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 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
  79 #  include <vtkOpenGLImageSliceMapper.h>
  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     mImageReslice->UpdateInformation();
 421 #else
 422     mOverlayReslice->SetInputData(0, mOverlay->GetFirstVTKImageData());
 423 #endif
 424     mOverlayReslice->Update();
 425
 426     if (!mOverlayMapper)
 427       mOverlayMapper = vtkSmartPointer<vtkImageMapToWindowLevelColors>::New();
 428 #if VTK_MAJOR_VERSION <= 5
 429     mOverlayMapper->SetInput(mOverlayReslice->GetOutput());
 430 #else
 431     mOverlayMapper->SetInputConnection(mOverlayReslice->GetOutputPort(0));
 432 #endif
 433
 434     if (!mOverlayActor) {
 435       mOverlayActor = vtkSmartPointer<vvBlendImageActor>::New();
 436 #if VTK_MAJOR_VERSION <= 5
 437       mOverlayActor->SetInput(mOverlayMapper->GetOutput());
 438 #else
 439       mOverlayActor->GetMapper()->SetInputConnection(mOverlayMapper->GetOutputPort());
 440 #endif
 441       mOverlayActor->SetPickable(0);
 442       mOverlayActor->SetVisibility(true);
 443       mOverlayActor->SetOpacity(0.5);
 444 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 445       mOverlayActor->GetMapper()->BorderOn();
 446 #endif
 447       }
 448
 449     //stupid but necessary : the Overlay need to be rendered before fusion
 450     if (mFusionActor) {
 451       this->GetRenderer()->RemoveActor(mFusionActor);
 452       this->GetRenderer()->AddActor(mOverlayActor);
 453       this->GetRenderer()->AddActor(mFusionActor);
 454     } else
 455       this->GetRenderer()->AddActor(mOverlayActor);
 456
 457     //Synchronize orientation and slice
 458     AdjustResliceToSliceOrientation(mOverlayReslice);
 459     this->UpdateDisplayExtent();
 460     this->SetTSlice(mCurrentTSlice);
 461   }
 462 }
 463 //------------------------------------------------------------------------------
 464
 465
 466 //------------------------------------------------------------------------------
 467 void vvSlicer::SetFusion(vvImage::Pointer fusion, int fusionSequenceCode)
 468 {
 469         mFusionSequenceCode = fusionSequenceCode;
 470   if (fusion->GetVTKImages().size()) {
 471     mFusion = fusion;
 472     mFusionVisibility = true;
 473
 474     if (!mFusionReslice) {
 475       mFusionReslice = vtkSmartPointer<vtkImageReslice>::New();
 476       mFusionReslice->SetInterpolationModeToLinear();
 477       mFusionReslice->AutoCropOutputOn();
 478       mFusionReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 479     }
 480
 481     mConcatenatedFusionTransform->Identity();
 482     mConcatenatedFusionTransform->Concatenate(mFusion->GetTransform()[0]);
 483     mConcatenatedFusionTransform->Concatenate(mSlicingTransform);
 484     mFusionReslice->SetResliceTransform(mConcatenatedFusionTransform);
 485 #if VTK_MAJOR_VERSION <= 5
 486     mFusionReslice->SetInput(0, mFusion->GetFirstVTKImageData());
 487     mFusionReslice->UpdateInformation();
 488 #else
 489     mFusionReslice->SetInputData(0, mFusion->GetFirstVTKImageData());
 490 #endif
 491     mFusionReslice->Update();
 492
 493     if (!mFusionMapper)
 494       mFusionMapper = vtkSmartPointer<vtkImageMapToColors>::New();
 495
 496     vtkSmartPointer<vtkLookupTable> lut = vtkLookupTable::New();
 497     lut->SetRange(0, 1);
 498     lut->SetValueRange(0, 1);
 499     lut->SetSaturationRange(0, 0);
 500     lut->Build();
 501     mFusionMapper->SetLookupTable(lut);
 502 #if VTK_MAJOR_VERSION <= 5
 503     mFusionMapper->SetInput(mFusionReslice->GetOutput());
 504 #else
 505     mFusionMapper->SetInputConnection(mFusionReslice->GetOutputPort(0));
 506 #endif
 507
 508     if (!mFusionActor) {
 509       mFusionActor = vtkSmartPointer<vtkImageActor>::New();
 510 #if VTK_MAJOR_VERSION <= 5
 511       mFusionActor->SetInput(mFusionMapper->GetOutput());
 512 #else
 513       mFusionActor->GetMapper()->SetInputConnection(mFusionMapper->GetOutputPort());
 514 #endif
 515       mFusionActor->SetPickable(0);
 516       mFusionActor->SetVisibility(true);
 517       mFusionActor->SetOpacity(0.7);
 518 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 519       mFusionActor->GetMapper()->BorderOn();
 520 #endif
 521
 522       this->GetRenderer()->AddActor(mFusionActor);
 523     }
 524
 525     //Synchronize orientation and slice
 526     AdjustResliceToSliceOrientation(mFusionReslice);
 527     this->UpdateDisplayExtent();
 528     this->SetTSlice(mCurrentTSlice);
 529   }
 530 }
 531 //------------------------------------------------------------------------------
 532
 533
 534 //------------------------------------------------------------------------------
 535 bool vvSlicer::GetActorVisibility(const std::string& actor_type, int overlay_index)
 536 {
 537   bool vis = false;
 538   if (actor_type == "image")
 539     vis = mImageVisibility;
 540   else if (actor_type == "vector")
 541     vis = mVFVisibility;
 542   else if (actor_type == "overlay")
 543     vis = mOverlayVisibility;
 544   else if ( (actor_type == "fusion") || (actor_type == "fusionSequence") )
 545     vis = mFusionVisibility;
 546   else if (actor_type == "contour")
 547     vis = this->mSurfaceCutActors[overlay_index]->GetActor()->GetVisibility();
 548   return vis;
 549 }
 550 //------------------------------------------------------------------------------
 551
 552 //------------------------------------------------------------------------------
 553 void vvSlicer::SetActorVisibility(const std::string& actor_type, int overlay_index ,bool vis)
 554 {
 555   if (actor_type == "image")
 556     mImageVisibility = vis;
 557   else if (actor_type == "vector")
 558     mVFVisibility = vis;
 559   else if (actor_type == "overlay")
 560     mOverlayVisibility = vis;
 561   else if ( (actor_type == "fusion") || (actor_type == "fusionSequence") )
 562     mFusionVisibility = vis;
 563   else if (actor_type == "contour")
 564     this->mSurfaceCutActors[overlay_index]->GetActor()->SetVisibility(vis);
 565   UpdateDisplayExtent();
 566 }
 567 //------------------------------------------------------------------------------
 568
 569 //------------------------------------------------------------------------------
 570 void vvSlicer::SetVF(vvImage::Pointer vf)
 571 {
 572   if (vf->GetVTKImages().size()) {
 573     mVF = vf;
 574     mVFVisibility = true;
 575
 576     if (!mAAFilter) {
 577       mAAFilter= vtkSmartPointer<vtkAssignAttribute>::New();
 578       mVOIFilter = vtkSmartPointer<vtkExtractVOI>::New();
 579       mVOIFilter->SetSampleRate(mSubSampling,mSubSampling,mSubSampling);
 580     }
 581 #if VTK_MAJOR_VERSION <= 5
 582     mVOIFilter->SetInput(vf->GetFirstVTKImageData());
 583     mAAFilter->SetInput(mVOIFilter->GetOutput());
 584 #else
 585     mVOIFilter->SetInputData(vf->GetFirstVTKImageData());
 586     mAAFilter->SetInputConnection(mVOIFilter->GetOutputPort());
 587 #endif
 588     ///This tells VTK to use the scalar (pixel) data of the image to draw the little arrows
 589     mAAFilter->Assign(vtkDataSetAttributes::SCALARS, vtkDataSetAttributes::VECTORS, vtkAssignAttribute::POINT_DATA);
 590
 591     if (!mArrow)
 592       mArrow = vtkSmartPointer<vvGlyphSource>::New();
 593     mArrow->SetGlyphTypeToSpecificArrow();
 594     mArrow->SetScale(mScale);
 595     mArrow->FilledOff();
 596
 597     // Glyph the gradient vector (with arrows)
 598     if (!mGlyphFilter)
 599       mGlyphFilter = vtkSmartPointer<vvGlyph2D>::New();
 600 #if VTK_MAJOR_VERSION <= 5
 601     mGlyphFilter->SetInput(mAAFilter->GetOutput());
 602     mGlyphFilter->SetSource(mArrow->GetOutput());
 603 #else
 604     mGlyphFilter->SetInputConnection(mAAFilter->GetOutputPort());
 605     mGlyphFilter->SetSourceConnection(mArrow->GetOutputPort());
 606 #endif
 607     mGlyphFilter->ScalingOn();
 608     mGlyphFilter->SetScaleModeToScaleByVector();
 609     mGlyphFilter->OrientOn();
