vv/vvSlicer.cxx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://www.centreleonberard.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17   ===========================================================================**/
  18
  19 #include <QMessageBox>
  20 #include <QString>
  21
  22 #include "vvSlicer.h"
  23 #include "vvImage.h"
  24 #include "vvSlicerManagerCommand.h"
  25 #include "vvGlyphSource.h"
  26 #include "vvGlyph2D.h"
  27
  28 #include <vtkVersion.h>
  29 #include <vtkExtentTranslator.h>
  30 #include <vtkAlgorithm.h>
  31 #include <vtkExecutive.h>
  32 #include <vtkStreamingDemandDrivenPipeline.h>
  33 #include <vtkInformation.h>
  34 #include <vtkTextProperty.h>
  35 #include <vtkTextActor.h>
  36 #include <vtkTextSource.h>
  37 #include <vtkActor2D.h>
  38 #include <vtkCursor2D.h>
  39 #include <vtkPolyDataMapper2D.h>
  40 #include <vtkProperty2D.h>
  41 #include <vtkCornerAnnotation.h>
  42 #include <vtkImageMapToWindowLevelColors.h>
  43 #include <vtkImageData.h>
  44 #include <vtkImageActor.h>
  45 #include <vvBlendImageActor.h>
  46 #include <vtkToolkits.h>
  47 #include <vtkObjectFactory.h>
  48 #include <vtkPointData.h>
  49 #include <vtkDataArray.h>
  50 #include <vtkFloatArray.h>
  51 #include <vtkClipPolyData.h>
  52 #include <vtkActor2DCollection.h>
  53 #include <vtkGlyph3D.h>
  54 #include <vtkMath.h>
  55 #include <vtkCursor3D.h>
  56 #include <vtkProperty.h>
  57 #include <vtkLight.h>
  58 #include <vtkLightCollection.h>
  59 #include <vtkScalarBarActor.h>
  60 #include <vtkLookupTable.h>
  61
  62 #include <vtkRenderer.h>
  63 #include <vtkRendererCollection.h>
  64 #include <vtkRenderWindow.h>
  65 #include <vtkRenderWindowInteractor.h>
  66 #include <vtkCamera.h>
  67 #include <vtkCallbackCommand.h>
  68 #include <vtkCommand.h>
  69 #include <vtkPolyDataMapper.h>
  70 #include <vtkBox.h>
  71
  72 #include <vtkExtractVOI.h>
  73 #include <vtkSphereSource.h>
  74 #include <vtkCutter.h>
  75 #include <vtkAssignAttribute.h>
  76 #include <vtkImageAccumulate.h>
  77 #include <vtkImageReslice.h>
  78 #include <vtkOpenGLImageSliceMapper.h>
  79 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
  80 #  include <vtkImageMapper3D.h>
  81 #  include <vtkImageSliceMapper.h>
  82 #endif
  83
  84 vtkStandardNewMacro(vvSlicer);
  85 static void copyExtent(int* in, int* to){
  86  for(int i=0; i<6; ++i)
  87  {
  88         to[i]=in[i];
  89  }
  90 }
  91 //------------------------------------------------------------------------------
  92 vvSlicer::vvSlicer()
  93 {
  94         mFusionSequenceCode = -1;
  95   this->UnInstallPipeline();
  96   mImage = NULL;
  97   mReducedExtent = new int[6];
  98   mRegisterExtent = NULL;
  99   mCurrentTSlice = 0;
 100   mCurrentFusionTSlice = 0;
 101   mCurrentOverlayTSlice = 0;
 102   mUseReducedExtent = false;
 103
 104   mCurrent[0] = -VTK_DOUBLE_MAX;
 105   mCurrent[1] = -VTK_DOUBLE_MAX;
 106   mCurrent[2] = -VTK_DOUBLE_MAX;
 107
 108   mCursor[0] = 0;//-VTK_DOUBLE_MAX;
 109   mCursor[1] = 0;//-VTK_DOUBLE_MAX;
 110   mCursor[2] = 0;//-VTK_DOUBLE_MAX;
 111   mCursor[3] = 0;//-VTK_DOUBLE_MAX;
 112
 113   mSubSampling = 5;
 114   mScale = 1;
 115   mVFLog = 0;
 116   mVFWidth = 1;
 117   mVFColor[0] = 0;
 118   mVFColor[1] = 1;
 119   mVFColor[2] = 0;
 120
 121   crossCursor = vtkSmartPointer<vtkCursor2D>::New();
 122   crossCursor->AllOff();
 123   crossCursor->AxesOn();
 124   crossCursor->SetTranslationMode(1);
 125   crossCursor->SetRadius(2);
 126
 127   pdm = vtkSmartPointer<vtkPolyDataMapper2D>::New();
 128 #if VTK_MAJOR_VERSION <= 5
 129   pdm->SetInput(crossCursor->GetOutput());
 130 #else
 131   pdm->SetInputConnection(crossCursor->GetOutputPort(0));
 132 #endif
 133
 134   pdmA = vtkSmartPointer<vtkActor2D>::New();
 135   pdmA->SetMapper(pdm);
 136   pdmA->GetProperty()->SetColor(255,10,212);
 137   pdmA->SetVisibility(0);
 138   pdmA->SetPickable(0);
 139
 140   ca = vtkSmartPointer<vtkCornerAnnotation>::New();
 141   ca->GetTextProperty()->SetColor(255,10,212);
 142   ca->SetVisibility(1);
 143   mFileName = "";
 144
 145   mVF = NULL;
 146   mOverlay = NULL;
 147   mFusion = NULL;
 148   mLandmarks = NULL;
 149
 150   legend = vtkSmartPointer<vtkScalarBarActor>::New();
 151   //legend->SetTitle("test!");
 152   legend->SetPosition(0.82,0.18);
 153   legend->SetWidth(0.1);
 154   legend->SetVisibility(0);
 155   legend->SetLabelFormat("%.1f");
 156   this->GetRenderer()->AddActor(legend);
 157   showFusionLegend = false;
 158
 159   this->InstallPipeline();
 160
 161   mLinkOverlayWindowLevel = true;
 162   mImageVisibility = true;
 163
 164 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 165   this->GetImageActor()->GetMapper()->BorderOn();
 166 #endif
 167
 168   mSlicingTransform = vtkSmartPointer<vtkTransform>::New();
 169   mConcatenatedTransform = vtkSmartPointer<vtkTransform>::New();
 170   mConcatenatedFusionTransform = vtkSmartPointer<vtkTransform>::New();
 171   mConcatenatedOverlayTransform = vtkSmartPointer<vtkTransform>::New();
 172   mFirstSetSliceOrientation = true;
 173 }
 174 //------------------------------------------------------------------------------
 175
 176
 177 //------------------------------------------------------------------------------
 178 vtkImageMapToWindowLevelColors* vvSlicer::GetOverlayMapper()
 179 {
 180   return mOverlayMapper.GetPointer();
 181 }
 182 //------------------------------------------------------------------------------
 183
 184
 185 //------------------------------------------------------------------------------
 186 vvBlendImageActor* vvSlicer::GetOverlayActor()
 187 {
 188   return mOverlayActor.GetPointer();
 189 }
 190 //------------------------------------------------------------------------------
 191
 192
 193 //------------------------------------------------------------------------------
 194 vtkImageMapToColors* vvSlicer::GetFusionMapper()
 195 {
 196   return mFusionMapper.GetPointer();
 197 }
 198 //------------------------------------------------------------------------------
 199
 200
 201 //------------------------------------------------------------------------------
 202 vtkImageActor* vvSlicer::GetFusionActor()
 203 {
 204   return mFusionActor.GetPointer();
 205 }
 206 //------------------------------------------------------------------------------
 207
 208
 209 //------------------------------------------------------------------------------
 210 vtkActor* vvSlicer::GetVFActor()
 211 {
 212   return mVFActor.GetPointer();
 213 }
 214 //------------------------------------------------------------------------------
 215
 216
 217 //------------------------------------------------------------------------------
 218 vtkCornerAnnotation* vvSlicer::GetAnnotation()
 219 {
 220   return ca.GetPointer();
 221 }
 222 //------------------------------------------------------------------------------
 223
 224
 225 //------------------------------------------------------------------------------
 226 void vvSlicer::EnableReducedExtent(bool b)
 227 {
 228   mUseReducedExtent = b;
 229 }
 230 //------------------------------------------------------------------------------
 231
 232
 233 //------------------------------------------------------------------------------
 234 void vvSlicer::SetReducedExtent(int * ext)
 235 {
 236   copyExtent(ext, mReducedExtent);
 237 }
 238 //------------------------------------------------------------------------------
 239
 240
 241 //------------------------------------------------------------------------------
 242 void vvSlicer::AddContour(vvMesh::Pointer contour,bool propagate)
 243 {
 244
 245   mSurfaceCutActors.push_back(new vvMeshActor());
 246   if (propagate)
 247     mSurfaceCutActors.back()->Init(contour,mCurrentTSlice,mVF);
 248   else
 249     mSurfaceCutActors.back()->Init(contour,mCurrentTSlice);
 250   mSurfaceCutActors.back()->SetSlicingOrientation(SliceOrientation);
 251   this->GetRenderer()->AddActor(mSurfaceCutActors.back()->GetActor());
 252
 253   SetContourSlice();
 254 }
 255 //------------------------------------------------------------------------------
 256
 257
 258 //------------------------------------------------------------------------------
 259 void vvSlicer::ToggleContourSuperposition()
 260 {
 261   for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 262        i!=mSurfaceCutActors.end(); i++)
 263     (*i)->ToggleSuperposition();
 264 }
 265 //------------------------------------------------------------------------------
 266
 267
 268 //------------------------------------------------------------------------------
 269 void vvSlicer::SetCursorColor(int r,int g, int b)
 270 {
 271   pdmA->GetProperty()->SetColor(r,g,b);
 272 }
 273 //------------------------------------------------------------------------------
 274
 275
 276 //------------------------------------------------------------------------------
 277 void vvSlicer::SetCursorVisibility(bool s)
 278 {
 279   pdmA->SetVisibility(s);
 280 }
 281 //------------------------------------------------------------------------------
 282
 283
 284 //------------------------------------------------------------------------------
 285 bool vvSlicer::GetCursorVisibility()
 286 {
 287   return pdmA->GetVisibility();
 288 }
 289 //------------------------------------------------------------------------------
 290
 291
 292 //------------------------------------------------------------------------------
 293 void vvSlicer::SetCornerAnnotationVisibility(bool s)
