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 "vvSlicer.h"
  20 #include "vvImage.h"
  21 #include "vvSlicerManagerCommand.h"
  22 #include "vvGlyphSource.h"
  23 #include "vvGlyph2D.h"
  24
  25 #include <vtkTextProperty.h>
  26 #include <vtkTextActor.h>
  27 #include <vtkTextSource.h>
  28 #include <vtkActor2D.h>
  29 #include <vtkCursor2D.h>
  30 #include <vtkPolyDataMapper2D.h>
  31 #include <vtkProperty2D.h>
  32 #include <vtkCornerAnnotation.h>
  33 #include <vtkImageMapToWindowLevelColors.h>
  34 #include <vtkImageData.h>
  35 #include <vtkImageActor.h>
  36 #include <vvBlendImageActor.h>
  37 #include <vtkToolkits.h>
  38 #include <vtkObjectFactory.h>
  39 #include <vtkPointData.h>
  40 #include <vtkDataArray.h>
  41 #include <vtkFloatArray.h>
  42 #include <vtkClipPolyData.h>
  43 #include <vtkActor2DCollection.h>
  44 #include <vtkGlyph3D.h>
  45 #include <vtkMath.h>
  46 #include <vtkCursor3D.h>
  47 #include <vtkProperty.h>
  48 #include <vtkLight.h>
  49 #include <vtkLightCollection.h>
  50 #include <vtkScalarBarActor.h>
  51 #include <vtkLookupTable.h>
  52
  53 #include <vtkRenderer.h>
  54 #include <vtkRendererCollection.h>
  55 #include <vtkRenderWindow.h>
  56 #include <vtkRenderWindowInteractor.h>
  57 #include <vtkCamera.h>
  58 #include <vtkCallbackCommand.h>
  59 #include <vtkCommand.h>
  60 #include <vtkPolyDataMapper.h>
  61 #include <vtkBox.h>
  62
  63 #include <vtkExtractVOI.h>
  64 #include <vtkSphereSource.h>
  65 #include <vtkCutter.h>
  66 #include <vtkAssignAttribute.h>
  67 #include <vtkImageAccumulate.h>
  68 #include <vtkImageReslice.h>
  69 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
  70 #  include <vtkImageMapper3D.h>
  71 #endif
  72
  73 vtkCxxRevisionMacro(vvSlicer, "DummyRevision");
  74 vtkStandardNewMacro(vvSlicer);
  75 static void copyExtent(int* in, int* to){
  76  for(int i=0; i<6; ++i) to[i]=in[i];
  77 }
  78 //------------------------------------------------------------------------------
  79 vvSlicer::vvSlicer()
  80 {
  81   this->UnInstallPipeline();
  82   mImage = NULL;
  83   mReducedExtent = new int[6];
  84   mCurrentTSlice = 0;
  85   mCurrentFusionTSlice = 0;
  86   mCurrentOverlayTSlice = 0;
  87   mUseReducedExtent = false;
  88
  89   mCurrent[0] = -VTK_DOUBLE_MAX;
  90   mCurrent[1] = -VTK_DOUBLE_MAX;
  91   mCurrent[2] = -VTK_DOUBLE_MAX;
  92
  93   mCursor[0] = 0;//-VTK_DOUBLE_MAX;
  94   mCursor[1] = 0;//-VTK_DOUBLE_MAX;
  95   mCursor[2] = 0;//-VTK_DOUBLE_MAX;
  96   mCursor[3] = 0;//-VTK_DOUBLE_MAX;
  97
  98   mSubSampling = 5;
  99   mScale = 1;
 100   mVFLog = 0;
 101   mVFWidth = 1;
 102   mVFColor[0] = 0;
 103   mVFColor[1] = 1;
 104   mVFColor[2] = 0;
 105
 106   crossCursor = vtkSmartPointer<vtkCursor2D>::New();
 107   crossCursor->AllOff();
 108   crossCursor->AxesOn();
 109   crossCursor->SetTranslationMode(1);
 110   crossCursor->SetRadius(2);
 111
 112   pdm = vtkSmartPointer<vtkPolyDataMapper2D>::New();
 113   pdm->SetInput(crossCursor->GetOutput());
 114
 115   pdmA = vtkSmartPointer<vtkActor2D>::New();
 116   pdmA->SetMapper(pdm);
 117   pdmA->GetProperty()->SetColor(255,10,212);
 118   pdmA->SetVisibility(0);
 119   pdmA->SetPickable(0);
 120
 121   ca = vtkSmartPointer<vtkCornerAnnotation>::New();
 122   ca->GetTextProperty()->SetColor(255,10,212);
 123   ca->SetVisibility(1);
 124   mFileName = "";
 125
 126   mVF = NULL;
 127   mOverlay = NULL;
 128   mFusion = NULL;
 129   mLandmarks = NULL;
 130
 131   legend = vtkSmartPointer<vtkScalarBarActor>::New();
 132   //legend->SetTitle("test!");
 133   legend->SetPosition(0.82,0.18);
 134   legend->SetWidth(0.1);
 135   legend->SetVisibility(0);
 136   legend->SetLabelFormat("%.1f");
 137   this->GetRenderer()->AddActor(legend);
 138   showFusionLegend = false;
 139
 140   this->InstallPipeline();
 141
 142   mLinkOverlayWindowLevel = true;
 143
 144 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 145   this->GetImageActor()->GetMapper()->BorderOn();
 146 #endif
 147
 148   mSlicingTransform = vtkSmartPointer<vtkTransform>::New();
 149   mConcatenatedTransform = vtkSmartPointer<vtkTransform>::New();
 150   mConcatenatedFusionTransform = vtkSmartPointer<vtkTransform>::New();
 151   mConcatenatedOverlayTransform = vtkSmartPointer<vtkTransform>::New();
 152 }
 153 //------------------------------------------------------------------------------
 154
 155
 156 //------------------------------------------------------------------------------
 157 vtkImageMapToWindowLevelColors* vvSlicer::GetOverlayMapper()
 158 {
 159   return mOverlayMapper.GetPointer();
 160 }
 161 //------------------------------------------------------------------------------
 162
 163
 164 //------------------------------------------------------------------------------
 165 vvBlendImageActor* vvSlicer::GetOverlayActor()
 166 {
 167   return mOverlayActor.GetPointer();
 168 }
 169 //------------------------------------------------------------------------------
 170
 171
 172 //------------------------------------------------------------------------------
 173 vtkImageMapToColors* vvSlicer::GetFusionMapper()
 174 {
 175   return mFusionMapper.GetPointer();
 176 }
 177 //------------------------------------------------------------------------------
 178
 179
 180 //------------------------------------------------------------------------------
 181 vtkImageActor* vvSlicer::GetFusionActor()
 182 {
 183   return mFusionActor.GetPointer();
 184 }
 185 //------------------------------------------------------------------------------
 186
 187
 188 //------------------------------------------------------------------------------
 189 vtkActor* vvSlicer::GetVFActor()
 190 {
 191   return mVFActor.GetPointer();
 192 }
 193 //------------------------------------------------------------------------------
 194
 195
 196 //------------------------------------------------------------------------------
 197 vtkCornerAnnotation* vvSlicer::GetAnnotation()
 198 {
 199   return ca.GetPointer();
 200 }
 201 //------------------------------------------------------------------------------
 202
 203
 204 //------------------------------------------------------------------------------
 205 void vvSlicer::EnableReducedExtent(bool b)
 206 {
 207   mUseReducedExtent = b;
 208 }
 209 //------------------------------------------------------------------------------
 210
 211
 212 //------------------------------------------------------------------------------
 213 void vvSlicer::SetReducedExtent(int * ext)
 214 {
 215   copyExtent(ext, mReducedExtent);
 216 }
 217 //------------------------------------------------------------------------------
 218
 219
 220 //------------------------------------------------------------------------------
 221 void vvSlicer::AddContour(vvMesh::Pointer contour,bool propagate)
 222 {
 223
 224   mSurfaceCutActors.push_back(new vvMeshActor());
 225   if (propagate)
 226     mSurfaceCutActors.back()->Init(contour,mCurrentTSlice,mVF);
 227   else
 228     mSurfaceCutActors.back()->Init(contour,mCurrentTSlice);
 229   mSurfaceCutActors.back()->SetSlicingOrientation(SliceOrientation);
 230   this->GetRenderer()->AddActor(mSurfaceCutActors.back()->GetActor());
 231
 232   SetContourSlice();
 233 }
 234 //------------------------------------------------------------------------------
 235
 236
 237 //------------------------------------------------------------------------------
 238 void vvSlicer::ToggleContourSuperposition()
 239 {
 240   for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 241        i!=mSurfaceCutActors.end(); i++)
 242     (*i)->ToggleSuperposition();
 243 }
 244 //------------------------------------------------------------------------------
 245
 246
 247 //------------------------------------------------------------------------------
