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 && mOverlayActor->GetVisibility())
 920     t = std::max(t, mCurrentOverlayTSlice);
 921   if(mFusion&& (mFusionSequenceCode<0) && mFusionActor->GetVisibility()) //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     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       double positionCamera[3], originTemp[3];
1234       this->Renderer->GetActiveCamera()->GetPosition(positionCamera);
1235       this->Renderer->ResetCameraClippingRange();
1236       originTemp[0] = mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[0];
1237       originTemp[1] = mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[1];
1238       originTemp[2] = mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[2];
1239       mConcatenatedTransform->GetInverse()->TransformPoint(originTemp, originTemp);
1240       positionCamera[this->SliceOrientation] = originTemp[this->SliceOrientation]-1;
1241       this->Renderer->GetActiveCamera()->SetPosition(positionCamera);
1242     } else {
1243       vtkCamera *cam = this->Renderer->GetActiveCamera();
1244       if (cam) {
1245         double bounds[6];
1246         this->ImageActor->GetBounds(bounds);
1247         double spos = (double)bounds[this->SliceOrientation * 2];
1248         double cpos = (double)cam->GetPosition()[this->SliceOrientation];
1249         double range = fabs(spos - cpos);
1250         double *spacing = input->GetSpacing();
1251         double sumSpacing = spacing[0] + spacing[1] + spacing[2];
1252         cam->SetClippingRange(range - sumSpacing, range + sumSpacing);
1253       }
1254     }
1255
1256     if (mLandActor) {
1257         if (mClipBox) {
1258             DisplayLandmarks();
1259         }
1260     }
1261   }
1262   emit UpdateDisplayExtentEnd(mSlicerNumber);
1263 }
1264 //----------------------------------------------------------------------------
1265
1266 //----------------------------------------------------------------------------
1267 void vvSlicer::ConvertImageToImageDisplayExtent(vtkInformation *sourceImage, const int sourceExtent[6],
1268                                                 vtkImageData *targetImage, int targetExtent[6])
1269 {
1270   double dExtents[6];
1271   double *origin, *spacing;
1272   origin = sourceImage->Get(vtkDataObject::ORIGIN());
1273   spacing = sourceImage->Get(vtkDataObject::SPACING());
1274   for(unsigned int i=0; i<6; i++) {
1275     // From source voxel coordinates to world coordinates
1276     dExtents[i] = origin[i/2] + spacing[i/2] * sourceExtent[i];
1277
1278     // From world coordinates to floating point target voxel coordinates
1279     dExtents[i] = (dExtents[i]- targetImage->GetOrigin()[i/2]) / targetImage->GetSpacing()[i/2];
1280
1281     // Round to current slice or larger extent
1282     if(i/2==this->GetOrientation())
1283       targetExtent[i] = itk::Math::Round<double>(dExtents[i]);
1284     else if(i%2==1)
1285       targetExtent[i] = itk::Math::Ceil<double>(dExtents[i]);
1286     else
1287       targetExtent[i] = itk::Math::Floor<double>(dExtents[i]);
1288   }
1289 }
1290 //----------------------------------------------------------------------------
1291
1292 //----------------------------------------------------------------------------
1293 void vvSlicer::ConvertImageToImageDisplayExtent(vtkImageData *sourceImage, const int sourceExtent[6],
1294                                                 vtkImageData *targetImage, int targetExtent[6])
1295 {
1296   double dExtents[6];
1297   for(unsigned int i=0; i<6; i++) {
1298     // From source voxel coordinates to world coordinates
1299     dExtents[i] = sourceImage->GetOrigin()[i/2] + sourceImage->GetSpacing()[i/2] * sourceExtent[i];
1300
1301     // From world coordinates to floating point target voxel coordinates
1302     dExtents[i] = (dExtents[i]- targetImage->GetOrigin()[i/2]) / targetImage->GetSpacing()[i/2];
1303
1304     // Round to current slice or larger extent
1305     if(i/2==this->GetOrientation())