 294 {
 295   ca->SetVisibility(s);
 296 }
 297 //------------------------------------------------------------------------------
 298
 299
 300 //------------------------------------------------------------------------------
 301 bool vvSlicer::GetCornerAnnotationVisibility()
 302 {
 303   return ca->GetVisibility();
 304 }
 305 //------------------------------------------------------------------------------
 306
 307
 308 //------------------------------------------------------------------------------
 309 vvSlicer::~vvSlicer()
 310 {
 311   for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 312        i!=mSurfaceCutActors.end(); i++)
 313     delete (*i);
 314   delete [] mReducedExtent;
 315 }
 316 //------------------------------------------------------------------------------
 317
 318 //------------------------------------------------------------------------------
 319 double* vvSlicer::GetCurrentPosition()
 320 {
 321   return mCurrentBeforeSlicingTransform;
 322 }
 323 //------------------------------------------------------------------------------
 324
 325 //------------------------------------------------------------------------------
 326 void vvSlicer::SetCurrentPosition(double x, double y, double z, int t)
 327 {
 328   mCurrentBeforeSlicingTransform[0]=x;
 329   mCurrentBeforeSlicingTransform[1]=y;
 330   mCurrentBeforeSlicingTransform[2]=z;
 331   mSlicingTransform->GetInverse()->TransformPoint(mCurrentBeforeSlicingTransform,mCurrent);
 332   if (t>=0) SetTSlice(t);
 333 }
 334 //------------------------------------------------------------------------------
 335
 336
 337 //------------------------------------------------------------------------------
 338 void vvSlicer::SetImage(vvImage::Pointer image)
 339 {
 340   if (image->GetVTKImages().size()) {
 341     mImage = image;
 342
 343     if (!mImageReslice) {
 344       mImageReslice = vtkSmartPointer<vtkImageReslice>::New();
 345       mImageReslice->SetInterpolationModeToLinear();
 346       mImageReslice->AutoCropOutputOn();
 347       mImageReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 348     }
 349
 350     mConcatenatedTransform->Identity();
 351     mConcatenatedTransform->Concatenate(mImage->GetTransform()[0]);
 352     mConcatenatedTransform->Concatenate(mSlicingTransform);
 353     mImageReslice->SetResliceTransform(mConcatenatedTransform);
 354 #if VTK_MAJOR_VERSION <= 5
 355     mImageReslice->SetInput(0, mImage->GetFirstVTKImageData());
 356 #else
 357     mImageReslice->SetInputData(0, mImage->GetFirstVTKImageData());
 358 #endif
 359     mImageReslice->UpdateInformation();
 360
 361 #if VTK_MAJOR_VERSION <= 5
 362     this->Superclass::SetInput(mImageReslice->GetOutput());
 363 #else
 364     this->Superclass::SetInputConnection(mImageReslice->GetOutputPort());
 365 #endif
 366
 367     int extent[6];
 368 #if VTK_MAJOR_VERSION <= 5
 369     this->GetInput()->GetWholeExtent(extent);
 370 #else
 371     int* ext = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
 372     copyExtent(ext, extent);
 373 #endif
 374
 375     // Prevent crash when reload -> change slice if outside extent
 376     if (Slice < extent[SliceOrientation*2] || Slice>=extent[SliceOrientation*2+1]) {
 377       Slice = (extent[SliceOrientation*2+1]+extent[SliceOrientation*2])/2.0;
 378     }
 379
 380     // Make sure that the required part image has been computed
 381     extent[SliceOrientation*2] = Slice;
 382     extent[SliceOrientation*2+1] = Slice;
 383 #if VTK_MAJOR_VERSION <= 5
 384     mImageReslice->GetOutput()->SetUpdateExtent(extent);
 385     mImageReslice->GetOutput()->Update();
 386 #else
 387     //mImageReslice->SetUpdateExtent(extent);
 388     mImageReslice->Update();
 389 #endif
 390
 391     this->UpdateDisplayExtent();
 392
 393     mCurrentTSlice = 0;
 394     ca->SetText(0,mFileName.c_str());
 395   }
 396 }
 397 //------------------------------------------------------------------------------
 398
 399
 400 //------------------------------------------------------------------------------
 401 void vvSlicer::SetOverlay(vvImage::Pointer overlay)
 402 {
 403   if (overlay->GetVTKImages().size()) {
 404     mOverlay = overlay;
 405     mOverlayVisibility = true;
 406
 407     if (!mOverlayReslice) {
 408       mOverlayReslice = vtkSmartPointer<vtkImageReslice>::New();
 409       mOverlayReslice->SetInterpolationModeToLinear();
 410       mOverlayReslice->AutoCropOutputOn();
 411       mOverlayReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 412     }
 413
 414     mConcatenatedOverlayTransform->Identity();
 415     mConcatenatedOverlayTransform->Concatenate(mOverlay->GetTransform()[0]);
 416     mConcatenatedOverlayTransform->Concatenate(mSlicingTransform);
 417     mOverlayReslice->SetResliceTransform(mConcatenatedOverlayTransform);
 418 #if VTK_MAJOR_VERSION <= 5
 419     mOverlayReslice->SetInput(0, mOverlay->GetFirstVTKImageData());
 420 #else
 421     mOverlayReslice->SetInputData(0, mOverlay->GetFirstVTKImageData());
 422 #endif
 423     mOverlayReslice->Update();
 424
 425     if (!mOverlayMapper)
 426       mOverlayMapper = vtkSmartPointer<vtkImageMapToWindowLevelColors>::New();
 427 #if VTK_MAJOR_VERSION <= 5
 428     mOverlayMapper->SetInput(mOverlayReslice->GetOutput());
 429 #else
 430     mOverlayMapper->SetInputConnection(mOverlayReslice->GetOutputPort(0));
 431 #endif
 432
 433     if (!mOverlayActor) {
 434       mOverlayActor = vtkSmartPointer<vvBlendImageActor>::New();
 435 #if VTK_MAJOR_VERSION <= 5
 436       mOverlayActor->SetInput(mOverlayMapper->GetOutput());
 437 #else
 438       mOverlayActor->GetMapper()->SetInputConnection(mOverlayMapper->GetOutputPort());
 439 #endif
 440       mOverlayActor->SetPickable(0);
 441       mOverlayActor->SetVisibility(true);
 442       mOverlayActor->SetOpacity(0.5);
 443 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 444       mOverlayActor->GetMapper()->BorderOn();
 445 #endif
 446       }
 447
 448     //stupid but necessary : the Overlay need to be rendered before fusion
 449     if (mFusionActor) {
 450       this->GetRenderer()->RemoveActor(mFusionActor);
 451       this->GetRenderer()->AddActor(mOverlayActor);
 452       this->GetRenderer()->AddActor(mFusionActor);
 453     } else
 454       this->GetRenderer()->AddActor(mOverlayActor);
 455
 456     //Synchronize orientation and slice
 457     AdjustResliceToSliceOrientation(mOverlayReslice);
 458     this->UpdateDisplayExtent();
 459     this->SetTSlice(mCurrentTSlice);
 460   }
 461 }
 462 //------------------------------------------------------------------------------
 463
 464
 465 //------------------------------------------------------------------------------
 466 void vvSlicer::SetFusion(vvImage::Pointer fusion, int fusionSequenceCode)
 467 {
 468         mFusionSequenceCode = fusionSequenceCode;
 469   if (fusion->GetVTKImages().size()) {
 470     mFusion = fusion;
 471     mFusionVisibility = true;
 472
 473     if (!mFusionReslice) {
 474       mFusionReslice = vtkSmartPointer<vtkImageReslice>::New();
 475       mFusionReslice->SetInterpolationModeToLinear();
 476       mFusionReslice->AutoCropOutputOn();
 477       mFusionReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 478     }
 479
 480     mConcatenatedFusionTransform->Identity();
 481     mConcatenatedFusionTransform->Concatenate(mFusion->GetTransform()[0]);
 482     mConcatenatedFusionTransform->Concatenate(mSlicingTransform);
 483     mFusionReslice->SetResliceTransform(mConcatenatedFusionTransform);
 484 #if VTK_MAJOR_VERSION <= 5
 485     mFusionReslice->SetInput(0, mFusion->GetFirstVTKImageData());
 486 #else
 487     mFusionReslice->SetInputData(0, mFusion->GetFirstVTKImageData());
 488 #endif
 489     mFusionReslice->Update();
 490
 491     if (!mFusionMapper)
 492       mFusionMapper = vtkSmartPointer<vtkImageMapToColors>::New();
 493
 494     vtkSmartPointer<vtkLookupTable> lut = vtkLookupTable::New();
 495     lut->SetRange(0, 1);
 496     lut->SetValueRange(0, 1);
 497     lut->SetSaturationRange(0, 0);
 498     lut->Build();
 499     mFusionMapper->SetLookupTable(lut);
 500 #if VTK_MAJOR_VERSION <= 5
 501     mFusionMapper->SetInput(mFusionReslice->GetOutput());
 502 #else
 503     mFusionMapper->SetInputConnection(mFusionReslice->GetOutputPort(0));
 504 #endif
 505
 506     if (!mFusionActor) {
 507       mFusionActor = vtkSmartPointer<vtkImageActor>::New();
 508 #if VTK_MAJOR_VERSION <= 5
 509       mFusionActor->SetInput(mFusionMapper->GetOutput());
 510 #else
 511       mFusionActor->GetMapper()->SetInputConnection(mFusionMapper->GetOutputPort());
 512 #endif
 513       mFusionActor->SetPickable(0);
 514       mFusionActor->SetVisibility(true);
 515       mFusionActor->SetOpacity(0.7);
 516 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 517       mFusionActor->GetMapper()->BorderOn();
 518 #endif
 519
 520       this->GetRenderer()->AddActor(mFusionActor);
 521     }
 522
 523     //Synchronize orientation and slice
 524     AdjustResliceToSliceOrientation(mFusionReslice);
 525     this->UpdateDisplayExtent();
 526     this->SetTSlice(mCurrentTSlice);
 527   }
 528 }
 529 //------------------------------------------------------------------------------
 530
 531
 532 //------------------------------------------------------------------------------
 533 bool vvSlicer::GetActorVisibility(const std::string& actor_type, int overlay_index)
 534 {
 535   bool vis = false;
 536   if (actor_type == "image")