 610     mGlyphFilter->SetVectorModeToUseVector();
 611     mGlyphFilter->SetColorModeToColorByVector();
 612
 613     if (!mVFColorLUT)
 614       mVFColorLUT = vtkSmartPointer<vtkLookupTable>::New();
 615
 616     double mVFColorHSV[3];
 617     vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
 618     mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
 619     mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
 620     mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
 621
 622     if (!mVFMapper)
 623       mVFMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
 624 #if VTK_MAJOR_VERSION <= 5
 625     mVFMapper->SetInput(mGlyphFilter->GetOutput());
 626 #else
 627     mVFMapper->SetInputConnection(mGlyphFilter->GetOutputPort());
 628 #endif
 629     mVFMapper->ImmediateModeRenderingOn();
 630     mVFMapper->SetLookupTable(mVFColorLUT);
 631
 632     if (!mVFActor)
 633       mVFActor = vtkSmartPointer<vtkActor>::New();
 634     mVFActor->SetMapper(mVFMapper);
 635     mVFActor->SetPickable(0);
 636     mVFActor->GetProperty()->SetLineWidth(mVFWidth);
 637     this->UpdateDisplayExtent();
 638     this->GetRenderer()->AddActor(mVFActor);
 639
 640     //Synchronize slice
 641     SetTSlice(mCurrentTSlice);
 642   }
 643 }
 644 //------------------------------------------------------------------------------
 645
 646
 647 //------------------------------------------------------------------------------
 648 void vvSlicer::SetLandmarks(vvLandmarks* landmarks)
 649 {
 650   mLandmarks = landmarks;
 651   if (landmarks) {
 652
 653     if (!mCross)
 654       mCross = vtkSmartPointer<vtkCursor3D>::New();
 655         if (!mClipBox)
 656       mClipBox = vtkSmartPointer<vtkBox>::New();
 657     if (!mLandClipper)
 658       mLandClipper = vtkSmartPointer<vvClipPolyData>::New();
 659     if (!mLandGlyph)
 660       mLandGlyph = vtkSmartPointer<vtkGlyph3D>::New();
 661     if (!mLandMapper)
 662       mLandMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
 663     if (!mLandActor)
 664       mLandActor = vtkSmartPointer<vtkActor>::New();
 665
 666     mCross->SetFocalPoint(0.0,0.0,0.0);
 667     mCross->SetModelBounds(-10,10,-10,10,-10,10);
 668     mCross->AllOff();
 669     mCross->AxesOn();
 670
 671     mLandClipper->SetClipFunction(mClipBox);
 672     mLandClipper->InsideOutOn();
 673 #if VTK_MAJOR_VERSION <= 5
 674     mLandmarkTransform = vtkSmartPointer<vtkTransformPolyDataFilter>::New();
 675     mLandmarkTransform->SetInput(mLandmarks->GetOutput());
 676     mConcatenatedTransform->Identity();
 677     mConcatenatedTransform->Concatenate(mImage->GetTransform()[0]);
 678     mConcatenatedTransform->Concatenate(mSlicingTransform);
 679     mLandmarkTransform->SetTransform(mConcatenatedTransform->GetInverse());
 680     mLandClipper->SetInput(mLandmarkTransform->GetOutput());
 681
 682     mLandGlyph->SetSource(mCross->GetOutput());
 683     mLandGlyph->SetInput(mLandClipper->GetOutput());
 684 #else
 685     mLandmarkTransform = vtkSmartPointer<vtkTransformPolyDataFilter>::New();
 686     mLandmarkTransform->SetInputData(mLandmarks->GetOutput());
 687     mConcatenatedTransform->Identity();
 688     mConcatenatedTransform->Concatenate(mImage->GetTransform()[0]);
 689     mConcatenatedTransform->Concatenate(mSlicingTransform);
 690     mLandmarkTransform->SetTransform(mConcatenatedTransform->GetInverse());
 691     mLandClipper->SetInputConnection(mLandmarkTransform->GetOutputPort());
 692
 693     mLandGlyph->SetSourceConnection(mCross->GetOutputPort());
 694     mLandGlyph->SetInputConnection(mLandClipper->GetOutputPort());
 695 #endif
 696     //mLandGlyph->SetIndexModeToScalar();
 697     //mLandGlyph->SetRange(0,1);
 698     //mLandGlyph->ScalingOff();
 699
 700     //mLandGlyph->SetColorModeToColorByScalar();
 701
 702     mLandGlyph->SetScaleModeToDataScalingOff();
 703     mLandGlyph->SetIndexModeToOff();
 704
 705     mLandMapper->SetInputConnection(mLandGlyph->GetOutputPort());
 706     //mLandMapper->ScalarVisibilityOff();
 707
 708     mLandActor->SetMapper(mLandMapper);
 709     mLandActor->GetProperty()->SetOpacity(0.995);  //in order to get VTK to turn on the alpha-blending in OpenGL
 710     mLandActor->GetProperty()->SetColor(255,10,212);
 711     mLandActor->SetPickable(0);
 712     mLandActor->SetVisibility(true);
 713     this->UpdateDisplayExtent();
 714   }
 715 }
 716 //------------------------------------------------------------------------------
 717
 718 //------------------------------------------------------------------------------
 719 //FIXME: this function leaks memory, we should fix it someday :)
 720 void vvSlicer::RemoveActor(const std::string& actor_type, int overlay_index)
 721 {
 722   if (actor_type == "vector") {
 723     Renderer->RemoveActor(mVFActor);
 724     mGlyphFilter=NULL;
 725     mVF = NULL;
 726     mArrow = NULL;
 727     mAAFilter=NULL;
 728     mVOIFilter = NULL;
 729     mVFMapper = NULL;
 730     mVFActor = NULL;
 731   }
 732   if (actor_type == "overlay") {
 733     Renderer->RemoveActor(mOverlayActor);
 734     mOverlay = NULL;
 735     mOverlayActor = NULL;
 736     mOverlayMapper = NULL;
 737   }
 738   if ( (actor_type == "fusion") || (actor_type == "fusionSequence") ) {
 739     Renderer->RemoveActor(mFusionActor);
 740     mFusion = NULL;
 741     mFusionActor = NULL;
 742     mFusionMapper = NULL;
 743   }
 744   if (actor_type == "contour") {
 745     Renderer->RemoveActor(this->mSurfaceCutActors[overlay_index]->GetActor());
 746     mSurfaceCutActors.erase(mSurfaceCutActors.begin()+overlay_index);
 747   }
 748 }
 749 //------------------------------------------------------------------------------
 750
 751
 752 //------------------------------------------------------------------------------
 753 void vvSlicer::SetVFSubSampling(int sub)
 754 {
 755   if (mVOIFilter) {
 756     mVOIFilter->SetSampleRate(mSubSampling,mSubSampling,mSubSampling);
 757     mSubSampling = sub;
 758   }
 759   UpdateDisplayExtent();
 760   Render();
 761 }
 762 //------------------------------------------------------------------------------
 763
 764
 765 //------------------------------------------------------------------------------
 766 void vvSlicer::SetVFScale(int scale)
 767 {
 768   mScale = scale;
 769   if (mArrow)
 770     mArrow->SetScale(mScale);
 771   UpdateDisplayExtent();
 772   Render();
 773 }
 774 //------------------------------------------------------------------------------
 775
 776 //------------------------------------------------------------------------------
 777 void vvSlicer::SetVFWidth(int width)
 778 {
 779   mVFWidth = width;
 780   if (mVFActor)
 781     mVFActor->GetProperty()->SetLineWidth(mVFWidth);
 782   UpdateDisplayExtent();
 783   Render();
 784 }
 785 //------------------------------------------------------------------------------
 786
 787
 788 //------------------------------------------------------------------------------
 789 void vvSlicer::SetVFLog(int log)
 790 {
 791   mVFLog = log;
 792   if (mGlyphFilter) {
 793     mGlyphFilter->SetUseLog(mVFLog);
 794     mGlyphFilter->Modified();
 795   }
 796   UpdateDisplayExtent();
 797   Render();
 798 }
 799 //------------------------------------------------------------------------------
 800
 801
 802 //------------------------------------------------------------------------------
 803 void vvSlicer::SetTSlice(int t, bool updateLinkedImages)
 804 {
 805         if (!updateLinkedImages) {
 806                 mCurrentTSlice = t;
 807 #if VTK_MAJOR_VERSION <= 5
 808                 mImageReslice->SetInput( mImage->GetVTKImages()[mCurrentTSlice] );
 809 #else
 810                 mImageReslice->SetInputData( mImage->GetVTKImages()[mCurrentTSlice] );
 811 #endif
 812                 // Update transform
 813                 mConcatenatedTransform->Identity();
 814                 mConcatenatedTransform->Concatenate(mImage->GetTransform()[mCurrentTSlice]);
