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 <vtkImageProperty.h>
  61 #include <vtkLookupTable.h>
  62
  63 #include <vtkRenderer.h>
  64 #include <vtkRendererCollection.h>
  65 #include <vtkRenderWindow.h>
  66 #include <vtkRenderWindowInteractor.h>
  67 #include <vtkCamera.h>
  68 #include <vtkCallbackCommand.h>
  69 #include <vtkCommand.h>
  70 #include <vtkPolyDataMapper.h>
  71 #include <vtkBox.h>
  72
  73 #include <vtkExtractVOI.h>
  74 #include <vtkSphereSource.h>
  75 #include <vtkCutter.h>
  76 #include <vtkAssignAttribute.h>
  77 #include <vtkImageAccumulate.h>
  78 #include <vtkImageReslice.h>
  79 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
  80 #  include <vtkOpenGLImageSliceMapper.h>
  81 #  include <vtkImageMapper3D.h>
  82 #  include <vtkImageSliceMapper.h>
  83 #endif
  84
  85 vtkStandardNewMacro(vvSlicer);
  86 static void copyExtent(int* in, int* to){
  87  for(int i=0; i<6; ++i)
  88  {
  89         to[i]=in[i];
  90  }
  91 }
  92 //------------------------------------------------------------------------------
  93 vvSlicer::vvSlicer()
  94 {
  95         mFusionSequenceCode = -1;
  96   this->UnInstallPipeline();
  97   mImage = NULL;
  98   mReducedExtent = new int[6];
  99   mRegisterExtent = NULL;
 100   mCurrentTSlice = 0;
 101   mCurrentFusionTSlice = 0;
 102   mCurrentOverlayTSlice = 0;
 103   mUseReducedExtent = false;
 104
 105   mCurrent[0] = -VTK_DOUBLE_MAX;
 106   mCurrent[1] = -VTK_DOUBLE_MAX;
 107   mCurrent[2] = -VTK_DOUBLE_MAX;
 108
 109   mCursor[0] = 0;//-VTK_DOUBLE_MAX;
 110   mCursor[1] = 0;//-VTK_DOUBLE_MAX;
 111   mCursor[2] = 0;//-VTK_DOUBLE_MAX;
 112   mCursor[3] = 0;//-VTK_DOUBLE_MAX;
 113
 114   mSubSampling = 5;
 115   mScale = 1;
 116   mVFLog = 0;
 117   mVFWidth = 1;
 118   mVFColor[0] = 0;
 119   mVFColor[1] = 1;
 120   mVFColor[2] = 0;
 121
 122   crossCursor = vtkSmartPointer<vtkCursor2D>::New();
 123   crossCursor->AllOff();
 124   crossCursor->AxesOn();
 125   crossCursor->SetTranslationMode(1);
 126   crossCursor->SetRadius(2);
 127
 128   pdm = vtkSmartPointer<vtkPolyDataMapper2D>::New();
 129 #if VTK_MAJOR_VERSION <= 5
 130   pdm->SetInput(crossCursor->GetOutput());
 131 #else
 132   pdm->SetInputConnection(crossCursor->GetOutputPort(0));
 133 #endif
 134
 135   pdmA = vtkSmartPointer<vtkActor2D>::New();
 136   pdmA->SetMapper(pdm);
 137   pdmA->GetProperty()->SetColor(255,10,212);
 138   pdmA->SetVisibility(0);
 139   pdmA->SetPickable(0);
 140
 141   ca = vtkSmartPointer<vtkCornerAnnotation>::New();
 142   ca->GetTextProperty()->SetColor(255,10,212);
 143   ca->SetVisibility(1);
 144   mFileName = "";
 145
 146   mVF = NULL;
 147   mOverlay = NULL;
 148   mFusion = NULL;
 149   mLandmarks = NULL;
 150
 151   legend = vtkSmartPointer<vtkScalarBarActor>::New();
 152   //legend->SetTitle("test!");
 153   legend->SetPosition(0.82,0.08);
 154   //legend->SetWidth(0.1);
 155   legend->SetVisibility(0);
 156   legend->SetLabelFormat("%.1e");
 157   this->GetRenderer()->AddActor(legend);
 158   showFusionLegend = false;
 159
 160   this->InstallPipeline();
 161
 162   mLinkOverlayWindowLevel = true;
 163   mImageVisibility = true;
 164
 165 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 166   this->GetImageActor()->GetMapper()->BorderOn();
 167 #endif
 168
 169   mSlicingTransform = vtkSmartPointer<vtkTransform>::New();
 170   mConcatenatedTransform = vtkSmartPointer<vtkTransform>::New();
 171   mConcatenatedFusionTransform = vtkSmartPointer<vtkTransform>::New();
 172   mConcatenatedOverlayTransform = vtkSmartPointer<vtkTransform>::New();
 173   mConcatenatedVFTransform = vtkSmartPointer<vtkTransform>::New();
 174   mFirstSetSliceOrientation = true;
 175 }
 176 //------------------------------------------------------------------------------
 177
 178
 179 //------------------------------------------------------------------------------
 180 vtkImageMapToWindowLevelColors* vvSlicer::GetOverlayMapper()
 181 {
 182   return mOverlayMapper.GetPointer();
 183 }
 184 //------------------------------------------------------------------------------
 185
 186
 187 //------------------------------------------------------------------------------
 188 vvBlendImageActor* vvSlicer::GetOverlayActor()
 189 {
 190   return mOverlayActor.GetPointer();
 191 }
 192 //------------------------------------------------------------------------------
 193
 194
 195 //------------------------------------------------------------------------------
 196 vtkImageMapToColors* vvSlicer::GetFusionMapper()
 197 {
 198   return mFusionMapper.GetPointer();
 199 }
 200 //------------------------------------------------------------------------------
 201
 202
 203 //------------------------------------------------------------------------------
 204 vtkImageActor* vvSlicer::GetFusionActor()
 205 {
 206   return mFusionActor.GetPointer();
 207 }
 208 //------------------------------------------------------------------------------
 209
 210
 211 //------------------------------------------------------------------------------
 212 vtkActor* vvSlicer::GetVFActor()
 213 {
 214   return mVFActor.GetPointer();
 215 }
 216 //------------------------------------------------------------------------------
 217
 218
 219 //------------------------------------------------------------------------------
 220 vtkCornerAnnotation* vvSlicer::GetAnnotation()
 221 {
 222   return ca.GetPointer();
 223 }
 224 //------------------------------------------------------------------------------
 225
 226
 227 //------------------------------------------------------------------------------
 228 void vvSlicer::EnableReducedExtent(bool b)
 229 {
 230   mUseReducedExtent = b;
 231 }
 232 //------------------------------------------------------------------------------
 233
 234
 235 //------------------------------------------------------------------------------
 236 void vvSlicer::SetReducedExtent(int * ext)
 237 {
 238   copyExtent(ext, mReducedExtent);
 239 }
 240 //------------------------------------------------------------------------------
 241
 242
 243 //------------------------------------------------------------------------------
 244 void vvSlicer::AddContour(vvMesh::Pointer contour,bool propagate)
 245 {
 246
 247   mSurfaceCutActors.push_back(new vvMeshActor());
 248   if (propagate)
 249     mSurfaceCutActors.back()->Init(contour,mCurrentTSlice,mVF);
 250   else
 251     mSurfaceCutActors.back()->Init(contour,mCurrentTSlice);
 252   mSurfaceCutActors.back()->SetSlicingOrientation(SliceOrientation);
 253   this->GetRenderer()->AddActor(mSurfaceCutActors.back()->GetActor());
 254
 255   SetContourSlice();
 256 }
 257 //------------------------------------------------------------------------------
 258
 259
 260 //------------------------------------------------------------------------------
 261 void vvSlicer::ToggleContourSuperposition()
 262 {
 263   for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 264        i!=mSurfaceCutActors.end(); i++)
 265     (*i)->ToggleSuperposition();
 266 }
 267 //------------------------------------------------------------------------------
 268
 269
 270 //------------------------------------------------------------------------------
 271 void vvSlicer::SetCursorColor(int r,int g, int b)
 272 {
 273   pdmA->GetProperty()->SetColor(r,g,b);
 274 }
 275 //------------------------------------------------------------------------------
 276
 277
 278 //------------------------------------------------------------------------------
 279 void vvSlicer::SetCursorVisibility(bool s)
 280 {
 281   pdmA->SetVisibility(s);
 282 }
 283 //------------------------------------------------------------------------------
 284
 285
 286 //------------------------------------------------------------------------------
 287 bool vvSlicer::GetCursorVisibility()
 288 {
 289   return pdmA->GetVisibility();
 290 }
 291 //------------------------------------------------------------------------------
 292
 293
 294 //------------------------------------------------------------------------------
 295 void vvSlicer::SetCornerAnnotationVisibility(bool s)
 296 {
 297   ca->SetVisibility(s);
 298 }
 299 //------------------------------------------------------------------------------
 300
 301
 302 //------------------------------------------------------------------------------
 303 bool vvSlicer::GetCornerAnnotationVisibility()
 304 {
 305   return ca->GetVisibility();
 306 }
 307 //------------------------------------------------------------------------------
 308
 309
 310 //------------------------------------------------------------------------------
 311 vvSlicer::~vvSlicer()
 312 {
 313   for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 314        i!=mSurfaceCutActors.end(); i++)
 315     delete (*i);
 316   delete [] mReducedExtent;
 317 }
 318 //------------------------------------------------------------------------------
 319
 320 //------------------------------------------------------------------------------
 321 double* vvSlicer::GetCurrentPosition()
 322 {
 323   return mCurrentBeforeSlicingTransform;
 324 }
 325 //------------------------------------------------------------------------------
 326
 327 //------------------------------------------------------------------------------
 328 void vvSlicer::SetInterpolationImageReslice(int interpolation)
 329 {
 330   mImageReslice->SetInterpolationMode(interpolation);
 331 }
 332 //------------------------------------------------------------------------------
 333