 248 void vvSlicer::SetCursorColor(int r,int g, int b)
 249 {
 250   pdmA->GetProperty()->SetColor(r,g,b);
 251 }
 252 //------------------------------------------------------------------------------
 253
 254
 255 //------------------------------------------------------------------------------
 256 void vvSlicer::SetCursorVisibility(bool s)
 257 {
 258   pdmA->SetVisibility(s);
 259 }
 260 //------------------------------------------------------------------------------
 261
 262
 263 //------------------------------------------------------------------------------
 264 bool vvSlicer::GetCursorVisibility()
 265 {
 266   return pdmA->GetVisibility();
 267 }
 268 //------------------------------------------------------------------------------
 269
 270
 271 //------------------------------------------------------------------------------
 272 void vvSlicer::SetCornerAnnotationVisibility(bool s)
 273 {
 274   ca->SetVisibility(s);
 275 }
 276 //------------------------------------------------------------------------------
 277
 278
 279 //------------------------------------------------------------------------------
 280 bool vvSlicer::GetCornerAnnotationVisibility()
 281 {
 282   return ca->GetVisibility();
 283 }
 284 //------------------------------------------------------------------------------
 285
 286
 287 //------------------------------------------------------------------------------
 288 vvSlicer::~vvSlicer()
 289 {
 290   for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 291        i!=mSurfaceCutActors.end(); i++)
 292     delete (*i);
 293   delete [] mReducedExtent;
 294 }
 295 //------------------------------------------------------------------------------
 296
 297 //------------------------------------------------------------------------------
 298 double* vvSlicer::GetCurrentPosition()
 299 {
 300   return mCurrentBeforeSlicingTransform;
 301 }
 302 //------------------------------------------------------------------------------
 303
 304 //------------------------------------------------------------------------------
 305 void vvSlicer::SetCurrentPosition(double x, double y, double z, int t)
 306 {
 307   mCurrentBeforeSlicingTransform[0]=x;
 308   mCurrentBeforeSlicingTransform[1]=y;
 309   mCurrentBeforeSlicingTransform[2]=z;
 310   mSlicingTransform->GetInverse()->TransformPoint(mCurrentBeforeSlicingTransform,mCurrent);
 311   SetTSlice(t);
 312 }
 313 //------------------------------------------------------------------------------
 314
 315
 316 //------------------------------------------------------------------------------
 317 void vvSlicer::SetImage(vvImage::Pointer image)
 318 {
 319   if (image->GetVTKImages().size()) {
 320     mImage = image;
 321
 322     if (!mImageReslice) {
 323       mImageReslice = vtkSmartPointer<vtkImageReslice>::New();
 324       mImageReslice->SetInterpolationModeToLinear();
 325       mImageReslice->AutoCropOutputOn();
 326       mImageReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 327     }
 328
 329     mConcatenatedTransform->Identity();
 330     mConcatenatedTransform->Concatenate(mImage->GetTransform()[0]);
 331     mConcatenatedTransform->Concatenate(mSlicingTransform);
 332     mImageReslice->SetResliceTransform(mConcatenatedTransform);
 333     mImageReslice->SetInput(0, mImage->GetFirstVTKImageData());
 334     mImageReslice->UpdateInformation();
 335
 336     this->Superclass::SetInput(mImageReslice->GetOutput());
 337
 338     int extent[6];
 339     this->GetInput()->GetWholeExtent(extent);
 340
 341     // Prevent crash when reload -> change slice if outside extent
 342     if (Slice < extent[SliceOrientation*2] || Slice>=extent[SliceOrientation*2+1]) {
 343       Slice = (extent[SliceOrientation*2+1]+extent[SliceOrientation*2])/2.0;
 344     }
 345
 346     // Make sure that the required part image has been computed
 347     extent[SliceOrientation*2] = Slice;
 348     extent[SliceOrientation*2+1] = Slice;
 349     mImageReslice->GetOutput()->SetUpdateExtent(extent);
 350     mImageReslice->GetOutput()->Update();
 351
 352     this->UpdateDisplayExtent();
 353
 354     mCurrentTSlice = 0;
 355     ca->SetText(0,mFileName.c_str());
 356   }
 357 }
 358 //------------------------------------------------------------------------------
 359
 360
 361 //------------------------------------------------------------------------------
 362 void vvSlicer::SetOverlay(vvImage::Pointer overlay)
 363 {
 364   if (overlay->GetVTKImages().size()) {
 365     mOverlay = overlay;
 366
 367     if (!mOverlayReslice) {
 368       mOverlayReslice = vtkSmartPointer<vtkImageReslice>::New();
 369       mOverlayReslice->SetInterpolationModeToLinear();
 370       mOverlayReslice->AutoCropOutputOn();
 371       mOverlayReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 372     }
 373
 374     mConcatenatedOverlayTransform->Identity();
 375     mConcatenatedOverlayTransform->Concatenate(mOverlay->GetTransform()[0]);
 376     mConcatenatedOverlayTransform->Concatenate(mSlicingTransform);
 377     mOverlayReslice->SetResliceTransform(mConcatenatedOverlayTransform);
 378     mOverlayReslice->SetInput(0, mOverlay->GetFirstVTKImageData());
 379     mImageReslice->UpdateInformation();
 380
 381     if (!mOverlayMapper)
 382       mOverlayMapper = vtkSmartPointer<vtkImageMapToWindowLevelColors>::New();
 383     mOverlayMapper->SetInput(mOverlayReslice->GetOutput());
 384
 385     if (!mOverlayActor) {
 386       mOverlayActor = vtkSmartPointer<vvBlendImageActor>::New();
 387       mOverlayActor->SetInput(mOverlayMapper->GetOutput());
 388       mOverlayActor->SetPickable(0);
 389       mOverlayActor->SetVisibility(true);
 390       mOverlayActor->SetOpacity(0.5);
 391 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 392       mOverlayActor->GetMapper()->BorderOn();
 393 #endif
 394       }
 395
 396     //stupid but necessary : the Overlay need to be rendered before fusion
 397     if (mFusionActor) {
 398       this->GetRenderer()->RemoveActor(mFusionActor);
 399       this->GetRenderer()->AddActor(mOverlayActor);
 400       this->GetRenderer()->AddActor(mFusionActor);
 401     } else
 402       this->GetRenderer()->AddActor(mOverlayActor);
 403
 404     //Synchronize orientation and slice
 405     AdjustResliceToSliceOrientation(mOverlayReslice);
 406     this->UpdateDisplayExtent();
 407     this->SetTSlice(mCurrentTSlice);
 408   }
 409 }
 410 //------------------------------------------------------------------------------
 411
 412
 413 //------------------------------------------------------------------------------
 414 void vvSlicer::SetFusion(vvImage::Pointer fusion)
 415 {
 416   if (fusion->GetVTKImages().size()) {
 417     mFusion = fusion;
 418
 419     if (!mFusionReslice) {
 420       mFusionReslice = vtkSmartPointer<vtkImageReslice>::New();
 421       mFusionReslice->SetInterpolationModeToLinear();
 422       mFusionReslice->AutoCropOutputOn();
 423       mFusionReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 424     }
 425
 426     mConcatenatedFusionTransform->Identity();
 427     mConcatenatedFusionTransform->Concatenate(mFusion->GetTransform()[0]);
 428     mConcatenatedFusionTransform->Concatenate(mSlicingTransform);
 429     mFusionReslice->SetResliceTransform(mConcatenatedFusionTransform);
 430     mFusionReslice->SetInput(0, mFusion->GetFirstVTKImageData());
 431     mFusionReslice->UpdateInformation();
 432
 433     if (!mFusionMapper)
 434       mFusionMapper = vtkSmartPointer<vtkImageMapToColors>::New();
 435
 436     vtkSmartPointer<vtkLookupTable> lut = vtkLookupTable::New();
 437     lut->SetRange(0, 1);
 438     lut->SetValueRange(0, 1);
 439     lut->SetSaturationRange(0, 0);
 440     lut->Build();