 815                 mConcatenatedTransform->Concatenate(mSlicingTransform);
 816                 UpdateDisplayExtent();
 817                 return;
 818         }
 819   if (t < 0)
 820     mCurrentTSlice = 0;
 821   else if ((unsigned int)t >= mImage->GetVTKImages().size())
 822     mCurrentTSlice = mImage->GetVTKImages().size() -1;
 823   else
 824     mCurrentTSlice = t;
 825
 826   // Update transform
 827   mConcatenatedTransform->Identity();
 828   mConcatenatedTransform->Concatenate(mImage->GetTransform()[mCurrentTSlice]);
 829   mConcatenatedTransform->Concatenate(mSlicingTransform);
 830
 831   // Update image data
 832 #if VTK_MAJOR_VERSION <= 5
 833    mImageReslice->SetInput( mImage->GetVTKImages()[mCurrentTSlice] );
 834 #else
 835   mImageReslice->SetInputData( mImage->GetVTKImages()[mCurrentTSlice] );
 836 #endif
 837   if (mVF && mVFActor->GetVisibility()) {
 838     if (mVF->GetVTKImages().size() > (unsigned int)mCurrentTSlice)
 839 #if VTK_MAJOR_VERSION <= 5
 840       mVOIFilter->SetInput(mVF->GetVTKImages()[mCurrentTSlice]);
 841 #else
 842       mVOIFilter->SetInputData(mVF->GetVTKImages()[mCurrentTSlice]);
 843 #endif
 844   }
 845   //update the overlay
 846   if (mOverlay && mOverlayActor->GetVisibility()) {
 847     if (mOverlay->GetVTKImages().size() > (unsigned int)t) {
 848       mCurrentOverlayTSlice = t;
 849 #if VTK_MAJOR_VERSION <= 5
 850       mOverlayReslice->SetInput( mOverlay->GetVTKImages()[mCurrentOverlayTSlice] );
 851 #else
 852       mOverlayReslice->SetInputData( mOverlay->GetVTKImages()[mCurrentOverlayTSlice] );
 853 #endif
 854       // Update overlay transform
 855       mConcatenatedOverlayTransform->Identity();
 856       mConcatenatedOverlayTransform->Concatenate(mOverlay->GetTransform()[mCurrentOverlayTSlice]);
 857       mConcatenatedOverlayTransform->Concatenate(mSlicingTransform);
 858     }
 859   }
 860   //update the fusion ; except in case this is a fusionSequence, in which case both 'times' should be independent.
 861   if (mFusion && mFusionActor->GetVisibility() && (mFusionSequenceCode<0)) {
 862     if (mFusion->GetVTKImages().size() > (unsigned int)t) {
 863       mCurrentFusionTSlice = t;
 864 #if VTK_MAJOR_VERSION <= 5
 865       mFusionReslice->SetInput( mFusion->GetVTKImages()[mCurrentFusionTSlice]);
 866 #else
 867       mFusionReslice->SetInputData( mFusion->GetVTKImages()[mCurrentFusionTSlice]);
 868 #endif
 869
 870       // Update fusion transform
 871       mConcatenatedFusionTransform->Identity();
 872       mConcatenatedFusionTransform->Concatenate(mFusion->GetTransform()[mCurrentFusionTSlice]);
 873       mConcatenatedFusionTransform->Concatenate(mSlicingTransform);
 874     }
 875   }
 876   if (mSurfaceCutActors.size() > 0)
 877     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 878          i!=mSurfaceCutActors.end(); i++)
 879       (*i)->SetTimeSlice(mCurrentTSlice);
 880   UpdateDisplayExtent();
 881 }
 882 //------------------------------------------------------------------------------
 883
 884
 885 //------------------------------------------------------------------------------
 886 void vvSlicer::SetFusionSequenceTSlice(int t)
 887 {
 888   if (mFusion && mFusionActor->GetVisibility() && (mFusionSequenceCode>=0)) {
 889     if (mFusion->GetVTKImages().size() > (unsigned int)t) {
 890       mCurrentFusionTSlice = t;
 891 #if VTK_MAJOR_VERSION <= 5
 892       mFusionReslice->SetInput( mFusion->GetVTKImages()[mCurrentFusionTSlice] );
 893 #else
 894       mFusionReslice->SetInputData( mFusion->GetVTKImages()[mCurrentFusionTSlice] );
 895 #endif
 896       // Update fusion transform
 897       mConcatenatedFusionTransform->Identity();
 898       mConcatenatedFusionTransform->Concatenate(mFusion->GetTransform()[mCurrentFusionTSlice]); //not really useful...
 899       mConcatenatedFusionTransform->Concatenate(mSlicingTransform);
 900     }
 901   }
 902
 903   UpdateDisplayExtent();
 904 }
 905 //------------------------------------------------------------------------------
 906
 907
 908 //------------------------------------------------------------------------------
 909 int vvSlicer::GetTSlice()
 910 {
 911   return mCurrentTSlice;
 912 }
 913 //------------------------------------------------------------------------------
 914
 915 //------------------------------------------------------------------------------
 916 int vvSlicer::GetMaxCurrentTSlice()
 917 {
 918   int t = mCurrentTSlice;
 919   if(mOverlay)
 920     t = std::max(t, mCurrentOverlayTSlice);
 921   if(mFusion&& (mFusionSequenceCode<0)) //ignore fusionSequence data: for these, the times are not to be related (this way)
 922     t = std::max(t, mCurrentFusionTSlice);
 923   return t;
 924 }
 925 //------------------------------------------------------------------------------
 926
 927 //------------------------------------------------------------------------------
 928 int vvSlicer::GetFusionTSlice()
 929 {
 930   return mCurrentFusionTSlice;
 931 }
 932 //------------------------------------------------------------------------------
 933
 934 //------------------------------------------------------------------------------
 935 int vvSlicer::GetOverlayTSlice()
 936 {
 937   return mCurrentOverlayTSlice;
 938 }
 939 //------------------------------------------------------------------------------
 940
 941 //------------------------------------------------------------------------------
 942 void vvSlicer::SetSliceOrientation(int orientation)
 943 {
 944   //if 2D image, force to watch in Axial View
 945   int extent[6];
 946 #if VTK_MAJOR_VERSION <= 5
 947     this->GetInput()->GetWholeExtent(extent);
 948 #else
 949     int* ext = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
 950     copyExtent(ext, extent);
 951 #endif
 952
 953   if (extent[5]-extent[4] <= 2)
 954     orientation = vtkImageViewer2::SLICE_ORIENTATION_XY;
 955
 956   if (orientation < vtkImageViewer2::SLICE_ORIENTATION_YZ ||
 957       orientation > vtkImageViewer2::SLICE_ORIENTATION_XY) {
 958     vtkErrorMacro("Error - invalid slice orientation " << orientation);
 959     return;
 960   }
 961
 962   this->SliceOrientation = orientation;
 963
 964   if(mFusion)
 965     AdjustResliceToSliceOrientation(mFusionReslice);
 966
 967   if(mOverlay)
 968     AdjustResliceToSliceOrientation(mOverlayReslice);
 969
 970   // Update the viewer
 971
 972   // Go to current cursor position
 973   // double* cursorPos = GetCursorPosition();
 974   // DDV(cursorPos, 3);
 975   // SetCurrentPosition(cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
 976
 977   if (mFirstSetSliceOrientation) {
 978     int *range = this->GetSliceRange();
 979     if (range)
 980       this->Slice = static_cast<int>((range[0] + range[1]) * 0.5);
 981 #if VTK_MAJOR_VERSION <= 5
 982       mFirstSetSliceOrientation = false;
 983 #endif
 984   }
 985   else if (this->Renderer && this->GetInput()) {
 986     double s = mCursor[orientation];
 987     double sCursor = (s - this->GetInput()->GetOrigin()[orientation])/this->GetInput()->GetSpacing()[orientation];
 988     this->Slice = static_cast<int>(sCursor);
 989   }
 990
 991   this->UpdateOrientation();
 992
 993   this->UpdateDisplayExtent();
 994
 995   if (mFirstSetSliceOrientation) {
 996     mFirstSetSliceOrientation = false;
 997   }
 998
 999   if (this->Renderer && this->GetInput()) {
1000     double scale = this->Renderer->GetActiveCamera()->GetParallelScale();
1001     this->Renderer->ResetCamera();
1002     this->Renderer->GetActiveCamera()->SetParallelScale(scale);
1003   }
1004
1005   SetContourSlice();
1006 }
1007 //----------------------------------------------------------------------------
1008
1009 //------------------------------------------------------------------------------
1010 // This function ensures that we sample the slices of a vtkImageReslice filter
1011 // in the direction of the slicer (SliceOrientation) similarly as mImageReslice.