 537     vis = mImageVisibility;
 538   else if (actor_type == "vector")
 539     vis = mVFVisibility;
 540   else if (actor_type == "overlay")
 541     vis = mOverlayVisibility;
 542   else if ( (actor_type == "fusion") || (actor_type == "fusionSequence") )
 543     vis = mFusionVisibility;
 544   else if (actor_type == "contour")
 545     vis = this->mSurfaceCutActors[overlay_index]->GetActor()->GetVisibility();
 546   return vis;
 547 }
 548 //------------------------------------------------------------------------------
 549
 550 //------------------------------------------------------------------------------
 551 void vvSlicer::SetActorVisibility(const std::string& actor_type, int overlay_index ,bool vis)
 552 {
 553   if (actor_type == "image")
 554     mImageVisibility = vis;
 555   else if (actor_type == "vector")
 556     mVFVisibility = vis;
 557   else if (actor_type == "overlay")
 558     mOverlayVisibility = vis;
 559   else if ( (actor_type == "fusion") || (actor_type == "fusionSequence") )
 560     mFusionVisibility = vis;
 561   else if (actor_type == "contour")
 562     this->mSurfaceCutActors[overlay_index]->GetActor()->SetVisibility(vis);
 563   UpdateDisplayExtent();
 564 }
 565 //------------------------------------------------------------------------------
 566
 567 //------------------------------------------------------------------------------
 568 void vvSlicer::SetVF(vvImage::Pointer vf)
 569 {
 570   if (vf->GetVTKImages().size()) {
 571     mVF = vf;
 572     mVFVisibility = true;
 573
 574     if (!mAAFilter) {
 575       mAAFilter= vtkSmartPointer<vtkAssignAttribute>::New();
 576       mVOIFilter = vtkSmartPointer<vtkExtractVOI>::New();
 577       mVOIFilter->SetSampleRate(mSubSampling,mSubSampling,mSubSampling);
 578     }
 579 #if VTK_MAJOR_VERSION <= 5
 580     mVOIFilter->SetInput(vf->GetFirstVTKImageData());
 581     mAAFilter->SetInput(mVOIFilter->GetOutput());
 582 #else
 583     mVOIFilter->SetInputData(vf->GetFirstVTKImageData());
 584     mAAFilter->SetInputConnection(mVOIFilter->GetOutputPort());
 585 #endif
 586     ///This tells VTK to use the scalar (pixel) data of the image to draw the little arrows
 587     mAAFilter->Assign(vtkDataSetAttributes::SCALARS, vtkDataSetAttributes::VECTORS, vtkAssignAttribute::POINT_DATA);
 588
 589     if (!mArrow)
 590       mArrow = vtkSmartPointer<vvGlyphSource>::New();
 591     mArrow->SetGlyphTypeToSpecificArrow();
 592     mArrow->SetScale(mScale);
 593     mArrow->FilledOff();
 594
 595     // Glyph the gradient vector (with arrows)
 596     if (!mGlyphFilter)
 597       mGlyphFilter = vtkSmartPointer<vvGlyph2D>::New();
 598 #if VTK_MAJOR_VERSION <= 5
 599     mGlyphFilter->SetInput(mAAFilter->GetOutput());
 600     mGlyphFilter->SetSource(mArrow->GetOutput());
 601 #else
 602     mGlyphFilter->SetInputConnection(mAAFilter->GetOutputPort());
 603     mGlyphFilter->SetSourceConnection(mArrow->GetOutputPort());
 604 #endif
 605     mGlyphFilter->ScalingOn();
 606     mGlyphFilter->SetScaleModeToScaleByVector();
 607     mGlyphFilter->OrientOn();
 608     mGlyphFilter->SetVectorModeToUseVector();
 609     mGlyphFilter->SetColorModeToColorByVector();
 610
 611     if (!mVFColorLUT)
 612       mVFColorLUT = vtkSmartPointer<vtkLookupTable>::New();
 613
 614     double mVFColorHSV[3];
 615     vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
 616     mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
 617     mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
 618     mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
 619
 620     if (!mVFMapper)
 621       mVFMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
 622 #if VTK_MAJOR_VERSION <= 5
 623     mVFMapper->SetInput(mGlyphFilter->GetOutput());
 624 #else
 625     mVFMapper->SetInputConnection(mGlyphFilter->GetOutputPort());
 626 #endif
 627     mVFMapper->ImmediateModeRenderingOn();
 628     mVFMapper->SetLookupTable(mVFColorLUT);
 629
 630     if (!mVFActor)
 631       mVFActor = vtkSmartPointer<vtkActor>::New();
 632     mVFActor->SetMapper(mVFMapper);
 633     mVFActor->SetPickable(0);
 634     mVFActor->GetProperty()->SetLineWidth(mVFWidth);
 635     this->UpdateDisplayExtent();
 636     this->GetRenderer()->AddActor(mVFActor);
 637
 638     //Synchronize slice
 639     SetTSlice(mCurrentTSlice);
 640   }
 641 }
 642 //------------------------------------------------------------------------------
 643
 644
 645 //------------------------------------------------------------------------------
 646 void vvSlicer::SetLandmarks(vvLandmarks* landmarks)
 647 {
 648   mLandmarks = landmarks;
 649   if (landmarks) {
 650
 651     if (!mCross)
 652       mCross = vtkSmartPointer<vtkCursor3D>::New();
 653         if (!mClipBox)
 654       mClipBox = vtkSmartPointer<vtkBox>::New();
 655     if (!mLandClipper)
 656       mLandClipper = vtkSmartPointer<vvClipPolyData>::New();
 657     if (!mLandGlyph)
 658       mLandGlyph = vtkSmartPointer<vtkGlyph3D>::New();
 659     if (!mLandMapper)
 660       mLandMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
 661     if (!mLandActor)
 662       mLandActor = vtkSmartPointer<vtkActor>::New();
 663
 664     mCross->SetFocalPoint(0.0,0.0,0.0);
 665     mCross->SetModelBounds(-10,10,-10,10,-10,10);
 666     mCross->AllOff();
 667     mCross->AxesOn();
 668
 669     mLandClipper->SetClipFunction(mClipBox);
 670     mLandClipper->InsideOutOn();
 671 #if VTK_MAJOR_VERSION <= 5
 672     mLandmarkTransform = vtkSmartPointer<vtkTransformPolyDataFilter>::New();
 673     mLandmarkTransform->SetInput(mLandmarks->GetOutput());
 674     mConcatenatedTransform->Identity();
 675     mConcatenatedTransform->Concatenate(mImage->GetTransform()[0]);
 676     mConcatenatedTransform->Concatenate(mSlicingTransform);
 677     mLandmarkTransform->SetTransform(mConcatenatedTransform->GetInverse());
 678     mLandClipper->SetInput(mLandmarkTransform->GetOutput());
 679
 680     mLandGlyph->SetSource(mCross->GetOutput());
 681     mLandGlyph->SetInput(mLandClipper->GetOutput());
 682 #else
 683     mLandmarkTransform = vtkSmartPointer<vtkTransformPolyDataFilter>::New();
 684     mLandmarkTransform->SetInputData(mLandmarks->GetOutput());
 685     mConcatenatedTransform->Identity();
 686     mConcatenatedTransform->Concatenate(mImage->GetTransform()[0]);
 687     mConcatenatedTransform->Concatenate(mSlicingTransform);
 688     mLandmarkTransform->SetTransform(mConcatenatedTransform->GetInverse());
 689     mLandClipper->SetInputConnection(mLandmarkTransform->GetOutputPort());
 690
 691     mLandGlyph->SetSourceConnection(mCross->GetOutputPort());
 692     mLandGlyph->SetInputConnection(mLandClipper->GetOutputPort());
 693 #endif
 694     //mLandGlyph->SetIndexModeToScalar();
 695     //mLandGlyph->SetRange(0,1);
 696     //mLandGlyph->ScalingOff();
 697
 698     //mLandGlyph->SetColorModeToColorByScalar();
 699
 700     mLandGlyph->SetScaleModeToDataScalingOff();
 701     mLandGlyph->SetIndexModeToOff();
 702
 703     mLandMapper->SetInputConnection(mLandGlyph->GetOutputPort());
 704     //mLandMapper->ScalarVisibilityOff();
 705
 706     mLandActor->SetMapper(mLandMapper);
 707     mLandActor->GetProperty()->SetOpacity(0.995);  //in order to get VTK to turn on the alpha-blending in OpenGL
 708     mLandActor->GetProperty()->SetColor(255,10,212);
 709     mLandActor->SetPickable(0);
 710     mLandActor->SetVisibility(true);
 711     this->UpdateDisplayExtent();
 712   }
 713 }
 714 //------------------------------------------------------------------------------
 715
 716 //------------------------------------------------------------------------------
 717 //FIXME: this function leaks memory, we should fix it someday :)
 718 void vvSlicer::RemoveActor(const std::string& actor_type, int overlay_index)
 719 {
 720   if (actor_type == "vector") {
 721     Renderer->RemoveActor(mVFActor);
 722     mGlyphFilter=NULL;
 723     mVF = NULL;
 724     mArrow = NULL;
 725     mAAFilter=NULL;
 726     mVOIFilter = NULL;
 727     mVFMapper = NULL;
 728     mVFActor = NULL;
 729   }
 730   if (actor_type == "overlay") {
 731     Renderer->RemoveActor(mOverlayActor);
 732     mOverlay = NULL;
 733     mOverlayActor = NULL;
 734     mOverlayMapper = NULL;
 735   }
 736   if ( (actor_type == "fusion") || (actor_type == "fusionSequence") ) {
 737     Renderer->RemoveActor(mFusionActor);
 738     mFusion = NULL;
 739     mFusionActor = NULL;
 740     mFusionMapper = NULL;
 741   }
 742   if (actor_type == "contour") {
 743     Renderer->RemoveActor(this->mSurfaceCutActors[overlay_index]->GetActor());
 744     mSurfaceCutActors.erase(mSurfaceCutActors.begin()+overlay_index);
 745   }
 746 }
 747 //------------------------------------------------------------------------------
 748
 749
 750 //------------------------------------------------------------------------------
 751 void vvSlicer::SetVFSubSampling(int sub)
 752 {
 753   if (mVOIFilter) {
 754     mVOIFilter->SetSampleRate(mSubSampling,mSubSampling,mSubSampling);
 755     mSubSampling = sub;
 756   }
 757   UpdateDisplayExtent();
 758   Render();
 759 }
 760 //------------------------------------------------------------------------------
 761
 762
 763 //------------------------------------------------------------------------------
 764 void vvSlicer::SetVFScale(int scale)
 765 {
 766   mScale = scale;
 767   if (mArrow)
 768     mArrow->SetScale(mScale);
 769   UpdateDisplayExtent();
 770   Render();
 771 }
