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 #include "vvImageMapToWLColors.h"
  25
  26 #include <vtkTextProperty.h>
  27 #include <vtkTextActor.h>
  28 #include <vtkTextSource.h>
  29 #include <vtkActor2D.h>
  30 #include <vtkCursor2D.h>
  31 #include <vtkPolyDataMapper2D.h>
  32 #include <vtkProperty2D.h>
  33 #include <vtkCornerAnnotation.h>
  34 #include <vtkImageMapToWindowLevelColors.h>
  35 #include <vtkImageData.h>
  36 #include <vtkImageActor.h>
  37 #include <vvBlendImageActor.h>
  38 #include <vtkToolkits.h>
  39 #include <vtkObjectFactory.h>
  40 #include <vtkPointData.h>
  41 #include <vtkDataArray.h>
  42 #include <vtkFloatArray.h>
  43 #include <vtkClipPolyData.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   mUseReducedExtent = false;
  86
  87   mCurrent[0] = -VTK_DOUBLE_MAX;
  88   mCurrent[1] = -VTK_DOUBLE_MAX;
  89   mCurrent[2] = -VTK_DOUBLE_MAX;
  90
  91   mCursor[0] = -VTK_DOUBLE_MAX;
  92   mCursor[1] = -VTK_DOUBLE_MAX;
  93   mCursor[2] = -VTK_DOUBLE_MAX;
  94   mCursor[3] = -VTK_DOUBLE_MAX;
  95
  96   mSubSampling = 5;
  97   mScale = 1;
  98   mVFLog = 0;
  99   mVFWidth = 1;
 100   mVFColor[0] = 0;
 101   mVFColor[1] = 1;
 102   mVFColor[2] = 0;
 103
 104   crossCursor = vtkSmartPointer<vtkCursor2D>::New();
 105   crossCursor->AllOff();
 106   crossCursor->AxesOn();
 107   crossCursor->SetTranslationMode(1);
 108   crossCursor->SetRadius(2);
 109
 110   pdm = vtkSmartPointer<vtkPolyDataMapper2D>::New();
 111   pdm->SetInput(crossCursor->GetOutput());
 112
 113   pdmA = vtkSmartPointer<vtkActor2D>::New();
 114   pdmA->SetMapper(pdm);
 115   pdmA->GetProperty()->SetColor(255,10,212);
 116   pdmA->SetVisibility(0);
 117   pdmA->SetPickable(0);
 118
 119   ca = vtkSmartPointer<vtkCornerAnnotation>::New();
 120   ca->GetTextProperty()->SetColor(255,10,212);
 121   ca->SetVisibility(1);
 122   mFileName = "";
 123
 124   mVF = NULL;
 125   mOverlay = NULL;
 126   mFusion = NULL;
 127   mLandmarks = NULL;
 128
 129   legend = vtkSmartPointer<vtkScalarBarActor>::New();
 130   //legend->SetTitle("test!");
 131   legend->SetPosition(0.82,0.18);
 132   legend->SetWidth(0.1);
 133   legend->SetVisibility(0);
 134   legend->SetLabelFormat("%.1f");
 135   this->GetRenderer()->AddActor(legend);
 136   showFusionLegend = false;
 137
 138   this->WindowLevel->Delete();
 139   this->WindowLevel = vvImageMapToWLColors::New();
 140
 141   this->InstallPipeline();
 142
 143   mLinkOverlayWindowLevel = true;
 144
 145 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 146   this->GetImageActor()->GetMapper()->BorderOn();
 147 #endif
 148
 149   mSlicingTransform = vtkSmartPointer<vtkTransform>::New();
 150   mConcatenatedTransform = vtkSmartPointer<vtkTransform>::New();
 151 }
 152 //------------------------------------------------------------------------------
 153
 154
 155 //------------------------------------------------------------------------------
 156 vtkImageMapToWindowLevelColors* vvSlicer::GetOverlayMapper()
 157 {
 158   return mOverlayMapper.GetPointer();
 159 }
 160 //------------------------------------------------------------------------------
 161
 162
 163 //------------------------------------------------------------------------------
 164 vvBlendImageActor* vvSlicer::GetOverlayActor()
 165 {
 166   return mOverlayActor.GetPointer();
 167 }
 168 //------------------------------------------------------------------------------
 169
 170
 171 //------------------------------------------------------------------------------
 172 vtkImageMapToColors* vvSlicer::GetFusionMapper()
 173 {
 174   return mFusionMapper.GetPointer();
 175 }
 176 //------------------------------------------------------------------------------
 177
 178
 179 //------------------------------------------------------------------------------
 180 vtkImageActor* vvSlicer::GetFusionActor()
 181 {
 182   return mFusionActor.GetPointer();
 183 }
 184 //------------------------------------------------------------------------------
 185
 186
 187 //------------------------------------------------------------------------------