1012 // In other words, we change the grid of the reslice in the same way as the grid
1013 // of the displayed image in the slicing direction.
1014 void vvSlicer::AdjustResliceToSliceOrientation(vtkImageReslice *reslice)
1015 {
1016   // Reset autocrop and update output information
1017   reslice->SetOutputOriginToDefault();
1018   reslice->SetOutputSpacingToDefault();
1019 #if VTK_MAJOR_VERSION <= 5
1020   reslice->GetOutput()->UpdateInformation();
1021 #else
1022   reslice->UpdateInformation();
1023 #endif
1024
1025   // Ge new origin / spacing
1026   double origin[3];
1027   double spacing[3];
1028   reslice->GetOutput()->GetOrigin(origin);
1029   reslice->GetOutput()->GetSpacing(spacing);
1030
1031   // Use similar spacing as the image in the direction SliceOrientation
1032   spacing[this->SliceOrientation] = mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
1033
1034   // Modify origin to be on the image grid in the direction SliceOrientation in 3 steps
1035   // Step 1: from world coordinates to image coordinates
1036   origin[this->SliceOrientation] -= mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
1037   origin[this->SliceOrientation] /= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
1038
1039   // Step 2: round to nearest grid positionInc. This has been validated as the only
1040   // way to have something consistent with the thickness of a 2D slice visible on the
1041   // other slices. The thickness is accounted for so if the 2D slice is to thin and
1042   // between two slices, one will never be able to see this 2D slice (bug #1883).
1043   origin[this->SliceOrientation] = itk::Math::Round<double>(origin[this->SliceOrientation]);
1044
1045   // Step 3: back to world coordinates
1046   origin[this->SliceOrientation] *= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
1047   origin[this->SliceOrientation] += mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
1048
1049   // Set new spacing and origin
1050   reslice->SetOutputOrigin(origin);
1051   reslice->SetOutputSpacing(spacing);
1052   reslice->UpdateInformation();
1053 #if VTK_MAJOR_VERSION <= 5
1054   reslice->GetOutput()->UpdateInformation();
1055 #endif
1056 }
1057 //------------------------------------------------------------------------------
1058
1059 //----------------------------------------------------------------------------
1060 int * vvSlicer::GetExtent()
1061 {
1062   int *w_ext;
1063   if (mUseReducedExtent) {
1064     w_ext = mReducedExtent;
1065   }
1066   else {
1067 #if VTK_MAJOR_VERSION <= 5
1068     w_ext = GetInput()->GetWholeExtent();
1069 #else
1070     w_ext = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
1071 #endif
1072   }
1073   return w_ext;
1074 }
1075 //----------------------------------------------------------------------------
1076
1077
1078 //----------------------------------------------------------------------------
1079 int vvSlicer::GetOrientation()
1080 {
1081   return this->SliceOrientation;
1082 }
1083 //----------------------------------------------------------------------------
1084
1085
1086 //----------------------------------------------------------------------------
1087 void vvSlicer::UpdateDisplayExtent()
1088 {
1089   emit UpdateDisplayExtentBegin(mSlicerNumber);
1090   vtkImageData *input = this->GetInput();
1091   if (!input || !this->ImageActor) {
1092     return;
1093   }
1094
1095 #if VTK_MAJOR_VERSION <= 5
1096   input->UpdateInformation();
1097 #else
1098   mRegisterExtent = mImageReslice->GetOutputInformation(0)->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
1099 #endif
1100   this->SetSlice( this->GetSlice() ); //SR: make sure the update let the slice in extents
1101
1102   // Local copy of extent
1103   int w_ext[6];
1104 #if VTK_MAJOR_VERSION <= 5
1105   int* ext = GetExtent();
1106 #else
1107   int* ext = mImageReslice->GetOutputInformation(0)->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
1108 #endif
1109   copyExtent(ext, w_ext);
1110   if (mUseReducedExtent) {
1111         copyExtent(mReducedExtent, w_ext);
1112     }
1113   // Set slice value
1114
1115   w_ext[ this->SliceOrientation*2   ] = this->Slice;
1116   w_ext[ this->SliceOrientation*2+1 ] = this->Slice;
1117
1118   // Image actor
1119   this->ImageActor->SetVisibility(mImageVisibility);
1120   this->ImageActor->SetDisplayExtent(w_ext);
1121
1122 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
1123   // Fix for bug #1882
1124   dynamic_cast<vtkImageSliceMapper *>(this->ImageActor->GetMapper())->SetOrientation(this->GetOrientation());
1125 #endif
1126
1127   // Overlay image actor
1128   if (mOverlay && mOverlayVisibility) {
1129     AdjustResliceToSliceOrientation(mOverlayReslice);
1130     int overExtent[6];
1131 #if VTK_MAJOR_VERSION <= 5
1132     this->ConvertImageToImageDisplayExtent(input, w_ext, mOverlayReslice->GetOutput(), overExtent);
1133     bool out = ClipDisplayedExtent(overExtent, mOverlayMapper->GetInput()->GetWholeExtent());
1134 #else
1135     this->ConvertImageToImageDisplayExtent(mImageReslice->GetOutputInformation(0), w_ext, mOverlayReslice->GetOutput(), overExtent);
1136     bool out = ClipDisplayedExtent(overExtent, mOverlayMapper->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT()));
1137 #endif
1138     mOverlayActor->SetVisibility(!out);
1139     mOverlayActor->SetDisplayExtent( overExtent );
1140 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
1141     // Fix for bug #1882
1142     dynamic_cast<vtkImageSliceMapper *>(mOverlayActor->GetMapper())->SetOrientation(this->GetOrientation());
1143 #endif
1144   }
1145   else if(mOverlay)
1146     mOverlayActor->SetVisibility(false);
1147
1148   // Fusion image actor
1149   if (mFusion && mFusionVisibility) {
1150     AdjustResliceToSliceOrientation(mFusionReslice);
1151     int fusExtent[6];
1152 #if VTK_MAJOR_VERSION <= 5
1153     this->ConvertImageToImageDisplayExtent(input, w_ext, mFusionReslice->GetOutput(), fusExtent);
1154     bool out = ClipDisplayedExtent(fusExtent, mFusionMapper->GetInput()->GetWholeExtent());
1155 #else
1156     this->ConvertImageToImageDisplayExtent(mImageReslice->GetOutputInformation(0), w_ext, mFusionReslice->GetOutput(), fusExtent);
1157     bool out = ClipDisplayedExtent(fusExtent, mFusionMapper->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT()));
1158 #endif
1159     mFusionActor->SetVisibility(!out);
1160     mFusionActor->SetDisplayExtent( fusExtent );
1161 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
1162     // Fix for bug #1882
1163     dynamic_cast<vtkImageSliceMapper *>(mFusionActor->GetMapper())->SetOrientation(this->GetOrientation());
1164 #endif
1165   }
1166   else if(mFusion)
1167     mFusionActor->SetVisibility(false);
1168   // Vector field actor
1169   double* camera = Renderer->GetActiveCamera()->GetPosition();
1170   double* image_bounds = ImageActor->GetBounds();
1171   double position[3] = {0, 0, 0};
1172   position[this->SliceOrientation] = image_bounds[this->SliceOrientation*2];
1173
1174   //print_vector<double, 6>("camera", camera);
1175   //print_vector<double, 6>("image_bounds", image_bounds);
1176   //print_vector<double, 3>("position", position);
1177
1178   // find where to place the VF actor. to deal with
1179   // z-buffer issues, the VF is placed right in front of the image,
1180   // subject to a small offset. the position actually depends on the
1181   // the location of the camera relative to the image.