 441     mFusionMapper->SetLookupTable(lut);
 442     mFusionMapper->SetInput(mFusionReslice->GetOutput());
 443
 444     if (!mFusionActor) {
 445       mFusionActor = vtkSmartPointer<vtkImageActor>::New();
 446       mFusionActor->SetInput(mFusionMapper->GetOutput());
 447       mFusionActor->SetPickable(0);
 448       mFusionActor->SetVisibility(true);
 449       mFusionActor->SetOpacity(0.7);
 450 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 451       mFusionActor->GetMapper()->BorderOn();
 452 #endif
 453       this->GetRenderer()->AddActor(mFusionActor);
 454     }
 455
 456     //Synchronize orientation and slice
 457     AdjustResliceToSliceOrientation(mFusionReslice);
 458     this->UpdateDisplayExtent();
 459     this->SetTSlice(mCurrentTSlice);
 460   }
 461 }
 462 //------------------------------------------------------------------------------
 463
 464
 465 //------------------------------------------------------------------------------
 466 bool vvSlicer::GetActorVisibility(const std::string& actor_type, int overlay_index)
 467 {
 468   bool vis = false;
 469   if (actor_type == "image") {
 470     vis = this->ImageActor->GetVisibility();
 471   }
 472   else if (actor_type == "vector") {
 473     vis = this->mVFActor->GetVisibility();
 474   }
 475   else if (actor_type == "overlay") {
 476     vis = this->mOverlayActor->GetVisibility();
 477   }
 478   else if (actor_type == "fusion") {
 479     vis = this->mFusionActor->GetVisibility();
 480   }
 481   else if (actor_type == "contour")
 482     vis = this->mSurfaceCutActors[overlay_index]->GetActor()->GetVisibility();
 483
 484   return vis;
 485 }
 486 //------------------------------------------------------------------------------
 487
 488 //------------------------------------------------------------------------------
 489 void vvSlicer::SetActorVisibility(const std::string& actor_type, int overlay_index ,bool vis)
 490 {
 491   if (actor_type == "image") {
 492     this->ImageActor->SetVisibility(vis);
 493   }
 494   else if (actor_type == "vector") {
 495     this->mVFActor->SetVisibility(vis);
 496   }
 497   else if (actor_type == "overlay") {
 498     this->mOverlayActor->SetVisibility(vis);
 499   }
 500   else if (actor_type == "fusion") {
 501     this->mFusionActor->SetVisibility(vis);
 502   }
 503   else if (actor_type == "contour")
 504     this->mSurfaceCutActors[overlay_index]->GetActor()->SetVisibility(vis);
 505   UpdateDisplayExtent();
 506 }
 507 //------------------------------------------------------------------------------
 508
 509 //------------------------------------------------------------------------------
 510 void vvSlicer::SetVF(vvImage::Pointer vf)
 511 {
 512   if (vf->GetVTKImages().size()) {
 513     mVF = vf;
 514
 515     if (!mAAFilter) {
 516       mAAFilter= vtkSmartPointer<vtkAssignAttribute>::New();
 517       mVOIFilter = vtkSmartPointer<vtkExtractVOI>::New();
 518       mVOIFilter->SetSampleRate(mSubSampling,mSubSampling,mSubSampling);
 519     }
 520     mVOIFilter->SetInput(vf->GetFirstVTKImageData());
 521     mAAFilter->SetInput(mVOIFilter->GetOutput());
 522     ///This tells VTK to use the scalar (pixel) data of the image to draw the little arrows
 523     mAAFilter->Assign(vtkDataSetAttributes::SCALARS, vtkDataSetAttributes::VECTORS, vtkAssignAttribute::POINT_DATA);
 524
 525     if (!mArrow)
 526       mArrow = vtkSmartPointer<vvGlyphSource>::New();
 527     mArrow->SetGlyphTypeToSpecificArrow();
 528     mArrow->SetScale(mScale);
 529     mArrow->FilledOff();
 530
 531     // Glyph the gradient vector (with arrows)
 532     if (!mGlyphFilter)
 533       mGlyphFilter = vtkSmartPointer<vvGlyph2D>::New();
 534     mGlyphFilter->SetInput(mAAFilter->GetOutput());
 535     mGlyphFilter->SetSource(mArrow->GetOutput());
 536     mGlyphFilter->ScalingOn();
 537     mGlyphFilter->SetScaleModeToScaleByVector();
 538     mGlyphFilter->OrientOn();
 539     mGlyphFilter->SetVectorModeToUseVector();
 540     mGlyphFilter->SetColorModeToColorByVector();
 541
 542     if (!mVFColorLUT)
 543       mVFColorLUT = vtkSmartPointer<vtkLookupTable>::New();
 544
 545     double mVFColorHSV[3];
 546     vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
 547     mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
 548     mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
 549     mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
 550
 551     if (!mVFMapper)
 552       mVFMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
 553     mVFMapper->SetInput(mGlyphFilter->GetOutput());
 554     mVFMapper->ImmediateModeRenderingOn();
 555     mVFMapper->SetLookupTable(mVFColorLUT);
 556
 557     if (!mVFActor)
 558       mVFActor = vtkSmartPointer<vtkActor>::New();
 559     mVFActor->SetMapper(mVFMapper);
 560     mVFActor->SetPickable(0);
 561     mVFActor->GetProperty()->SetLineWidth(mVFWidth);
 562     this->UpdateDisplayExtent();
 563     this->GetRenderer()->AddActor(mVFActor);
 564
 565     //Synchronize slice
 566     SetTSlice(mCurrentTSlice);
 567   }
 568 }
 569 //------------------------------------------------------------------------------
 570
 571
 572 //------------------------------------------------------------------------------
 573 void vvSlicer::SetLandmarks(vvLandmarks* landmarks)
 574 {
 575   mLandmarks = landmarks;
 576   if (landmarks) {
 577
 578     if (!mCross)
 579       mCross = vtkSmartPointer<vtkCursor3D>::New();
 580         if (!mClipBox)
 581       mClipBox = vtkSmartPointer<vtkBox>::New();
 582     if (!mLandClipper)
 583       mLandClipper = vtkSmartPointer<vvClipPolyData>::New();
 584     if (!mLandGlyph)
 585       mLandGlyph = vtkSmartPointer<vtkGlyph3D>::New();
 586     if (!mLandMapper)
 587       mLandMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
 588     if (!mLandActor)
 589       mLandActor = vtkSmartPointer<vtkActor>::New();
 590
 591     mCross->SetFocalPoint(0.0,0.0,0.0);
 592     mCross->SetModelBounds(-10,10,-10,10,-10,10);
 593     mCross->AllOff();
 594     mCross->AxesOn();
 595
 596     mLandClipper->SetClipFunction(mClipBox);
 597     mLandClipper->InsideOutOn();
 598     mLandClipper->SetInput(mLandmarks->GetOutput());
 599
 600     mLandGlyph->SetSource(mCross->GetOutput());
 601     mLandGlyph->SetInput(mLandClipper->GetOutput());
 602     //mLandGlyph->SetIndexModeToScalar();
 603     //mLandGlyph->SetRange(0,1);
 604     //mLandGlyph->ScalingOff();
 605
 606     //mLandGlyph->SetColorModeToColorByScalar();
 607
 608     mLandGlyph->SetScaleModeToDataScalingOff();
 609     mLandGlyph->SetIndexModeToOff();
 610
 611     mLandMapper->SetInputConnection(mLandGlyph->GetOutputPort());
 612     //mLandMapper->ScalarVisibilityOff();
 613
 614     mLandActor->SetMapper(mLandMapper);
 615     mLandActor->GetProperty()->SetColor(255,10,212);
 616     mLandActor->SetPickable(0);
 617     mLandActor->SetVisibility(true);
 618     this->UpdateDisplayExtent();
 619     this->GetRenderer()->AddActor(mLandActor);
 620   }
 621 }
 622 //------------------------------------------------------------------------------
 623
 624 //------------------------------------------------------------------------------
 625 //FIXME: this function leaks memory, we should fix it someday :)
 626 void vvSlicer::RemoveActor(const std::string& actor_type, int overlay_index)
 627 {
 628   if (actor_type == "vector") {
 629     Renderer->RemoveActor(mVFActor);
 630     mGlyphFilter=NULL;
 631     mVF = NULL;
 632     mArrow = NULL;
 633     mAAFilter=NULL;
 634     mVOIFilter = NULL;
 635     mVFMapper = NULL;
 636     mVFActor = NULL;
 637   }
 638   if (actor_type == "overlay") {
 639     Renderer->RemoveActor(mOverlayActor);
 640     mOverlay = NULL;
 641     mOverlayActor = NULL;