 188 vtkActor* vvSlicer::GetVFActor()
 189 {
 190   return mVFActor.GetPointer();
 191 }
 192 //------------------------------------------------------------------------------
 193
 194
 195 //------------------------------------------------------------------------------
 196 vtkCornerAnnotation* vvSlicer::GetAnnotation()
 197 {
 198   return ca.GetPointer();
 199 }
 200 //------------------------------------------------------------------------------
 201
 202
 203 //------------------------------------------------------------------------------
 204 void vvSlicer::EnableReducedExtent(bool b)
 205 {
 206   mUseReducedExtent = b;
 207 }
 208 //------------------------------------------------------------------------------
 209
 210
 211 //------------------------------------------------------------------------------
 212 void vvSlicer::SetReducedExtent(int * ext)
 213 {
 214   copyExtent(ext, mReducedExtent);
 215 }
 216 //------------------------------------------------------------------------------
 217
 218
 219 //------------------------------------------------------------------------------
 220 void vvSlicer::AddContour(vvMesh::Pointer contour,bool propagate)
 221 {
 222
 223   mSurfaceCutActors.push_back(new vvMeshActor());
 224   if (propagate)
 225     mSurfaceCutActors.back()->Init(contour,mCurrentTSlice,mVF);
 226   else
 227     mSurfaceCutActors.back()->Init(contour,mCurrentTSlice);
 228   mSurfaceCutActors.back()->SetSlicingOrientation(SliceOrientation);
 229   this->GetRenderer()->AddActor(mSurfaceCutActors.back()->GetActor());
 230
 231   SetContourSlice();
 232 }
 233 //------------------------------------------------------------------------------
 234
 235
 236 //------------------------------------------------------------------------------
 237 void vvSlicer::ToggleContourSuperposition()
 238 {
 239   for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 240        i!=mSurfaceCutActors.end(); i++)
 241     (*i)->ToggleSuperposition();
 242 }
 243 //------------------------------------------------------------------------------
 244
 245
 246 //------------------------------------------------------------------------------
 247 void vvSlicer::SetCursorColor(int r,int g, int b)
 248 {
 249   pdmA->GetProperty()->SetColor(r,g,b);
 250 }
 251 //------------------------------------------------------------------------------
 252
 253
 254 //------------------------------------------------------------------------------
 255 void vvSlicer::SetCursorVisibility(bool s)
 256 {
 257   pdmA->SetVisibility(s);
 258 }
 259 //------------------------------------------------------------------------------
 260
 261
 262 //------------------------------------------------------------------------------
 263 bool vvSlicer::GetCursorVisibility()
 264 {
 265   return pdmA->GetVisibility();
 266 }
 267 //------------------------------------------------------------------------------
 268
 269
 270 //------------------------------------------------------------------------------
 271 void vvSlicer::SetCornerAnnotationVisibility(bool s)
 272 {
 273   ca->SetVisibility(s);
 274 }
 275 //------------------------------------------------------------------------------
 276
 277
 278 //------------------------------------------------------------------------------
 279 bool vvSlicer::GetCornerAnnotationVisibility()
 280 {
 281   return ca->GetVisibility();
 282 }
 283 //------------------------------------------------------------------------------
 284
 285
 286 //------------------------------------------------------------------------------
 287 vvSlicer::~vvSlicer()
 288 {
 289   for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 290        i!=mSurfaceCutActors.end(); i++)
 291     delete (*i);
 292   delete [] mReducedExtent;
 293 }
 294 //------------------------------------------------------------------------------
 295
 296 //------------------------------------------------------------------------------
 297 double* vvSlicer::GetCurrentPosition()
 298 {
 299   return mCurrentBeforeSlicingTransform;