 772 //------------------------------------------------------------------------------
 773
 774 //------------------------------------------------------------------------------
 775 void vvSlicer::SetVFWidth(int width)
 776 {
 777   mVFWidth = width;
 778   if (mVFActor)
 779     mVFActor->GetProperty()->SetLineWidth(mVFWidth);
 780   UpdateDisplayExtent();
 781   Render();
 782 }
 783 //------------------------------------------------------------------------------
 784
 785
 786 //------------------------------------------------------------------------------
 787 void vvSlicer::SetVFLog(int log)
 788 {
 789   mVFLog = log;
 790   if (mGlyphFilter) {
 791     mGlyphFilter->SetUseLog(mVFLog);
 792     mGlyphFilter->Modified();
 793   }
 794   UpdateDisplayExtent();
 795   Render();
 796 }
 797 //------------------------------------------------------------------------------
 798
 799
 800 //------------------------------------------------------------------------------
 801 void vvSlicer::SetTSlice(int t, bool updateLinkedImages)
 802 {
 803         if (!updateLinkedImages) {
 804                 mCurrentTSlice = t;
 805 #if VTK_MAJOR_VERSION <= 5
 806                 mImageReslice->SetInput( mImage->GetVTKImages()[mCurrentTSlice] );
 807 #else
 808                 mImageReslice->SetInputData( mImage->GetVTKImages()[mCurrentTSlice] );
 809 #endif
 810                 // Update transform
 811                 mConcatenatedTransform->Identity();
 812                 mConcatenatedTransform->Concatenate(mImage->GetTransform()[mCurrentTSlice]);
 813                 mConcatenatedTransform->Concatenate(mSlicingTransform);
 814                 UpdateDisplayExtent();
 815                 return;
 816         }
 817   if (t < 0)
 818     mCurrentTSlice = 0;
 819   else if ((unsigned int)t >= mImage->GetVTKImages().size())
 820     mCurrentTSlice = mImage->GetVTKImages().size() -1;
 821   else
 822     mCurrentTSlice = t;
 823
 824   // Update transform
 825   mConcatenatedTransform->Identity();
 826   mConcatenatedTransform->Concatenate(mImage->GetTransform()[mCurrentTSlice]);
 827   mConcatenatedTransform->Concatenate(mSlicingTransform);
 828
 829   // Update image data
 830 #if VTK_MAJOR_VERSION <= 5
 831    mImageReslice->SetInput( mImage->GetVTKImages()[mCurrentTSlice] );
 832 #else
 833   mImageReslice->SetInputData( mImage->GetVTKImages()[mCurrentTSlice] );
 834 #endif
 835   if (mVF && mVFActor->GetVisibility()) {
 836     if (mVF->GetVTKImages().size() > (unsigned int)mCurrentTSlice)
 837 #if VTK_MAJOR_VERSION <= 5
 838       mVOIFilter->SetInput(mVF->GetVTKImages()[mCurrentTSlice]);
 839 #else
 840       mVOIFilter->SetInputData(mVF->GetVTKImages()[mCurrentTSlice]);
 841 #endif
 842   }
 843   //update the overlay
 844   if (mOverlay && mOverlayActor->GetVisibility()) {
 845     if (mOverlay->GetVTKImages().size() > (unsigned int)t) {
 846       mCurrentOverlayTSlice = t;
 847 #if VTK_MAJOR_VERSION <= 5
 848       mOverlayReslice->SetInput( mOverlay->GetVTKImages()[mCurrentOverlayTSlice] );
 849 #else
 850       mOverlayReslice->SetInputData( mOverlay->GetVTKImages()[mCurrentOverlayTSlice] );
 851 #endif
 852       // Update overlay transform
 853       mConcatenatedOverlayTransform->Identity();
 854       mConcatenatedOverlayTransform->Concatenate(mOverlay->GetTransform()[mCurrentOverlayTSlice]);
 855       mConcatenatedOverlayTransform->Concatenate(mSlicingTransform);
 856     }
 857   }
 858   //update the fusion ; except in case this is a fusionSequence, in which case both 'times' should be independent.
 859   if (mFusion && mFusionActor->GetVisibility() && (mFusionSequenceCode<0)) {
 860     if (mFusion->GetVTKImages().size() > (unsigned int)t) {
 861       mCurrentFusionTSlice = t;
 862 #if VTK_MAJOR_VERSION <= 5
 863       mFusionReslice->SetInput( mFusion->GetVTKImages()[mCurrentFusionTSlice]);
 864 #else
 865       mFusionReslice->SetInputData( mFusion->GetVTKImages()[mCurrentFusionTSlice]);
 866 #endif
 867
 868       // Update fusion transform
 869       mConcatenatedFusionTransform->Identity();
 870       mConcatenatedFusionTransform->Concatenate(mFusion->GetTransform()[mCurrentFusionTSlice]);
 871       mConcatenatedFusionTransform->Concatenate(mSlicingTransform);
 872     }
 873   }
 874   if (mSurfaceCutActors.size() > 0)
 875     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 876          i!=mSurfaceCutActors.end(); i++)
 877       (*i)->SetTimeSlice(mCurrentTSlice);
 878   UpdateDisplayExtent();
 879 }
 880 //------------------------------------------------------------------------------
 881
 882
 883 //------------------------------------------------------------------------------
 884 void vvSlicer::SetFusionSequenceTSlice(int t)
 885 {
 886   if (mFusion && mFusionActor->GetVisibility() && (mFusionSequenceCode>=0)) {
 887     if (mFusion->GetVTKImages().size() > (unsigned int)t) {
 888       mCurrentFusionTSlice = t;
 889 #if VTK_MAJOR_VERSION <= 5
 890       mFusionReslice->SetInput( mFusion->GetVTKImages()[mCurrentFusionTSlice] );
 891 #else
 892       mFusionReslice->SetInputData( mFusion->GetVTKImages()[mCurrentFusionTSlice] );
 893 #endif
 894       // Update fusion transform
 895       mConcatenatedFusionTransform->Identity();
 896       mConcatenatedFusionTransform->Concatenate(mFusion->GetTransform()[mCurrentFusionTSlice]); //not really useful...
 897       mConcatenatedFusionTransform->Concatenate(mSlicingTransform);
 898     }
 899   }
 900
 901   UpdateDisplayExtent();
 902 }
 903 //------------------------------------------------------------------------------
 904
 905
 906 //------------------------------------------------------------------------------
 907 int vvSlicer::GetTSlice()
 908 {
 909   return mCurrentTSlice;
 910 }
 911 //------------------------------------------------------------------------------
 912
 913 //------------------------------------------------------------------------------
 914 int vvSlicer::GetMaxCurrentTSlice()
 915 {
 916   int t = mCurrentTSlice;
 917   if(mOverlay)
 918     t = std::max(t, mCurrentOverlayTSlice);
 919   if(mFusion&& (mFusionSequenceCode<0)) //ignore fusionSequence data: for these, the times are not to be related (this way)
 920     t = std::max(t, mCurrentFusionTSlice);
 921   return t;
 922 }
 923 //------------------------------------------------------------------------------
 924
 925 //------------------------------------------------------------------------------
 926 int vvSlicer::GetFusionTSlice()
 927 {
 928   return mCurrentFusionTSlice;
 929 }
 930 //------------------------------------------------------------------------------
 931
 932 //------------------------------------------------------------------------------
 933 int vvSlicer::GetOverlayTSlice()
 934 {
 935   return mCurrentOverlayTSlice;
 936 }
 937 //------------------------------------------------------------------------------
 938
 939 //------------------------------------------------------------------------------
 940 void vvSlicer::SetSliceOrientation(int orientation)
 941 {
 942   //if 2D image, force to watch in Axial View
 943   int extent[6];
 944 #if VTK_MAJOR_VERSION <= 5
 945     this->GetInput()->GetWholeExtent(extent);
 946 #else
 947     int* ext = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
 948     copyExtent(ext, extent);
 949 #endif
 950
 951   if (extent[5]-extent[4] <= 2)
 952     orientation = vtkImageViewer2::SLICE_ORIENTATION_XY;
 953
 954   if (orientation < vtkImageViewer2::SLICE_ORIENTATION_YZ ||
 955       orientation > vtkImageViewer2::SLICE_ORIENTATION_XY) {
 956     vtkErrorMacro("Error - invalid slice orientation " << orientation);
 957     return;
 958   }
 959
 960   this->SliceOrientation = orientation;
 961
 962   if(mFusion)
 963     AdjustResliceToSliceOrientation(mFusionReslice);
 964
 965   if(mOverlay)
 966     AdjustResliceToSliceOrientation(mOverlayReslice);
 967
 968   // Update the viewer
 969
 970   // Go to current cursor position
 971   // double* cursorPos = GetCursorPosition();
 972   // DDV(cursorPos, 3);
 973   // SetCurrentPosition(cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
 974
 975   if (mFirstSetSliceOrientation) {
 976     int *range = this->GetSliceRange();
 977     if (range)
 978       this->Slice = static_cast<int>((range[0] + range[1]) * 0.5);
 979 #if VTK_MAJOR_VERSION <= 5
 980       mFirstSetSliceOrientation = false;
 981 #endif
 982   }
 983   else if (this->Renderer && this->GetInput()) {
 984     double s = mCursor[orientation];
 985     double sCursor = (s - this->GetInput()->GetOrigin()[orientation])/this->GetInput()->GetSpacing()[orientation];
 986     this->Slice = static_cast<int>(sCursor);
 987   }
 988
 989   this->UpdateOrientation();
 990
 991   this->UpdateDisplayExtent();
 992
 993   if (mFirstSetSliceOrientation) {
 994     mFirstSetSliceOrientation = false;
 995   }
 996
 997   if (this->Renderer && this->GetInput()) {
 998     double scale = this->Renderer->GetActiveCamera()->GetParallelScale();
 999     this->Renderer->ResetCamera();
1000     this->Renderer->GetActiveCamera()->SetParallelScale(scale);
1001   }
1002
1003   SetContourSlice();
1004 }
1005 //----------------------------------------------------------------------------
1006
1007 //------------------------------------------------------------------------------
1008 // This function ensures that we sample the slices of a vtkImageReslice filter
1009 // in the direction of the slicer (SliceOrientation) similarly as mImageReslice.