1306       targetExtent[i] = itk::Math::Round<double>(dExtents[i]);
1307     else if(i%2==1)
1308       targetExtent[i] = itk::Math::Ceil<double>(dExtents[i]);
1309     else
1310       targetExtent[i] = itk::Math::Floor<double>(dExtents[i]);
1311   }
1312 }
1313 //----------------------------------------------------------------------------
1314
1315 //----------------------------------------------------------------------------
1316 bool vvSlicer::ClipDisplayedExtent(int extent[6], int refExtent[6])
1317 {
1318   bool out = false;
1319   int maxBound = 6;
1320
1321   for (int i = 0; i < maxBound; i = i+2) {
1322     //if we are totally outside the image
1323     if ( extent[i] > refExtent[i+1] || extent[i+1] < refExtent[i] ) {
1324       out = true;
1325       break;
1326     }
1327     //crop to the limit of the image
1328     extent[i] = std::max(extent[i], refExtent[i]);
1329     extent[i] = std::min(extent[i], refExtent[i+1]);;
1330     extent[i+1] = std::max(extent[i+1], refExtent[i]);
1331     extent[i+1] = std::min(extent[i+1], refExtent[i+1]);;
1332   }
1333   if (out)
1334     for (int i = 0; i < maxBound; i = i+2) {
1335       extent[i] = refExtent[i];
1336       extent[i+1] = refExtent[i];
1337     }
1338   return out;
1339 }
1340 //----------------------------------------------------------------------------
1341
1342
1343 //----------------------------------------------------------------------------
1344 void vvSlicer::UpdateOrientation()
1345 {
1346   // Set the camera position
1347   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1348   if (cam) {
1349     switch (this->SliceOrientation) {
1350     case vtkImageViewer2::SLICE_ORIENTATION_XY:
1351       cam->SetFocalPoint(0,0,0);
1352       cam->SetPosition(0,0,-1); // -1 if medical ?
1353       cam->SetViewUp(0,-1,0);
1354       break;
1355
1356     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
1357       cam->SetFocalPoint(0,0,0);
1358       cam->SetPosition(0,-1,0); // 1 if medical ?
1359       cam->SetViewUp(0,0,1);
1360       break;
1361
1362     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1363       cam->SetFocalPoint(0,0,0);
1364       cam->SetPosition(-1,0,0); // -1 if medical ?
1365       cam->SetViewUp(0,0,1);
1366       break;
1367     }
1368   }
1369 }
1370 //----------------------------------------------------------------------------
1371
1372
1373 //----------------------------------------------------------------------------
1374 void vvSlicer::SetOpacity(double s)
1375 {
1376   this->GetImageActor()->SetOpacity(s);
1377 }
1378 //----------------------------------------------------------------------------
1379
1380
1381 //----------------------------------------------------------------------------
1382 void vvSlicer::SetRenderWindow(int orientation, vtkRenderWindow * rw)
1383 {
1384   this->Superclass::SetRenderWindow(rw);
1385   this->SetupInteractor(rw->GetInteractor());
1386   ca->SetImageActor(this->GetImageActor());
1387   ca->SetWindowLevel(this->GetWindowLevel());
1388   ca->SetText(3, "<window>\n<level>");
1389
1390   double bounds[6];
1391   double max = 65000;
1392
1393   bounds[0] = -max;
1394   bounds[1] = max;
1395   bounds[2] = -max;
1396   bounds[3] = max;
1397   bounds[4] = -max;
1398   bounds[5] = max;
1399   crossCursor->SetModelBounds(bounds);
1400
1401   this->GetRenderer()->AddActor(pdmA);
1402   this->GetRenderer()->AddActor(ca);
1403
1404   //this is just a mapping between the labeling of the orientations presented to the user and
1405   //the one used by vtk
1406   SetSliceOrientation(2-(orientation%3));
1407   ResetCamera();
1408 }
1409 //----------------------------------------------------------------------------
1410
1411
1412 //----------------------------------------------------------------------------
1413 void vvSlicer::ResetCamera()
1414 {
1415   this->GetRenderer()->ResetCamera();
1416 }
1417 //----------------------------------------------------------------------------
1418
1419