 642     mOverlayMapper = NULL;
 643   }
 644   if (actor_type == "fusion") {
 645     Renderer->RemoveActor(mFusionActor);
 646     mFusion = NULL;
 647     mFusionActor = NULL;
 648     mFusionMapper = NULL;
 649   }
 650   if (actor_type == "contour") {
 651     Renderer->RemoveActor(this->mSurfaceCutActors[overlay_index]->GetActor());
 652     mSurfaceCutActors.erase(mSurfaceCutActors.begin()+overlay_index);
 653   }
 654 }
 655 //------------------------------------------------------------------------------
 656
 657
 658 //------------------------------------------------------------------------------
 659 void vvSlicer::SetVFSubSampling(int sub)
 660 {
 661   if (mVOIFilter) {
 662     mVOIFilter->SetSampleRate(mSubSampling,mSubSampling,mSubSampling);
 663     mSubSampling = sub;
 664   }
 665   UpdateDisplayExtent();
 666   Render();
 667 }
 668 //------------------------------------------------------------------------------
 669
 670
 671 //------------------------------------------------------------------------------
 672 void vvSlicer::SetVFScale(int scale)
 673 {
 674   mScale = scale;
 675   if (mArrow)
 676     mArrow->SetScale(mScale);
 677   UpdateDisplayExtent();
 678   Render();
 679 }
 680 //------------------------------------------------------------------------------
 681
 682 //------------------------------------------------------------------------------
 683 void vvSlicer::SetVFWidth(int width)
 684 {
 685   mVFWidth = width;
 686   if (mVFActor)
 687     mVFActor->GetProperty()->SetLineWidth(mVFWidth);
 688   UpdateDisplayExtent();
 689   Render();
 690 }
 691 //------------------------------------------------------------------------------
 692
 693
 694 //------------------------------------------------------------------------------
 695 void vvSlicer::SetVFLog(int log)
 696 {
 697   mVFLog = log;
 698   if (mGlyphFilter) {
 699     mGlyphFilter->SetUseLog(mVFLog);
 700     mGlyphFilter->Modified();
 701   }
 702   UpdateDisplayExtent();
 703   Render();
 704 }
 705 //------------------------------------------------------------------------------
 706
 707
 708 //------------------------------------------------------------------------------
 709 void vvSlicer::SetTSlice(int t)
 710 {
 711   if (t < 0)
 712     mCurrentTSlice = 0;
 713   else if ((unsigned int)t >= mImage->GetVTKImages().size())
 714     mCurrentTSlice = mImage->GetVTKImages().size() -1;
 715   else
 716     mCurrentTSlice = t;
 717
 718   // Update transform
 719   mConcatenatedTransform->Identity();
 720   mConcatenatedTransform->Concatenate(mImage->GetTransform()[mCurrentTSlice]);
 721   mConcatenatedTransform->Concatenate(mSlicingTransform);
 722
 723   // Update image data
 724   mImageReslice->SetInput( mImage->GetVTKImages()[mCurrentTSlice] );
 725   if (mVF && mVFActor->GetVisibility()) {
 726     if (mVF->GetVTKImages().size() > (unsigned int)mCurrentTSlice)
 727       mVOIFilter->SetInput(mVF->GetVTKImages()[mCurrentTSlice]);
 728   }
 729   if (mOverlay && mOverlayActor->GetVisibility()) {
 730     if (mOverlay->GetVTKImages().size() > (unsigned int)t) {
 731       mCurrentOverlayTSlice = t;
 732       mOverlayReslice->SetInput( mOverlay->GetVTKImages()[mCurrentOverlayTSlice] );
 733
 734       // Update overlay transform
 735       mConcatenatedOverlayTransform->Identity();
 736       mConcatenatedOverlayTransform->Concatenate(mOverlay->GetTransform()[mCurrentOverlayTSlice]);
 737       mConcatenatedOverlayTransform->Concatenate(mSlicingTransform);
 738     }
 739   }
 740   if (mFusion && mFusionActor->GetVisibility()) {
 741     if (mFusion->GetVTKImages().size() > (unsigned int)t) {
 742       mCurrentFusionTSlice = t;
 743       mFusionReslice->SetInput( mFusion->GetVTKImages()[mCurrentFusionTSlice]);
 744
 745       // Update fusion transform
 746       mConcatenatedFusionTransform->Identity();
 747       mConcatenatedFusionTransform->Concatenate(mFusion->GetTransform()[mCurrentFusionTSlice]);
 748       mConcatenatedFusionTransform->Concatenate(mSlicingTransform);
 749     }
 750   }
 751   if (mSurfaceCutActors.size() > 0)
 752     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 753          i!=mSurfaceCutActors.end(); i++)
 754       (*i)->SetTimeSlice(mCurrentTSlice);
 755   UpdateDisplayExtent();
 756 }
 757 //------------------------------------------------------------------------------
 758
 759
 760 //------------------------------------------------------------------------------
 761 int vvSlicer::GetTSlice()
 762 {
 763   return mCurrentTSlice;
 764 }
 765 //------------------------------------------------------------------------------
 766
 767 //------------------------------------------------------------------------------
 768 int vvSlicer::GetMaxCurrentTSlice()
 769 {
 770   int t = mCurrentTSlice;
 771   if(mOverlay)
 772     t = std::max(t, mCurrentOverlayTSlice);
 773   if(mFusion)
 774     t = std::max(t, mCurrentFusionTSlice);
 775   return t;
 776 }
 777 //------------------------------------------------------------------------------
 778
 779 //------------------------------------------------------------------------------
 780 int vvSlicer::GetFusionTSlice()
 781 {
 782   return mCurrentFusionTSlice;
 783 }
 784 //------------------------------------------------------------------------------
 785
 786 //------------------------------------------------------------------------------
 787 int vvSlicer::GetOverlayTSlice()
 788 {
 789   return mCurrentOverlayTSlice;
 790 }
 791 //------------------------------------------------------------------------------
 792
 793 //------------------------------------------------------------------------------
 794 void vvSlicer::SetSliceOrientation(int orientation)
 795 {
 796   //if 2D image, force to watch in Axial View
 797   int extent[6];
 798   this->GetInput()->GetWholeExtent(extent);
 799   if (extent[5]-extent[4] <= 2)
 800     orientation = vtkImageViewer2::SLICE_ORIENTATION_XY;
 801
 802   if (orientation < vtkImageViewer2::SLICE_ORIENTATION_YZ ||
 803       orientation > vtkImageViewer2::SLICE_ORIENTATION_XY) {
 804     vtkErrorMacro("Error - invalid slice orientation " << orientation);
 805     return;
 806   }
 807
 808   this->SliceOrientation = orientation;
 809
 810   if(mFusion)
 811     AdjustResliceToSliceOrientation(mFusionReslice);
 812
 813   if(mOverlay)
 814     AdjustResliceToSliceOrientation(mOverlayReslice);
 815
 816   // Update the viewer
 817
 818   // Go to current cursor position
 819   // double* cursorPos = GetCursorPosition();
 820   // DDV(cursorPos, 3);
 821   // SetCurrentPosition(cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
 822
 823   if (this->Renderer && this->GetInput()) {
 824     double s = mCursor[orientation];
 825     double sCursor = (s - this->GetInput()->GetOrigin()[orientation])/this->GetInput()->GetSpacing()[orientation];
 826     this->Slice = static_cast<int>(sCursor);
 827   }
 828
 829 //   int *range = this->GetSliceRange();
 830 //   if (range)
 831 //     this->Slice = static_cast<int>((range[0] + range[1]) * 0.5);
 832
 833   this->UpdateOrientation();
 834   this->UpdateDisplayExtent();
 835
 836   if (this->Renderer && this->GetInput()) {
 837     double scale = this->Renderer->GetActiveCamera()->GetParallelScale();
 838     this->Renderer->ResetCamera();
 839     this->Renderer->GetActiveCamera()->SetParallelScale(scale);
 840   }
 841
 842   SetContourSlice();
 843 }
 844 //----------------------------------------------------------------------------
 845
 846 //------------------------------------------------------------------------------
 847 // This function ensures that we sample the slices of a vtkImageReslice filter
 848 // in the direction of the slicer (SliceOrientation) similarly as mImageReslice.