1010 // In other words, we change the grid of the reslice in the same way as the grid
1011 // of the displayed image in the slicing direction.
1012 void vvSlicer::AdjustResliceToSliceOrientation(vtkImageReslice *reslice)
1013 {
1014   // Reset autocrop and update output information
1015   reslice->SetOutputOriginToDefault();
1016   reslice->SetOutputSpacingToDefault();
1017 #if VTK_MAJOR_VERSION <= 5
1018   reslice->GetOutput()->UpdateInformation();
1019 #else
1020   reslice->UpdateInformation();
1021 #endif
1022
1023   // Ge new origin / spacing
1024   double origin[3];
1025   double spacing[3];
1026   reslice->GetOutput()->GetOrigin(origin);
1027   reslice->GetOutput()->GetSpacing(spacing);
1028
1029   // Use similar spacing as the image in the direction SliceOrientation
1030   spacing[this->SliceOrientation] = mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
1031
1032   // Modify origin to be on the image grid in the direction SliceOrientation in 3 steps
1033   // Step 1: from world coordinates to image coordinates
1034   origin[this->SliceOrientation] -= mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
1035   origin[this->SliceOrientation] /= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
1036
1037   // Step 2: round to nearest grid positionInc. This has been validated as the only
1038   // way to have something consistent with the thickness of a 2D slice visible on the
1039   // other slices. The thickness is accounted for so if the 2D slice is to thin and
1040   // between two slices, one will never be able to see this 2D slice (bug #1883).
1041   origin[this->SliceOrientation] = itk::Math::Round<double>(origin[this->SliceOrientation]);
1042
1043   // Step 3: back to world coordinates
1044   origin[this->SliceOrientation] *= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
1045   origin[this->SliceOrientation] += mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
1046
1047   // Set new spacing and origin
1048   reslice->SetOutputOrigin(origin);
1049   reslice->SetOutputSpacing(spacing);
1050   reslice->UpdateInformation();
1051 }
1052 //------------------------------------------------------------------------------
1053
1054 //----------------------------------------------------------------------------
1055 int * vvSlicer::GetExtent()
1056 {
1057   int *w_ext;
1058   if (mUseReducedExtent) {
1059     w_ext = mReducedExtent;
1060   }
1061   else {
1062 #if VTK_MAJOR_VERSION <= 5
1063     w_ext = GetInput()->GetWholeExtent();
1064 #else
1065     w_ext = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
1066 #endif
1067   }
1068   return w_ext;
1069 }
1070 //----------------------------------------------------------------------------
1071
1072
1073 //----------------------------------------------------------------------------
1074 int vvSlicer::GetOrientation()
1075 {
1076   return this->SliceOrientation;
1077 }
1078 //----------------------------------------------------------------------------
1079
1080
1081 //----------------------------------------------------------------------------
1082 void vvSlicer::UpdateDisplayExtent()
1083 {
1084   emit UpdateDisplayExtentBegin(mSlicerNumber);
1085   vtkImageData *input = this->GetInput();
1086   if (!input || !this->ImageActor) {
1087     return;
1088   }
1089
1090 #if VTK_MAJOR_VERSION <= 5
1091   input->UpdateInformation();
1092 #else
1093   mRegisterExtent = mImageReslice->GetOutputInformation(0)->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
1094 #endif
1095   this->SetSlice( this->GetSlice() ); //SR: make sure the update let the slice in extents
1096
1097   // Local copy of extent
1098   int w_ext[6];
1099 #if VTK_MAJOR_VERSION <= 5
1100   int* ext = GetExtent();
1101 #else
1102   int* ext = mImageReslice->GetOutputInformation(0)->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
1103 #endif
1104   copyExtent(ext, w_ext);
1105   if (mUseReducedExtent) {
1106         copyExtent(mReducedExtent, w_ext);
1107     }
1108   // Set slice value
1109
1110   w_ext[ this->SliceOrientation*2   ] = this->Slice;
1111   w_ext[ this->SliceOrientation*2+1 ] = this->Slice;
1112
1113   // Image actor
1114   this->ImageActor->SetVisibility(mImageVisibility);
1115   this->ImageActor->SetDisplayExtent(w_ext);
1116
1117 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
1118   // Fix for bug #1882
1119   dynamic_cast<vtkImageSliceMapper *>(this->ImageActor->GetMapper())->SetOrientation(this->GetOrientation());
1120 #endif
1121
1122   // Overlay image actor
1123   if (mOverlay && mOverlayVisibility) {
1124     AdjustResliceToSliceOrientation(mOverlayReslice);
1125     int overExtent[6];
1126 #if VTK_MAJOR_VERSION <= 5
1127     this->ConvertImageToImageDisplayExtent(input, w_ext, mOverlayReslice->GetOutput(), overExtent);
1128     bool out = ClipDisplayedExtent(overExtent, mOverlayMapper->GetInput()->GetWholeExtent());
1129 #else
1130     this->ConvertImageToImageDisplayExtent(mImageReslice->GetOutputInformation(0), w_ext, mOverlayReslice->GetOutput(), overExtent);
1131     bool out = ClipDisplayedExtent(overExtent, mOverlayMapper->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT()));
1132 #endif
1133     mOverlayActor->SetVisibility(!out);
1134     mOverlayActor->SetDisplayExtent( overExtent );
1135 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
1136     // Fix for bug #1882
1137     dynamic_cast<vtkImageSliceMapper *>(mOverlayActor->GetMapper())->SetOrientation(this->GetOrientation());
1138 #endif
1139   }
1140   else if(mOverlay)
1141     mOverlayActor->SetVisibility(false);
1142
1143   // Fusion image actor
1144   if (mFusion && mFusionVisibility) {
1145     AdjustResliceToSliceOrientation(mFusionReslice);
1146     int fusExtent[6];
1147 #if VTK_MAJOR_VERSION <= 5
1148     this->ConvertImageToImageDisplayExtent(input, w_ext, mFusionReslice->GetOutput(), fusExtent);
1149     bool out = ClipDisplayedExtent(fusExtent, mFusionMapper->GetInput()->GetWholeExtent());
1150 #else
1151     this->ConvertImageToImageDisplayExtent(mImageReslice->GetOutputInformation(0), w_ext, mFusionReslice->GetOutput(), fusExtent);
1152     bool out = ClipDisplayedExtent(fusExtent, mFusionMapper->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT()));
1153 #endif
1154     mFusionActor->SetVisibility(!out);
1155     mFusionActor->SetDisplayExtent( fusExtent );
1156 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
1157     // Fix for bug #1882
1158     dynamic_cast<vtkImageSliceMapper *>(mFusionActor->GetMapper())->SetOrientation(this->GetOrientation());
1159 #endif
1160   }
1161   else if(mFusion)
1162     mFusionActor->SetVisibility(false);
1163   // Vector field actor
1164   double* camera = Renderer->GetActiveCamera()->GetPosition();
1165   double* image_bounds = ImageActor->GetBounds();
1166   double position[3] = {0, 0, 0};
1167   position[this->SliceOrientation] = image_bounds[this->SliceOrientation*2];
1168
1169   //print_vector<double, 6>("camera", camera);
1170   //print_vector<double, 6>("image_bounds", image_bounds);
1171   //print_vector<double, 3>("position", position);
1172
1173   // find where to place the VF actor. to deal with
1174   // z-buffer issues, the VF is placed right in front of the image,
1175   // subject to a small offset. the position actually depends on the
1176   // the location of the camera relative to the image.