1420 //----------------------------------------------------------------------------
1421 void vvSlicer::SetDisplayMode(bool i)
1422 {
1423         this->GetRenderer()->SetDraw(i);
1424         if (i) UpdateDisplayExtent();
1425 }
1426 //----------------------------------------------------------------------------
1427
1428
1429 //----------------------------------------------------------------------------
1430 void vvSlicer::FlipHorizontalView()
1431 {
1432   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1433   if (cam) {
1434     double *position = cam->GetPosition();
1435     double factor[3] = {1, 1, 1};
1436     factor[this->SliceOrientation] = -1;
1437     cam->SetPosition(factor[0]*position[0],factor[1]*position[1],factor[2]*position[2]);
1438
1439 /*    switch (this->SliceOrientation) {
1440     case vtkImageViewer2::SLICE_ORIENTATION_XY:
1441       cam->SetPosition(position[0],position[1],-position[2]);
1442       break;
1443
1444     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
1445       cam->SetPosition(position[0],-position[1],position[2]);
1446       break;
1447
1448     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1449       cam->SetPosition(-position[0],position[1],position[2]);
1450       break;
1451     }*/
1452
1453     this->Renderer->ResetCameraClippingRange();
1454     this->UpdateDisplayExtent();
1455   }
1456 }
1457 //----------------------------------------------------------------------------
1458
1459
1460 //----------------------------------------------------------------------------
1461 void vvSlicer::FlipVerticalView()
1462 {
1463   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1464   if (cam) {
1465     FlipHorizontalView();
1466     double *viewup = cam->GetViewUp();
1467     cam->SetViewUp(-viewup[0],-viewup[1],-viewup[2]);
1468     this->UpdateDisplayExtent();
1469   }
1470 }
1471 //----------------------------------------------------------------------------
1472
1473
1474 //----------------------------------------------------------------------------
1475 void vvSlicer::SetColorWindow(double window)
1476 {
1477   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1478   if ( LUT ) {
1479     double level = this->GetWindowLevel()->GetLevel();
1480     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1481     LUT->Build();
1482   }
1483   this->vtkImageViewer2::SetColorWindow(window);
1484 }
1485 //----------------------------------------------------------------------------
1486
1487 //----------------------------------------------------------------------------
1488 void vvSlicer::SetColorLevel(double level)
1489 {
1490   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1491   if ( LUT ) {
1492     double window = this->GetWindowLevel()->GetWindow();
1493     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1494     LUT->Build();
1495   }
1496   this->vtkImageViewer2::SetColorLevel(level);
1497 }
1498 //----------------------------------------------------------------------------
1499
1500 //----------------------------------------------------------------------------
1501 double vvSlicer::GetOverlayColorWindow()
1502 {
1503   if(mOverlayMapper)
1504     return mOverlayMapper->GetWindow();
1505   else
1506     return 0.;
1507 }
1508 //----------------------------------------------------------------------------
1509
1510 //----------------------------------------------------------------------------
1511 double vvSlicer::GetOverlayColorLevel()
1512 {
1513   if(mOverlayMapper)
1514     return mOverlayMapper->GetLevel();
1515   else
1516     return 0.;
1517 }
1518 //----------------------------------------------------------------------------
1519
1520 //----------------------------------------------------------------------------
1521 void vvSlicer::SetOverlayColorWindow(double window)
1522 {
1523   if(mOverlayMapper)
1524     mOverlayMapper->SetWindow(window);
1525 }
1526 //----------------------------------------------------------------------------
1527