 334 //------------------------------------------------------------------------------
 335 void vvSlicer::SetCurrentPosition(double x, double y, double z, int t)
 336 {
 337   mCurrentBeforeSlicingTransform[0]=x;
 338   mCurrentBeforeSlicingTransform[1]=y;
 339   mCurrentBeforeSlicingTransform[2]=z;
 340   mSlicingTransform->GetInverse()->TransformPoint(mCurrentBeforeSlicingTransform,mCurrent);
 341   if (t>=0) SetTSlice(t);
 342 }
 343 //------------------------------------------------------------------------------
 344
 345
 346 //------------------------------------------------------------------------------
 347 void vvSlicer::SetImage(vvImage::Pointer image)
 348 {
 349   if (image->GetVTKImages().size()) {
 350     mImage = image;
 351
 352     if (!mImageReslice) {
 353       mImageReslice = vtkSmartPointer<vtkImageReslice>::New();
 354       mImageReslice->SetInterpolationModeToLinear();
 355       mImageReslice->AutoCropOutputOn();
 356       mImageReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 357     }
 358
 359     mConcatenatedTransform->Identity();
 360     mConcatenatedTransform->Concatenate(mImage->GetTransform()[0]);
 361     mConcatenatedTransform->Concatenate(mSlicingTransform);
 362     mImageReslice->SetResliceTransform(mConcatenatedTransform);
 363     //mImageReslice->SetResliceAxes(mConcatenatedTransform->GetMatrix());
 364 #if VTK_MAJOR_VERSION <= 5
 365     mImageReslice->SetInput(0, mImage->GetFirstVTKImageData());
 366 #else
 367     mImageReslice->SetInputData(0, mImage->GetFirstVTKImageData());
 368 #endif
 369     mImageReslice->UpdateInformation();
 370
 371 #if VTK_MAJOR_VERSION <= 5
 372     this->Superclass::SetInput(mImageReslice->GetOutput());
 373 #else
 374     this->Superclass::SetInputConnection(mImageReslice->GetOutputPort());
 375 #endif
 376
 377     int extent[6];
 378 #if VTK_MAJOR_VERSION <= 5
 379     this->GetInput()->GetWholeExtent(extent);
 380 #else
 381     int* ext = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
 382     copyExtent(ext, extent);
 383 #endif
 384
 385     // Prevent crash when reload -> change slice if outside extent
 386     if (Slice < extent[SliceOrientation*2] || Slice>=extent[SliceOrientation*2+1]) {
 387       Slice = (extent[SliceOrientation*2+1]+extent[SliceOrientation*2])/2.0;
 388     }
 389
 390     // Make sure that the required part image has been computed
 391     extent[SliceOrientation*2] = Slice;
 392     extent[SliceOrientation*2+1] = Slice;
 393 #if VTK_MAJOR_VERSION <= 5
 394     mImageReslice->GetOutput()->SetUpdateExtent(extent);
 395     mImageReslice->GetOutput()->Update();
 396 #else
 397     mImageReslice->SetUpdateExtent(extent);
 398     mImageReslice->Update();
 399 #endif
 400
 401     this->UpdateDisplayExtent();
 402
 403     mCurrentTSlice = 0;
 404     ca->SetText(0,mFileName.c_str());
 405   }
 406 }
 407 //------------------------------------------------------------------------------
 408
 409
 410 //------------------------------------------------------------------------------
 411 void vvSlicer::SetOverlay(vvImage::Pointer overlay)
 412 {
 413   if (overlay->GetVTKImages().size()) {
 414     mOverlay = overlay;
 415     mOverlayVisibility = true;
 416
 417     if (!mOverlayReslice) {
 418       mOverlayReslice = vtkSmartPointer<vtkImageReslice>::New();
 419       mOverlayReslice->SetInterpolationModeToLinear();
 420       mOverlayReslice->AutoCropOutputOn();
 421       mOverlayReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 422     }
 423
 424     mConcatenatedOverlayTransform->Identity();
 425     mConcatenatedOverlayTransform->Concatenate(mOverlay->GetTransform()[0]);
 426     mConcatenatedOverlayTransform->Concatenate(mSlicingTransform);
 427     mOverlayReslice->SetResliceTransform(mConcatenatedOverlayTransform);
 428 #if VTK_MAJOR_VERSION <= 5
 429     mOverlayReslice->SetInput(0, mOverlay->GetFirstVTKImageData());
 430     mImageReslice->UpdateInformation();
 431 #else
 432     mOverlayReslice->SetInputData(0, mOverlay->GetFirstVTKImageData());
 433 #endif
 434     mOverlayReslice->Update();
 435
 436     if (!mOverlayMapper)
 437       mOverlayMapper = vtkSmartPointer<vtkImageMapToWindowLevelColors>::New();
 438 #if VTK_MAJOR_VERSION <= 5
 439     mOverlayMapper->SetInput(mOverlayReslice->GetOutput());
 440 #else
 441     mOverlayMapper->SetInputConnection(mOverlayReslice->GetOutputPort(0));
 442 #endif
 443
 444     if (!mOverlayActor) {
 445       mOverlayActor = vtkSmartPointer<vvBlendImageActor>::New();
 446 #if VTK_MAJOR_VERSION <= 5
 447       mOverlayActor->SetInput(mOverlayMapper->GetOutput());
 448 #else
 449       mOverlayActor->GetMapper()->SetInputConnection(mOverlayMapper->GetOutputPort());
 450 #endif
 451       mOverlayActor->SetPickable(0);
 452       mOverlayActor->SetVisibility(true);
 453       mOverlayActor->SetOpacity(0.5);
 454 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 455       mOverlayActor->GetMapper()->BorderOn();
 456 #endif
 457       }
 458
 459     //stupid but necessary : the Overlay need to be rendered before fusion
 460     if (mFusionActor) {
 461       this->GetRenderer()->RemoveActor(mFusionActor);
 462       this->GetRenderer()->AddActor(mOverlayActor);
 463       this->GetRenderer()->AddActor(mFusionActor);
 464     } else
 465       this->GetRenderer()->AddActor(mOverlayActor);
 466
 467     //Synchronize orientation and slice
 468     AdjustResliceToSliceOrientation(mOverlayReslice);
 469     this->UpdateDisplayExtent();
 470     this->SetTSlice(mCurrentTSlice);
 471   }
 472 }
 473 //------------------------------------------------------------------------------
 474
 475
 476 //------------------------------------------------------------------------------
 477 void vvSlicer::SetFusion(vvImage::Pointer fusion, int fusionSequenceCode)
 478 {
 479         mFusionSequenceCode = fusionSequenceCode;
 480   if (fusion->GetVTKImages().size()) {
 481     mFusion = fusion;
 482     mFusionVisibility = true;
 483
 484     if (!mFusionReslice) {
 485       mFusionReslice = vtkSmartPointer<vtkImageReslice>::New();
 486       mFusionReslice->SetInterpolationModeToLinear();
 487       mFusionReslice->AutoCropOutputOn();
 488       mFusionReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 489     }
 490
 491     mConcatenatedFusionTransform->Identity();
 492     mConcatenatedFusionTransform->Concatenate(mFusion->GetTransform()[0]);
 493     mConcatenatedFusionTransform->Concatenate(mSlicingTransform);
 494     mFusionReslice->SetResliceTransform(mConcatenatedFusionTransform);
 495 #if VTK_MAJOR_VERSION <= 5
 496     mFusionReslice->SetInput(0, mFusion->GetFirstVTKImageData());
 497     mFusionReslice->UpdateInformation();
 498 #else
 499     mFusionReslice->SetInputData(0, mFusion->GetFirstVTKImageData());
 500 #endif
 501     mFusionReslice->Update();
 502
 503     if (!mFusionMapper)
 504       mFusionMapper = vtkSmartPointer<vtkImageMapToColors>::New();
 505
 506     vtkSmartPointer<vtkLookupTable> lut = vtkLookupTable::New();
 507     lut->SetRange(0, 1);
 508     lut->SetValueRange(0, 1);
 509     lut->SetSaturationRange(0, 0);
 510     lut->Build();
 511     mFusionMapper->SetLookupTable(lut);
 512 #if VTK_MAJOR_VERSION <= 5
 513     mFusionMapper->SetInput(mFusionReslice->GetOutput());
 514 #else
 515     mFusionMapper->SetInputConnection(mFusionReslice->GetOutputPort(0));
 516 #endif
 517
 518     if (!mFusionActor) {
 519       mFusionActor = vtkSmartPointer<vtkImageActor>::New();
 520 #if VTK_MAJOR_VERSION <= 5
 521       mFusionActor->SetInput(mFusionMapper->GetOutput());
 522 #else
 523       mFusionActor->GetMapper()->SetInputConnection(mFusionMapper->GetOutputPort());
 524 #endif
 525       mFusionActor->SetPickable(0);
 526       mFusionActor->SetVisibility(true);
 527       mFusionActor->SetOpacity(0.7);
 528 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 529       mFusionActor->GetMapper()->BorderOn();
 530 #endif
 531
 532       this->GetRenderer()->AddActor(mFusionActor);
 533     }
 534
 535     //Synchronize orientation and slice
 536     AdjustResliceToSliceOrientation(mFusionReslice);
 537     this->UpdateDisplayExtent();
 538     this->SetTSlice(mCurrentTSlice);
 539   }
 540 }
 541 //------------------------------------------------------------------------------
 542
 543
 544 //------------------------------------------------------------------------------
 545 bool vvSlicer::GetActorVisibility(const std::string& actor_type, int overlay_index)
 546 {
 547   bool vis = false;
 548   if (actor_type == "image")
 549     vis = mImageVisibility;
 550   else if (actor_type == "vector")
 551     vis = mVFVisibility;
 552   else if (actor_type == "overlay")
 553     vis = mOverlayVisibility;
 554   else if ( (actor_type == "fusion") || (actor_type == "fusionSequence") )
 555     vis = mFusionVisibility;
 556   else if (actor_type == "contour")
 557     vis = this->mSurfaceCutActors[overlay_index]->GetActor()->GetVisibility();
 558   return vis;
 559 }
 560 //------------------------------------------------------------------------------
 561
 562 //------------------------------------------------------------------------------
 563 void vvSlicer::SetActorVisibility(const std::string& actor_type, int overlay_index ,bool vis)
 564 {
 565   if (actor_type == "image")
 566     mImageVisibility = vis;
 567   else if (actor_type == "vector")
 568     mVFVisibility = vis;
 569   else if (actor_type == "overlay")
 570     mOverlayVisibility = vis;
 571   else if ( (actor_type == "fusion") || (actor_type == "fusionSequence") )