1177   double offset = 1;
1178   if (camera[this->SliceOrientation] < image_bounds[this->SliceOrientation*2])
1179     offset = -1;
1180
1181   if (mVF && mVFVisibility) {
1182     int vfExtent[6];
1183 #if VTK_MAJOR_VERSION <= 5
1184     mVF->GetVTKImages()[0]->UpdateInformation();
1185     this->ConvertImageToImageDisplayExtent(input, w_ext, mVF->GetVTKImages()[0], vfExtent);
1186     bool out = ClipDisplayedExtent(vfExtent, mVOIFilter->GetInput()->GetWholeExtent());
1187 #else
1188     //this->UpdateInformation();
1189     this->ConvertImageToImageDisplayExtent(mImageReslice->GetOutputInformation(0), w_ext, mVF->GetVTKImages()[0], vfExtent);
1190     bool out = ClipDisplayedExtent(vfExtent, mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT()));
1191 #endif
1192     mVFActor->SetVisibility(!out);
1193     mVOIFilter->SetVOI(vfExtent);
1194     int orientation[3] = {1,1,1};
1195     orientation[this->SliceOrientation] = 0;
1196     mGlyphFilter->SetOrientation(orientation[0], orientation[1], orientation[2]);
1197     position[this->SliceOrientation] += offset;
1198     mVFActor->SetPosition(position);
1199     mVFActor->GetProperty()->SetOpacity(0.995); //in order to get VTK to turn on the alpha-blending in OpenGL
1200     mVFMapper->Update();
1201
1202   }
1203   else if(mVF)
1204     mVFActor->SetVisibility(false);
1205
1206
1207     double boundsT [6];
1208       for(unsigned int i=0; i<6; i++)
1209         boundsT[i] = ImageActor->GetBounds()[i];
1210       boundsT[ this->SliceOrientation*2   ] = ImageActor->GetBounds()[ this->SliceOrientation*2  ]-fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
1211       boundsT[ this->SliceOrientation*2+1 ] = ImageActor->GetBounds()[ this->SliceOrientation*2+1 ]+fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
1212
1213
1214   // Landmarks actor
1215   if (mLandActor) {
1216     if (mClipBox) {
1217       RemoveLandmarks();
1218     }
1219
1220     position[this->SliceOrientation] = offset;
1221     mLandActor->SetPosition(position);
1222   }
1223
1224   // Figure out the correct clipping range
1225   if (this->Renderer) {
1226     if (this->InteractorStyle &&
1227         this->InteractorStyle->GetAutoAdjustCameraClippingRange()) {
1228       this->Renderer->ResetCameraClippingRange();
1229     } else {
1230       vtkCamera *cam = this->Renderer->GetActiveCamera();
1231       if (cam) {
1232         double bounds[6];
1233         this->ImageActor->GetBounds(bounds);
1234         double spos = (double)bounds[this->SliceOrientation * 2];
1235         double cpos = (double)cam->GetPosition()[this->SliceOrientation];
1236         double range = fabs(spos - cpos);
1237         double *spacing = input->GetSpacing();
1238         double sumSpacing = spacing[0] + spacing[1] + spacing[2];
1239         cam->SetClippingRange(range - sumSpacing, range + sumSpacing);
1240       }
1241     }
1242
1243     if (mLandActor) {
1244         if (mClipBox) {
1245             DisplayLandmarks();
1246         }
1247     }
1248   }
1249   emit UpdateDisplayExtentEnd(mSlicerNumber);
1250 }
1251 //----------------------------------------------------------------------------
1252
1253 //----------------------------------------------------------------------------
1254 void vvSlicer::ConvertImageToImageDisplayExtent(vtkInformation *sourceImage, const int sourceExtent[6],
1255                                                 vtkImageData *targetImage, int targetExtent[6])
1256 {
1257   double dExtents[6];
1258   double *origin, *spacing;
1259   origin = sourceImage->Get(vtkDataObject::ORIGIN());
1260   spacing = sourceImage->Get(vtkDataObject::SPACING());
1261   for(unsigned int i=0; i<6; i++) {
1262     // From source voxel coordinates to world coordinates
1263     dExtents[i] = origin[i/2] + spacing[i/2] * sourceExtent[i];
1264
1265     // From world coordinates to floating point target voxel coordinates
1266     dExtents[i] = (dExtents[i]- targetImage->GetOrigin()[i/2]) / targetImage->GetSpacing()[i/2];
1267
1268     // Round to current slice or larger extent
1269     if(i/2==this->GetOrientation())
1270       targetExtent[i] = itk::Math::Round<double>(dExtents[i]);
1271     else if(i%2==1)
1272       targetExtent[i] = itk::Math::Ceil<double>(dExtents[i]);
1273     else
1274       targetExtent[i] = itk::Math::Floor<double>(dExtents[i]);
1275   }
1276 }
1277 //----------------------------------------------------------------------------
1278
1279 //----------------------------------------------------------------------------
1280 void vvSlicer::ConvertImageToImageDisplayExtent(vtkImageData *sourceImage, const int sourceExtent[6],
1281                                                 vtkImageData *targetImage, int targetExtent[6])
1282 {
1283   double dExtents[6];
1284   for(unsigned int i=0; i<6; i++) {
1285     // From source voxel coordinates to world coordinates
1286     dExtents[i] = sourceImage->GetOrigin()[i/2] + sourceImage->GetSpacing()[i/2] * sourceExtent[i];
1287
1288     // From world coordinates to floating point target voxel coordinates
1289     dExtents[i] = (dExtents[i]- targetImage->GetOrigin()[i/2]) / targetImage->GetSpacing()[i/2];
1290
1291     // Round to current slice or larger extent
1292     if(i/2==this->GetOrientation())
1293       targetExtent[i] = itk::Math::Round<double>(dExtents[i]);
1294     else if(i%2==1)
1295       targetExtent[i] = itk::Math::Ceil<double>(dExtents[i]);
1296     else
1297       targetExtent[i] = itk::Math::Floor<double>(dExtents[i]);
1298   }
1299 }
1300 //----------------------------------------------------------------------------
1301
1302 //----------------------------------------------------------------------------
1303 bool vvSlicer::ClipDisplayedExtent(int extent[6], int refExtent[6])
1304 {
1305   bool out = false;
1306   int maxBound = 6;
1307
1308   for (int i = 0; i < maxBound; i = i+2) {
1309     //if we are totally outside the image
1310     if ( extent[i] > refExtent[i+1] || extent[i+1] < refExtent[i] ) {
1311       out = true;
1312       break;
1313     }
1314     //crop to the limit of the image
1315     extent[i] = std::max(extent[i], refExtent[i]);
1316     extent[i] = std::min(extent[i], refExtent[i+1]);;
1317     extent[i+1] = std::max(extent[i+1], refExtent[i]);
1318     extent[i+1] = std::min(extent[i+1], refExtent[i+1]);;
1319   }
1320   if (out)
1321     for (int i = 0; i < maxBound; i = i+2) {
1322       extent[i] = refExtent[i];
1323       extent[i+1] = refExtent[i];
1324     }
1325   return out;
1326 }
1327 //----------------------------------------------------------------------------
1328
1329
1330 //----------------------------------------------------------------------------
1331 void vvSlicer::UpdateOrientation()
1332 {
1333   // Set the camera position
1334   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1335   if (cam) {
1336     switch (this->SliceOrientation) {
1337     case vtkImageViewer2::SLICE_ORIENTATION_XY:
1338       cam->SetFocalPoint(0,0,0);
1339       cam->SetPosition(0,0,-1); // -1 if medical ?
1340       cam->SetViewUp(0,-1,0);
1341       break;
1342
1343     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
1344       cam->SetFocalPoint(0,0,0);
1345       cam->SetPosition(0,-1,0); // 1 if medical ?
1346       cam->SetViewUp(0,0,1);
1347       break;
1348
1349     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1350       cam->SetFocalPoint(0,0,0);
1351       cam->SetPosition(-1,0,0); // -1 if medical ?
1352       cam->SetViewUp(0,0,1);
1353       break;
1354     }
1355   }
1356 }
1357 //----------------------------------------------------------------------------
1358
1359
1360 //----------------------------------------------------------------------------
1361 void vvSlicer::SetOpacity(double s)
1362 {
1363   this->GetImageActor()->SetOpacity(s);
1364 }
1365 //----------------------------------------------------------------------------
1366
1367
1368 //----------------------------------------------------------------------------
1369 void vvSlicer::SetRenderWindow(int orientation, vtkRenderWindow * rw)
1370 {
1371   this->Superclass::SetRenderWindow(rw);
1372   this->SetupInteractor(rw->GetInteractor());
1373   ca->SetImageActor(this->GetImageActor());
1374   ca->SetWindowLevel(this->GetWindowLevel());
1375   ca->SetText(3, "<window>\n<level>");
1376
1377   double bounds[6];
1378   double max = 65000;
1379
1380   bounds[0] = -max;
1381   bounds[1] = max;
1382   bounds[2] = -max;
1383   bounds[3] = max;
1384   bounds[4] = -max;
1385   bounds[5] = max;
1386   crossCursor->SetModelBounds(bounds);
1387
1388   this->GetRenderer()->AddActor(pdmA);
1389   this->GetRenderer()->AddActor(ca);
1390   this->GetRenderer()->ResetCamera();
1391
1392   //this is just a mapping between the labeling of the orientations presented to the user and
1393   //the one used by vtk
1394   SetSliceOrientation(2-(orientation%3));
1395   ResetCamera();
1396 }
1397 //----------------------------------------------------------------------------
1398
1399
1400 //----------------------------------------------------------------------------
1401 void vvSlicer::ResetCamera()
1402 {
1403   this->GetRenderer()->ResetCamera();
1404 }
1405 //----------------------------------------------------------------------------
1406
1407
1408 //----------------------------------------------------------------------------
1409 void vvSlicer::SetDisplayMode(bool i)
1410 {
1411         this->GetRenderer()->SetDraw(i);
1412         if (i) UpdateDisplayExtent();
1413 }
1414 //----------------------------------------------------------------------------
1415
1416
1417 //----------------------------------------------------------------------------
1418 void vvSlicer::FlipHorizontalView()
1419 {
1420   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1421   if (cam) {
1422     double *position = cam->GetPosition();
1423     double factor[3] = {1, 1, 1};
1424     factor[this->SliceOrientation] = -1;
1425     cam->SetPosition(factor[0]*position[0],factor[1]*position[1],factor[2]*position[2]);
1426
1427 /*    switch (this->SliceOrientation) {
1428     case vtkImageViewer2::SLICE_ORIENTATION_XY:
1429       cam->SetPosition(position[0],position[1],-position[2]);
1430       break;
1431
1432     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
1433       cam->SetPosition(position[0],-position[1],position[2]);
1434       break;
1435
1436     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1437       cam->SetPosition(-position[0],position[1],position[2]);
1438       break;
1439     }*/
1440
1441     this->Renderer->ResetCameraClippingRange();
1442     this->UpdateDisplayExtent();
1443   }
1444 }
1445 //----------------------------------------------------------------------------
1446
1447
1448 //----------------------------------------------------------------------------
1449 void vvSlicer::FlipVerticalView()
1450 {
1451   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1452   if (cam) {
1453     FlipHorizontalView();
1454     double *viewup = cam->GetViewUp();
1455     cam->SetViewUp(-viewup[0],-viewup[1],-viewup[2]);