1528 //----------------------------------------------------------------------------
1529 void vvSlicer::SetOverlayColorLevel(double level)
1530 {
1531   if(mOverlayMapper)
1532     mOverlayMapper->SetLevel(level);
1533 }
1534 //----------------------------------------------------------------------------
1535
1536 //----------------------------------------------------------------------------
1537 // Returns the min an the max value in a 20%x20% region around the mouse pointer
1538 void vvSlicer::GetExtremasAroundMousePointer(double & min, double & max, vtkImageData *image, vtkTransform *transform)
1539 {
1540   //Get mouse pointer position in view coordinates
1541   double corner1[3];
1542   double corner2[3];
1543   for(int i=0; i<3; i++) {
1544     corner1[i] = mCurrent[i];
1545     corner2[i] = mCurrent[i];
1546   }
1547
1548   this->Renderer->WorldToView(corner1[0], corner1[1], corner1[2]);
1549   this->Renderer->WorldToView(corner2[0], corner2[1], corner2[2]);
1550
1551   // In view coordinates, x is the slicer width and y is the slicer height are the in-plane axis
1552   int w, h;
1553   this->Renderer->GetTiledSize(&w, &h);
1554   corner1[0] -= 0.2*h/(double)w;
1555   corner2[0] += 0.2*h/(double)w;
1556   corner1[1] -= 0.2;
1557   corner2[1] += 0.2;
1558   this->Renderer->ViewToWorld(corner1[0], corner1[1], corner1[2]);
1559   this->Renderer->ViewToWorld(corner2[0], corner2[1], corner2[2]);
1560
1561   //Convert to image pixel coordinates (rounded)
1562   transform->TransformPoint(corner1, corner1);
1563   transform->TransformPoint(corner2, corner2);
1564   int iLocalExtents[6];
1565   for(int i=0; i<3; i++) {
1566     corner1[i] = (corner1[i] - image->GetOrigin()[i])/image->GetSpacing()[i];
1567     corner2[i] = (corner2[i] - image->GetOrigin()[i])/image->GetSpacing()[i];
1568
1569     iLocalExtents[i*2  ] = lrint(corner1[i]);
1570     iLocalExtents[i*2+1] = lrint(corner2[i]);
1571
1572     if(iLocalExtents[i*2  ]>iLocalExtents[i*2+1])
1573       std::swap(iLocalExtents[i*2], iLocalExtents[i*2+1]);
1574
1575 #if VTK_MAJOR_VERSION > 5
1576     for(int j=0;j<2; j++) {
1577       if(iLocalExtents[i*2+j]< mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT())[2*i])
1578         iLocalExtents[i*2+j] = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT())[2*i];
1579
1580       if(iLocalExtents[i*2+j]> mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT())[2*i+1])
1581         iLocalExtents[i*2+j] = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT())[2*i+1];
1582     }
1583 #endif
1584   }
1585
1586   vtkSmartPointer<vtkExtractVOI> voiFilter = vtkSmartPointer<vtkExtractVOI>::New();
1587 #if VTK_MAJOR_VERSION <= 5
1588   voiFilter->SetInput(image);
1589 #else
1590   voiFilter->SetInputData(image);
1591 #endif
1592   voiFilter->SetVOI(iLocalExtents);
1593   voiFilter->Update();
1594   if (!voiFilter->GetOutput()->GetNumberOfPoints()) {
1595     min = 0;
1596     max = 0;
1597     return;
1598   }
1599
1600   vtkSmartPointer<vtkImageAccumulate> accFilter = vtkSmartPointer<vtkImageAccumulate>::New();
1601 #if VTK_MAJOR_VERSION <= 5
1602   accFilter->SetInput(voiFilter->GetOutput());
1603 #else
1604   accFilter->SetInputConnection(voiFilter->GetOutputPort(0));
1605 #endif
1606   accFilter->Update();
1607
1608   min = *(accFilter->GetMin());
1609   max = *(accFilter->GetMax());
1610 }
1611 //----------------------------------------------------------------------------
1612
1613 //----------------------------------------------------------------------------
1614 double vvSlicer::GetScalarComponentAsDouble(vtkImageData *image, double X, double Y, double Z, int &ix, int &iy, int &iz, int component)
1615 {
1616   ix = lrint(X);
1617   iy = lrint(Y);
1618   iz = lrint(Z);
1619 #if VTK_MAJOR_VERSION <= 5
1620   if (ix < image->GetWholeExtent()[0] ||
1621       ix > image->GetWholeExtent()[1] ||
1622       iy < image->GetWholeExtent()[2] ||
1623       iy > image->GetWholeExtent()[3] ||
1624       iz < image->GetWholeExtent()[4] ||