 300 }
 301 //------------------------------------------------------------------------------
 302
 303 //------------------------------------------------------------------------------
 304 void vvSlicer::SetCurrentPosition(double x, double y, double z, int t)
 305 {
 306   mCurrentBeforeSlicingTransform[0]=x;
 307   mCurrentBeforeSlicingTransform[1]=y;
 308   mCurrentBeforeSlicingTransform[2]=z;
 309   mSlicingTransform->GetInverse()->TransformPoint(mCurrentBeforeSlicingTransform,mCurrent);
 310   mCurrentTSlice = t;
 311 }
 312 //------------------------------------------------------------------------------
 313
 314
 315 //------------------------------------------------------------------------------
 316 void vvSlicer::SetImage(vvImage::Pointer image)
 317 {
 318   if (image->GetVTKImages().size()) {
 319     mImage = image;
 320
 321     if (!mImageReslice) {
 322       mImageReslice = vtkSmartPointer<vtkImageReslice>::New();
 323       mImageReslice->SetInterpolationModeToLinear();
 324       mImageReslice->AutoCropOutputOn();
 325       mImageReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 326     }
 327
 328     mConcatenatedTransform->Identity();
 329     mConcatenatedTransform->Concatenate(mImage->GetTransform()[0]);
 330     mConcatenatedTransform->Concatenate(mSlicingTransform);
 331     mImageReslice->SetResliceTransform(mConcatenatedTransform);
 332     mImageReslice->SetInput(0, mImage->GetFirstVTKImageData());
 333     mImageReslice->UpdateInformation();
 334
 335     this->Superclass::SetInput(mImageReslice->GetOutput());
 336
 337     int extent[6];
 338     this->GetInput()->GetWholeExtent(extent);
 339
 340     // Prevent crash when reload -> change slice if outside extent
 341     if (Slice < extent[SliceOrientation*2] || Slice>=extent[SliceOrientation*2+1]) {
 342       Slice = (extent[SliceOrientation*2+1]+extent[SliceOrientation*2])/2.0;
 343     }
 344
 345     // Make sure that the required part image has been computed
 346     extent[SliceOrientation*2] = Slice;
 347     extent[SliceOrientation*2+1] = Slice;
 348     mImageReslice->GetOutput()->SetUpdateExtent(extent);
 349     mImageReslice->GetOutput()->Update();
 350
 351     this->UpdateDisplayExtent();
 352
 353     mCurrentTSlice = 0;
 354     ca->SetText(0,mFileName.c_str());
 355   }
 356 }
 357 //------------------------------------------------------------------------------
 358
 359
 360 //------------------------------------------------------------------------------
 361 void vvSlicer::SetOverlay(vvImage::Pointer overlay)
 362 {
 363   if (overlay->GetVTKImages().size()) {
 364     mOverlay = overlay;
 365
 366     if (!mOverlayReslice) {
 367       mOverlayReslice = vtkSmartPointer<vtkImageReslice>::New();
 368       mOverlayReslice->SetInterpolationModeToLinear();
 369       mOverlayReslice->AutoCropOutputOn();
 370       mOverlayReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 371     }
 372     mOverlayReslice->SetResliceTransform(mOverlay->GetTransform()[0]);
 373     mOverlayReslice->SetInput(0, mOverlay->GetFirstVTKImageData());
 374
 375     if (!mOverlayMapper)
 376       mOverlayMapper = vtkSmartPointer<vtkImageMapToWindowLevelColors>::New();
 377     mOverlayMapper->SetInput(mOverlayReslice->GetOutput());
 378
 379     if (!mOverlayActor) {
 380       mOverlayActor = vtkSmartPointer<vvBlendImageActor>::New();
 381       mOverlayActor->SetInput(mOverlayMapper->GetOutput());
 382       mOverlayActor->SetPickable(0);
 383       mOverlayActor->SetVisibility(true);
 384       mOverlayActor->SetOpacity(0.5);
 385 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 386       mOverlayActor->GetMapper()->BorderOn();
 387 #endif
 388       }
 389
 390     //stupid but necessary : the Overlay need to be rendered before fusion
 391     if (mFusionActor) {
 392       this->GetRenderer()->RemoveActor(mFusionActor);
 393       this->GetRenderer()->AddActor(mOverlayActor);
 394       this->GetRenderer()->AddActor(mFusionActor);
 395     } else
 396       this->GetRenderer()->AddActor(mOverlayActor);