1182   double offset = 1;
1183   if (camera[this->SliceOrientation] < image_bounds[this->SliceOrientation*2])
1184     offset = -1;
1185
1186   if (mVF && mVFVisibility) {
1187     int vfExtent[6];
1188 #if VTK_MAJOR_VERSION <= 5
1189     mVF->GetVTKImages()[0]->UpdateInformation();
1190     this->ConvertImageToImageDisplayExtent(input, w_ext, mVF->GetVTKImages()[0], vfExtent);
1191     bool out = ClipDisplayedExtent(vfExtent, mVOIFilter->GetInput()->GetWholeExtent());
1192 #else
1193     mVOIFilter->Update();
1194     this->ConvertImageToImageDisplayExtent(mImageReslice->GetOutputInformation(0), w_ext, mVF->GetVTKImages()[0], vfExtent);
1195     bool out = ClipDisplayedExtent(vfExtent, mVOIFilter->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT()));
1196 #endif
1197     mVFActor->SetVisibility(!out);
1198     mVOIFilter->SetVOI(vfExtent);
1199     int orientation[3] = {1,1,1};
1200     orientation[this->SliceOrientation] = 0;
1201     mGlyphFilter->SetOrientation(orientation[0], orientation[1], orientation[2]);
1202     position[this->SliceOrientation] += offset;
1203     mVFActor->SetPosition(position);
1204     mVFActor->GetProperty()->SetOpacity(0.995); //in order to get VTK to turn on the alpha-blending in OpenGL
1205     mVFMapper->Update();
1206
1207   }
1208   else if(mVF)
1209     mVFActor->SetVisibility(false);
1210
1211
1212     double boundsT [6];
1213       for(unsigned int i=0; i<6; i++)
1214         boundsT[i] = ImageActor->GetBounds()[i];
1215       boundsT[ this->SliceOrientation*2   ] = ImageActor->GetBounds()[ this->SliceOrientation*2  ]-fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
1216       boundsT[ this->SliceOrientation*2+1 ] = ImageActor->GetBounds()[ this->SliceOrientation*2+1 ]+fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
1217
1218
1219   // Landmarks actor
1220   if (mLandActor) {
1221     if (mClipBox) {
1222       RemoveLandmarks();
1223     }
1224
1225     position[this->SliceOrientation] = offset;
1226     mLandActor->SetPosition(position);
1227   }
1228
1229   // Figure out the correct clipping range
1230   if (this->Renderer) {
1231     if (this->InteractorStyle &&
1232         this->InteractorStyle->GetAutoAdjustCameraClippingRange()) {
1233       this->Renderer->ResetCameraClippingRange();
1234     } else {
1235       vtkCamera *cam = this->Renderer->GetActiveCamera();
1236       if (cam) {
1237         double bounds[6];
1238         this->ImageActor->GetBounds(bounds);
1239         double spos = (double)bounds[this->SliceOrientation * 2];
1240         double cpos = (double)cam->GetPosition()[this->SliceOrientation];
1241         double range = fabs(spos - cpos);
1242         double *spacing = input->GetSpacing();
1243         double sumSpacing = spacing[0] + spacing[1] + spacing[2];
1244         cam->SetClippingRange(range - sumSpacing, range + sumSpacing);
1245       }
1246     }
1247
1248     if (mLandActor) {
1249         if (mClipBox) {
1250             DisplayLandmarks();
1251         }
1252     }
1253   }
1254   emit UpdateDisplayExtentEnd(mSlicerNumber);
1255 }
1256 //----------------------------------------------------------------------------
1257
1258 //----------------------------------------------------------------------------
1259 void vvSlicer::ConvertImageToImageDisplayExtent(vtkInformation *sourceImage, const int sourceExtent[6],
1260                                                 vtkImageData *targetImage, int targetExtent[6])
1261 {
1262   double dExtents[6];
1263   double *origin, *spacing;
1264   origin = sourceImage->Get(vtkDataObject::ORIGIN());
1265   spacing = sourceImage->Get(vtkDataObject::SPACING());
1266   for(unsigned int i=0; i<6; i++) {
1267     // From source voxel coordinates to world coordinates
1268     dExtents[i] = origin[i/2] + spacing[i/2] * sourceExtent[i];
1269
1270     // From world coordinates to floating point target voxel coordinates
1271     dExtents[i] = (dExtents[i]- targetImage->GetOrigin()[i/2]) / targetImage->GetSpacing()[i/2];
1272
1273     // Round to current slice or larger extent
1274     if(i/2==this->GetOrientation())
1275       targetExtent[i] = itk::Math::Round<double>(dExtents[i]);
1276     else if(i%2==1)
1277       targetExtent[i] = itk::Math::Ceil<double>(dExtents[i]);
1278     else
1279       targetExtent[i] = itk::Math::Floor<double>(dExtents[i]);
1280   }
1281 }
1282 //----------------------------------------------------------------------------
1283
1284 //----------------------------------------------------------------------------
1285 void vvSlicer::ConvertImageToImageDisplayExtent(vtkImageData *sourceImage, const int sourceExtent[6],
1286                                                 vtkImageData *targetImage, int targetExtent[6])
1287 {
1288   double dExtents[6];
1289   for(unsigned int i=0; i<6; i++) {
1290     // From source voxel coordinates to world coordinates
1291     dExtents[i] = sourceImage->GetOrigin()[i/2] + sourceImage->GetSpacing()[i/2] * sourceExtent[i];
1292
1293     // From world coordinates to floating point target voxel coordinates
1294     dExtents[i] = (dExtents[i]- targetImage->GetOrigin()[i/2]) / targetImage->GetSpacing()[i/2];
1295
1296     // Round to current slice or larger extent
1297     if(i/2==this->GetOrientation())
1298       targetExtent[i] = itk::Math::Round<double>(dExtents[i]);
1299     else if(i%2==1)
1300       targetExtent[i] = itk::Math::Ceil<double>(dExtents[i]);
1301     else
1302       targetExtent[i] = itk::Math::Floor<double>(dExtents[i]);
1303   }
1304 }
1305 //----------------------------------------------------------------------------
1306
1307 //----------------------------------------------------------------------------
1308 bool vvSlicer::ClipDisplayedExtent(int extent[6], int refExtent[6])
1309 {
1310   bool out = false;
1311   int maxBound = 6;
1312
1313   for (int i = 0; i < maxBound; i = i+2) {
1314     //if we are totally outside the image
1315     if ( extent[i] > refExtent[i+1] || extent[i+1] < refExtent[i] ) {
1316       out = true;
1317       break;
1318     }
1319     //crop to the limit of the image
1320     extent[i] = std::max(extent[i], refExtent[i]);
1321     extent[i] = std::min(extent[i], refExtent[i+1]);;
1322     extent[i+1] = std::max(extent[i+1], refExtent[i]);
1323     extent[i+1] = std::min(extent[i+1], refExtent[i+1]);;
1324   }
1325   if (out)
1326     for (int i = 0; i < maxBound; i = i+2) {
1327       extent[i] = refExtent[i];
1328       extent[i+1] = refExtent[i];
1329     }
1330   return out;
1331 }
1332 //----------------------------------------------------------------------------
1333
1334
1335 //----------------------------------------------------------------------------
1336 void vvSlicer::UpdateOrientation()
1337 {
1338   // Set the camera position
1339   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1340   if (cam) {
1341     switch (this->SliceOrientation) {
1342     case vtkImageViewer2::SLICE_ORIENTATION_XY:
1343       cam->SetFocalPoint(0,0,0);
1344       cam->SetPosition(0,0,-1); // -1 if medical ?
1345       cam->SetViewUp(0,-1,0);
1346       break;
1347
1348     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
1349       cam->SetFocalPoint(0,0,0);
1350       cam->SetPosition(0,-1,0); // 1 if medical ?
1351       cam->SetViewUp(0,0,1);
1352       break;
1353
1354     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1355       cam->SetFocalPoint(0,0,0);
1356       cam->SetPosition(-1,0,0); // -1 if medical ?