1625       iz > image->GetWholeExtent()[5] )
1626     return std::numeric_limits<double>::quiet_NaN();
1627   image->SetUpdateExtent(ix, ix, iy, iy, iz, iz);
1628   image->Update();
1629 #else
1630   if (ix < image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[0] ||
1631       ix > image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[1] ||
1632       iy < image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[2] ||
1633       iy > image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[3] ||
1634       iz < image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[4] ||
1635       iz > image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[5] )
1636     return std::numeric_limits<double>::quiet_NaN();
1637   //image->SetUpdateExtent(ix, ix, iy, iy, iz, iz);
1638   //image->Update();
1639 #endif
1640
1641   return image->GetScalarComponentAsDouble(ix, iy, iz, component);
1642 }
1643 //----------------------------------------------------------------------------
1644
1645 //----------------------------------------------------------------------------
1646 void vvSlicer::Render()
1647 {
1648   if (this->mFusion && mFusionActor->GetVisibility() && showFusionLegend) {
1649     legend->SetLookupTable(this->GetFusionMapper()->GetLookupTable());
1650     legend->UseOpacityOn();
1651     legend->SetVisibility(1);
1652   }
1653   else if (this->GetWindowLevel()->GetLookupTable() && !this->mOverlay)  {
1654     legend->SetLookupTable(this->GetWindowLevel()->GetLookupTable());
1655     legend->UseOpacityOff();
1656     legend->SetVisibility(1);
1657   } else legend->SetVisibility(0);
1658
1659   if (ca->GetVisibility()) {
1660
1661     std::stringstream worldPos(" ");
1662     double pt[3];
1663     mConcatenatedTransform->TransformPoint(mCurrent, pt);
1664     double X = (pt[0] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[0])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[0];
1665     double Y = (pt[1] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[1])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[1];
1666     double Z = (pt[2] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[2])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[2];
1667 #if VTK_MAJOR_VERSION <= 5
1668     if (X >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[0]-0.5 &&
1669         X <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[1]+0.5 &&
1670         Y >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[2]-0.5 &&
1671         Y <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[3]+0.5 &&
1672         Z >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[4]-0.5 &&
1673         Z <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[5]+0.5) {
1674
1675
1676       int ix, iy, iz;
1677       double value = this->GetScalarComponentAsDouble(mImage->GetVTKImages()[mCurrentTSlice], X, Y, Z, ix, iy, iz);
1678
1679       if(ImageActor->GetVisibility())
1680         worldPos << "data value : " << value << std::endl;
1681
1682       worldPos << "mm : " << lrint(mCurrentBeforeSlicingTransform[0]) << ' '
1683                           << lrint(mCurrentBeforeSlicingTransform[1]) << ' '
1684                           << lrint(mCurrentBeforeSlicingTransform[2]) << ' '
1685                           << mCurrentTSlice
1686                           << std::endl;
1687       worldPos << "pixel : " << ix << ' '
1688                              << iy << ' '
1689                              << iz << ' '
1690                              << mCurrentTSlice
1691                              << std::endl;
1692     }
1693 #else
1694     if (X >= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[0]-0.5 &&
1695         X <= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[1]+0.5 &&
1696         Y >= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[2]-0.5 &&
1697         Y <= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[3]+0.5 &&
1698         Z >= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[4]-0.5 &&