 397
 398     //Synchronize orientation and slice
 399     AdjustResliceToSliceOrientation(mOverlayReslice);
 400     this->UpdateDisplayExtent();
 401     this->SetTSlice(mCurrentTSlice);
 402   }
 403 }
 404 //------------------------------------------------------------------------------
 405
 406
 407 //------------------------------------------------------------------------------
 408 void vvSlicer::SetFusion(vvImage::Pointer fusion)
 409 {
 410   if (fusion->GetVTKImages().size()) {
 411     mFusion = fusion;
 412
 413     if (!mFusionReslice) {
 414       mFusionReslice = vtkSmartPointer<vtkImageReslice>::New();
 415       mFusionReslice->SetInterpolationModeToLinear();
 416       mFusionReslice->AutoCropOutputOn();
 417       mFusionReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 418     }
 419     mFusionReslice->SetResliceTransform(mFusion->GetTransform()[0]);
 420     mFusionReslice->SetInput(0, mFusion->GetFirstVTKImageData());
 421
 422     if (!mFusionMapper)
 423       mFusionMapper = vtkSmartPointer<vtkImageMapToColors>::New();
 424
 425     vtkSmartPointer<vtkLookupTable> lut = vtkLookupTable::New();
 426     lut->SetRange(0, 1);
 427     lut->SetValueRange(0, 1);
 428     lut->SetSaturationRange(0, 0);
 429     lut->Build();
 430     mFusionMapper->SetLookupTable(lut);
 431     mFusionMapper->SetInput(mFusionReslice->GetOutput());
 432
 433     if (!mFusionActor) {
 434       mFusionActor = vtkSmartPointer<vtkImageActor>::New();
 435       mFusionActor->SetInput(mFusionMapper->GetOutput());
 436       mFusionActor->SetPickable(0);
 437       mFusionActor->SetVisibility(true);
 438       mFusionActor->SetOpacity(0.7);
 439 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 440       mFusionActor->GetMapper()->BorderOn();
 441 #endif
 442       this->GetRenderer()->AddActor(mFusionActor);
 443     }
 444
 445     //Synchronize orientation and slice
 446     AdjustResliceToSliceOrientation(mFusionReslice);
 447     this->UpdateDisplayExtent();
 448     this->SetTSlice(mCurrentTSlice);
 449   }
 450 }
 451 //------------------------------------------------------------------------------
 452
 453
 454 //------------------------------------------------------------------------------
 455 bool vvSlicer::GetActorVisibility(const std::string& actor_type, int overlay_index)
 456 {
 457   bool vis = false;
 458   if (actor_type == "image") {
 459     vis = this->ImageActor->GetVisibility();
 460   }
 461   else if (actor_type == "vector") {
 462     vis = this->mVFActor->GetVisibility();
 463   }
 464   else if (actor_type == "overlay") {
 465     vis = this->mOverlayActor->GetVisibility();
 466   }
 467   else if (actor_type == "fusion") {
 468     vis = this->mFusionActor->GetVisibility();
 469   }
 470   else if (actor_type == "contour")
 471     vis = this->mSurfaceCutActors[overlay_index]->GetActor()->GetVisibility();
 472
 473   return vis;
 474 }
 475 //------------------------------------------------------------------------------
 476
 477 //------------------------------------------------------------------------------
 478 void vvSlicer::SetActorVisibility(const std::string& actor_type, int overlay_index ,bool vis)
 479 {
 480   if (actor_type == "image") {
 481     this->ImageActor->SetVisibility(vis);
 482   }
 483   else if (actor_type == "vector") {
 484     this->mVFActor->SetVisibility(vis);
 485   }
 486   else if (actor_type == "overlay") {
 487     this->mOverlayActor->SetVisibility(vis);
 488   }
 489   else if (actor_type == "fusion") {
 490     this->mFusionActor->SetVisibility(vis);
 491   }
 492   else if (actor_type == "contour")
 493     this->mSurfaceCutActors[overlay_index]->GetActor()->SetVisibility(vis);
 494   UpdateDisplayExtent();
 495 }
 496 //------------------------------------------------------------------------------
 497
 498 //------------------------------------------------------------------------------
 499 void vvSlicer::SetVF(vvImage::Pointer vf)
 500 {
 501   if (vf->GetVTKImages().size()) {
 502     mVF = vf;
 503
 504     if (!mAAFilter) {