 572     mFusionVisibility = vis;
 573   else if (actor_type == "contour")
 574     this->mSurfaceCutActors[overlay_index]->GetActor()->SetVisibility(vis);
 575   UpdateDisplayExtent();
 576 }
 577 //------------------------------------------------------------------------------
 578
 579 //------------------------------------------------------------------------------
 580 void vvSlicer::SetVF(vvImage::Pointer vf)
 581 {
 582   if (vf->GetVTKImages().size()) {
 583     mVF = vf;
 584     mVFVisibility = true;
 585
 586     if (!mAAFilter) {
 587       mVFReslice = vtkSmartPointer<vtkImageReslice>::New();
 588       mVFReslice->SetInterpolationModeToLinear();
 589       mVFReslice->AutoCropOutputOn();
 590       mVFReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 591       mAAFilter= vtkSmartPointer<vtkAssignAttribute>::New();
 592       mVOIFilter = vtkSmartPointer<vtkExtractVOI>::New();
 593       mVOIFilter->SetSampleRate(mSubSampling,mSubSampling,mSubSampling);
 594     }
 595
 596     mConcatenatedVFTransform->Identity();
 597     mConcatenatedVFTransform->Concatenate(mVF->GetTransform()[0]);
 598     mConcatenatedVFTransform->Concatenate(mSlicingTransform);
 599     mVFReslice->SetResliceTransform(mConcatenatedVFTransform);
 600 #if VTK_MAJOR_VERSION <= 5
 601     mVFReslice->SetInput(0, mVF->GetFirstVTKImageData());
 602 #else
 603     mVFReslice->SetInputData(0, mVF->GetFirstVTKImageData());
 604 #endif
 605     mVFReslice->Update();
 606
 607 #if VTK_MAJOR_VERSION <= 5
 608     mVOIFilter->SetInput(mVFReslice->GetOutput());
 609     mAAFilter->SetInput(mVOIFilter->GetOutput());
 610 #else
 611     mVOIFilter->SetInputConnection(mVFReslice->GetOutputPort());
 612     mAAFilter->SetInputConnection(mVOIFilter->GetOutputPort());
 613 #endif
 614     ///This tells VTK to use the scalar (pixel) data of the image to draw the little arrows
 615     mAAFilter->Assign(vtkDataSetAttributes::SCALARS, vtkDataSetAttributes::VECTORS, vtkAssignAttribute::POINT_DATA);
 616
 617     if (!mArrow)
 618       mArrow = vtkSmartPointer<vvGlyphSource>::New();
 619     mArrow->SetGlyphTypeToSpecificArrow();
 620     mArrow->SetScale(mScale);
 621     mArrow->FilledOff();
 622
 623     // Glyph the gradient vector (with arrows)
 624     if (!mGlyphFilter)
 625       mGlyphFilter = vtkSmartPointer<vvGlyph2D>::New();
 626 #if VTK_MAJOR_VERSION <= 5
 627     mGlyphFilter->SetInput(mAAFilter->GetOutput());
 628     mGlyphFilter->SetSource(mArrow->GetOutput());
 629 #else
 630     mGlyphFilter->SetInputConnection(mAAFilter->GetOutputPort());
 631     mGlyphFilter->SetSourceConnection(mArrow->GetOutputPort());
 632 #endif
 633     mGlyphFilter->ScalingOn();
 634     mGlyphFilter->SetScaleModeToScaleByVector();
 635     mGlyphFilter->OrientOn();
 636     mGlyphFilter->SetVectorModeToUseVector();
 637     mGlyphFilter->SetColorModeToColorByVector();
 638
 639     if (!mVFColorLUT)
 640       mVFColorLUT = vtkSmartPointer<vtkLookupTable>::New();
 641
 642     double mVFColorHSV[3];
 643     vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
 644     mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
 645     mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
 646     mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
 647
 648     if (!mVFMapper)
 649       mVFMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
 650 #if VTK_MAJOR_VERSION <= 5
 651     mVFMapper->SetInput(mGlyphFilter->GetOutput());
 652 #else
 653     mVFMapper->SetInputConnection(mGlyphFilter->GetOutputPort());
 654 #endif
 655     mVFMapper->ImmediateModeRenderingOn();
 656     mVFMapper->SetLookupTable(mVFColorLUT);
 657
 658     if (!mVFActor)
 659       mVFActor = vtkSmartPointer<vtkActor>::New();
 660     mVFActor->SetMapper(mVFMapper);
 661     mVFActor->SetPickable(0);
 662     mVFActor->GetProperty()->SetLineWidth(mVFWidth);
 663     this->UpdateDisplayExtent();
 664     this->GetRenderer()->AddActor(mVFActor);
 665
 666     //Synchronize slice
 667     SetTSlice(mCurrentTSlice);
 668   }
 669 }
 670 //------------------------------------------------------------------------------
 671
 672
 673 //------------------------------------------------------------------------------
 674 void vvSlicer::SetLandmarks(vvLandmarks* landmarks)
 675 {
 676   mLandmarks = landmarks;
 677   if (landmarks) {
 678
 679     if (!mCross)
 680       mCross = vtkSmartPointer<vtkCursor3D>::New();
 681         if (!mClipBox)
 682       mClipBox = vtkSmartPointer<vtkBox>::New();
 683     if (!mLandClipper)
 684       mLandClipper = vtkSmartPointer<vvClipPolyData>::New();
 685     if (!mLandGlyph)
 686       mLandGlyph = vtkSmartPointer<vtkGlyph3D>::New();
 687     if (!mLandMapper)
 688       mLandMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
 689     if (!mLandActor)
 690       mLandActor = vtkSmartPointer<vtkActor>::New();
 691
 692     mCross->SetFocalPoint(0.0,0.0,0.0);
 693     mCross->SetModelBounds(-10,10,-10,10,-10,10);
 694     mCross->AllOff();
 695     mCross->AxesOn();
 696
 697     mLandClipper->SetClipFunction(mClipBox);
 698     mLandClipper->InsideOutOn();
 699 #if VTK_MAJOR_VERSION <= 5
 700     mLandmarkTransform = vtkSmartPointer<vtkTransformPolyDataFilter>::New();
 701     mLandmarkTransform->SetInput(mLandmarks->GetOutput());
 702     mConcatenatedTransform->Identity();
 703     mConcatenatedTransform->Concatenate(mImage->GetTransform()[0]);
 704     mConcatenatedTransform->Concatenate(mSlicingTransform);
 705     mLandmarkTransform->SetTransform(mConcatenatedTransform->GetInverse());
 706     mLandClipper->SetInput(mLandmarkTransform->GetOutput());
 707
 708     mLandGlyph->SetSource(mCross->GetOutput());
 709     mLandGlyph->SetInput(mLandClipper->GetOutput());
 710 #else
 711     mLandmarkTransform = vtkSmartPointer<vtkTransformPolyDataFilter>::New();
 712     mLandmarkTransform->SetInputData(mLandmarks->GetOutput());
 713     mConcatenatedTransform->Identity();
 714     mConcatenatedTransform->Concatenate(mImage->GetTransform()[0]);
 715     mConcatenatedTransform->Concatenate(mSlicingTransform);
 716     mLandmarkTransform->SetTransform(mConcatenatedTransform->GetInverse());
 717     mLandClipper->SetInputConnection(mLandmarkTransform->GetOutputPort());
 718
 719     mLandGlyph->SetSourceConnection(mCross->GetOutputPort());
 720     mLandGlyph->SetInputConnection(mLandClipper->GetOutputPort());
 721 #endif
 722     //mLandGlyph->SetIndexModeToScalar();
 723     //mLandGlyph->SetRange(0,1);
 724     //mLandGlyph->ScalingOff();
 725
 726     //mLandGlyph->SetColorModeToColorByScalar();
 727
 728     mLandGlyph->SetScaleModeToDataScalingOff();
 729     mLandGlyph->SetIndexModeToOff();
 730
 731     mLandMapper->SetInputConnection(mLandGlyph->GetOutputPort());
 732     //mLandMapper->ScalarVisibilityOff();
 733
 734     mLandActor->SetMapper(mLandMapper);
 735     mLandActor->GetProperty()->SetOpacity(0.995);  //in order to get VTK to turn on the alpha-blending in OpenGL
 736     mLandActor->GetProperty()->SetColor(255,10,212);
 737     mLandActor->SetPickable(0);
 738     mLandActor->SetVisibility(true);
 739     this->UpdateDisplayExtent();
 740   }
 741 }
 742 //------------------------------------------------------------------------------
 743
 744 //------------------------------------------------------------------------------
 745 //FIXME: this function leaks memory, we should fix it someday :)
 746 void vvSlicer::RemoveActor(const std::string& actor_type, int overlay_index)
 747 {
 748   if (actor_type == "vector") {
 749     Renderer->RemoveActor(mVFActor);
 750     mGlyphFilter=NULL;
 751     mVF = NULL;
 752     mArrow = NULL;
 753     mAAFilter=NULL;
 754     mVOIFilter = NULL;
 755     mVFMapper = NULL;
 756     mVFActor = NULL;
 757   }
 758   if (actor_type == "overlay") {
 759     Renderer->RemoveActor(mOverlayActor);
 760     mOverlay = NULL;
 761     mOverlayActor = NULL;
 762     mOverlayMapper = NULL;
 763   }
 764   if ( (actor_type == "fusion") || (actor_type == "fusionSequence") ) {
 765     Renderer->RemoveActor(mFusionActor);
 766     mFusion = NULL;
 767     mFusionActor = NULL;
 768     mFusionMapper = NULL;
 769   }
 770   if (actor_type == "contour") {
 771     Renderer->RemoveActor(this->mSurfaceCutActors[overlay_index]->GetActor());
 772     mSurfaceCutActors.erase(mSurfaceCutActors.begin()+overlay_index);
 773   }
 774 }
 775 //------------------------------------------------------------------------------
 776
 777
 778 //------------------------------------------------------------------------------
 779 void vvSlicer::SetVFSubSampling(int sub)
 780 {
 781   if (mVOIFilter) {
 782     mVOIFilter->SetSampleRate(mSubSampling,mSubSampling,mSubSampling);
 783     mSubSampling = sub;
 784   }
 785   UpdateDisplayExtent();
 786   Render();
 787 }
 788 //------------------------------------------------------------------------------
 789
 790
 791 //------------------------------------------------------------------------------
 792 void vvSlicer::SetVFScale(int scale)
 793 {
 794   mScale = scale;
 795   if (mArrow)
 796     mArrow->SetScale(mScale);
 797   UpdateDisplayExtent();
 798   Render();
 799 }
 800 //------------------------------------------------------------------------------
 801
 802 //------------------------------------------------------------------------------
 803 void vvSlicer::SetVFWidth(int width)
 804 {
 805   mVFWidth = width;
 806   if (mVFActor)
 807     mVFActor->GetProperty()->SetLineWidth(mVFWidth);
 808   UpdateDisplayExtent();