1699         Z <= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[5]+0.5) {
1700
1701       int ix, iy, iz;
1702       double value = this->GetScalarComponentAsDouble(mImage->GetVTKImages()[mCurrentTSlice], X, Y, Z, ix, iy, iz);
1703
1704       if(ImageActor->GetVisibility())
1705         worldPos << "data value : " << value << std::endl;
1706
1707       worldPos << "mm : " << lrint(mCurrentBeforeSlicingTransform[0]) << ' '
1708                           << lrint(mCurrentBeforeSlicingTransform[1]) << ' '
1709                           << lrint(mCurrentBeforeSlicingTransform[2]) << ' '
1710                           << mCurrentTSlice
1711                           << std::endl;
1712       worldPos << "pixel : " << ix << ' '
1713                              << iy << ' '
1714                              << iz << ' '
1715                              << mCurrentTSlice
1716                              << std::endl;
1717
1718     }
1719 #endif
1720     ca->SetText(1,worldPos.str().c_str());
1721
1722     std::stringstream slicePos;
1723     slicePos << "Slice: " << this->GetSlice();
1724     ca->SetText(2, slicePos.str().c_str());
1725   }
1726
1727   if (pdmA->GetVisibility()) {
1728     double x = mCursor[0];
1729     double y = mCursor[1];
1730     double z = mCursor[2];
1731     double xCursor = (x - this->GetInput()->GetOrigin()[0])/this->GetInput()->GetSpacing()[0];
1732     double yCursor = (y - this->GetInput()->GetOrigin()[1])/this->GetInput()->GetSpacing()[1];
1733     double zCursor = (z - this->GetInput()->GetOrigin()[2])/this->GetInput()->GetSpacing()[2];
1734 #if VTK_MAJOR_VERSION <= 5
1735     if (xCursor >= this->GetImageActor()->GetDisplayExtent()[0]-0.5 &&
1736         xCursor < this->GetImageActor()->GetDisplayExtent()[1]+0.5 &&
1737         yCursor >= this->GetImageActor()->GetDisplayExtent()[2]-0.5 &&
1738         yCursor < this->GetImageActor()->GetDisplayExtent()[3]+0.5 &&
1739         zCursor >= this->GetImageActor()->GetDisplayExtent()[4]-0.5 &&
1740         zCursor < this->GetImageActor()->GetDisplayExtent()[5]+0.5 ) {
1741       vtkRenderer * renderer = this->Renderer;
1742
1743       renderer->WorldToView(x,y,z);
1744       renderer->ViewToNormalizedViewport(x,y,z);
1745       renderer->NormalizedViewportToViewport(x,y);
1746       renderer->ViewportToNormalizedDisplay(x,y);
1747       renderer->NormalizedDisplayToDisplay(x,y);
1748       crossCursor->SetFocalPoint(x,y,z);
1749     } else
1750       crossCursor->SetFocalPoint(-1,-1,z);
1751     crossCursor->Update();
1752   }
1753 #else
1754     vtkSmartPointer<vtkOpenGLImageSliceMapper> mapperOpenGL= vtkSmartPointer<vtkOpenGLImageSliceMapper>::New();
1755     try {
1756         mapperOpenGL = dynamic_cast<vtkOpenGLImageSliceMapper*>(GetImageActor()->GetMapper());
1757     } catch (const std::bad_cast& e) {
1758                 std::cerr << e.what() << std::endl;
1759                 std::cerr << "Conversion error" << std::endl;
1760                 return;
1761         }
1762
1763     if (xCursor >= mapperOpenGL->GetCroppingRegion()[0]-0.5 &&
1764         xCursor < mapperOpenGL->GetCroppingRegion()[1]+0.5 &&
1765         yCursor >= mapperOpenGL->GetCroppingRegion()[2]-0.5 &&
1766         yCursor < mapperOpenGL->GetCroppingRegion()[3]+0.5 &&
1767         zCursor >= mapperOpenGL->GetCroppingRegion()[4]-0.5 &&
1768         zCursor < mapperOpenGL->GetCroppingRegion()[5]+0.5 ) {
1769       vtkRenderer * renderer = this->Renderer;
1770
1771       renderer->WorldToView(x,y,z);
1772       renderer->ViewToNormalizedViewport(x,y,z);
1773       renderer->NormalizedViewportToViewport(x,y);
1774       renderer->ViewportToNormalizedDisplay(x,y);
1775       renderer->NormalizedDisplayToDisplay(x,y);
1776       crossCursor->SetFocalPoint(x,y,z);
1777     } else
1778       crossCursor->SetFocalPoint(-1,-1,z);
1779     crossCursor->Update();
1780   }
1781 #endif
1782
1783   if (mOverlay && mOverlayActor->GetVisibility()) {
1784     if(mLinkOverlayWindowLevel) {