1456     this->UpdateDisplayExtent();
1457   }
1458 }
1459 //----------------------------------------------------------------------------
1460
1461
1462 //----------------------------------------------------------------------------
1463 void vvSlicer::SetColorWindow(double window)
1464 {
1465   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1466   if ( LUT ) {
1467     double level = this->GetWindowLevel()->GetLevel();
1468     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1469     LUT->Build();
1470   }
1471   this->vtkImageViewer2::SetColorWindow(window);
1472 }
1473 //----------------------------------------------------------------------------
1474
1475 //----------------------------------------------------------------------------
1476 void vvSlicer::SetColorLevel(double level)
1477 {
1478   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1479   if ( LUT ) {
1480     double window = this->GetWindowLevel()->GetWindow();
1481     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1482     LUT->Build();
1483   }
1484   this->vtkImageViewer2::SetColorLevel(level);
1485 }
1486 //----------------------------------------------------------------------------
1487
1488 //----------------------------------------------------------------------------
1489 double vvSlicer::GetOverlayColorWindow()
1490 {
1491   if(mOverlayMapper)
1492     return mOverlayMapper->GetWindow();
1493   else
1494     return 0.;
1495 }
1496 //----------------------------------------------------------------------------
1497
1498 //----------------------------------------------------------------------------
1499 double vvSlicer::GetOverlayColorLevel()
1500 {
1501   if(mOverlayMapper)
1502     return mOverlayMapper->GetLevel();
1503   else
1504     return 0.;
1505 }
1506 //----------------------------------------------------------------------------
1507
1508 //----------------------------------------------------------------------------
1509 void vvSlicer::SetOverlayColorWindow(double window)
1510 {
1511   if(mOverlayMapper)
1512     mOverlayMapper->SetWindow(window);
1513 }
1514 //----------------------------------------------------------------------------
1515
1516 //----------------------------------------------------------------------------
1517 void vvSlicer::SetOverlayColorLevel(double level)
1518 {
1519   if(mOverlayMapper)
1520     mOverlayMapper->SetLevel(level);
1521 }
1522 //----------------------------------------------------------------------------
1523
1524 //----------------------------------------------------------------------------
1525 // Returns the min an the max value in a 20%x20% region around the mouse pointer
1526 void vvSlicer::GetExtremasAroundMousePointer(double & min, double & max, vtkImageData *image, vtkTransform *transform)
1527 {
1528   //Get mouse pointer position in view coordinates
1529   double corner1[3];
1530   double corner2[3];
1531   for(int i=0; i<3; i++) {
1532     corner1[i] = mCurrent[i];
1533     corner2[i] = mCurrent[i];
1534   }
1535
1536   this->Renderer->WorldToView(corner1[0], corner1[1], corner1[2]);
1537   this->Renderer->WorldToView(corner2[0], corner2[1], corner2[2]);
1538
1539   // In view coordinates, x is the slicer width and y is the slicer height are the in-plane axis
1540   int w, h;
1541   this->Renderer->GetTiledSize(&w, &h);
1542   corner1[0] -= 0.2*h/(double)w;
1543   corner2[0] += 0.2*h/(double)w;
1544   corner1[1] -= 0.2;
1545   corner2[1] += 0.2;
1546   this->Renderer->ViewToWorld(corner1[0], corner1[1], corner1[2]);
1547   this->Renderer->ViewToWorld(corner2[0], corner2[1], corner2[2]);
1548
1549   //Convert to image pixel coordinates (rounded)
1550   transform->TransformPoint(corner1, corner1);
1551   transform->TransformPoint(corner2, corner2);
1552   int iLocalExtents[6];
1553   for(int i=0; i<3; i++) {
1554     corner1[i] = (corner1[i] - image->GetOrigin()[i])/image->GetSpacing()[i];
1555     corner2[i] = (corner2[i] - image->GetOrigin()[i])/image->GetSpacing()[i];
1556
1557     iLocalExtents[i*2  ] = lrint(corner1[i]);
1558     iLocalExtents[i*2+1] = lrint(corner2[i]);
1559
1560     if(iLocalExtents[i*2  ]>iLocalExtents[i*2+1])
1561       std::swap(iLocalExtents[i*2], iLocalExtents[i*2+1]);
1562
1563 #if VTK_MAJOR_VERSION > 5
1564     for(int j=0;j<2; j++) {
1565       if(iLocalExtents[i*2+j]< mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT())[2*i])
1566         iLocalExtents[i*2+j] = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT())[2*i];
1567
1568       if(iLocalExtents[i*2+j]> mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT())[2*i+1])
1569         iLocalExtents[i*2+j] = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT())[2*i+1];
1570     }
1571 #endif
1572   }
1573
1574   vtkSmartPointer<vtkExtractVOI> voiFilter = vtkSmartPointer<vtkExtractVOI>::New();
1575 #if VTK_MAJOR_VERSION <= 5
1576   voiFilter->SetInput(image);
1577 #else
1578   voiFilter->SetInputData(image);
1579 #endif
1580   voiFilter->SetVOI(iLocalExtents);
1581   voiFilter->Update();
1582   if (!voiFilter->GetOutput()->GetNumberOfPoints()) {
1583     min = 0;
1584     max = 0;
1585     return;
1586   }
1587
1588   vtkSmartPointer<vtkImageAccumulate> accFilter = vtkSmartPointer<vtkImageAccumulate>::New();
1589 #if VTK_MAJOR_VERSION <= 5
1590   accFilter->SetInput(voiFilter->GetOutput());
1591 #else
1592   accFilter->SetInputConnection(voiFilter->GetOutputPort(0));
1593 #endif
1594   accFilter->Update();
1595
1596   min = *(accFilter->GetMin());
1597   max = *(accFilter->GetMax());
1598 }
1599 //----------------------------------------------------------------------------
1600
1601 //----------------------------------------------------------------------------
1602 double vvSlicer::GetScalarComponentAsDouble(vtkImageData *image, double X, double Y, double Z, int &ix, int &iy, int &iz, int component)
1603 {
1604   ix = lrint(X);
1605   iy = lrint(Y);
1606   iz = lrint(Z);
1607 #if VTK_MAJOR_VERSION <= 5
1608   if (ix < image->GetWholeExtent()[0] ||
1609       ix > image->GetWholeExtent()[1] ||
1610       iy < image->GetWholeExtent()[2] ||
1611       iy > image->GetWholeExtent()[3] ||
1612       iz < image->GetWholeExtent()[4] ||
1613       iz > image->GetWholeExtent()[5] )
1614     return std::numeric_limits<double>::quiet_NaN();
1615   image->SetUpdateExtent(ix, ix, iy, iy, iz, iz);
1616   image->Update();
1617 #else
1618   if (ix < image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[0] ||
1619       ix > image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[1] ||
1620       iy < image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[2] ||
1621       iy > image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[3] ||
1622       iz < image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[4] ||
1623       iz > image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[5] )
1624     return std::numeric_limits<double>::quiet_NaN();
1625   //image->SetUpdateExtent(ix, ix, iy, iy, iz, iz);
1626   //image->Update();
1627 #endif
1628
1629   return image->GetScalarComponentAsDouble(ix, iy, iz, component);
1630 }
1631 //----------------------------------------------------------------------------
1632
1633 //----------------------------------------------------------------------------
1634 void vvSlicer::Render()
1635 {
1636   if (this->mFusion && mFusionActor->GetVisibility() && showFusionLegend) {
1637     legend->SetLookupTable(this->GetFusionMapper()->GetLookupTable());
1638     legend->UseOpacityOn();
1639     legend->SetVisibility(1);
1640   }
1641   else if (this->GetWindowLevel()->GetLookupTable() && !this->mOverlay)  {
1642     legend->SetLookupTable(this->GetWindowLevel()->GetLookupTable());
1643     legend->UseOpacityOff();
1644     legend->SetVisibility(1);
1645   } else legend->SetVisibility(0);
1646
1647   if (ca->GetVisibility()) {
1648
1649     std::stringstream worldPos(" ");
1650     double pt[3];
1651     mConcatenatedTransform->TransformPoint(mCurrent, pt);
1652     double X = (pt[0] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[0])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[0];
1653     double Y = (pt[1] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[1])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[1];
1654     double Z = (pt[2] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[2])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[2];
1655 #if VTK_MAJOR_VERSION <= 5
1656     if (X >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[0]-0.5 &&
1657         X <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[1]+0.5 &&
1658         Y >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[2]-0.5 &&
1659         Y <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[3]+0.5 &&
1660         Z >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[4]-0.5 &&
1661         Z <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[5]+0.5) {
1662
1663
1664       int ix, iy, iz;
1665       double value = this->GetScalarComponentAsDouble(mImage->GetVTKImages()[mCurrentTSlice], X, Y, Z, ix, iy, iz);
1666
1667       if(ImageActor->GetVisibility())
1668         worldPos << "data value : " << value << std::endl;
1669
1670       worldPos << "mm : " << lrint(mCurrentBeforeSlicingTransform[0]) << ' '
1671                           << lrint(mCurrentBeforeSlicingTransform[1]) << ' '
1672                           << lrint(mCurrentBeforeSlicingTransform[2]) << ' '
1673                           << mCurrentTSlice
1674                           << std::endl;
1675       worldPos << "pixel : " << ix << ' '
1676                              << iy << ' '
1677                              << iz << ' '
1678                              << mCurrentTSlice
1679                              << std::endl;
1680     }
1681 #else
1682     if (X >= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[0]-0.5 &&
1683         X <= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[1]+0.5 &&
1684         Y >= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[2]-0.5 &&
1685         Y <= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[3]+0.5 &&
1686         Z >= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[4]-0.5 &&
1687         Z <= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[5]+0.5) {
1688
1689       int ix, iy, iz;
1690       double value = this->GetScalarComponentAsDouble(mImage->GetVTKImages()[mCurrentTSlice], X, Y, Z, ix, iy, iz);
1691
1692       if(ImageActor->GetVisibility())
1693         worldPos << "data value : " << value << std::endl;
1694
1695       worldPos << "mm : " << lrint(mCurrentBeforeSlicingTransform[0]) << ' '
1696                           << lrint(mCurrentBeforeSlicingTransform[1]) << ' '
1697                           << lrint(mCurrentBeforeSlicingTransform[2]) << ' '
1698                           << mCurrentTSlice
1699                           << std::endl;
1700       worldPos << "pixel : " << ix << ' '
1701                              << iy << ' '
1702                              << iz << ' '
1703                              << mCurrentTSlice
1704                              << std::endl;