1357       cam->SetViewUp(0,0,1);
1358       break;
1359     }
1360   }
1361 }
1362 //----------------------------------------------------------------------------
1363
1364
1365 //----------------------------------------------------------------------------
1366 void vvSlicer::SetOpacity(double s)
1367 {
1368   this->GetImageActor()->SetOpacity(s);
1369 }
1370 //----------------------------------------------------------------------------
1371
1372
1373 //----------------------------------------------------------------------------
1374 void vvSlicer::SetRenderWindow(int orientation, vtkRenderWindow * rw)
1375 {
1376   this->Superclass::SetRenderWindow(rw);
1377   this->SetupInteractor(rw->GetInteractor());
1378   ca->SetImageActor(this->GetImageActor());
1379   ca->SetWindowLevel(this->GetWindowLevel());
1380   ca->SetText(3, "<window>\n<level>");
1381
1382   double bounds[6];
1383   double max = 65000;
1384
1385   bounds[0] = -max;
1386   bounds[1] = max;
1387   bounds[2] = -max;
1388   bounds[3] = max;
1389   bounds[4] = -max;
1390   bounds[5] = max;
1391   crossCursor->SetModelBounds(bounds);
1392
1393   this->GetRenderer()->AddActor(pdmA);
1394   this->GetRenderer()->AddActor(ca);
1395   this->GetRenderer()->ResetCamera();
1396
1397   //this is just a mapping between the labeling of the orientations presented to the user and
1398   //the one used by vtk
1399   SetSliceOrientation(2-(orientation%3));
1400   ResetCamera();
1401 }
1402 //----------------------------------------------------------------------------
1403
1404
1405 //----------------------------------------------------------------------------
1406 void vvSlicer::ResetCamera()
1407 {
1408   this->GetRenderer()->ResetCamera();
1409 }
1410 //----------------------------------------------------------------------------
1411
1412
1413 //----------------------------------------------------------------------------
1414 void vvSlicer::SetDisplayMode(bool i)
1415 {
1416         this->GetRenderer()->SetDraw(i);
1417         if (i) UpdateDisplayExtent();
1418 }
1419 //----------------------------------------------------------------------------
1420
1421
1422 //----------------------------------------------------------------------------
1423 void vvSlicer::FlipHorizontalView()
1424 {
1425   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1426   if (cam) {
1427     double *position = cam->GetPosition();
1428     double factor[3] = {1, 1, 1};
1429     factor[this->SliceOrientation] = -1;
1430     cam->SetPosition(factor[0]*position[0],factor[1]*position[1],factor[2]*position[2]);
1431
1432 /*    switch (this->SliceOrientation) {
1433     case vtkImageViewer2::SLICE_ORIENTATION_XY:
1434       cam->SetPosition(position[0],position[1],-position[2]);
1435       break;
1436
1437     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
1438       cam->SetPosition(position[0],-position[1],position[2]);
1439       break;
1440
1441     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1442       cam->SetPosition(-position[0],position[1],position[2]);
1443       break;
1444     }*/
1445
1446     this->Renderer->ResetCameraClippingRange();
1447     this->UpdateDisplayExtent();
1448   }
1449 }
1450 //----------------------------------------------------------------------------
1451
1452
1453 //----------------------------------------------------------------------------
1454 void vvSlicer::FlipVerticalView()
1455 {
1456   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1457   if (cam) {
1458     FlipHorizontalView();
1459     double *viewup = cam->GetViewUp();
1460     cam->SetViewUp(-viewup[0],-viewup[1],-viewup[2]);
1461     this->UpdateDisplayExtent();
1462   }
1463 }
1464 //----------------------------------------------------------------------------
1465
1466
1467 //----------------------------------------------------------------------------
1468 void vvSlicer::SetColorWindow(double window)
1469 {
1470   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1471   if ( LUT ) {
1472     double level = this->GetWindowLevel()->GetLevel();
1473     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1474     LUT->Build();
1475   }
1476   this->vtkImageViewer2::SetColorWindow(window);
1477 }
1478 //----------------------------------------------------------------------------
1479
1480 //----------------------------------------------------------------------------
1481 void vvSlicer::SetColorLevel(double level)
1482 {
1483   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1484   if ( LUT ) {
1485     double window = this->GetWindowLevel()->GetWindow();
1486     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1487     LUT->Build();
1488   }
1489   this->vtkImageViewer2::SetColorLevel(level);
1490 }
1491 //----------------------------------------------------------------------------
1492
1493 //----------------------------------------------------------------------------
1494 double vvSlicer::GetOverlayColorWindow()
1495 {
1496   if(mOverlayMapper)
1497     return mOverlayMapper->GetWindow();
1498   else
1499     return 0.;
1500 }
1501 //----------------------------------------------------------------------------
1502
1503 //----------------------------------------------------------------------------
1504 double vvSlicer::GetOverlayColorLevel()
1505 {
1506   if(mOverlayMapper)
1507     return mOverlayMapper->GetLevel();
1508   else
1509     return 0.;
1510 }
1511 //----------------------------------------------------------------------------
1512
1513 //----------------------------------------------------------------------------
1514 void vvSlicer::SetOverlayColorWindow(double window)
1515 {
1516   if(mOverlayMapper)
1517     mOverlayMapper->SetWindow(window);
1518 }
1519 //----------------------------------------------------------------------------
1520
1521 //----------------------------------------------------------------------------
1522 void vvSlicer::SetOverlayColorLevel(double level)
1523 {
1524   if(mOverlayMapper)
1525     mOverlayMapper->SetLevel(level);
1526 }
1527 //----------------------------------------------------------------------------
1528
1529 //----------------------------------------------------------------------------
1530 // Returns the min an the max value in a 20%x20% region around the mouse pointer
1531 void vvSlicer::GetExtremasAroundMousePointer(double & min, double & max, vtkImageData *image, vtkTransform *transform)
1532 {
1533   //Get mouse pointer position in view coordinates
1534   double corner1[3];
1535   double corner2[3];
1536   for(int i=0; i<3; i++) {
1537     corner1[i] = mCurrent[i];
1538     corner2[i] = mCurrent[i];
1539   }
1540
1541   this->Renderer->WorldToView(corner1[0], corner1[1], corner1[2]);
1542   this->Renderer->WorldToView(corner2[0], corner2[1], corner2[2]);
1543
1544   // In view coordinates, x is the slicer width and y is the slicer height are the in-plane axis
1545   int w, h;
1546   this->Renderer->GetTiledSize(&w, &h);
1547   corner1[0] -= 0.2*h/(double)w;
1548   corner2[0] += 0.2*h/(double)w;
1549   corner1[1] -= 0.2;
1550   corner2[1] += 0.2;
1551   this->Renderer->ViewToWorld(corner1[0], corner1[1], corner1[2]);
1552   this->Renderer->ViewToWorld(corner2[0], corner2[1], corner2[2]);
1553
1554   //Convert to image pixel coordinates (rounded)
1555   transform->TransformPoint(corner1, corner1);
1556   transform->TransformPoint(corner2, corner2);
1557   int iLocalExtents[6];
1558   for(int i=0; i<3; i++) {
1559     corner1[i] = (corner1[i] - image->GetOrigin()[i])/image->GetSpacing()[i];
1560     corner2[i] = (corner2[i] - image->GetOrigin()[i])/image->GetSpacing()[i];
1561
1562     iLocalExtents[i*2  ] = lrint(corner1[i]);
1563     iLocalExtents[i*2+1] = lrint(corner2[i]);
1564
1565     if(iLocalExtents[i*2  ]>iLocalExtents[i*2+1])
1566       std::swap(iLocalExtents[i*2], iLocalExtents[i*2+1]);
1567
1568 #if VTK_MAJOR_VERSION > 5
1569     for(int j=0;j<2; j++) {
1570       if(iLocalExtents[i*2+j]< mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT())[2*i])
1571         iLocalExtents[i*2+j] = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT())[2*i];
1572
1573       if(iLocalExtents[i*2+j]> mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT())[2*i+1])
1574         iLocalExtents[i*2+j] = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT())[2*i+1];
1575     }
1576 #endif
1577   }
1578
1579   vtkSmartPointer<vtkExtractVOI> voiFilter = vtkSmartPointer<vtkExtractVOI>::New();
1580 #if VTK_MAJOR_VERSION <= 5
1581   voiFilter->SetInput(image);
1582 #else
1583   voiFilter->SetInputData(image);
1584 #endif
1585   voiFilter->SetVOI(iLocalExtents);