1785       mOverlayMapper->SetWindow(this->GetColorWindow());
1786       mOverlayMapper->SetLevel(this->GetColorLevel());
1787     }
1788 #if VTK_MAJOR_VERSION <= 5
1789     mOverlayMapper->GetOutput()->SetUpdateExtent(mOverlayActor->GetDisplayExtent());
1790 #else
1791     mOverlayMapper->SetUpdateExtent(mOverlayActor->GetDisplayExtent());
1792 #endif
1793     mOverlayMapper->Update();
1794   }
1795   if (mFusion && mFusionActor->GetVisibility()) {
1796 #if VTK_MAJOR_VERSION <= 5
1797     mFusionMapper->GetOutput()->SetUpdateExtent(mFusionActor->GetDisplayExtent());
1798 #else
1799     mFusionMapper->SetUpdateExtent(mFusionActor->GetDisplayExtent());
1800 #endif
1801     mFusionMapper->Update();
1802   }
1803   if (mLandMapper) {
1804     RemoveLandmarks();
1805     DisplayLandmarks();
1806   }
1807
1808     this->GetRenderWindow()->Render();
1809 }
1810 //----------------------------------------------------------------------------
1811
1812
1813 //----------------------------------------------------------------------------
1814 void vvSlicer::UpdateCursorPosition()
1815 {
1816   pdmA->SetVisibility(true);
1817   mCursor[0] = mCurrent[0];
1818   mCursor[1] = mCurrent[1];
1819   mCursor[2] = mCurrent[2];
1820   mCursor[3] = mCurrentTSlice;
1821 }
1822 //----------------------------------------------------------------------------
1823
1824
1825 //----------------------------------------------------------------------------
1826 void vvSlicer::RemoveLandmarks()
1827 {
1828   vtkPolyData *pd = static_cast<vtkPolyData*>(mLandmarks->GetOutput());
1829   if (pd->GetPoints()) {
1830
1831     //First remove all captions:
1832     for(unsigned int i=0;i<mLandLabelActors.size();i++) {
1833         this->Renderer->RemoveActor2D(mLandLabelActors[i]);
1834         //allActors2D->Remove (mLandLabelActors[i]);
1835     }
1836     mLandLabelActors.clear();
1837   }
1838 }
1839 //----------------------------------------------------------------------------
1840
1841
1842 //----------------------------------------------------------------------------
1843 void vvSlicer::DisplayLandmarks()
1844 {
1845
1846   double bounds [6];
1847   for(unsigned int i=0; i<6; i++)
1848     bounds[i] = ImageActor->GetBounds()[i];
1849   bounds[ this->SliceOrientation*2   ] = ImageActor->GetBounds()[ this->SliceOrientation*2  ]-fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
1850   bounds[ this->SliceOrientation*2+1 ] = ImageActor->GetBounds()[ this->SliceOrientation*2+1 ]+fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
1851   mClipBox->SetBounds(bounds);
1852
1853
1854   vtkPolyData *pd = static_cast<vtkPolyData*>(mLandmarks->GetOutput());
1855   if (pd->GetPoints()) {
1856     this->GetRenderer()->AddActor(mLandActor);
1857     //mLandGlyph->SetRange(0,1);
1858     //mLandGlyph->Modified();
1859     //mLandGlyph->Update();
1860     mClipBox->Modified();
1861     mLandClipper->Update();
1862     mLandMapper->Update();
1863     //Next add the captions to the displayed points
1864     for (vtkIdType id=0; id<mLandClipper->GetOutput()->GetNumberOfPoints(); id++) {
1865           double *position = mLandClipper->GetOutput()->GetPoint(id);
1866       vtkStdString label = static_cast<vtkStringArray*>(mLandClipper->GetOutput()->GetPointData()->GetAbstractArray("labels"))->GetValue(id);
1867       vtkSmartPointer<vtkCaptionActor2D> label_actor = vtkSmartPointer<vtkCaptionActor2D>::New();
1868       label_actor->SetCaption(label);
1869       label_actor->SetAttachmentPoint(position);
1870       label_actor->GetCaptionTextProperty()->SetColor(1,0,0);
1871       label_actor->GetCaptionTextProperty()->SetOrientation(33.333333);
1872       label_actor->GetCaptionTextProperty()->SetFontFamilyToTimes();
1873       label_actor->GetCaptionTextProperty()->SetBold(0);
1874       label_actor->GetCaptionTextProperty()->SetFontSize(6);
1875       label_actor->BorderOff();
1876       label_actor->LeaderOff();
1877       label_actor->ThreeDimensionalLeaderOff();
1878       mLandLabelActors.push_back(label_actor);