1705
1706     }
1707 #endif
1708     ca->SetText(1,worldPos.str().c_str());
1709
1710     std::stringstream slicePos;
1711     slicePos << "Slice: " << this->GetSlice();
1712     ca->SetText(2, slicePos.str().c_str());
1713   }
1714
1715   if (pdmA->GetVisibility()) {
1716     double x = mCursor[0];
1717     double y = mCursor[1];
1718     double z = mCursor[2];
1719     double xCursor = (x - this->GetInput()->GetOrigin()[0])/this->GetInput()->GetSpacing()[0];
1720     double yCursor = (y - this->GetInput()->GetOrigin()[1])/this->GetInput()->GetSpacing()[1];
1721     double zCursor = (z - this->GetInput()->GetOrigin()[2])/this->GetInput()->GetSpacing()[2];
1722 #if VTK_MAJOR_VERSION <= 5
1723     if (xCursor >= this->GetImageActor()->GetDisplayExtent()[0]-0.5 &&
1724         xCursor < this->GetImageActor()->GetDisplayExtent()[1]+0.5 &&
1725         yCursor >= this->GetImageActor()->GetDisplayExtent()[2]-0.5 &&
1726         yCursor < this->GetImageActor()->GetDisplayExtent()[3]+0.5 &&
1727         zCursor >= this->GetImageActor()->GetDisplayExtent()[4]-0.5 &&
1728         zCursor < this->GetImageActor()->GetDisplayExtent()[5]+0.5 ) {
1729       vtkRenderer * renderer = this->Renderer;
1730
1731       renderer->WorldToView(x,y,z);
1732       renderer->ViewToNormalizedViewport(x,y,z);
1733       renderer->NormalizedViewportToViewport(x,y);
1734       renderer->ViewportToNormalizedDisplay(x,y);
1735       renderer->NormalizedDisplayToDisplay(x,y);
1736       crossCursor->SetFocalPoint(x,y,z);
1737     } else
1738       crossCursor->SetFocalPoint(-1,-1,z);
1739     crossCursor->Update();
1740   }
1741 #else
1742     vtkSmartPointer<vtkOpenGLImageSliceMapper> mapperOpenGL= vtkSmartPointer<vtkOpenGLImageSliceMapper>::New();
1743     try {
1744         mapperOpenGL = dynamic_cast<vtkOpenGLImageSliceMapper*>(GetImageActor()->GetMapper());
1745     } catch (const std::bad_cast& e) {
1746                 std::cerr << e.what() << std::endl;
1747                 std::cerr << "Conversion error" << std::endl;
1748                 return;
1749         }
1750
1751     if (xCursor >= mapperOpenGL->GetCroppingRegion()[0]-0.5 &&
1752         xCursor < mapperOpenGL->GetCroppingRegion()[1]+0.5 &&
1753         yCursor >= mapperOpenGL->GetCroppingRegion()[2]-0.5 &&
1754         yCursor < mapperOpenGL->GetCroppingRegion()[3]+0.5 &&
1755         zCursor >= mapperOpenGL->GetCroppingRegion()[4]-0.5 &&
1756         zCursor < mapperOpenGL->GetCroppingRegion()[5]+0.5 ) {
1757       vtkRenderer * renderer = this->Renderer;
1758
1759       renderer->WorldToView(x,y,z);
1760       renderer->ViewToNormalizedViewport(x,y,z);
1761       renderer->NormalizedViewportToViewport(x,y);
1762       renderer->ViewportToNormalizedDisplay(x,y);
1763       renderer->NormalizedDisplayToDisplay(x,y);
1764       crossCursor->SetFocalPoint(x,y,z);
1765     } else
1766       crossCursor->SetFocalPoint(-1,-1,z);
1767     crossCursor->Update();
1768   }
1769 #endif
1770
1771   if (mOverlay && mOverlayActor->GetVisibility()) {
1772     if(mLinkOverlayWindowLevel) {
1773       mOverlayMapper->SetWindow(this->GetColorWindow());
1774       mOverlayMapper->SetLevel(this->GetColorLevel());
1775     }
1776 #if VTK_MAJOR_VERSION <= 5
1777     mOverlayMapper->GetOutput()->SetUpdateExtent(mOverlayActor->GetDisplayExtent());
1778 #else
1779     mOverlayMapper->SetUpdateExtent(mOverlayActor->GetDisplayExtent());
1780 #endif
1781     mOverlayMapper->Update();
1782   }
1783   if (mFusion && mFusionActor->GetVisibility()) {
1784 #if VTK_MAJOR_VERSION <= 5
1785     mFusionMapper->GetOutput()->SetUpdateExtent(mFusionActor->GetDisplayExtent());
1786 #else
1787     mFusionMapper->SetUpdateExtent(mFusionActor->GetDisplayExtent());
1788 #endif
1789     mFusionMapper->Update();
1790   }
1791   if (mLandMapper) {
1792     RemoveLandmarks();
1793     DisplayLandmarks();
1794   }
1795
1796     this->GetRenderWindow()->Render();
1797 }
1798 //----------------------------------------------------------------------------
1799
1800
1801 //----------------------------------------------------------------------------
1802 void vvSlicer::UpdateCursorPosition()
1803 {
1804   pdmA->SetVisibility(true);
1805   mCursor[0] = mCurrent[0];
1806   mCursor[1] = mCurrent[1];
1807   mCursor[2] = mCurrent[2];
1808   mCursor[3] = mCurrentTSlice;
1809 }
1810 //----------------------------------------------------------------------------
1811
1812
1813 //----------------------------------------------------------------------------
1814 void vvSlicer::RemoveLandmarks()
1815 {
1816   vtkPolyData *pd = static_cast<vtkPolyData*>(mLandmarks->GetOutput());
1817   if (pd->GetPoints()) {
1818
1819     //First remove all captions:
1820     for(unsigned int i=0;i<mLandLabelActors.size();i++) {
1821         this->Renderer->RemoveActor2D(mLandLabelActors[i]);
1822         //allActors2D->Remove (mLandLabelActors[i]);
1823     }
1824     mLandLabelActors.clear();
1825   }
1826 }
1827 //----------------------------------------------------------------------------
1828
1829
1830 //----------------------------------------------------------------------------
1831 void vvSlicer::DisplayLandmarks()
1832 {
1833
1834   double bounds [6];
1835   for(unsigned int i=0; i<6; i++)
1836     bounds[i] = ImageActor->GetBounds()[i];
1837   bounds[ this->SliceOrientation*2   ] = ImageActor->GetBounds()[ this->SliceOrientation*2  ]-fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
1838   bounds[ this->SliceOrientation*2+1 ] = ImageActor->GetBounds()[ this->SliceOrientation*2+1 ]+fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
1839   mClipBox->SetBounds(bounds);
1840
1841
1842   vtkPolyData *pd = static_cast<vtkPolyData*>(mLandmarks->GetOutput());
1843   if (pd->GetPoints()) {
1844     this->GetRenderer()->AddActor(mLandActor);
1845     //mLandGlyph->SetRange(0,1);
1846     //mLandGlyph->Modified();
1847     //mLandGlyph->Update();
1848     mClipBox->Modified();
1849     mLandClipper->Update();
1850     mLandMapper->Update();
1851     //Next add the captions to the displayed points
1852     for (vtkIdType id=0; id<mLandClipper->GetOutput()->GetNumberOfPoints(); id++) {
1853           double *position = mLandClipper->GetOutput()->GetPoint(id);
1854       vtkStdString label = static_cast<vtkStringArray*>(mLandClipper->GetOutput()->GetPointData()->GetAbstractArray("labels"))->GetValue(id);
1855       vtkSmartPointer<vtkCaptionActor2D> label_actor = vtkSmartPointer<vtkCaptionActor2D>::New();
1856       label_actor->SetCaption(label);
1857       label_actor->SetAttachmentPoint(position);
1858       label_actor->GetCaptionTextProperty()->SetColor(1,0,0);
1859       label_actor->GetCaptionTextProperty()->SetOrientation(33.333333);
1860       label_actor->GetCaptionTextProperty()->SetFontFamilyToTimes();
1861       label_actor->GetCaptionTextProperty()->SetBold(0);
1862       label_actor->GetCaptionTextProperty()->SetFontSize(6);
1863       label_actor->BorderOff();
1864       label_actor->LeaderOff();
1865       label_actor->ThreeDimensionalLeaderOff();
1866       mLandLabelActors.push_back(label_actor);
1867       this->Renderer->AddActor2D(mLandLabelActors[id]);
1868      }
1869   }
1870
1871 }
1872 //----------------------------------------------------------------------------
1873
1874
1875 //----------------------------------------------------------------------------
1876 void vvSlicer::SetSlice(int slice)
1877 {
1878   int *range = this->GetSliceRange();
1879   if (range) {
1880     if (slice < range[0]) {
1881       slice = range[0];
1882     } else if (slice > range[1]) {
1883       slice = range[1];
1884     }
1885   }
1886
1887   if (this->Slice == slice) {
1888     return;
1889   }
1890
1891   this->Slice = slice;
1892   SetContourSlice();
1893   this->Modified();
1894   this->UpdateDisplayExtent();
1895
1896   // Seems to work without this line
1897   //this->Render();
1898 }
1899 //----------------------------------------------------------------------------
1900
1901 //----------------------------------------------------------------------------
1902 int vvSlicer::GetTMax()
1903 {
1904   int tmax = (int)mImage->GetVTKImages().size() - 1;
1905   if(mOverlay)
1906     tmax = std::max(tmax, (int)mOverlay->GetVTKImages().size()-1);
1907   return tmax;
1908 }
1909 //----------------------------------------------------------------------------
1910
1911 //----------------------------------------------------------------------------
1912 void vvSlicer::SetContourSlice()
1913 {
1914   if (mSurfaceCutActors.size() > 0)
1915     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
1916          i!=mSurfaceCutActors.end(); i++) {
1917
1918       (*i)->SetSlicingOrientation(this->SliceOrientation);
1919       (*i)->SetCutSlice((this->Slice)*this->GetImage()->GetSpacing()[this->SliceOrientation]+
1920                         this->GetImage()->GetOrigin()[this->SliceOrientation]);
1921     }
1922 }
1923 //----------------------------------------------------------------------------
1924
1925
1926 //----------------------------------------------------------------------------
1927 void vvSlicer::ForceUpdateDisplayExtent()
1928 {
1929   this->UpdateDisplayExtent();
1930 }
1931 //----------------------------------------------------------------------------
1932
1933
1934 //----------------------------------------------------------------------------
1935 int* vvSlicer::GetDisplayExtent()
1936 {
1937   return this->GetImageActor()->GetDisplayExtent();
1938 }
1939 //----------------------------------------------------------------------------
1940
1941
1942 //----------------------------------------------------------------------------
1943 void vvSlicer::PrintSelf(ostream& os, vtkIndent indent)
1944 {
1945   this->Superclass::PrintSelf(os, indent);
1946 }
1947 //----------------------------------------------------------------------------
1948
1949
1950 //----------------------------------------------------------------------------
1951 void vvSlicer::SetVFColor(double r, double g, double b)
1952 {
1953   double mVFColorHSV[3];
1954   mVFColor[0] = r;
1955   mVFColor[1] = g;
1956   mVFColor[2] = b;
1957
1958   vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
1959   mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
1960   mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
1961   mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
1962
1963   this->Render();
1964 }
1965 //----------------------------------------------------------------------------
1966
1967
1968 //----------------------------------------------------------------------------
1969 void vvSlicer::SetRegisterExtent(int ext[6])
1970 {
1971     copyExtent(ext, mRegisterExtent);
1972 }
1973 //----------------------------------------------------------------------------
1974
1975
1976 //----------------------------------------------------------------------------
1977 void vvSlicer::GetRegisterExtent(int ext[6])
1978 {
1979     copyExtent(mRegisterExtent, ext);
1980 }
1981 //----------------------------------------------------------------------------
1982