------------------------------------------------
2139 void vvMainWindow::SetOverlayProperty(int color) {
2140   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2141   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
2142     {
2143       mSlicerManagers[index]->SetOverlayColor(color);
2144       mSlicerManagers[index]->SetColorMap(0);
2145       mSlicerManagers[index]->Render();
2146     }
2147 }
2148 //------------------------------------------------------------------------------
2149
2150 //------------------------------------------------------------------------------
2151 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level) {
2152   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2153   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion())
2154     {
2155       mSlicerManagers[index]->SetFusionOpacity(opacity);
2156       mSlicerManagers[index]->SetFusionColorMap(colormap);
2157       mSlicerManagers[index]->SetFusionWindow(window);
2158       mSlicerManagers[index]->SetFusionLevel(level);
2159       mSlicerManagers[index]->SetColorMap(0);
2160       mSlicerManagers[index]->Render();
2161     }
2162 }
2163 //------------------------------------------------------------------------------
2164
2165 //------------------------------------------------------------------------------
2166 void vvMainWindow::SaveAs() {
2167   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector")
2168     {
2169       QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2170       return;
2171     }
2172
2173   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2174   int dimension = mSlicerManagers[index]->GetDimension();
2175   QStringList OutputListeFormat;
2176   OutputListeFormat.clear();
2177   if (dimension == 1)
2178     {
2179       OutputListeFormat.push_back(".mhd");
2180     }
2181   if (dimension == 2)
2182     {
2183       OutputListeFormat.push_back(".bmp");
2184       OutputListeFormat.push_back(".png");
2185       OutputListeFormat.push_back(".jpeg");
2186       OutputListeFormat.push_back(".tif");
2187       OutputListeFormat.push_back(".mhd");
2188       OutputListeFormat.push_back(".hdr");
2189       OutputListeFormat.push_back(".vox");
2190     }
2191   else if (dimension == 3)
2192     {
2193       OutputListeFormat.push_back(".mhd");
2194       OutputListeFormat.push_back(".hdr");
2195       OutputListeFormat.push_back(".vox");
2196     }
2197   else if (dimension == 4)
2198     {
2199       OutputListeFormat.push_back(".mhd");
2200     }
2201   QString Extensions = "AllFiles(*.*)";
2202   for (int i = 0; i < OutputListeFormat.count(); i++)
2203     {
2204       Extensions += ";;Images ( *";
2205       Extensions += OutputListeFormat[i];
2206       Extensions += ")";
2207     }
2208   QString fileName = QFileDialog::getSaveFileName(this,
2209                                                   tr("Save As"),
2210                                                   mSlicerManagers[index]->GetFileName().c_str(),
2211                                                   Extensions);
2212   if (!fileName.isEmpty())
2213     {
2214       std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2215       if (OutputListeFormat.contains(
2216                                      fileformat.c_str()))
2217         {
2218           QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2219           std::string action = "Saving";
2220           vvProgressDialog progress("Saving "+fileName.toStdString());
2221           qApp->processEvents();
2222           vvImageWriter *writer = new vvImageWriter;
2223           writer->SetOutputFileName(fileName.toStdString());
2224           writer->SetInput(mSlicerManagers[index]->GetImage());
2225           writer->Update();
2226           QApplication::restoreOverrideCursor();
2227           if (writer->GetLastError().size())
2228             {
2229               QString error = "Saving did not succeed\n";
2230               error += writer->GetLastError().c_str();
2231               QMessageBox::information(this,tr("Saving Problem"),error);
2232               SaveAs();
2233             }
2234         }
2235       else
2236         {
2237           QString error = fileformat.c_str();
2238           if (error.isEmpty())
2239             error += "no file format specified !";
2240           else
2241             error += " format unknown !!!\n";
2242           QMessageBox::information(this,tr("Saving Problem"),error);
2243           SaveAs();
2244         }
2245     }
2246 }
2247 //------------------------------------------------------------------------------
2248
2249 //------------------------------------------------------------------------------
2250 void vvMainWindow::AddLink(QString image1,QString image2) {
2251   for (unsigned int i = 0; i < mSlicerManagers.size();i++)
2252     {
2253       if (image1.toStdString() == mSlicerManagers[i]->GetId())
2254         {
2255           mSlicerManagers[i]->AddLink(image2.toStdString());
2256         }
2257       if (image2.toStdString() == mSlicerManagers[i]->GetId())
2258         {
2259           mSlicerManagers[i]->AddLink(image1.toStdString());
2260         }
2261     }
2262 }
2263 //------------------------------------------------------------------------------
2264
2265 //------------------------------------------------------------------------------