 849 // In other words, we change the grid of the reslice in the same way as the grid
 850 // of the displayed image in the slicing direction.
 851 void vvSlicer::AdjustResliceToSliceOrientation(vtkImageReslice *reslice)
 852 {
 853   // Reset autocrop and update output information
 854   reslice->SetOutputOriginToDefault();
 855   reslice->SetOutputSpacingToDefault();
 856   reslice->GetOutput()->UpdateInformation();
 857
 858   // Ge new origin / spacing
 859   double origin[3];
 860   double spacing[3];
 861   reslice->GetOutput()->GetOrigin(origin);
 862   reslice->GetOutput()->GetSpacing(spacing);
 863
 864   // Use similar spacing as the image in the direction SliceOrientation
 865   spacing[this->SliceOrientation] = mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
 866
 867   // Modify origin to be on the image grid in the direction SliceOrientation in 3 steps
 868   // Step 1: from world coordinates to image coordinates
 869   origin[this->SliceOrientation] -= mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
 870   origin[this->SliceOrientation] /= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
 871   // Step 2: round to superior grid positionInc
 872   origin[this->SliceOrientation] = itk::Math::Ceil<double>(origin[this->SliceOrientation]);
 873   // Step 3: back to world coordinates
 874   origin[this->SliceOrientation] *= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
 875   origin[this->SliceOrientation] += mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
 876
 877   // Set new spacing and origin
 878   reslice->SetOutputOrigin(origin);
 879   reslice->SetOutputSpacing(spacing);
 880   reslice->UpdateInformation();
 881   reslice->GetOutput()->UpdateInformation();
 882 }
 883 //------------------------------------------------------------------------------
 884
 885 //----------------------------------------------------------------------------
 886 int * vvSlicer::GetExtent(){
 887   int *w_ext;
 888   if (mUseReducedExtent) {
 889     w_ext = mReducedExtent;
 890   } else w_ext = GetInput()->GetWholeExtent();
 891   return w_ext;
 892 }
 893 //----------------------------------------------------------------------------
 894
 895
 896 //----------------------------------------------------------------------------
 897 int vvSlicer::GetOrientation()
 898 {
 899   return this->SliceOrientation;
 900 }
 901 //----------------------------------------------------------------------------
 902
 903
 904 //----------------------------------------------------------------------------
 905 void vvSlicer::UpdateDisplayExtent()
 906 {
 907   vtkImageData *input = this->GetInput();
 908   if (!input || !this->ImageActor) {
 909     return;
 910   }
 911   input->UpdateInformation();
 912   this->SetSlice( this->GetSlice() ); //SR: make sure the update let the slice in extents
 913
 914   // Local copy of extent
 915   int w_ext[6];
 916   int* ext = GetExtent();
 917   copyExtent(ext, w_ext);
 918   // Set slice value
 919   w_ext[ this->SliceOrientation*2   ] = this->Slice;
 920   w_ext[ this->SliceOrientation*2+1 ] = this->Slice;
 921
 922   // Image actor
 923   this->ImageActor->SetDisplayExtent(w_ext);
 924
 925   // Overlay image actor
 926   if (mOverlay && mOverlayActor->GetVisibility()) {
 927     AdjustResliceToSliceOrientation(mOverlayReslice);
 928     int overExtent[6];
 929     this->ConvertImageToImageDisplayExtent(input, w_ext, mOverlayReslice->GetOutput(), overExtent);
 930     ClipDisplayedExtent(overExtent, mOverlayMapper->GetInput()->GetWholeExtent());
 931     mOverlayActor->SetDisplayExtent( overExtent );
 932   }
 933
 934   // Fusion image actor
 935   if (mFusion && mFusionActor->GetVisibility()) {
 936     AdjustResliceToSliceOrientation(mFusionReslice);
 937     int fusExtent[6];
 938     this->ConvertImageToImageDisplayExtent(input, w_ext, mFusionReslice->GetOutput(), fusExtent);
 939     ClipDisplayedExtent(fusExtent, mFusionMapper->GetInput()->GetWholeExtent());
 940     mFusionActor->SetDisplayExtent(fusExtent);
 941   }
 942
 943   // Vector field actor
 944   double* camera = Renderer->GetActiveCamera()->GetPosition();
 945   double* image_bounds = ImageActor->GetBounds();
 946   double position[3] = {0, 0, 0};
 947   position[this->SliceOrientation] = image_bounds[this->SliceOrientation*2];
 948
 949   //print_vector<double, 6>("camera", camera);
 950   //print_vector<double, 6>("image_bounds", image_bounds);
 951   //print_vector<double, 3>("position", position);
 952
 953   // find where to place the VF actor. to deal with
 954   // z-buffer issues, the VF is placed right in front of the image,
 955   // subject to a small offset. the position actually depends on the
 956   // the location of the camera relative to the image.