1879       this->Renderer->AddActor2D(mLandLabelActors[id]);
1880      }
1881   }
1882
1883 }
1884 //----------------------------------------------------------------------------
1885
1886
1887 //----------------------------------------------------------------------------
1888 void vvSlicer::SetSlice(int slice)
1889 {
1890   int *range = this->GetSliceRange();
1891   if (range) {
1892     if (slice < range[0]) {
1893       slice = range[0];
1894     } else if (slice > range[1]) {
1895       slice = range[1];
1896     }
1897   }
1898
1899   if (this->Slice == slice) {
1900     return;
1901   }
1902
1903   this->Slice = slice;
1904   SetContourSlice();
1905   this->Modified();
1906   this->UpdateDisplayExtent();
1907
1908   // Seems to work without this line
1909   //this->Render();
1910 }
1911 //----------------------------------------------------------------------------
1912
1913 //----------------------------------------------------------------------------
1914 int vvSlicer::GetTMax()
1915 {
1916   int tmax = (int)mImage->GetVTKImages().size() - 1;
1917   if(mOverlay)
1918     tmax = std::max(tmax, (int)mOverlay->GetVTKImages().size()-1);
1919   return tmax;
1920 }
1921 //----------------------------------------------------------------------------
1922
1923 //----------------------------------------------------------------------------
1924 void vvSlicer::SetContourSlice()
1925 {
1926   if (mSurfaceCutActors.size() > 0)
1927     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
1928          i!=mSurfaceCutActors.end(); i++) {
1929
1930       (*i)->SetSlicingOrientation(this->SliceOrientation);
1931       (*i)->SetCutSlice((this->Slice)*this->GetImage()->GetSpacing()[this->SliceOrientation]+
1932                         this->GetImage()->GetOrigin()[this->SliceOrientation]);
1933     }
1934 }
1935 //----------------------------------------------------------------------------
1936
1937
1938 //----------------------------------------------------------------------------
1939 void vvSlicer::ForceUpdateDisplayExtent()
1940 {
1941   this->UpdateDisplayExtent();
1942 }
1943 //----------------------------------------------------------------------------
1944
1945
1946 //----------------------------------------------------------------------------
1947 int* vvSlicer::GetDisplayExtent()
1948 {
1949   return this->GetImageActor()->GetDisplayExtent();
1950 }
1951 //----------------------------------------------------------------------------
1952
1953
1954 //----------------------------------------------------------------------------
1955 void vvSlicer::PrintSelf(ostream& os, vtkIndent indent)
1956 {
1957   this->Superclass::PrintSelf(os, indent);
1958 }
1959 //----------------------------------------------------------------------------
1960
1961
1962 //----------------------------------------------------------------------------
1963 void vvSlicer::SetVFColor(double r, double g, double b)
1964 {
1965   double mVFColorHSV[3];
1966   mVFColor[0] = r;
1967   mVFColor[1] = g;
1968   mVFColor[2] = b;
1969
1970   vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
1971   mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
1972   mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
1973   mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
1974
1975   this->Render();
1976 }
1977 //----------------------------------------------------------------------------
1978
1979
1980 //----------------------------------------------------------------------------
1981 void vvSlicer::SetRegisterExtent(int ext[6])
1982 {
1983     copyExtent(ext, mRegisterExtent);
1984 }
1985 //----------------------------------------------------------------------------
1986
1987
1988 //----------------------------------------------------------------------------
1989 void vvSlicer::GetRegisterExtent(int ext[6])
1990 {
1991     copyExtent(mRegisterExtent, ext);
1992 }
1993 //----------------------------------------------------------------------------
1994