 505       mAAFilter= vtkSmartPointer<vtkAssignAttribute>::New();
 506       mVOIFilter = vtkSmartPointer<vtkExtractVOI>::New();
 507       mVOIFilter->SetSampleRate(mSubSampling,mSubSampling,mSubSampling);
 508     }
 509     mVOIFilter->SetInput(vf->GetFirstVTKImageData());
 510     mAAFilter->SetInput(mVOIFilter->GetOutput());
 511     ///This tells VTK to use the scalar (pixel) data of the image to draw the little arrows
 512     mAAFilter->Assign(vtkDataSetAttributes::SCALARS, vtkDataSetAttributes::VECTORS, vtkAssignAttribute::POINT_DATA);
 513
 514     if (!mArrow)
 515       mArrow = vtkSmartPointer<vvGlyphSource>::New();
 516     mArrow->SetGlyphTypeToSpecificArrow();
 517     mArrow->SetScale(mScale);
 518     mArrow->FilledOff();
 519
 520     // Glyph the gradient vector (with arrows)
 521     if (!mGlyphFilter)
 522       mGlyphFilter = vtkSmartPointer<vvGlyph2D>::New();
 523     mGlyphFilter->SetInput(mAAFilter->GetOutput());
 524     mGlyphFilter->SetSource(mArrow->GetOutput());
 525     mGlyphFilter->ScalingOn();
 526     mGlyphFilter->SetScaleModeToScaleByVector();
 527     mGlyphFilter->OrientOn();
 528     mGlyphFilter->SetVectorModeToUseVector();
 529     mGlyphFilter->SetColorModeToColorByVector();
 530
 531     if (!mVFColorLUT)
 532       mVFColorLUT = vtkSmartPointer<vtkLookupTable>::New();
 533
 534     double mVFColorHSV[3];
 535     vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
 536     mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
 537     mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
 538     mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
 539
 540     if (!mVFMapper)
 541       mVFMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
 542     mVFMapper->SetInput(mGlyphFilter->GetOutput());
 543     mVFMapper->ImmediateModeRenderingOn();
 544     mVFMapper->SetLookupTable(mVFColorLUT);
 545
 546     if (!mVFActor)
 547       mVFActor = vtkSmartPointer<vtkActor>::New();
 548     mVFActor->SetMapper(mVFMapper);
 549     mVFActor->SetPickable(0);
 550     mVFActor->GetProperty()->SetLineWidth(mVFWidth);
 551     this->UpdateDisplayExtent();
 552     this->GetRenderer()->AddActor(mVFActor);
 553
 554     //Synchronize slice
 555     SetTSlice(mCurrentTSlice);
 556   }
 557 }
 558 //------------------------------------------------------------------------------
 559
 560
 561 //------------------------------------------------------------------------------
 562 void vvSlicer::SetLandmarks(vvLandmarks* landmarks)
 563 {
 564   mLandmarks = landmarks;
 565   if (landmarks) {
 566
 567     if (!mCross)
 568       mCross = vtkSmartPointer<vtkCursor3D>::New();
 569     mCross->SetFocalPoint(0.0,0.0,0.0);
 570     mCross->SetModelBounds(-10,10,-10,10,-10,10);
 571     mCross->AllOff();
 572     mCross->AxesOn();
 573
 574     if (!mLandGlyph)
 575       mLandGlyph = vtkSmartPointer<vtkGlyph3D>::New();
 576     mLandGlyph->SetSource(mCross->GetOutput());
 577     mLandGlyph->SetInput(landmarks->GetOutput());
 578     //mLandGlyph->SetIndexModeToScalar();
 579     mLandGlyph->SetRange(0,1);
 580     mLandGlyph->ScalingOff();
 581
 582     mLandGlyph->SetColorModeToColorByScalar();
 583
 584     if (!mClipBox)
 585       mClipBox = vtkSmartPointer<vtkBox>::New();
 586     if (!mLandClipper)
 587       mLandClipper = vtkSmartPointer<vtkClipPolyData>::New();
 588     mLandClipper->InsideOutOn();
 589     mLandClipper->SetInput(mLandGlyph->GetOutput());
 590     mLandClipper->SetClipFunction(mClipBox);
 591
 592     if (!mLandMapper)
 593       mLandMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
 594     mLandMapper->SetInputConnection(mLandClipper->GetOutputPort());
 595     //mLandMapper->ScalarVisibilityOff();
 596
 597     if (!mLandActor)
 598       mLandActor = vtkSmartPointer<vtkActor>::New();
 599     mLandActor->SetMapper(mLandMapper);
 600     mLandActor->GetProperty()->SetColor(255,10,212);
 601     mLandActor->SetPickable(0);
 602     mLandActor->SetVisibility(true);
 603     this->UpdateDisplayExtent();