 957   double offset = 1;
 958   if (camera[this->SliceOrientation] < image_bounds[this->SliceOrientation*2])
 959     offset = -1;
 960
 961   if (mVF && mVFActor->GetVisibility()) {
 962     int vfExtent[6];
 963     mVF->GetVTKImages()[0]->UpdateInformation();
 964     this->ConvertImageToImageDisplayExtent(input, w_ext, mVF->GetVTKImages()[0], vfExtent);
 965     ClipDisplayedExtent(vfExtent, mVOIFilter->GetInput()->GetWholeExtent());
 966     mVOIFilter->SetVOI(vfExtent);
 967     int orientation[3] = {1,1,1};
 968     orientation[this->SliceOrientation] = 0;
 969     mGlyphFilter->SetOrientation(orientation[0], orientation[1], orientation[2]);
 970     mVFMapper->Update();
 971
 972     position[this->SliceOrientation] += offset;
 973     mVFActor->SetPosition(position);
 974   }
 975
 976   // Landmarks actor
 977   if (mLandActor) {
 978     if (mClipBox) {
 979       double bounds [6];
 980       for(unsigned int i=0; i<6; i++)
 981         bounds[i] = ImageActor->GetBounds()[i];
 982       bounds[ this->SliceOrientation*2   ] = ImageActor->GetBounds()[ this->SliceOrientation*2  ]-fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
 983       bounds[ this->SliceOrientation*2+1 ] = ImageActor->GetBounds()[ this->SliceOrientation*2+1 ]+fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
 984       mClipBox->SetBounds(bounds);
 985       UpdateLandmarks();
 986     }
 987
 988     position[this->SliceOrientation] = offset;
 989     mLandActor->SetPosition(position);
 990   }
 991
 992   // Figure out the correct clipping range
 993   if (this->Renderer) {
 994     if (this->InteractorStyle &&
 995         this->InteractorStyle->GetAutoAdjustCameraClippingRange()) {
 996       this->Renderer->ResetCameraClippingRange();
 997     } else {
 998       vtkCamera *cam = this->Renderer->GetActiveCamera();
 999       if (cam) {
1000         double bounds[6];
1001         this->ImageActor->GetBounds(bounds);
1002         double spos = (double)bounds[this->SliceOrientation * 2];
1003         double cpos = (double)cam->GetPosition()[this->SliceOrientation];
1004         double range = fabs(spos - cpos);
1005         double *spacing = input->GetSpacing();
1006         double sumSpacing = spacing[0] + spacing[1] + spacing[2];
1007         cam->SetClippingRange(range - sumSpacing, range + sumSpacing);
1008       }
1009     }
1010   }
1011
1012 }
1013 //----------------------------------------------------------------------------
1014
1015 //----------------------------------------------------------------------------
1016 void vvSlicer::ConvertImageToImageDisplayExtent(vtkImageData *sourceImage, const int sourceExtent[6],
1017                                                 vtkImageData *targetImage, int targetExtent[6])
1018 {
1019   double dExtents[6];
1020   for(unsigned int i=0; i<6; i++) {
1021     // From source voxel coordinates to world coordinates
1022     dExtents[i] = sourceImage->GetOrigin()[i/2] + sourceImage->GetSpacing()[i/2] * sourceExtent[i];
1023
1024     // From world coordinates to floating point target voxel coordinates
1025     dExtents[i] = (dExtents[i]- targetImage->GetOrigin()[i/2]) / targetImage->GetSpacing()[i/2];
1026
1027     // Round to nearest
1028     //targetExtent[i] = itk::Math::Round<double>(dExtents[i]);
1029     targetExtent[i] = itk::Math::Floor<double>(dExtents[i]);
1030   }
1031 }
1032 //----------------------------------------------------------------------------
1033
1034 //----------------------------------------------------------------------------
1035 void vvSlicer::ClipDisplayedExtent(int extent[6], int refExtent[6])
1036 {
1037   bool out = false;
1038   int maxBound = 6;
1039
1040   //2D overlay on 3D image specific case
1041   if (refExtent[4] == refExtent[5]) {
1042     maxBound = 4;
1043     extent[4] = refExtent[4];
1044     extent[5] = refExtent[5];
1045   }
1046
1047   for (int i = 0; i < maxBound; i = i+2) {
1048     //if we are totally outside the image
1049     if ( extent[i] > refExtent[i+1] || extent[i+1] < refExtent[i] ) {
1050       out = true;
1051       break;
1052     }
1053     //crop to the limit of the image
1054     extent[i] = (extent[i] > refExtent[i]) ? extent[i] : refExtent[i];
1055     extent[i] = (extent[i] < refExtent[i+1]) ? extent[i] : refExtent[i+1];
1056     extent[i+1] = (extent[i+1] > refExtent[i]) ? extent[i+1] : refExtent[i];
1057     extent[i+1] = (extent[i+1] < refExtent[i+1]) ? extent[i+1] : refExtent[i+1];
1058   }
1059   if (out)
1060     for (int i = 0; i < maxBound; i = i+2) {
1061       extent[i] = refExtent[i];
1062       extent[i+1] = refExtent[i];
1063     }
1064 }
1065 //----------------------------------------------------------------------------
1066
1067
1068 //----------------------------------------------------------------------------
1069 void vvSlicer::UpdateOrientation()
1070 {
1071   // Set the camera position
1072   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1073   if (cam) {
1074     switch (this->SliceOrientation) {
1075     case vtkImageViewer2::SLICE_ORIENTATION_XY:
1076       cam->SetFocalPoint(0,0,0);
1077       cam->SetPosition(0,0,-1); // -1 if medical ?
1078       cam->SetViewUp(0,-1,0);
1079       break;
1080
1081     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
1082       cam->SetFocalPoint(0,0,0);
1083       cam->SetPosition(0,-1,0); // 1 if medical ?
1084       cam->SetViewUp(0,0,1);
1085       break;
1086
1087     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1088       cam->SetFocalPoint(0,0,0);
1089       cam->SetPosition(-1,0,0); // -1 if medical ?
1090       cam->SetViewUp(0,0,1);
1091       break;
1092     }
1093   }
1094 }
1095 //----------------------------------------------------------------------------
1096
1097
1098 //----------------------------------------------------------------------------
1099 void vvSlicer::SetOpacity(double s)
1100 {
1101   this->GetImageActor()->SetOpacity(s);
1102 }
1103 //----------------------------------------------------------------------------
1104
1105
1106 //----------------------------------------------------------------------------
1107 void vvSlicer::SetRenderWindow(int orientation, vtkRenderWindow * rw)
1108 {
1109   this->Superclass::SetRenderWindow(rw);
1110   this->SetupInteractor(rw->GetInteractor());
1111   ca->SetImageActor(this->GetImageActor());
1112   ca->SetWindowLevel(this->GetWindowLevel());
1113   ca->SetText(2, "<slice>");
1114   ca->SetText(3, "<window>\n<level>");
1115
1116   double bounds[6];
1117   double max = 65000;
1118
1119   bounds[0] = -max;
1120   bounds[1] = max;
1121   bounds[2] = -max;
1122   bounds[3] = max;
1123   bounds[4] = -max;
1124   bounds[5] = max;
1125
1126   crossCursor->SetModelBounds(bounds);
1127   this->GetRenderer()->AddActor(pdmA);
1128   this->GetRenderer()->AddActor(ca);
1129   this->GetRenderer()->ResetCamera();
1130
1131   //this is just a mapping between the labeling of the orientations presented to the user and
1132   //the one used by vtk
1133   SetSliceOrientation(2-(orientation%3));
1134   ResetCamera();
1135 }
1136 //----------------------------------------------------------------------------
1137
1138
1139 //----------------------------------------------------------------------------
1140 void vvSlicer::ResetCamera()
1141 {
1142   this->GetRenderer()->ResetCamera();
1143 }
1144 //----------------------------------------------------------------------------
1145
1146
1147 //----------------------------------------------------------------------------
1148 void vvSlicer::SetDisplayMode(bool i)
1149 {
1150   this->GetRenderer()->SetDraw(i);
1151   if (i)
1152     UpdateDisplayExtent();
1153 }
1154 //----------------------------------------------------------------------------
1155
1156
1157 //----------------------------------------------------------------------------
1158 void vvSlicer::FlipHorizontalView()
1159 {
1160   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1161   if (cam) {
1162     double *position = cam->GetPosition();
1163     double factor[3] = {1, 1, 1};
1164     factor[this->SliceOrientation] = -1;
1165     cam->SetPosition(factor[0]*position[0],factor[1]*position[1],factor[2]*position[2]);
1166
1167 /*    switch (this->SliceOrientation) {
1168     case vtkImageViewer2::SLICE_ORIENTATION_XY:
1169       cam->SetPosition(position[0],position[1],-position[2]);