2266 void vvMainWindow::RemoveLink(QString image1,QString image2) {
2267   for (unsigned int i = 0; i < mSlicerManagers.size();i++)
2268     {
2269       if (image1.toStdString() == mSlicerManagers[i]->GetId())
2270         {
2271           mSlicerManagers[i]->RemoveLink(image2.toStdString());
2272         }
2273       if (image2.toStdString() == mSlicerManagers[i]->GetId())
2274         {
2275           mSlicerManagers[i]->RemoveLink(image1.toStdString());
2276         }
2277     }
2278 }
2279 //------------------------------------------------------------------------------
2280
2281 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2282 {
2283   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2284     {
2285       if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1)
2286         {
2287           for (int j = 0; j < 4; j++)
2288             {
2289               mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2290               //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2291               //UpdateTSlice(j,value);
2292             }
2293           mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2294           break;
2295         }
2296     }
2297 }
2298
2299 //------------------------------------------------------------------------------
2300 void vvMainWindow::NOHorizontalSliderMoved() {
2301   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2302 }
2303 //------------------------------------------------------------------------------
2304
2305 //------------------------------------------------------------------------------
2306 void vvMainWindow::NEHorizontalSliderMoved() {
2307   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2308 }
2309 //------------------------------------------------------------------------------
2310
2311 //------------------------------------------------------------------------------
2312 void vvMainWindow::SOHorizontalSliderMoved() {
2313   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2314 }
2315 //------------------------------------------------------------------------------
2316
2317 //------------------------------------------------------------------------------
2318 void vvMainWindow::SEHorizontalSliderMoved() {
2319   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2320 }
2321 //------------------------------------------------------------------------------
2322
2323 //------------------------------------------------------------------------------
2324 void vvMainWindow::NOVerticalSliderChanged() {
2325   int value = NOVerticalSlider->value();
2326   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2327     {
2328       if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
2329         {
2330           mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2331           // mSlicerManagers[i]->UpdateSlice(0); // <-- too much update...
2332           break;
2333         }
2334     }
2335 }
2336 //------------------------------------------------------------------------------
2337
2338 //------------------------------------------------------------------------------
2339 void vvMainWindow::NEVerticalSliderChanged() {
2340   int value = NEVerticalSlider->value();
2341   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2342     {
2343       if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1)
2344         {
2345           mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2346           break;
2347         }
2348     }
2349 }
2350 //------------------------------------------------------------------------------
2351
2352 //------------------------------------------------------------------------------
2353 void vvMainWindow::SOVerticalSliderChanged() {
2354   int value = SOVerticalSlider->value();
2355   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2356     {
2357       if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
2358         {
2359           mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2360           break;
2361         }
2362     }
2363 }
2364 //------------------------------------------------------------------------------
2365
2366 //------------------------------------------------------------------------------
2367 void vvMainWindow::SEVerticalSliderChanged() {
2368   int value = SEVerticalSlider->value();
2369   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2370     {
2371       if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1)
2372         {
2373           mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2374           break;
2375         }
2376     }
2377 }
2378 //------------------------------------------------------------------------------
2379
2380 //------------------------------------------------------------------------------
2381 void vvMainWindow::UpdateSlice(int slicer, int slice) {
2382   if (slicer == 0)
2383     NOVerticalSlider->setValue(slice);
2384   else if (slicer == 1)
2385     NEVerticalSlider->setValue(slice);
2386   else if (slicer == 2)
2387     SOVerticalSlider->setValue(slice);
2388   else if (slicer == 3)
2389     SEVerticalSlider->setValue(slice);
2390 }
2391 //------------------------------------------------------------------------------
2392
2393 //------------------------------------------------------------------------------