 809   Render();
 810 }
 811 //------------------------------------------------------------------------------
 812
 813
 814 //------------------------------------------------------------------------------
 815 void vvSlicer::SetVFLog(int log)
 816 {
 817   mVFLog = log;
 818   if (mGlyphFilter) {
 819     mGlyphFilter->SetUseLog(mVFLog);
 820     mGlyphFilter->Modified();
 821   }
 822   UpdateDisplayExtent();
 823   Render();
 824 }
 825 //------------------------------------------------------------------------------
 826
 827
 828 //------------------------------------------------------------------------------
 829 void vvSlicer::SetTSlice(int t, bool updateLinkedImages)
 830 {
 831         if (!updateLinkedImages) {
 832                 mCurrentTSlice = t;
 833 #if VTK_MAJOR_VERSION <= 5
 834                 mImageReslice->SetInput( mImage->GetVTKImages()[mCurrentTSlice] );
 835 #else
 836                 mImageReslice->SetInputData( mImage->GetVTKImages()[mCurrentTSlice] );
 837 #endif
 838                 // Update transform
 839                 mConcatenatedTransform->Identity();
 840                 mConcatenatedTransform->Concatenate(mImage->GetTransform()[mCurrentTSlice]);
 841                 mConcatenatedTransform->Concatenate(mSlicingTransform);
 842                 UpdateDisplayExtent();
 843                 return;
 844         }
 845   if (t < 0)
 846     mCurrentTSlice = 0;
 847   else if ((unsigned int)t >= mImage->GetVTKImages().size())
 848     mCurrentTSlice = mImage->GetVTKImages().size() -1;
 849   else
 850     mCurrentTSlice = t;
 851
 852   // Update transform
 853   mConcatenatedTransform->Identity();
 854   mConcatenatedTransform->Concatenate(mImage->GetTransform()[mCurrentTSlice]);
 855   mConcatenatedTransform->Concatenate(mSlicingTransform);
 856
 857   // Update image data
 858 #if VTK_MAJOR_VERSION <= 5
 859    mImageReslice->SetInput( mImage->GetVTKImages()[mCurrentTSlice] );
 860 #else
 861   mImageReslice->SetInputData( mImage->GetVTKImages()[mCurrentTSlice] );
 862 #endif
 863   if (mVF && mVFActor->GetVisibility()) {
 864     if (mVF->GetVTKImages().size() > (unsigned int)mCurrentTSlice)
 865 #if VTK_MAJOR_VERSION <= 5
 866       mVFReslice->SetInput(mVF->GetVTKImages()[mCurrentTSlice]);
 867 #else
 868       mVFReslice->SetInputData(mVF->GetVTKImages()[mCurrentTSlice]);
 869 #endif
 870       // Update overlay transform
 871       mConcatenatedVFTransform->Identity();
 872       mConcatenatedVFTransform->Concatenate(mVF->GetTransform()[mCurrentTSlice]);
 873       mConcatenatedVFTransform->Concatenate(mSlicingTransform);
 874   }
 875   //update the overlay
 876   if (mOverlay && mOverlayActor->GetVisibility()) {
 877     if (mOverlay->GetVTKImages().size() > (unsigned int)t) {
 878       mCurrentOverlayTSlice = t;
 879 #if VTK_MAJOR_VERSION <= 5
 880       mOverlayReslice->SetInput( mOverlay->GetVTKImages()[mCurrentOverlayTSlice] );
 881 #else
 882       mOverlayReslice->SetInputData( mOverlay->GetVTKImages()[mCurrentOverlayTSlice] );
 883 #endif
 884       // Update overlay transform
 885       mConcatenatedOverlayTransform->Identity();
 886       mConcatenatedOverlayTransform->Concatenate(mOverlay->GetTransform()[mCurrentOverlayTSlice]);
 887       mConcatenatedOverlayTransform->Concatenate(mSlicingTransform);
 888     }
 889   }
 890   //update the fusion ; except in case this is a fusionSequence, in which case both 'times' should be independent.
 891   if (mFusion && mFusionActor->GetVisibility() && (mFusionSequenceCode<0)) {
 892     if (mFusion->GetVTKImages().size() > (unsigned int)t) {
 893       mCurrentFusionTSlice = t;
 894 #if VTK_MAJOR_VERSION <= 5
 895       mFusionReslice->SetInput( mFusion->GetVTKImages()[mCurrentFusionTSlice]);
 896 #else
 897       mFusionReslice->SetInputData( mFusion->GetVTKImages()[mCurrentFusionTSlice]);
 898 #endif
 899
 900       // Update fusion transform
 901       mConcatenatedFusionTransform->Identity();
 902       mConcatenatedFusionTransform->Concatenate(mFusion->GetTransform()[mCurrentFusionTSlice]);
 903       mConcatenatedFusionTransform->Concatenate(mSlicingTransform);
 904     }
 905   }
 906   if (mSurfaceCutActors.size() > 0)
 907     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 908          i!=mSurfaceCutActors.end(); i++)
 909       (*i)->SetTimeSlice(mCurrentTSlice);
 910   UpdateDisplayExtent();
 911 }
 912 //------------------------------------------------------------------------------
 913
 914
 915 //------------------------------------------------------------------------------
 916 void vvSlicer::SetFusionSequenceTSlice(int t)
 917 {
 918   if (mFusion && mFusionActor->GetVisibility() && (mFusionSequenceCode>=0)) {
 919     if (mFusion->GetVTKImages().size() > (unsigned int)t) {
 920       mCurrentFusionTSlice = t;
 921 #if VTK_MAJOR_VERSION <= 5
 922       mFusionReslice->SetInput( mFusion->GetVTKImages()[mCurrentFusionTSlice] );
 923 #else
 924       mFusionReslice->SetInputData( mFusion->GetVTKImages()[mCurrentFusionTSlice] );
 925 #endif
 926       // Update fusion transform
 927       mConcatenatedFusionTransform->Identity();
 928       mConcatenatedFusionTransform->Concatenate(mFusion->GetTransform()[mCurrentFusionTSlice]); //not really useful...
 929       mConcatenatedFusionTransform->Concatenate(mSlicingTransform);
 930     }
 931   }
 932
 933   UpdateDisplayExtent();
 934 }
 935 //------------------------------------------------------------------------------
 936
 937
 938 //------------------------------------------------------------------------------
 939 int vvSlicer::GetTSlice()
 940 {
 941   return mCurrentTSlice;
 942 }
 943 //------------------------------------------------------------------------------
 944
 945 //------------------------------------------------------------------------------
 946 int vvSlicer::GetMaxCurrentTSlice()
 947 {
 948   int t = mCurrentTSlice;
 949   if(mOverlay && mOverlayActor->GetVisibility())
 950     t = std::max(t, mCurrentOverlayTSlice);
 951   if(mFusion&& (mFusionSequenceCode<0) && mFusionActor->GetVisibility()) //ignore fusionSequence data: for these, the times are not to be related (this way)
 952     t = std::max(t, mCurrentFusionTSlice);
 953   return t;
 954 }
 955 //------------------------------------------------------------------------------
 956
 957 //------------------------------------------------------------------------------
 958 int vvSlicer::GetFusionTSlice()
 959 {
 960   return mCurrentFusionTSlice;
 961 }
 962 //------------------------------------------------------------------------------
 963
 964 //------------------------------------------------------------------------------
 965 int vvSlicer::GetOverlayTSlice()
 966 {
 967   return mCurrentOverlayTSlice;
 968 }
 969 //------------------------------------------------------------------------------
 970
 971 //------------------------------------------------------------------------------
 972 void vvSlicer::SetSliceOrientation(int orientation)
 973 {
 974   //if 2D image, force to watch in Axial View
 975   int extent[6];
 976 #if VTK_MAJOR_VERSION <= 5
 977     this->GetInput()->GetWholeExtent(extent);
 978 #else
 979     int* ext = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
 980     copyExtent(ext, extent);
 981 #endif
 982
 983   if (extent[5]-extent[4] <= 2)
 984     orientation = vtkImageViewer2::SLICE_ORIENTATION_XY;
 985
 986   if (orientation < vtkImageViewer2::SLICE_ORIENTATION_YZ ||
 987       orientation > vtkImageViewer2::SLICE_ORIENTATION_XY) {
 988     vtkErrorMacro("Error - invalid slice orientation " << orientation);
 989     return;
 990   }
 991
 992   this->SliceOrientation = orientation;
 993
 994   if(mFusion)
 995     AdjustResliceToSliceOrientation(mFusionReslice);
 996
 997   if(mOverlay)
 998     AdjustResliceToSliceOrientation(mOverlayReslice);
 999
1000   if(mVF)
1001     AdjustResliceToSliceOrientation(mVFReslice);
1002
1003   // Update the viewer
1004
1005   // Go to current cursor position
1006   // double* cursorPos = GetCursorPosition();
1007   // DDV(cursorPos, 3);
1008   // SetCurrentPosition(cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
1009
1010   if (mFirstSetSliceOrientation) {
1011     int *range = this->GetSliceRange();
1012     if (range)
1013       this->Slice = static_cast<int>((range[0] + range[1]) * 0.5);
1014 #if VTK_MAJOR_VERSION <= 5
1015       mFirstSetSliceOrientation = false;
1016 #endif
1017   }
1018   else if (this->Renderer && this->GetInput()) {
1019     double s = mCursor[orientation];
1020     double sCursor = (s - this->GetInput()->GetOrigin()[orientation])/this->GetInput()->GetSpacing()[orientation];
1021     this->Slice = static_cast<int>(sCursor);
1022   }
1023
1024   this->UpdateOrientation();
1025
1026   this->UpdateDisplayExtent();
1027
1028   if (mFirstSetSliceOrientation) {
1029     mFirstSetSliceOrientation = false;
1030   }
1031
1032   if (this->Renderer && this->GetInput()) {
1033     double scale = this->Renderer->GetActiveCamera()->GetParallelScale();
1034     this->Renderer->ResetCamera();
1035     this->Renderer->GetActiveCamera()->SetParallelScale(scale);
1036   }
1037
1038   SetContourSlice();
1039 }
1040 //----------------------------------------------------------------------------
1041
1042 //------------------------------------------------------------------------------
1043 // This function ensures that we sample the slices of a vtkImageReslice filter
1044 // in the direction of the slicer (SliceOrientation) similarly as mImageReslice.