1170       break;
1171
1172     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
1173       cam->SetPosition(position[0],-position[1],position[2]);
1174       break;
1175
1176     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1177       cam->SetPosition(-position[0],position[1],position[2]);
1178       break;
1179     }*/
1180
1181     this->Renderer->ResetCameraClippingRange();
1182     this->UpdateDisplayExtent();
1183   }
1184 }
1185 //----------------------------------------------------------------------------
1186
1187
1188 //----------------------------------------------------------------------------
1189 void vvSlicer::FlipVerticalView()
1190 {
1191   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1192   if (cam) {
1193     FlipHorizontalView();
1194     double *viewup = cam->GetViewUp();
1195     cam->SetViewUp(-viewup[0],-viewup[1],-viewup[2]);
1196     this->UpdateDisplayExtent();
1197   }
1198 }
1199 //----------------------------------------------------------------------------
1200
1201
1202 //----------------------------------------------------------------------------
1203 void vvSlicer::SetColorWindow(double window)
1204 {
1205   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1206   if ( LUT ) {
1207     double level = this->GetWindowLevel()->GetLevel();
1208     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1209     LUT->Build();
1210   }
1211   this->vtkImageViewer2::SetColorWindow(window);
1212 }
1213 //----------------------------------------------------------------------------
1214
1215 //----------------------------------------------------------------------------
1216 void vvSlicer::SetColorLevel(double level)
1217 {
1218   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1219   if ( LUT ) {
1220     double window = this->GetWindowLevel()->GetWindow();
1221     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1222     LUT->Build();
1223   }
1224   this->vtkImageViewer2::SetColorLevel(level);
1225 }
1226 //----------------------------------------------------------------------------
1227
1228 //----------------------------------------------------------------------------
1229 double vvSlicer::GetOverlayColorWindow()
1230 {
1231   if(mOverlayMapper)
1232     return mOverlayMapper->GetWindow();
1233   else
1234     return 0.;
1235 }
1236 //----------------------------------------------------------------------------
1237
1238 //----------------------------------------------------------------------------
1239 double vvSlicer::GetOverlayColorLevel()
1240 {
1241   if(mOverlayMapper)
1242     return mOverlayMapper->GetLevel();
1243   else
1244     return 0.;
1245 }
1246 //----------------------------------------------------------------------------
1247
1248 //----------------------------------------------------------------------------
1249 void vvSlicer::SetOverlayColorWindow(double window)
1250 {
1251   mOverlayMapper->SetWindow(window);
1252 }
1253 //----------------------------------------------------------------------------
1254
1255 //----------------------------------------------------------------------------
1256 void vvSlicer::SetOverlayColorLevel(double level)
1257 {
1258   mOverlayMapper->SetLevel(level);
1259 }
1260 //----------------------------------------------------------------------------
1261
1262 //----------------------------------------------------------------------------
1263 // Returns the min an the max value in a 20%x20% region around the mouse pointer
1264 void vvSlicer::GetExtremasAroundMousePointer(double & min, double & max, vtkImageData *image, vtkTransform *transform)
1265 {
1266   //Get mouse pointer position in view coordinates
1267   double corner1[3];
1268   double corner2[3];
1269   for(int i=0; i<3; i++) {
1270     corner1[i] = mCurrent[i];
1271     corner2[i] = mCurrent[i];
1272   }
1273
1274   this->Renderer->WorldToView(corner1[0], corner1[1], corner1[2]);
1275   this->Renderer->WorldToView(corner2[0], corner2[1], corner2[2]);
1276
1277   // In view coordinates, x is the slicer width and y is the slicer height are the in-plane axis
1278   int w, h;
1279   this->Renderer->GetTiledSize(&w, &h);
1280   corner1[0] -= 0.2*h/(double)w;
1281   corner2[0] += 0.2*h/(double)w;
1282   corner1[1] -= 0.2;
1283   corner2[1] += 0.2;
1284   this->Renderer->ViewToWorld(corner1[0], corner1[1], corner1[2]);
1285   this->Renderer->ViewToWorld(corner2[0], corner2[1], corner2[2]);
1286
1287   //Convert to image pixel coordinates (rounded)
1288   transform->TransformPoint(corner1, corner1);
1289   transform->TransformPoint(corner2, corner2);
1290   int iLocalExtents[6];
1291   for(int i=0; i<3; i++) {
1292     corner1[i] = (corner1[i] - image->GetOrigin()[i])/image->GetSpacing()[i];
1293     corner2[i] = (corner2[i] - image->GetOrigin()[i])/image->GetSpacing()[i];
1294
1295     iLocalExtents[i*2  ] = lrint(corner1[i]);
1296     iLocalExtents[i*2+1] = lrint(corner2[i]);
1297
1298     if(iLocalExtents[i*2  ]>iLocalExtents[i*2+1])
1299       std::swap(iLocalExtents[i*2], iLocalExtents[i*2+1]);
1300   }
1301
1302   vtkSmartPointer<vtkExtractVOI> voiFilter = vtkSmartPointer<vtkExtractVOI>::New();
1303   voiFilter->SetInput(image);
1304   voiFilter->SetVOI(iLocalExtents);
1305   voiFilter->Update();
1306   if (!voiFilter->GetOutput()->GetNumberOfPoints()) {
1307     min = 0;
1308     max = 0;
1309     return;
1310   }
1311
1312   vtkSmartPointer<vtkImageAccumulate> accFilter = vtkSmartPointer<vtkImageAccumulate>::New();
1313   accFilter->SetInput(voiFilter->GetOutput());
1314   accFilter->Update();
1315
1316   min = *(accFilter->GetMin());
1317   max = *(accFilter->GetMax());
1318 }
1319 //----------------------------------------------------------------------------
1320
1321 //----------------------------------------------------------------------------
1322 double vvSlicer::GetScalarComponentAsDouble(vtkImageData *image, double X, double Y, double Z, int &ix, int &iy, int &iz, int component)
1323 {
1324   ix = lrint(X);
1325   iy = lrint(Y);
1326   iz = lrint(Z);
1327   if (ix < image->GetWholeExtent()[0] ||
1328       ix > image->GetWholeExtent()[1] ||
1329       iy < image->GetWholeExtent()[2] ||
1330       iy > image->GetWholeExtent()[3] ||
1331       iz < image->GetWholeExtent()[4] ||
1332       iz > image->GetWholeExtent()[5] )
1333     return std::numeric_limits<double>::quiet_NaN();
1334
1335   image->SetUpdateExtent(ix, ix, iy, iy, iz, iz);
1336   image->Update();
1337   return image->GetScalarComponentAsDouble(ix, iy, iz, component);
1338 }
1339 //----------------------------------------------------------------------------
1340
1341 //----------------------------------------------------------------------------
1342 void vvSlicer::Render()
1343 {
1344   if (this->mFusion && mFusionActor->GetVisibility() && showFusionLegend) {
1345     legend->SetLookupTable(this->GetFusionMapper()->GetLookupTable());
1346     legend->UseOpacityOn();
1347     legend->SetVisibility(1);
1348   }
1349   else if (this->GetWindowLevel()->GetLookupTable() && !this->mOverlay)  {
1350     legend->SetLookupTable(this->GetWindowLevel()->GetLookupTable());
1351     legend->UseOpacityOff();
1352     legend->SetVisibility(1);
1353   } else legend->SetVisibility(0);
1354
1355   if (ca->GetVisibility()) {
1356     std::stringstream worldPos;
1357     double pt[3];
1358     mConcatenatedTransform->TransformPoint(mCurrent, pt);
1359     double X = (pt[0] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[0])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[0];
1360     double Y = (pt[1] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[1])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[1];
1361     double Z = (pt[2] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[2])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[2];
1362
1363     if (X >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[0]-0.5 &&
1364         X <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[1]+0.5 &&
1365         Y >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[2]-0.5 &&
1366         Y <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[3]+0.5 &&
1367         Z >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[4]-0.5 &&
1368         Z <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[5]+0.5) {
1369
1370
1371       int ix, iy, iz;