2394 void vvMainWindow::UpdateTSlice(int slicer, int slice) {
2395   switch (slicer)
2396     {
2397     case 0:
2398       NOHorizontalSlider->setValue(slice);
2399       break;
2400     case 1:
2401       NEHorizontalSlider->setValue(slice);
2402       break;
2403     case 2:
2404       SOHorizontalSlider->setValue(slice);
2405       break;
2406     case 3:
2407       SEHorizontalSlider->setValue(slice);
2408       break;
2409     }
2410 }
2411 //------------------------------------------------------------------------------
2412
2413 //------------------------------------------------------------------------------
2414 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax) {
2415   int position = int((min+max)/2);
2416   int tPosition = int((tmin+tmax)/2);
2417   if (slicer == 0)
2418     {
2419       NOVerticalSlider->setValue(position);
2420       NOVerticalSlider->setRange(min,max);
2421       NOHorizontalSlider->setRange(tmin,tmax);
2422       NOHorizontalSlider->setValue(tPosition);
2423     }
2424   else if (slicer == 1)
2425     {
2426       NEVerticalSlider->setValue(position);
2427       NEVerticalSlider->setRange(min,max);
2428       NEHorizontalSlider->setRange(tmin,tmax);
2429       NEHorizontalSlider->setValue(tPosition);
2430     }
2431   else if (slicer == 2)
2432     {
2433       SOVerticalSlider->setValue(position);
2434       SOVerticalSlider->setRange(min,max);
2435       SOHorizontalSlider->setRange(tmin,tmax);
2436       SOHorizontalSlider->setValue(tPosition);
2437     }
2438   else if (slicer == 3)
2439     {
2440       SEVerticalSlider->setValue(position);
2441       SEVerticalSlider->setRange(min,max);
2442       SEHorizontalSlider->setRange(tmin,tmax);
2443       SEHorizontalSlider->setValue(tPosition);
2444     }
2445 }
2446 //------------------------------------------------------------------------------
2447
2448 //------------------------------------------------------------------------------
2449 void vvMainWindow::SaveNOScreenshot() {
2450   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2451   w2i->SetInput(NOViewWidget->GetRenderWindow());
2452   w2i->Update();
2453   SaveScreenshot(w2i->GetOutput());
2454   w2i->Delete();
2455 }
2456 //------------------------------------------------------------------------------
2457
2458 //------------------------------------------------------------------------------
2459 void vvMainWindow::SaveNEScreenshot() {
2460   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2461   w2i->SetInput(NEViewWidget->GetRenderWindow());
2462   w2i->Update();
2463   SaveScreenshot(w2i->GetOutput());
2464   w2i->Delete();
2465 }
2466 //------------------------------------------------------------------------------
2467
2468 //------------------------------------------------------------------------------
2469 void vvMainWindow::SaveSOScreenshot() {
2470   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2471   w2i->SetInput(SOViewWidget->GetRenderWindow());
2472   w2i->Update();
2473   SaveScreenshot(w2i->GetOutput());
2474   w2i->Delete();
2475 }
2476 //------------------------------------------------------------------------------
2477
2478 //------------------------------------------------------------------------------
2479 void vvMainWindow::SaveSEScreenshot() {
2480   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2481   w2i->SetInput(SEViewWidget->GetRenderWindow());
2482   w2i->Update();
2483   SaveScreenshot(w2i->GetOutput());
2484   w2i->Delete();
2485 }
2486 //------------------------------------------------------------------------------
2487
2488 //------------------------------------------------------------------------------
2489 void vvMainWindow::SaveScreenshot(vtkImageData* image) {
2490   QString Extensions = "Images( *.png);;";
2491   Extensions += "Images( *.jpg);;";
2492   Extensions += "Images( *.bmp);;";
2493   Extensions += "Images( *.tif);;";
2494   Extensions += "Images( *.ppm)";
2495   QString fileName = QFileDialog::getSaveFileName(this,
2496                                                   tr("Save As"),
2497                                                   itksys::SystemTools::GetFilenamePath(
2498                                                                                        mSlicerManagers[0]->GetFileName()).c_str(),
2499                                                   Extensions);
2500   if (!fileName.isEmpty())
2501     {
2502       const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2503       if (!strcmp(ext, ".bmp"))
2504         {
2505           vtkBMPWriter *bmp = vtkBMPWriter::New();
2506           bmp->SetInput(image);
2507           bmp->SetFileName(fileName.toStdString().c_str());
2508           bmp->Write();
2509           bmp->Delete();
2510         }
2511       else if (!strcmp(ext, ".tif"))
2512         {
2513           vtkTIFFWriter *tif = vtkTIFFWriter::New();
2514           tif->SetInput(image);
2515           tif->SetFileName(fileName.toStdString().c_str());
2516           tif->Write();
2517           tif->Delete();
2518         }
2519       else if (!strcmp(ext, ".ppm"))
2520         {
2521           vtkPNMWriter *pnm = vtkPNMWriter::New();
2522           pnm->SetInput(image);
2523           pnm->SetFileName(fileName.toStdString().c_str());