1045 // In other words, we change the grid of the reslice in the same way as the grid
1046 // of the displayed image in the slicing direction.
1047 void vvSlicer::AdjustResliceToSliceOrientation(vtkImageReslice *reslice)
1048 {
1049   // Reset autocrop and update output information
1050   reslice->SetOutputOriginToDefault();
1051   reslice->SetOutputSpacingToDefault();
1052 #if VTK_MAJOR_VERSION <= 5
1053   reslice->GetOutput()->UpdateInformation();
1054 #else
1055   reslice->UpdateInformation();
1056 #endif
1057
1058   // Ge new origin / spacing
1059   double origin[3];
1060   double spacing[3];
1061   reslice->GetOutput()->GetOrigin(origin);
1062   reslice->GetOutput()->GetSpacing(spacing);
1063
1064   // Use similar spacing as the image in the direction SliceOrientation
1065   spacing[this->SliceOrientation] = mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
1066
1067   // Modify origin to be on the image grid in the direction SliceOrientation in 3 steps
1068   // Step 1: from world coordinates to image coordinates
1069   origin[this->SliceOrientation] -= mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
1070   origin[this->SliceOrientation] /= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
1071
1072   // Step 2: round to nearest grid positionInc. This has been validated as the only
1073   // way to have something consistent with the thickness of a 2D slice visible on the
1074   // other slices. The thickness is accounted for so if the 2D slice is to thin and
1075   // between two slices, one will never be able to see this 2D slice (bug #1883).
1076   origin[this->SliceOrientation] = itk::Math::Round<double>(origin[this->SliceOrientation]);
1077
1078   // Step 3: back to world coordinates
1079   origin[this->SliceOrientation] *= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
1080   origin[this->SliceOrientation] += mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
1081
1082   // Set new spacing and origin
1083   reslice->SetOutputOrigin(origin);
1084   reslice->SetOutputSpacing(spacing);
1085   reslice->UpdateInformation();
1086 #if VTK_MAJOR_VERSION <= 5
1087   reslice->GetOutput()->UpdateInformation();
1088 #endif
1089 }
1090 //------------------------------------------------------------------------------
1091
1092 //----------------------------------------------------------------------------
1093 int * vvSlicer::GetExtent()
1094 {
1095   int *w_ext;
1096   if (mUseReducedExtent) {
1097     w_ext = mReducedExtent;
1098   }
1099   else {
1100 #if VTK_MAJOR_VERSION <= 5
1101     w_ext = GetInput()->GetWholeExtent();
1102 #else
1103     w_ext = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
1104 #endif
1105   }
1106   return w_ext;
1107 }
1108 //----------------------------------------------------------------------------
1109
1110
1111 //----------------------------------------------------------------------------
1112 int vvSlicer::GetOrientation()
1113 {
1114   return this->SliceOrientation;
1115 }
1116 //----------------------------------------------------------------------------
1117
1118
1119 //----------------------------------------------------------------------------
1120 void vvSlicer::UpdateDisplayExtent()
1121 {
1122   emit UpdateDisplayExtentBegin(mSlicerNumber);
1123   vtkImageData *input = this->GetInput();
1124   if (!input || !this->ImageActor) {
1125     return;
1126   }
1127
1128 #if VTK_MAJOR_VERSION <= 5
1129   input->UpdateInformation();
1130 #else
1131   mRegisterExtent = mImageReslice->GetOutputInformation(0)->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
1132 #endif
1133   this->SetSlice( this->GetSlice() ); //SR: make sure the update let the slice in extents
1134
1135   // Local copy of extent
1136   int w_ext[6];
1137 #if VTK_MAJOR_VERSION <= 5
1138   int* ext = GetExtent();
1139 #else
1140   int* ext = mImageReslice->GetOutputInformation(0)->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
1141 #endif
1142   copyExtent(ext, w_ext);
1143   if (mUseReducedExtent) {
1144         copyExtent(mReducedExtent, w_ext);
1145     }
1146   // Set slice value
1147
1148   w_ext[ this->SliceOrientation*2   ] = this->Slice;
1149   w_ext[ this->SliceOrientation*2+1 ] = this->Slice;
1150
1151   // Image actor
1152   this->ImageActor->SetVisibility(mImageVisibility);
1153   this->ImageActor->SetDisplayExtent(w_ext);
1154
1155 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
1156   // Fix for bug #1882
1157   dynamic_cast<vtkImageSliceMapper *>(this->ImageActor->GetMapper())->SetOrientation(this->GetOrientation());
1158 #endif
1159
1160   // Overlay image actor
1161   if (mOverlay && mOverlayVisibility) {
1162     AdjustResliceToSliceOrientation(mOverlayReslice);
1163     int overExtent[6];
1164 #if VTK_MAJOR_VERSION <= 5
1165     this->ConvertImageToImageDisplayExtent(input, w_ext, mOverlayReslice->GetOutput(), overExtent);
1166     bool out = ClipDisplayedExtent(overExtent, mOverlayMapper->GetInput()->GetWholeExtent());
1167 #else
1168     this->ConvertImageToImageDisplayExtent(mImageReslice->GetOutputInformation(0), w_ext, mOverlayReslice->GetOutput(), overExtent);
1169     bool out = ClipDisplayedExtent(overExtent, mOverlayMapper->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT()));
1170 #endif
1171     mOverlayActor->SetVisibility(!out);
1172     mOverlayActor->SetDisplayExtent( overExtent );
1173 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
1174     // Fix for bug #1882
1175     dynamic_cast<vtkImageSliceMapper *>(mOverlayActor->GetMapper())->SetOrientation(this->GetOrientation());
1176 #endif
1177   }
1178   else if(mOverlay)
1179     mOverlayActor->SetVisibility(false);
1180
1181   // Fusion image actor
1182   if (mFusion && mFusionVisibility) {
1183     AdjustResliceToSliceOrientation(mFusionReslice);
1184     int fusExtent[6];
1185 #if VTK_MAJOR_VERSION <= 5
1186     this->ConvertImageToImageDisplayExtent(input, w_ext, mFusionReslice->GetOutput(), fusExtent);
1187     bool out = ClipDisplayedExtent(fusExtent, mFusionMapper->GetInput()->GetWholeExtent());
1188 #else
1189     this->ConvertImageToImageDisplayExtent(mImageReslice->GetOutputInformation(0), w_ext, mFusionReslice->GetOutput(), fusExtent);
1190     bool out = ClipDisplayedExtent(fusExtent, mFusionMapper->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT()));
1191 #endif
1192     mFusionActor->SetVisibility(!out);
1193     mFusionActor->SetDisplayExtent( fusExtent );
1194 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
1195     // Fix for bug #1882
1196     dynamic_cast<vtkImageSliceMapper *>(mFusionActor->GetMapper())->SetOrientation(this->GetOrientation());
1197 #endif
1198   }
1199   else if(mFusion)
1200     mFusionActor->SetVisibility(false);
1201   // Vector field actor
1202   double* camera = Renderer->GetActiveCamera()->GetPosition();
1203   double* image_bounds = ImageActor->GetBounds();
1204   double position[3] = {0, 0, 0};
1205   position[this->SliceOrientation] = image_bounds[this->SliceOrientation*2];
1206
1207   //print_vector<double, 6>("camera", camera);
1208   //print_vector<double, 6>("image_bounds", image_bounds);
1209   //print_vector<double, 3>("position", position);
1210
1211   // find where to place the VF actor. to deal with
1212   // z-buffer issues, the VF is placed right in front of the image,
1213   // subject to a small offset. the position actually depends on the
1214   // the location of the camera relative to the image.