1586   voiFilter->Update();
1587   if (!voiFilter->GetOutput()->GetNumberOfPoints()) {
1588     min = 0;
1589     max = 0;
1590     return;
1591   }
1592
1593   vtkSmartPointer<vtkImageAccumulate> accFilter = vtkSmartPointer<vtkImageAccumulate>::New();
1594 #if VTK_MAJOR_VERSION <= 5
1595   accFilter->SetInput(voiFilter->GetOutput());
1596 #else
1597   accFilter->SetInputConnection(voiFilter->GetOutputPort(0));
1598 #endif
1599   accFilter->Update();
1600
1601   min = *(accFilter->GetMin());
1602   max = *(accFilter->GetMax());
1603 }
1604 //----------------------------------------------------------------------------
1605
1606 //----------------------------------------------------------------------------
1607 double vvSlicer::GetScalarComponentAsDouble(vtkImageData *image, double X, double Y, double Z, int &ix, int &iy, int &iz, int component)
1608 {
1609   ix = lrint(X);
1610   iy = lrint(Y);
1611   iz = lrint(Z);
1612 #if VTK_MAJOR_VERSION <= 5
1613   if (ix < image->GetWholeExtent()[0] ||
1614       ix > image->GetWholeExtent()[1] ||
1615       iy < image->GetWholeExtent()[2] ||
1616       iy > image->GetWholeExtent()[3] ||
1617       iz < image->GetWholeExtent()[4] ||
1618       iz > image->GetWholeExtent()[5] )
1619     return std::numeric_limits<double>::quiet_NaN();
1620   image->SetUpdateExtent(ix, ix, iy, iy, iz, iz);
1621   image->Update();
1622 #else
1623   if (ix < image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[0] ||
1624       ix > image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[1] ||
1625       iy < image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[2] ||
1626       iy > image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[3] ||
1627       iz < image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[4] ||
1628       iz > image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[5] )
1629     return std::numeric_limits<double>::quiet_NaN();
1630   //image->SetUpdateExtent(ix, ix, iy, iy, iz, iz);
1631   //image->Update();
1632 #endif
1633
1634   return image->GetScalarComponentAsDouble(ix, iy, iz, component);
1635 }
1636 //----------------------------------------------------------------------------
1637
1638 //----------------------------------------------------------------------------
1639 void vvSlicer::Render()
1640 {
1641   if (this->mFusion && mFusionActor->GetVisibility() && showFusionLegend) {
1642     legend->SetLookupTable(this->GetFusionMapper()->GetLookupTable());
1643     legend->UseOpacityOn();
1644     legend->SetVisibility(1);
1645   }
1646   else if (this->GetWindowLevel()->GetLookupTable() && !this->mOverlay)  {
1647     legend->SetLookupTable(this->GetWindowLevel()->GetLookupTable());
1648     legend->UseOpacityOff();
1649     legend->SetVisibility(1);
1650   } else legend->SetVisibility(0);
1651
1652   if (ca->GetVisibility()) {
1653
1654     std::stringstream worldPos(" ");
1655     double pt[3];
1656     mConcatenatedTransform->TransformPoint(mCurrent, pt);
1657     double X = (pt[0] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[0])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[0];
1658     double Y = (pt[1] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[1])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[1];
1659     double Z = (pt[2] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[2])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[2];
1660 #if VTK_MAJOR_VERSION <= 5
1661     if (X >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[0]-0.5 &&
1662         X <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[1]+0.5 &&
1663         Y >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[2]-0.5 &&
1664         Y <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[3]+0.5 &&
1665         Z >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[4]-0.5 &&
1666         Z <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[5]+0.5) {
1667
1668
1669       int ix, iy, iz;
1670       double value = this->GetScalarComponentAsDouble(mImage->GetVTKImages()[mCurrentTSlice], X, Y, Z, ix, iy, iz);
1671
1672       if(ImageActor->GetVisibility())
1673         worldPos << "data value : " << value << std::endl;
1674
1675       worldPos << "mm : " << lrint(mCurrentBeforeSlicingTransform[0]) << ' '
1676                           << lrint(mCurrentBeforeSlicingTransform[1]) << ' '
1677                           << lrint(mCurrentBeforeSlicingTransform[2]) << ' '
1678                           << mCurrentTSlice
1679                           << std::endl;
1680       worldPos << "pixel : " << ix << ' '
1681                              << iy << ' '
1682                              << iz << ' '
1683                              << mCurrentTSlice
1684                              << std::endl;
1685     }
1686 #else
1687     if (X >= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[0]-0.5 &&
1688         X <= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[1]+0.5 &&
1689         Y >= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[2]-0.5 &&
1690         Y <= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[3]+0.5 &&
1691         Z >= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[4]-0.5 &&
1692         Z <= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[5]+0.5) {
1693
1694       int ix, iy, iz;
1695       double value = this->GetScalarComponentAsDouble(mImage->GetVTKImages()[mCurrentTSlice], X, Y, Z, ix, iy, iz);
1696
1697       if(ImageActor->GetVisibility())
1698         worldPos << "data value : " << value << std::endl;
1699
1700       worldPos << "mm : " << lrint(mCurrentBeforeSlicingTransform[0]) << ' '
1701                           << lrint(mCurrentBeforeSlicingTransform[1]) << ' '
1702                           << lrint(mCurrentBeforeSlicingTransform[2]) << ' '
1703                           << mCurrentTSlice
1704                           << std::endl;
1705       worldPos << "pixel : " << ix << ' '
1706                              << iy << ' '
1707                              << iz << ' '
1708                              << mCurrentTSlice
1709                              << std::endl;
1710
1711     }
1712 #endif
1713     ca->SetText(1,worldPos.str().c_str());
1714
1715     std::stringstream slicePos;
1716     slicePos << "Slice: " << this->GetSlice();
1717     ca->SetText(2, slicePos.str().c_str());
1718   }
1719
1720   if (pdmA->GetVisibility()) {
1721     double x = mCursor[0];
1722     double y = mCursor[1];
1723     double z = mCursor[2];
1724     double xCursor = (x - this->GetInput()->GetOrigin()[0])/this->GetInput()->GetSpacing()[0];
1725     double yCursor = (y - this->GetInput()->GetOrigin()[1])/this->GetInput()->GetSpacing()[1];
1726     double zCursor = (z - this->GetInput()->GetOrigin()[2])/this->GetInput()->GetSpacing()[2];
1727 #if VTK_MAJOR_VERSION <= 5
1728     if (xCursor >= this->GetImageActor()->GetDisplayExtent()[0]-0.5 &&
1729         xCursor < this->GetImageActor()->GetDisplayExtent()[1]+0.5 &&
1730         yCursor >= this->GetImageActor()->GetDisplayExtent()[2]-0.5 &&
1731         yCursor < this->GetImageActor()->GetDisplayExtent()[3]+0.5 &&
1732         zCursor >= this->GetImageActor()->GetDisplayExtent()[4]-0.5 &&
1733         zCursor < this->GetImageActor()->GetDisplayExtent()[5]+0.5 ) {
1734       vtkRenderer * renderer = this->Renderer;
1735
1736       renderer->WorldToView(x,y,z);
1737       renderer->ViewToNormalizedViewport(x,y,z);
1738       renderer->NormalizedViewportToViewport(x,y);
1739       renderer->ViewportToNormalizedDisplay(x,y);
1740       renderer->NormalizedDisplayToDisplay(x,y);
1741       crossCursor->SetFocalPoint(x,y,z);
1742     } else
1743       crossCursor->SetFocalPoint(-1,-1,z);
1744     crossCursor->Update();
1745   }
1746 #else
1747     vtkSmartPointer<vtkOpenGLImageSliceMapper> mapperOpenGL= vtkSmartPointer<vtkOpenGLImageSliceMapper>::New();
1748     try {
1749         mapperOpenGL = dynamic_cast<vtkOpenGLImageSliceMapper*>(GetImageActor()->GetMapper());
1750     } catch (const std::bad_cast& e) {
1751                 std::cerr << e.what() << std::endl;
1752                 std::cerr << "Conversion error" << std::endl;
1753                 return;
1754         }
1755
1756     if (xCursor >= mapperOpenGL->GetCroppingRegion()[0]-0.5 &&
1757         xCursor < mapperOpenGL->GetCroppingRegion()[1]+0.5 &&
1758         yCursor >= mapperOpenGL->GetCroppingRegion()[2]-0.5 &&
1759         yCursor < mapperOpenGL->GetCroppingRegion()[3]+0.5 &&
1760         zCursor >= mapperOpenGL->GetCroppingRegion()[4]-0.5 &&
1761         zCursor < mapperOpenGL->GetCroppingRegion()[5]+0.5 ) {