2524           pnm->Write();
2525           pnm->Delete();
2526         }
2527       else if (!strcmp(ext, ".png"))
2528         {
2529           vtkPNGWriter *png = vtkPNGWriter::New();
2530           png->SetInput(image);
2531           png->SetFileName(fileName.toStdString().c_str());
2532           png->Write();
2533           png->Delete();
2534         }
2535       else if (!strcmp(ext, ".jpg"))
2536         {
2537           vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2538           jpg->SetInput(image);
2539           jpg->SetFileName(fileName.toStdString().c_str());
2540           jpg->Write();
2541           jpg->Delete();
2542         }
2543       else
2544         {
2545           QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2546         }
2547     }
2548
2549 }
2550 //------------------------------------------------------------------------------
2551
2552 //------------------------------------------------------------------------------
2553 void vvMainWindow::GoToCursor() {
2554   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2555   for (int column = 1; column < 5; column++)
2556     {
2557       if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1)
2558         {
2559           double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2560           mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2561                                                                           cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2562           mSlicerManagers[index]->UpdateViews(1,column-1);
2563           mSlicerManagers[index]->UpdateLinked(column-1);
2564           break;
2565         }
2566     }
2567 }
2568 //------------------------------------------------------------------------------
2569
2570 //------------------------------------------------------------------------------
2571 void vvMainWindow::PlayPause() {
2572   if (playMode)
2573     {
2574       playMode = 0;
2575       playButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/player_play.png")));
2576       ImageInfoChanged();
2577       return;
2578     }
2579   else
2580     {
2581       int image_number=DataTree->topLevelItemCount();
2582       bool has_temporal;
2583       for (int i=0;i<image_number;i++)
2584         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1)
2585           {
2586             has_temporal=true;
2587             break;
2588           }
2589       if (has_temporal)
2590         {
2591           playMode = 1;
2592           playButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/player_pause.png")));
2593           QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2594         }
2595     }
2596 }
2597 //------------------------------------------------------------------------------
2598
2599 //------------------------------------------------------------------------------
2600 void vvMainWindow::PlayNext() {
2601   if (playMode && !this->isHidden())
2602     {
2603       int image_number=DataTree->topLevelItemCount();
2604       ///Only play one slicer per SM, and only if the SM is being displayed
2605       for (int i=0;i<image_number;i++)
2606         for (int j=0;j<4;j++)
2607           if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2608               DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0)
2609             {
2610               mSlicerManagers[i]->SetNextTSlice(j);
2611               break;
2612             }
2613       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2614     }
2615 }
2616 //------------------------------------------------------------------------------
2617
2618 void vvMainWindow::ShowLastImage()
2619 {
2620   if (mSlicerManagers.size() > 1)
2621     {
2622       QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2623       CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2624       item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2625       DisplayChanged(item,1);
2626     }
2627 }
2628
2629 //------------------------------------------------------------------------------
2630 void vvMainWindow::UpdateRenderWindows() {
2631   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2632   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2633   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2634   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2635 }
2636 //------------------------------------------------------------------------------
2637
2638 //------------------------------------------------------------------------------
2639 void vvMainWindow::ResampleCurrentImage() {
2640   vvResamplerDialog resampler;
2641   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2642   resampler.SetSlicerManagers(mSlicerManagers,index);
2643   if (resampler.exec())
2644     AddImage(resampler.GetOutput(),resampler.GetOutputFileName());
2645 }
2646 //------------------------------------------------------------------------------
2647
2648 //------------------------------------------------------------------------------
2649 void vvMainWindow::SegmentationOnCurrentImage() {
2650   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2651
2652   vvSegmentationDialog segmentation;
2653   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2654   segmentation.exec();
2655 }