1215   double offset = 1;
1216   if (camera[this->SliceOrientation] < image_bounds[this->SliceOrientation*2])
1217     offset = -1;
1218
1219   if (mVF && mVFVisibility) {
1220     AdjustResliceToSliceOrientation(mVFReslice);
1221     int vfExtent[6];
1222 #if VTK_MAJOR_VERSION <= 5
1223     mVF->GetVTKImages()[0]->UpdateInformation();
1224     this->ConvertImageToImageDisplayExtent(input, w_ext, mVFReslice->GetOutput(), vfExtent);
1225     bool out = ClipDisplayedExtent(vfExtent, mVOIFilter->GetInput()->GetWholeExtent());
1226 #else
1227     mVOIFilter->Update();
1228     this->ConvertImageToImageDisplayExtent(mImageReslice->GetOutputInformation(0), w_ext, mVFReslice->GetOutput(), vfExtent);
1229     bool out = ClipDisplayedExtent(vfExtent, mVOIFilter->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT()));
1230 #endif
1231     mVFActor->SetVisibility(!out);
1232     mVOIFilter->SetVOI(vfExtent);
1233     int orientation[3] = {1,1,1};
1234     orientation[this->SliceOrientation] = 0;
1235     mGlyphFilter->SetOrientation(orientation[0], orientation[1], orientation[2]);
1236     position[this->SliceOrientation] += offset;
1237     mVFActor->SetPosition(position);
1238     mVFActor->GetProperty()->SetOpacity(0.995); //in order to get VTK to turn on the alpha-blending in OpenGL
1239     mVFMapper->Update();
1240
1241   }
1242   else if(mVF)
1243     mVFActor->SetVisibility(false);
1244
1245
1246     double boundsT [6];
1247       for(unsigned int i=0; i<6; i++)
1248         boundsT[i] = ImageActor->GetBounds()[i];
1249       boundsT[ this->SliceOrientation*2   ] = ImageActor->GetBounds()[ this->SliceOrientation*2  ]-fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
1250       boundsT[ this->SliceOrientation*2+1 ] = ImageActor->GetBounds()[ this->SliceOrientation*2+1 ]+fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
1251
1252
1253   // Landmarks actor
1254   if (mLandActor) {
1255     if (mClipBox) {
1256       RemoveLandmarks();
1257     }
1258
1259     position[this->SliceOrientation] = offset;
1260     mLandActor->SetPosition(position);
1261   }
1262
1263   // Figure out the correct clipping range
1264   if (this->Renderer) {
1265     if (this->InteractorStyle &&
1266         this->InteractorStyle->GetAutoAdjustCameraClippingRange()) {
1267       this->Renderer->ResetCameraClippingRange();
1268     } else {
1269       vtkCamera *cam = this->Renderer->GetActiveCamera();
1270       if (cam) {
1271         double bounds[6];
1272         this->ImageActor->GetBounds(bounds);
1273         double spos = (double)bounds[this->SliceOrientation * 2];
1274         double cpos = (double)cam->GetPosition()[this->SliceOrientation];
1275         double range = fabs(spos - cpos);
1276         double *spacing = input->GetSpacing();
1277         double sumSpacing = spacing[0] + spacing[1] + spacing[2];
1278         cam->SetClippingRange(range - sumSpacing, range + sumSpacing);
1279       }
1280     }
1281
1282     if (mLandActor) {
1283         if (mClipBox) {
1284             DisplayLandmarks();
1285         }
1286     }
1287   }
1288   emit UpdateDisplayExtentEnd(mSlicerNumber);
1289 }
1290 //----------------------------------------------------------------------------
1291
1292 //----------------------------------------------------------------------------
1293 void vvSlicer::ConvertImageToImageDisplayExtent(vtkInformation *sourceImage, const int sourceExtent[6],
1294                                                 vtkImageData *targetImage, int targetExtent[6])
1295 {
1296   double dExtents[6];
1297   double *origin, *spacing;
1298   origin = sourceImage->Get(vtkDataObject::ORIGIN());
1299   spacing = sourceImage->Get(vtkDataObject::SPACING());
1300   for(unsigned int i=0; i<6; i++) {
1301     // From source voxel coordinates to world coordinates
1302     dExtents[i] = origin[i/2] + spacing[i/2] * sourceExtent[i];
1303
1304     // From world coordinates to floating point target voxel coordinates
1305     dExtents[i] = (dExtents[i]- targetImage->GetOrigin()[i/2]) / targetImage->GetSpacing()[i/2];
1306
1307     // Round to current slice or larger extent
1308     if(i/2==this->GetOrientation())
1309       targetExtent[i] = itk::Math::Round<double>(dExtents[i]);
1310     else if(i%2==1)
1311       targetExtent[i] = itk::Math::Ceil<double>(dExtents[i]);
1312     else
1313       targetExtent[i] = itk::Math::Floor<double>(dExtents[i]);
1314   }
1315 }
1316 //----------------------------------------------------------------------------
1317
1318 //----------------------------------------------------------------------------
1319 void vvSlicer::ConvertImageToImageDisplayExtent(vtkImageData *sourceImage, const int sourceExtent[6],
1320                                                 vtkImageData *targetImage, int targetExtent[6])
1321 {
1322   double dExtents[6];
1323   for(unsigned int i=0; i<6; i++) {
1324     // From source voxel coordinates to world coordinates
1325     dExtents[i] = sourceImage->GetOrigin()[i/2] + sourceImage->GetSpacing()[i/2] * sourceExtent[i];
1326
1327     // From world coordinates to floating point target voxel coordinates
1328     dExtents[i] = (dExtents[i]- targetImage->GetOrigin()[i/2]) / targetImage->GetSpacing()[i/2];
1329
1330     // Round to current slice or larger extent
1331     if(i/2==this->GetOrientation())
1332       targetExtent[i] = itk::Math::Round<double>(dExtents[i]);
1333     else if(i%2==1)
1334       targetExtent[i] = itk::Math::Ceil<double>(dExtents[i]);
1335     else
1336       targetExtent[i] = itk::Math::Floor<double>(dExtents[i]);
1337   }
1338 }
1339 //----------------------------------------------------------------------------
1340
1341 //----------------------------------------------------------------------------
1342 bool vvSlicer::ClipDisplayedExtent(int extent[6], int refExtent[6])
1343 {
1344   bool out = false;
1345   int maxBound = 6;
1346
1347   for (int i = 0; i < maxBound; i = i+2) {
1348     //if we are totally outside the image
1349     if ( extent[i] > refExtent[i+1] || extent[i+1] < refExtent[i] ) {
1350       out = true;
1351       break;
1352     }
1353     //crop to the limit of the image
1354     extent[i] = std::max(extent[i], refExtent[i]);
1355     extent[i] = std::min(extent[i], refExtent[i+1]);;
1356     extent[i+1] = std::max(extent[i+1], refExtent[i]);
1357     extent[i+1] = std::min(extent[i+1], refExtent[i+1]);;
1358   }
1359   if (out)
1360     for (int i = 0; i < maxBound; i = i+2) {
1361       extent[i] = refExtent[i];
1362       extent[i+1] = refExtent[i];
1363     }
1364   return out;
1365 }
1366 //----------------------------------------------------------------------------
1367
1368
1369 //----------------------------------------------------------------------------
1370 void vvSlicer::UpdateOrientation()
1371 {
1372   // Set the camera position
1373   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1374   if (cam) {
1375     switch (this->SliceOrientation) {
1376     case vtkImageViewer2::SLICE_ORIENTATION_XY:
1377       cam->SetFocalPoint(0,0,0);
1378       cam->SetPosition(0,0,-1); // -1 if medical ?
1379       cam->SetViewUp(0,-1,0);
1380       break;
1381
1382     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
1383       cam->SetFocalPoint(0,0,0);
1384       cam->SetPosition(0,-1,0); // 1 if medical ?
1385       cam->SetViewUp(0,0,1);
1386       break;
1387
1388     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1389       cam->SetFocalPoint(0,0,0);
1390       cam->SetPosition(-1,0,0); // -1 if medical ?
1391       cam->SetViewUp(0,0,1);
1392       break;
1393     }
1394   }
1395 }
1396 //----------------------------------------------------------------------------
1397
1398
1399 //----------------------------------------------------------------------------
1400 void vvSlicer::SetOpacity(double s)
1401 {
1402   this->GetImageActor()->SetOpacity(s);
1403 }
1404 //----------------------------------------------------------------------------
1405
1406
1407 //----------------------------------------------------------------------------
1408 void vvSlicer::SetRenderWindow(int orientation, vtkRenderWindow * rw)
1409 {
1410   this->Superclass::SetRenderWindow(rw);
1411   this->SetupInteractor(rw->GetInteractor());
1412   ca->SetImageActor(this->GetImageActor());
1413   ca->SetWindowLevel(this->GetWindowLevel());
1414   ca->SetText(3, "<window>\n<level>");
1415
1416   double bounds[6];
1417   double max = 65000;
1418
1419   bounds[0] = -max;
1420   bounds[1] = max;
1421   bounds[2] = -max;
1422   bounds[3] = max;
1423   bounds[4] = -max;
1424   bounds[5] = max;
1425   crossCursor->SetModelBounds(bounds);
1426
1427   this->GetRenderer()->AddActor(pdmA);
1428   this->GetRenderer()->AddActor(ca);
1429   this->GetRenderer()->ResetCamera();
1430
1431   //this is just a mapping between the labeling of the orientations presented to the user and
1432   //the one used by vtk
1433   SetSliceOrientation(2-(orientation%3));
1434   ResetCamera();
1435 }
1436 //----------------------------------------------------------------------------
1437
1438
1439 //----------------------------------------------------------------------------
1440 void vvSlicer::ResetCamera()
1441 {
1442   this->GetRenderer()->ResetCamera();
1443 }
1444 //----------------------------------------------------------------------------
1445
1446
1447 //----------------------------------------------------------------------------
1448 void vvSlicer::SetDisplayMode(bool i)
1449 {
1450         this->GetRenderer()->SetDraw(i);
1451         if (i) UpdateDisplayExtent();
1452 }
1453 //----------------------------------------------------------------------------
1454
1455
1456 //----------------------------------------------------------------------------
1457 void vvSlicer::FlipHorizontalView()
1458 {
1459   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1460   if (cam) {
1461     double *position = cam->GetPosition();
1462     double factor[3] = {1, 1, 1};
1463     factor[this->SliceOrientation] = -1;
1464     cam->SetPosition(factor[0]*position[0],factor[1]*position[1],factor[2]*position[2]);
1465
1466 /*    switch (this->SliceOrientation) {
1467     case vtkImageViewer2::SLICE_ORIENTATION_XY:
1468       cam->SetPosition(position[0],position[1],-position[2]);
1469       break;
1470
1471     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
1472       cam->SetPosition(position[0],-position[1],position[2]);
1473       break;
1474
1475     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1476       cam->SetPosition(-position[0],position[1],position[2]);
1477       break;
1478     }*/
1479
1480     this->Renderer->ResetCameraClippingRange();
1481     this->UpdateDisplayExtent();
1482   }
1483 }
1484 //----------------------------------------------------------------------------