1372       double value = this->GetScalarComponentAsDouble(mImage->GetVTKImages()[mCurrentTSlice], X, Y, Z, ix, iy, iz);
1373
1374       if(ImageActor->GetVisibility())
1375         worldPos << "data value : " << value << std::endl;
1376
1377       worldPos << "mm : " << lrint(mCurrentBeforeSlicingTransform[0]) << ' '
1378                           << lrint(mCurrentBeforeSlicingTransform[1]) << ' '
1379                           << lrint(mCurrentBeforeSlicingTransform[2]) << ' '
1380                           << mCurrentTSlice
1381                           << std::endl;
1382       worldPos << "pixel : " << ix << ' '
1383                              << iy << ' '
1384                              << iz << ' '
1385                              << mCurrentTSlice
1386                              << std::endl;
1387     }
1388     ca->SetText(1,worldPos.str().c_str());
1389   }
1390
1391   if (pdmA->GetVisibility()) {
1392     double x = mCursor[0];
1393     double y = mCursor[1];
1394     double z = mCursor[2];
1395     double xCursor = (x - this->GetInput()->GetOrigin()[0])/this->GetInput()->GetSpacing()[0];
1396     double yCursor = (y - this->GetInput()->GetOrigin()[1])/this->GetInput()->GetSpacing()[1];
1397     double zCursor = (z - this->GetInput()->GetOrigin()[2])/this->GetInput()->GetSpacing()[2];
1398
1399     if (xCursor >= this->GetImageActor()->GetDisplayExtent()[0]-0.5 &&
1400         xCursor < this->GetImageActor()->GetDisplayExtent()[1]+0.5 &&
1401         yCursor >= this->GetImageActor()->GetDisplayExtent()[2]-0.5 &&
1402         yCursor < this->GetImageActor()->GetDisplayExtent()[3]+0.5 &&
1403         zCursor >= this->GetImageActor()->GetDisplayExtent()[4]-0.5 &&
1404         zCursor < this->GetImageActor()->GetDisplayExtent()[5]+0.5 ) {
1405       vtkRenderer * renderer = this->Renderer;
1406
1407       renderer->WorldToView(x,y,z);
1408       renderer->ViewToNormalizedViewport(x,y,z);
1409       renderer->NormalizedViewportToViewport(x,y);
1410       renderer->ViewportToNormalizedDisplay(x,y);
1411       renderer->NormalizedDisplayToDisplay(x,y);
1412       crossCursor->SetFocalPoint(x,y,z);
1413     } else
1414       crossCursor->SetFocalPoint(-1,-1,z);
1415   }
1416
1417
1418   if (mOverlay && mOverlayActor->GetVisibility()) {
1419     if(mLinkOverlayWindowLevel) {
1420       mOverlayMapper->SetWindow(this->GetColorWindow());
1421       mOverlayMapper->SetLevel(this->GetColorLevel());
1422     }
1423     mOverlayMapper->GetOutput()->SetUpdateExtent(mOverlayActor->GetDisplayExtent());
1424     mOverlayMapper->GetOutput()->Update();
1425     mOverlayMapper->Update();
1426   }
1427   if (mLandMapper)
1428     UpdateLandmarks();
1429
1430   this->GetRenderWindow()->Render();
1431 }
1432 //----------------------------------------------------------------------------
1433
1434
1435 //----------------------------------------------------------------------------
1436 void vvSlicer::UpdateCursorPosition()
1437 {
1438   pdmA->SetVisibility(true);
1439   mCursor[0] = mCurrent[0];
1440   mCursor[1] = mCurrent[1];
1441   mCursor[2] = mCurrent[2];
1442   mCursor[3] = mCurrentTSlice;
1443 }
1444 //----------------------------------------------------------------------------
1445
1446
1447 //----------------------------------------------------------------------------
1448 void vvSlicer::UpdateLandmarks()
1449 {
1450   vtkPolyData *pd = static_cast<vtkPolyData*>(mLandClipper->GetInput());
1451   if (pd->GetPoints()) {
1452     //mLandGlyph->SetRange(0,1);
1453     //mLandGlyph->Modified();
1454     //mLandGlyph->Update();
1455
1456     mClipBox->Modified();
1457     mLandClipper->Update();
1458     mLandMapper->Update();
1459     //Let's add the captions
1460     //First remove all captions:
1461     for(unsigned int i=0;i<mLandLabelActors.size();i++) {
1462         this->Renderer->RemoveActor2D(mLandLabelActors[i]);
1463         //allActors2D->Remove (mLandLabelActors[i]);
1464     }
1465     mLandLabelActors.clear();
1466     //Next add the captions to the displayed points
1467     for (vtkIdType id=0; id<mLandClipper->GetOutput()->GetNumberOfPoints(); id++) {
1468           double *position = mLandClipper->GetOutput()->GetPoint(id);
1469       vtkStdString label = static_cast<vtkStringArray*>(mLandClipper->GetOutput()->GetPointData()->GetAbstractArray("labels"))->GetValue(id);
1470       vtkSmartPointer<vtkCaptionActor2D> label_actor = vtkSmartPointer<vtkCaptionActor2D>::New();
1471       label_actor->SetCaption(label);
1472       label_actor->SetAttachmentPoint(position);
1473       label_actor->GetCaptionTextProperty()->SetColor(1,0,0);
1474       label_actor->GetCaptionTextProperty()->SetOrientation(33.333333);
1475       label_actor->GetCaptionTextProperty()->SetFontFamilyToTimes();
1476       label_actor->GetCaptionTextProperty()->SetBold(0);
1477       label_actor->GetCaptionTextProperty()->SetFontSize(6);
1478       label_actor->BorderOff();
1479       label_actor->LeaderOff();
1480       label_actor->ThreeDimensionalLeaderOff();
1481       mLandLabelActors.push_back(label_actor);
1482       this->Renderer->AddActor2D(mLandLabelActors[id]);
1483      }
1484   }
1485
1486 }
1487 //----------------------------------------------------------------------------
1488
1489
1490 //----------------------------------------------------------------------------
1491 void vvSlicer::SetSlice(int slice)
1492 {
1493   int *range = this->GetSliceRange();
1494   if (range) {
1495     if (slice < range[0]) {
1496       slice = range[0];
1497     } else if (slice > range[1]) {
1498       slice = range[1];
1499     }
1500   }
1501
1502   if (this->Slice == slice) {
1503     return;
1504   }
1505
1506   this->Slice = slice;
1507   SetContourSlice();
1508   this->Modified();
1509   this->UpdateDisplayExtent();
1510
1511   // Seems to work without this line
1512   //this->Render();
1513 }
1514 //----------------------------------------------------------------------------
1515
1516 //----------------------------------------------------------------------------
1517 int vvSlicer::GetTMax() {
1518   int tmax = (int)mImage->GetVTKImages().size() - 1;
1519   if(mOverlay)
1520     tmax = std::max(tmax, (int)mOverlay->GetVTKImages().size()-1);
1521   return tmax;
1522 }
1523 //----------------------------------------------------------------------------
1524
1525 //----------------------------------------------------------------------------
1526 void vvSlicer::SetContourSlice()
1527 {
1528   if (mSurfaceCutActors.size() > 0)
1529     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
1530          i!=mSurfaceCutActors.end(); i++) {
1531
1532       (*i)->SetSlicingOrientation(this->SliceOrientation);
1533       (*i)->SetCutSlice((this->Slice)*this->GetImage()->GetSpacing()[this->SliceOrientation]+
1534                         this->GetImage()->GetOrigin()[this->SliceOrientation]);
1535     }
1536 }
1537 //----------------------------------------------------------------------------
1538
1539
1540 //----------------------------------------------------------------------------
1541 void vvSlicer::ForceUpdateDisplayExtent()
1542 {
1543   this->UpdateDisplayExtent();
1544 }
1545 //----------------------------------------------------------------------------
1546
1547
1548 //----------------------------------------------------------------------------
1549 int* vvSlicer::GetDisplayExtent()
1550 {
1551   return this->GetImageActor()->GetDisplayExtent();
1552 }
1553 //----------------------------------------------------------------------------
1554
1555
1556 //----------------------------------------------------------------------------
1557 void vvSlicer::PrintSelf(ostream& os, vtkIndent indent)
1558 {
1559   this->Superclass::PrintSelf(os, indent);
1560 }
1561 //----------------------------------------------------------------------------
1562
1563 //----------------------------------------------------------------------------
1564 void vvSlicer::SetVFColor(double r, double g, double b)
1565 {
1566   double mVFColorHSV[3];
1567   mVFColor[0] = r;
1568   mVFColor[1] = g;
1569   mVFColor[2] = b;
1570
1571   vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
1572   mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
1573   mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
1574   mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
1575
1576   this->Render();
1577 }
1578