2656 //------------------------------------------------------------------------------
2657
2658 void vvMainWindow::SurfaceViewerLaunch()
2659 {
2660   vvSurfaceViewerDialog surfaceViewer;
2661   surfaceViewer.exec();
2662 }
2663
2664 //------------------------------------------------------------------------------
2665 void vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2666 {
2667   vvSlicerManager* m = new vvSlicerManager(4);
2668   m->SetImage(image);
2669   m->SetFilename(filename);
2670   AddImage(m);
2671 }
2672
2673 //------------------------------------------------------------------------------
2674 void vvMainWindow::AddImage(vvSlicerManager * slicer_manager) {
2675   mSlicerManagers.push_back(slicer_manager);
2676
2677   std::string filename = slicer_manager->GetFileName();
2678
2679   //create an item in the tree with good settings
2680   QTreeWidgetItem *item = new QTreeWidgetItem();
2681   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2682   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
2683   qApp->processEvents();
2684
2685   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2686
2687   //Create the buttons for reload and close
2688   qApp->processEvents();
2689   QTreePushButton* cButton = new QTreePushButton;
2690   cButton->setItem(item);
2691   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2692   cButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/exit.png")));
2693   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2694           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2695
2696   QTreePushButton* rButton = new QTreePushButton;
2697   rButton->setItem(item);
2698   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2699   rButton->setIcon(QIcon(QString::fromUtf8(":/new/prefix1/icons/rotateright.png")));
2700   rButton->setEnabled(0);
2701   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2702           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2703
2704   DataTree->addTopLevelItem(item);
2705   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2706   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2707
2708   //set the id of the image
2709   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2710   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2711   mSlicerManagers.back()->SetId(id.toStdString());
2712
2713   linkPanel->addImage(filename, id.toStdString());
2714
2715   connect(mSlicerManagers.back(),SIGNAL(currentImageChanged(std::string)),
2716           this,SLOT(CurrentImageChanged(std::string)));
2717   connect(mSlicerManagers.back(),SIGNAL(
2718                                         UpdatePosition(int, double, double, double, double, double, double, double)),this,
2719           SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2720   connect(mSlicerManagers.back(),SIGNAL(UpdateVector(int, double, double, double, double)),
2721           this, SLOT(VectorChanged(int,double,double,double, double)));
2722   connect(mSlicerManagers.back(),SIGNAL(UpdateOverlay(int, double, double)),
2723           this, SLOT(OverlayChanged(int,double,double)));
2724   connect(mSlicerManagers.back(),SIGNAL(UpdateFusion(int, double)),
2725           this, SLOT(FusionChanged(int,double)));
2726   connect(mSlicerManagers.back(),SIGNAL(UpdateWindows(int, int, int)),
2727           this,SLOT(WindowsChanged(int, int, int)));
2728   connect(mSlicerManagers.back(),SIGNAL(WindowLevelChanged(double, double,int, int)),
2729           this,SLOT(WindowLevelChanged(double, double, int, int)));
2730   connect(mSlicerManagers.back(),SIGNAL(UpdateSlice(int,int)),
2731           this,SLOT(UpdateSlice(int,int)));
2732   connect(mSlicerManagers.back(),SIGNAL(UpdateTSlice(int, int)),
2733           this,SLOT(UpdateTSlice(int, int)));
2734   connect(mSlicerManagers.back(),SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2735           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2736   connect(mSlicerManagers.back(),SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2737           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2738   connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2739   UpdateTree();
2740   qApp->processEvents();
2741   InitSlicers();
2742   ShowLastImage();
2743   InitDisplay();
2744   qApp->processEvents();
2745
2746   // vvToolManager::GetInstance()->UpdateEnabledTool();
2747   // emit SlicerManagersHasChanged();
2748 }
2749 //------------------------------------------------------------------------------
2750
2751
2752 //------------------------------------------------------------------------------
2753 vvMainWindowToolInfo * vvMainWindow::GetInfoForTool() {
2754   DD("GetInfoForTool");
2755   if (mCurrentToolInfo ==0) mCurrentToolInfo = new vvMainWindowToolInfo;
2756
2757   mCurrentToolInfo->mMenuTools = menuTools;
2758   mCurrentToolInfo->mSlicerManagers = &mSlicerManagers;
2759   int index = -1;
2760   DD(DataTree->selectedItems().size());
2761   if (DataTree->selectedItems().size() > 0) {
2762     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2763     DD(DataTree->selectedItems()[0]);
2764     DD(index);
2765   }
2766   mCurrentToolInfo->mSlicerManagerCurrentIndex = index;
2767
2768   return mCurrentToolInfo;
2769 }
2770 //------------------------------------------------------------------------------
2771
2772