1485
1486
1487 //----------------------------------------------------------------------------
1488 void vvSlicer::FlipVerticalView()
1489 {
1490   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1491   if (cam) {
1492     FlipHorizontalView();
1493     double *viewup = cam->GetViewUp();
1494     cam->SetViewUp(-viewup[0],-viewup[1],-viewup[2]);
1495     this->UpdateDisplayExtent();
1496   }
1497 }
1498 //----------------------------------------------------------------------------
1499
1500
1501 //----------------------------------------------------------------------------
1502 void vvSlicer::SetColorWindow(double window)
1503 {
1504   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1505   if ( LUT ) {
1506     double level = this->GetWindowLevel()->GetLevel();
1507     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1508     LUT->Build();
1509   }
1510   this->vtkImageViewer2::SetColorWindow(window);
1511 }
1512 //----------------------------------------------------------------------------
1513
1514 //----------------------------------------------------------------------------
1515 void vvSlicer::SetColorLevel(double level)
1516 {
1517   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1518   if ( LUT ) {
1519     double window = this->GetWindowLevel()->GetWindow();
1520     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1521     LUT->Build();
1522   }
1523   this->vtkImageViewer2::SetColorLevel(level);
1524 }
1525 //----------------------------------------------------------------------------
1526
1527 //----------------------------------------------------------------------------
1528 double vvSlicer::GetOverlayColorWindow()
1529 {
1530   if(mOverlayMapper)
1531     return mOverlayMapper->GetWindow();
1532   else
1533     return 0.;
1534 }
1535 //----------------------------------------------------------------------------
1536
1537 //----------------------------------------------------------------------------
1538 double vvSlicer::GetOverlayColorLevel()
1539 {
1540   if(mOverlayMapper)
1541     return mOverlayMapper->GetLevel();
1542   else
1543     return 0.;
1544 }
1545 //----------------------------------------------------------------------------
1546
1547 //----------------------------------------------------------------------------
1548 void vvSlicer::SetOverlayColorWindow(double window)
1549 {
1550   if(mOverlayMapper)
1551     mOverlayMapper->SetWindow(window);
1552 }
1553 //----------------------------------------------------------------------------
1554
1555 //----------------------------------------------------------------------------
1556 void vvSlicer::SetOverlayColorLevel(double level)
1557 {
1558   if(mOverlayMapper)
1559     mOverlayMapper->SetLevel(level);
1560 }
1561 //----------------------------------------------------------------------------
1562
1563 //----------------------------------------------------------------------------
1564 // Returns the min an the max value in a 20%x20% region around the mouse pointer
1565 void vvSlicer::GetExtremasAroundMousePointer(double & min, double & max, vtkImageData *image, vtkTransform *transform)
1566 {
1567   //Get mouse pointer position in view coordinates
1568   double corner1[3];
1569   double corner2[3];
1570   for(int i=0; i<3; i++) {
1571     corner1[i] = mCurrent[i];
1572     corner2[i] = mCurrent[i];
1573   }
1574
1575   this->Renderer->WorldToView(corner1[0], corner1[1], corner1[2]);
1576   this->Renderer->WorldToView(corner2[0], corner2[1], corner2[2]);
1577
1578   // In view coordinates, x is the slicer width and y is the slicer height are the in-plane axis
1579   int w, h;
1580   this->Renderer->GetTiledSize(&w, &h);
1581   corner1[0] -= 0.2*h/(double)w;
1582   corner2[0] += 0.2*h/(double)w;
1583   corner1[1] -= 0.2;
1584   corner2[1] += 0.2;
1585   this->Renderer->ViewToWorld(corner1[0], corner1[1], corner1[2]);
1586   this->Renderer->ViewToWorld(corner2[0], corner2[1], corner2[2]);
1587
1588   //Convert to image pixel coordinates (rounded)
1589   transform->TransformPoint(corner1, corner1);
1590   transform->TransformPoint(corner2, corner2);
1591   int iLocalExtents[6];
1592   for(int i=0; i<3; i++) {
1593     corner1[i] = (corner1[i] - image->GetOrigin()[i])/image->GetSpacing()[i];
1594     corner2[i] = (corner2[i] - image->GetOrigin()[i])/image->GetSpacing()[i];
1595
1596     iLocalExtents[i*2  ] = lrint(corner1[i]);
1597     iLocalExtents[i*2+1] = lrint(corner2[i]);
1598
1599     if(iLocalExtents[i*2  ]>iLocalExtents[i*2+1])
1600       std::swap(iLocalExtents[i*2], iLocalExtents[i*2+1]);
1601
1602 #if VTK_MAJOR_VERSION > 5
1603     for(int j=0;j<2; j++) {
1604       if(iLocalExtents[i*2+j]< mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT())[2*i])
1605         iLocalExtents[i*2+j] = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT())[2*i];
1606
1607       if(iLocalExtents[i*2+j]> mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT())[2*i+1])
1608         iLocalExtents[i*2+j] = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT())[2*i+1];
1609     }
1610 #endif
1611   }
1612
1613   vtkSmartPointer<vtkExtractVOI> voiFilter = vtkSmartPointer<vtkExtractVOI>::New();
1614 #if VTK_MAJOR_VERSION <= 5
1615   voiFilter->SetInput(image);
1616 #else
1617   voiFilter->SetInputData(image);
1618 #endif
1619   voiFilter->SetVOI(iLocalExtents);
1620   voiFilter->Update();
1621   if (!voiFilter->GetOutput()->GetNumberOfPoints()) {
1622     min = 0;
1623     max = 0;
1624     return;
1625   }
1626
1627   vtkSmartPointer<vtkImageAccumulate> accFilter = vtkSmartPointer<vtkImageAccumulate>::New();
1628 #if VTK_MAJOR_VERSION <= 5
1629   accFilter->SetInput(voiFilter->GetOutput());
1630 #else
1631   accFilter->SetInputConnection(voiFilter->GetOutputPort(0));
1632 #endif
1633   accFilter->Update();
1634
1635   min = *(accFilter->GetMin());
1636   max = *(accFilter->GetMax());
1637 }
1638 //----------------------------------------------------------------------------
1639
1640 //----------------------------------------------------------------------------
1641 double vvSlicer::GetScalarComponentAsDouble(vtkImageData *image, double X, double Y, double Z, int &ix, int &iy, int &iz, int component)
1642 {
1643   ix = lrint(X);
1644   iy = lrint(Y);
1645   iz = lrint(Z);
1646 #if VTK_MAJOR_VERSION <= 5
1647   if (ix < image->GetWholeExtent()[0] ||
1648       ix > image->GetWholeExtent()[1] ||
1649       iy < image->GetWholeExtent()[2] ||
1650       iy > image->GetWholeExtent()[3] ||
1651       iz < image->GetWholeExtent()[4] ||
1652       iz > image->GetWholeExtent()[5] )
1653     return std::numeric_limits<double>::quiet_NaN();
1654   image->SetUpdateExtent(ix, ix, iy, iy, iz, iz);
1655   image->Update();
1656 #else
1657   if (ix < image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[0] ||
1658       ix > image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[1] ||
1659       iy < image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[2] ||
1660       iy > image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[3] ||
1661       iz < image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[4] ||
1662       iz > image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[5] )
1663     return std::numeric_limits<double>::quiet_NaN();
1664   //image->SetUpdateExtent(ix, ix, iy, iy, iz, iz);
1665   //image->Update();
1666 #endif
1667   return image->GetScalarComponentAsDouble(ix, iy, iz, component);
1668 }
1669 //----------------------------------------------------------------------------
1670
1671 //----------------------------------------------------------------------------
1672 void vvSlicer::Render()
1673 {
1674   if (this->mFusion && mFusionActor->GetVisibility() && showFusionLegend) {
1675     legend->SetLookupTable(this->GetFusionMapper()->GetLookupTable());
1676     legend->UseOpacityOn();
1677     legend->SetVisibility(1);
1678   }
1679   else if (this->GetWindowLevel()->GetLookupTable() && !this->mOverlay)  {
1680     legend->SetLookupTable(this->GetWindowLevel()->GetLookupTable());
1681     legend->UseOpacityOff();
1682     legend->SetVisibility(1);
1683   } else legend->SetVisibility(0);
1684
1685   if (ca->GetVisibility()) {
1686     std::stringstream worldPos(" ");
1687     double pt[3];
1688     mConcatenatedTransform->TransformPoint(mCurrent, pt);
1689     double X = (pt[0] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[0])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[0];
1690     double Y = (pt[1] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[1])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[1];
1691     double Z = (pt[2] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[2])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[2];
1692 #if VTK_MAJOR_VERSION <= 5
1693     if (X >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[0]-0.5 &&
1694         X <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[1]+0.5 &&
1695         Y >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[2]-0.5 &&
1696         Y <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[3]+0.5 &&
1697         Z >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[4]-0.5 &&
1698         Z <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[5]+0.5) {
1699 #else
1700     if (X >= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[0]-0.5 &&
1701         X <= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[1]+0.5 &&
1702         Y >= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[2]-0.5 &&
1703         Y <= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[3]+0.5 &&
1704         Z >= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[4]-0.5 &&
1705         Z <= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[5]+0.5) {
1706 #endif
1707       int ix, iy, iz;
1708       double value = this->GetScalarComponentAsDouble(mImage->GetVTKImages()[mCurrentTSlice], X, Y, Z, ix, iy, iz);
1709       if(ImageActor->GetVisibility())
1710         worldPos << "data value : " << value << std::endl;
1711       worldPos << "mm : " << lrint(mCurrent[0]) << ' '
1712                           << lrint(mCurrent[1]) << ' '
1713                           << lrint(mCurrent[2]) << ' '
1714                           << mCurrentTSlice
1715                           << std::endl;
1716       worldPos << "pixel : " << ix << ' '
1717                              << iy << ' '
1718                              << iz << ' '
1719                              << mCurrentTSlice
1720                              << std::endl;
1721
1722     }
1723     ca->SetText(1,worldPos.str().c_str());
1724
1725     std::stringstream slicePos;
1726     slicePos << "Slice: " << this->GetSlice();
1727     ca->SetText(2, slicePos.str().c_str());
1728   }
1729
1730   if (pdmA->GetVisibility()) {