1762       vtkRenderer * renderer = this->Renderer;
1763
1764       renderer->WorldToView(x,y,z);
1765       renderer->ViewToNormalizedViewport(x,y,z);
1766       renderer->NormalizedViewportToViewport(x,y);
1767       renderer->ViewportToNormalizedDisplay(x,y);
1768       renderer->NormalizedDisplayToDisplay(x,y);
1769       crossCursor->SetFocalPoint(x,y,z);
1770     } else
1771       crossCursor->SetFocalPoint(-1,-1,z);
1772     crossCursor->Update();
1773   }
1774 #endif
1775
1776   if (mOverlay && mOverlayActor->GetVisibility()) {
1777     if(mLinkOverlayWindowLevel) {
1778       mOverlayMapper->SetWindow(this->GetColorWindow());
1779       mOverlayMapper->SetLevel(this->GetColorLevel());
1780     }
1781 #if VTK_MAJOR_VERSION <= 5
1782     mOverlayMapper->GetOutput()->SetUpdateExtent(mOverlayActor->GetDisplayExtent());
1783 #else
1784     mOverlayMapper->SetUpdateExtent(mOverlayActor->GetDisplayExtent());
1785 #endif
1786     mOverlayMapper->Update();
1787   }
1788   if (mFusion && mFusionActor->GetVisibility()) {
1789 #if VTK_MAJOR_VERSION <= 5
1790     mFusionMapper->GetOutput()->SetUpdateExtent(mFusionActor->GetDisplayExtent());
1791 #else
1792     mFusionMapper->SetUpdateExtent(mFusionActor->GetDisplayExtent());
1793 #endif
1794     mFusionMapper->Update();
1795   }
1796   if (mLandMapper) {
1797     RemoveLandmarks();
1798     DisplayLandmarks();
1799   }
1800
1801     this->GetRenderWindow()->Render();
1802 }
1803 //----------------------------------------------------------------------------
1804
1805
1806 //----------------------------------------------------------------------------
1807 void vvSlicer::UpdateCursorPosition()
1808 {
1809   pdmA->SetVisibility(true);
1810   mCursor[0] = mCurrent[0];
1811   mCursor[1] = mCurrent[1];
1812   mCursor[2] = mCurrent[2];
1813   mCursor[3] = mCurrentTSlice;
1814 }
1815 //----------------------------------------------------------------------------
1816
1817
1818 //----------------------------------------------------------------------------
1819 void vvSlicer::RemoveLandmarks()
1820 {
1821   vtkPolyData *pd = static_cast<vtkPolyData*>(mLandmarks->GetOutput());
1822   if (pd->GetPoints()) {
1823
1824     //First remove all captions:
1825     for(unsigned int i=0;i<mLandLabelActors.size();i++) {
1826         this->Renderer->RemoveActor2D(mLandLabelActors[i]);
1827         //allActors2D->Remove (mLandLabelActors[i]);
1828     }
1829     mLandLabelActors.clear();
1830   }
1831 }
1832 //----------------------------------------------------------------------------
1833
1834
1835 //----------------------------------------------------------------------------
1836 void vvSlicer::DisplayLandmarks()
1837 {
1838
1839   double bounds [6];
1840   for(unsigned int i=0; i<6; i++)
1841     bounds[i] = ImageActor->GetBounds()[i];
1842   bounds[ this->SliceOrientation*2   ] = ImageActor->GetBounds()[ this->SliceOrientation*2  ]-fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
1843   bounds[ this->SliceOrientation*2+1 ] = ImageActor->GetBounds()[ this->SliceOrientation*2+1 ]+fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
1844   mClipBox->SetBounds(bounds);
1845
1846
1847   vtkPolyData *pd = static_cast<vtkPolyData*>(mLandmarks->GetOutput());
1848   if (pd->GetPoints()) {
1849     this->GetRenderer()->AddActor(mLandActor);
1850     //mLandGlyph->SetRange(0,1);
1851     //mLandGlyph->Modified();
1852     //mLandGlyph->Update();
1853     mClipBox->Modified();
1854     mLandClipper->Update();
1855     mLandMapper->Update();
1856     //Next add the captions to the displayed points
1857     for (vtkIdType id=0; id<mLandClipper->GetOutput()->GetNumberOfPoints(); id++) {
1858           double *position = mLandClipper->GetOutput()->GetPoint(id);
1859       vtkStdString label = static_cast<vtkStringArray*>(mLandClipper->GetOutput()->GetPointData()->GetAbstractArray("labels"))->GetValue(id);
1860       vtkSmartPointer<vtkCaptionActor2D> label_actor = vtkSmartPointer<vtkCaptionActor2D>::New();
1861       label_actor->SetCaption(label);
1862       label_actor->SetAttachmentPoint(position);
1863       label_actor->GetCaptionTextProperty()->SetColor(1,0,0);
1864       label_actor->GetCaptionTextProperty()->SetOrientation(33.333333);
1865       label_actor->GetCaptionTextProperty()->SetFontFamilyToTimes();
1866       label_actor->GetCaptionTextProperty()->SetBold(0);
1867       label_actor->GetCaptionTextProperty()->SetFontSize(6);
1868       label_actor->BorderOff();
1869       label_actor->LeaderOff();
1870       label_actor->ThreeDimensionalLeaderOff();
1871       mLandLabelActors.push_back(label_actor);
1872       this->Renderer->AddActor2D(mLandLabelActors[id]);
1873      }
1874   }
1875
1876 }
1877 //----------------------------------------------------------------------------
1878
1879
1880 //----------------------------------------------------------------------------
1881 void vvSlicer::SetSlice(int slice)
1882 {
1883   int *range = this->GetSliceRange();
1884   if (range) {
1885     if (slice < range[0]) {
1886       slice = range[0];
1887     } else if (slice > range[1]) {
1888       slice = range[1];
1889     }
1890   }
1891
1892   if (this->Slice == slice) {
1893     return;
1894   }
1895
1896   this->Slice = slice;
1897   SetContourSlice();
1898   this->Modified();
1899   this->UpdateDisplayExtent();
1900
1901   // Seems to work without this line
1902   //this->Render();
1903 }
1904 //----------------------------------------------------------------------------
1905
1906 //----------------------------------------------------------------------------
1907 int vvSlicer::GetTMax()
1908 {
1909   int tmax = (int)mImage->GetVTKImages().size() - 1;
1910   if(mOverlay)
1911     tmax = std::max(tmax, (int)mOverlay->GetVTKImages().size()-1);
1912   return tmax;
1913 }
1914 //----------------------------------------------------------------------------
1915
1916 //----------------------------------------------------------------------------
1917 void vvSlicer::SetContourSlice()
1918 {
1919   if (mSurfaceCutActors.size() > 0)
1920     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
1921          i!=mSurfaceCutActors.end(); i++) {
1922
1923       (*i)->SetSlicingOrientation(this->SliceOrientation);
1924       (*i)->SetCutSlice((this->Slice)*this->GetImage()->GetSpacing()[this->SliceOrientation]+
1925                         this->GetImage()->GetOrigin()[this->SliceOrientation]);
1926     }
1927 }
1928 //----------------------------------------------------------------------------
1929
1930
1931 //----------------------------------------------------------------------------
1932 void vvSlicer::ForceUpdateDisplayExtent()
1933 {
1934   this->UpdateDisplayExtent();
1935 }
1936 //----------------------------------------------------------------------------
1937
1938
1939 //----------------------------------------------------------------------------
1940 int* vvSlicer::GetDisplayExtent()
1941 {
1942   return this->GetImageActor()->GetDisplayExtent();
1943 }
1944 //----------------------------------------------------------------------------
1945
1946
1947 //----------------------------------------------------------------------------
1948 void vvSlicer::PrintSelf(ostream& os, vtkIndent indent)
1949 {
1950   this->Superclass::PrintSelf(os, indent);
1951 }
1952 //----------------------------------------------------------------------------
1953
1954
1955 //----------------------------------------------------------------------------
1956 void vvSlicer::SetVFColor(double r, double g, double b)
1957 {
1958   double mVFColorHSV[3];
1959   mVFColor[0] = r;
1960   mVFColor[1] = g;
1961   mVFColor[2] = b;
1962
1963   vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
1964   mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
1965   mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
1966   mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
1967
1968   this->Render();
1969 }
1970 //----------------------------------------------------------------------------
1971
1972
1973 //----------------------------------------------------------------------------
1974 void vvSlicer::SetRegisterExtent(int ext[6])
1975 {
1976     copyExtent(ext, mRegisterExtent);
1977 }
1978 //----------------------------------------------------------------------------
1979
1980
1981 //----------------------------------------------------------------------------
1982 void vvSlicer::GetRegisterExtent(int ext[6])
1983 {
1984     copyExtent(mRegisterExtent, ext);
1985 }
1986 //----------------------------------------------------------------------------
1987