1731     double x = mCursor[0];
1732     double y = mCursor[1];
1733     double z = mCursor[2];
1734     double xCursor = (x - this->GetInput()->GetOrigin()[0])/this->GetInput()->GetSpacing()[0];
1735     double yCursor = (y - this->GetInput()->GetOrigin()[1])/this->GetInput()->GetSpacing()[1];
1736     double zCursor = (z - this->GetInput()->GetOrigin()[2])/this->GetInput()->GetSpacing()[2];
1737 #if VTK_MAJOR_VERSION <= 5
1738     if (xCursor >= this->GetImageActor()->GetDisplayExtent()[0]-0.5 &&
1739         xCursor < this->GetImageActor()->GetDisplayExtent()[1]+0.5 &&
1740         yCursor >= this->GetImageActor()->GetDisplayExtent()[2]-0.5 &&
1741         yCursor < this->GetImageActor()->GetDisplayExtent()[3]+0.5 &&
1742         zCursor >= this->GetImageActor()->GetDisplayExtent()[4]-0.5 &&
1743         zCursor < this->GetImageActor()->GetDisplayExtent()[5]+0.5 ) {
1744       vtkRenderer * renderer = this->Renderer;
1745
1746       renderer->WorldToView(x,y,z);
1747       renderer->ViewToNormalizedViewport(x,y,z);
1748       renderer->NormalizedViewportToViewport(x,y);
1749       renderer->ViewportToNormalizedDisplay(x,y);
1750       renderer->NormalizedDisplayToDisplay(x,y);
1751       crossCursor->SetFocalPoint(x,y,z);
1752     } else
1753       crossCursor->SetFocalPoint(-1,-1,z);
1754     crossCursor->Update();
1755   }
1756 #else
1757     vtkSmartPointer<vtkOpenGLImageSliceMapper> mapperOpenGL= vtkSmartPointer<vtkOpenGLImageSliceMapper>::New();
1758     try {
1759         mapperOpenGL = dynamic_cast<vtkOpenGLImageSliceMapper*>(GetImageActor()->GetMapper());
1760     } catch (const std::bad_cast& e) {
1761                 std::cerr << e.what() << std::endl;
1762                 std::cerr << "Conversion error" << std::endl;
1763                 return;
1764         }
1765
1766     if (xCursor >= mapperOpenGL->GetCroppingRegion()[0]-0.5 &&
1767         xCursor < mapperOpenGL->GetCroppingRegion()[1]+0.5 &&
1768         yCursor >= mapperOpenGL->GetCroppingRegion()[2]-0.5 &&
1769         yCursor < mapperOpenGL->GetCroppingRegion()[3]+0.5 &&
1770         zCursor >= mapperOpenGL->GetCroppingRegion()[4]-0.5 &&
1771         zCursor < mapperOpenGL->GetCroppingRegion()[5]+0.5 ) {
1772       vtkRenderer * renderer = this->Renderer;
1773
1774       renderer->WorldToView(x,y,z);
1775       renderer->ViewToNormalizedViewport(x,y,z);
1776       renderer->NormalizedViewportToViewport(x,y);
1777       renderer->ViewportToNormalizedDisplay(x,y);
1778       renderer->NormalizedDisplayToDisplay(x,y);
1779       crossCursor->SetFocalPoint(x,y,z);
1780     } else
1781       crossCursor->SetFocalPoint(-1,-1,z);
1782     crossCursor->Update();
1783   }
1784 #endif
1785
1786   if (mOverlay && mOverlayActor->GetVisibility()) {
1787     if(mLinkOverlayWindowLevel) {
1788       mOverlayMapper->SetWindow(this->GetColorWindow());
1789       mOverlayMapper->SetLevel(this->GetColorLevel());
1790     }
1791 #if VTK_MAJOR_VERSION <= 5
1792     mOverlayMapper->GetOutput()->SetUpdateExtent(mOverlayActor->GetDisplayExtent());
1793 #else
1794     mOverlayMapper->SetUpdateExtent(mOverlayActor->GetDisplayExtent());
1795 #endif
1796     mOverlayMapper->Update();
1797   }
1798   if (mFusion && mFusionActor->GetVisibility()) {
1799 #if VTK_MAJOR_VERSION <= 5
1800     mFusionMapper->GetOutput()->SetUpdateExtent(mFusionActor->GetDisplayExtent());
1801 #else
1802     mFusionMapper->SetUpdateExtent(mFusionActor->GetDisplayExtent());
1803 #endif
1804     mFusionMapper->Update();
1805   }
1806   if (mLandMapper) {
1807     RemoveLandmarks();
1808     DisplayLandmarks();
1809   }
1810
1811     this->GetRenderWindow()->Render();
1812 }
1813 //----------------------------------------------------------------------------
1814
1815
1816 //----------------------------------------------------------------------------
1817 void vvSlicer::UpdateCursorPosition()
1818 {
1819   pdmA->SetVisibility(true);
1820   mCursor[0] = mCurrent[0];
1821   mCursor[1] = mCurrent[1];
1822   mCursor[2] = mCurrent[2];
1823   mCursor[3] = mCurrentTSlice;
1824 }
1825 //----------------------------------------------------------------------------
1826
1827
1828 //----------------------------------------------------------------------------
1829 void vvSlicer::RemoveLandmarks()
1830 {
1831   vtkPolyData *pd = static_cast<vtkPolyData*>(mLandmarks->GetOutput());
1832   if (pd->GetPoints()) {
1833
1834     //First remove all captions:
1835     for(unsigned int i=0;i<mLandLabelActors.size();i++) {
1836         this->Renderer->RemoveActor2D(mLandLabelActors[i]);
1837         //allActors2D->Remove (mLandLabelActors[i]);
1838     }
1839     mLandLabelActors.clear();
1840   }
1841 }
1842 //----------------------------------------------------------------------------
1843
1844
1845 //----------------------------------------------------------------------------
1846 void vvSlicer::DisplayLandmarks()
1847 {
1848
1849   double bounds [6];
1850   for(unsigned int i=0; i<6; i++)
1851     bounds[i] = ImageActor->GetBounds()[i];
1852   bounds[ this->SliceOrientation*2   ] = ImageActor->GetBounds()[ this->SliceOrientation*2  ]-fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
1853   bounds[ this->SliceOrientation*2+1 ] = ImageActor->GetBounds()[ this->SliceOrientation*2+1 ]+fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
1854   mClipBox->SetBounds(bounds);
1855
1856
1857   vtkPolyData *pd = static_cast<vtkPolyData*>(mLandmarks->GetOutput());
1858   if (pd->GetPoints()) {
1859     this->GetRenderer()->AddActor(mLandActor);
1860     //mLandGlyph->SetRange(0,1);
1861     //mLandGlyph->Modified();
1862     //mLandGlyph->Update();
1863     mClipBox->Modified();
1864     mLandClipper->Update();
1865     mLandMapper->Update();
1866     //Next add the captions to the displayed points
1867     for (vtkIdType id=0; id<mLandClipper->GetOutput()->GetNumberOfPoints(); id++) {
1868           double *position = mLandClipper->GetOutput()->GetPoint(id);
1869       vtkStdString label = static_cast<vtkStringArray*>(mLandClipper->GetOutput()->GetPointData()->GetAbstractArray("labels"))->GetValue(id);
1870       vtkSmartPointer<vtkCaptionActor2D> label_actor = vtkSmartPointer<vtkCaptionActor2D>::New();
1871       label_actor->SetCaption(label);
1872       label_actor->SetAttachmentPoint(position);
1873       label_actor->GetCaptionTextProperty()->SetColor(1,0,0);
1874       label_actor->GetCaptionTextProperty()->SetOrientation(33.333333);
1875       label_actor->GetCaptionTextProperty()->SetFontFamilyToTimes();
1876       label_actor->GetCaptionTextProperty()->SetBold(0);
1877       label_actor->GetCaptionTextProperty()->SetFontSize(6);
1878       label_actor->BorderOff();
1879       label_actor->LeaderOff();
1880       label_actor->ThreeDimensionalLeaderOff();
1881       mLandLabelActors.push_back(label_actor);
1882       this->Renderer->AddActor2D(mLandLabelActors[id]);
1883      }
1884   }
1885
1886 }
1887 //----------------------------------------------------------------------------
1888
1889
1890 //----------------------------------------------------------------------------
1891 void vvSlicer::SetSlice(int slice)
1892 {
1893   int *range = this->GetSliceRange();
1894   if (range) {
1895     if (slice < range[0]) {
1896       slice = range[0];
1897     } else if (slice > range[1]) {
1898       slice = range[1];
1899     }
1900   }
1901
1902   if (this->Slice == slice) {
1903     return;
1904   }
1905
1906   this->Slice = slice;
1907   SetContourSlice();
1908   this->Modified();
1909   this->UpdateDisplayExtent();
1910
1911   // Seems to work without this line
1912   //this->Render();
1913 }
1914 //----------------------------------------------------------------------------
1915
1916 //----------------------------------------------------------------------------
1917 int vvSlicer::GetTMax()
1918 {
1919   int tmax = (int)mImage->GetVTKImages().size() - 1;
1920   if(mOverlay)
1921     tmax = std::max(tmax, (int)mOverlay->GetVTKImages().size()-1);
1922   return tmax;
1923 }
1924 //----------------------------------------------------------------------------
1925
1926 //----------------------------------------------------------------------------
1927 void vvSlicer::SetContourSlice()
1928 {
1929   if (mSurfaceCutActors.size() > 0)
1930     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
1931          i!=mSurfaceCutActors.end(); i++) {
1932
1933       (*i)->SetSlicingOrientation(this->SliceOrientation);
1934       (*i)->SetCutSlice((this->Slice)*this->GetImage()->GetSpacing()[this->SliceOrientation]+
1935                         this->GetImage()->GetOrigin()[this->SliceOrientation]);
1936     }
1937 }
1938 //----------------------------------------------------------------------------
1939
1940
1941 //----------------------------------------------------------------------------
1942 void vvSlicer::ForceUpdateDisplayExtent()
1943 {
1944   this->UpdateDisplayExtent();
1945 }
1946 //----------------------------------------------------------------------------
1947
1948
1949 //----------------------------------------------------------------------------
1950 int* vvSlicer::GetDisplayExtent()
1951 {
1952   return this->GetImageActor()->GetDisplayExtent();
1953 }
1954 //----------------------------------------------------------------------------
1955
1956
1957 //----------------------------------------------------------------------------
1958 void vvSlicer::PrintSelf(ostream& os, vtkIndent indent)
1959 {
1960   this->Superclass::PrintSelf(os, indent);
1961 }
1962 //----------------------------------------------------------------------------
1963
1964
1965 //----------------------------------------------------------------------------
1966 void vvSlicer::SetVFColor(double r, double g, double b)
1967 {
1968   double mVFColorHSV[3];
1969   mVFColor[0] = r;
1970   mVFColor[1] = g;
1971   mVFColor[2] = b;
1972
1973   vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
1974   mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
1975   mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
1976   mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
1977
1978   this->Render();
1979 }
1980 //----------------------------------------------------------------------------
1981
1982
1983 //----------------------------------------------------------------------------
1984 void vvSlicer::SetRegisterExtent(int ext[6])
1985 {
1986     copyExtent(ext, mRegisterExtent);
1987 }
1988 //----------------------------------------------------------------------------
1989
1990
1991 //----------------------------------------------------------------------------
1992 void vvSlicer::GetRegisterExtent(int ext[6])
1993 {
1994     copyExtent(mRegisterExtent, ext);
1995 }
1996 //----------------------------------------------------------------------------
1997