 604     this->GetRenderer()->AddActor(mLandActor);
 605   }
 606 }
 607 //------------------------------------------------------------------------------
 608
 609 //------------------------------------------------------------------------------
 610 //FIXME: this function leaks memory, we should fix it someday :)
 611 void vvSlicer::RemoveActor(const std::string& actor_type, int overlay_index)
 612 {
 613   if (actor_type == "vector") {
 614     Renderer->RemoveActor(mVFActor);
 615     mGlyphFilter=NULL;
 616     mVF = NULL;
 617     mArrow = NULL;
 618     mAAFilter=NULL;
 619     mVOIFilter = NULL;
 620     mVFMapper = NULL;
 621     mVFActor = NULL;
 622   }
 623   if (actor_type == "overlay") {
 624     Renderer->RemoveActor(mOverlayActor);
 625     mOverlay = NULL;
 626     mOverlayActor = NULL;
 627     mOverlayMapper = NULL;
 628   }
 629   if (actor_type == "fusion") {
 630     Renderer->RemoveActor(mFusionActor);
 631     mFusion = NULL;
 632     mFusionActor = NULL;
 633     mFusionMapper = NULL;
 634   }
 635   if (actor_type == "contour") {
 636     Renderer->RemoveActor(this->mSurfaceCutActors[overlay_index]->GetActor());
 637     mSurfaceCutActors.erase(mSurfaceCutActors.begin()+overlay_index);
 638   }
 639 }
 640 //------------------------------------------------------------------------------
 641
 642
 643 //------------------------------------------------------------------------------
 644 void vvSlicer::SetVFSubSampling(int sub)
 645 {
 646   if (mVOIFilter) {
 647     mVOIFilter->SetSampleRate(mSubSampling,mSubSampling,mSubSampling);
 648     mSubSampling = sub;
 649   }
 650   UpdateDisplayExtent();
 651   Render();
 652 }
 653 //------------------------------------------------------------------------------
 654
 655
 656 //------------------------------------------------------------------------------
 657 void vvSlicer::SetVFScale(int scale)
 658 {
 659   mScale = scale;
 660   if (mArrow)
 661     mArrow->SetScale(mScale);
 662   UpdateDisplayExtent();
 663   Render();
 664 }
 665 //------------------------------------------------------------------------------
 666
 667 //------------------------------------------------------------------------------
 668 void vvSlicer::SetVFWidth(int width)
 669 {
 670   mVFWidth = width;
 671   if (mVFActor)
 672     mVFActor->GetProperty()->SetLineWidth(mVFWidth);
 673   UpdateDisplayExtent();
 674   Render();
 675 }
 676 //------------------------------------------------------------------------------
 677
 678
 679 //------------------------------------------------------------------------------
 680 void vvSlicer::SetVFLog(int log)
 681 {
 682   mVFLog = log;
 683   if (mGlyphFilter) {
 684     mGlyphFilter->SetUseLog(mVFLog);
 685     mGlyphFilter->Modified();
 686   }
 687   UpdateDisplayExtent();
 688   Render();
 689 }
 690 //------------------------------------------------------------------------------
 691
 692
 693 //------------------------------------------------------------------------------
 694 void vvSlicer::SetTSlice(int t)
 695 {
 696   if (t < 0)
 697     t = 0;
 698   else if ((unsigned int)t >= mImage->GetVTKImages().size())
 699     t = mImage->GetVTKImages().size() -1;
 700
 701   // Update transform
 702   mConcatenatedTransform->Identity();
 703   mConcatenatedTransform->Concatenate(mImage->GetTransform()[t]);
 704   mConcatenatedTransform->Concatenate(mSlicingTransform);
 705
 706   // Update image data
 707   mCurrentTSlice = t;
 708   mImageReslice->SetInput( mImage->GetVTKImages()[mCurrentTSlice] );
 709   if (mVF && mVFActor->GetVisibility()) {
 710     if (mVF->GetVTKImages().size() > (unsigned int)mCurrentTSlice)
 711       mVOIFilter->SetInput(mVF->GetVTKImages()[mCurrentTSlice]);
 712   }
 713   if (mOverlay && mOverlayActor->GetVisibility()) {
 714     if (mOverlay->GetVTKImages().size() > (unsigned int)mCurrentTSlice)
 715       mOverlayReslice->SetInput( mOverlay->GetVTKImages()[mCurrentTSlice] );
 716   }
 717   if (mFusion && mFusionActor->GetVisibility()) {
 718     if (mFusion->GetVTKImages().size() > (unsigned int)mCurrentTSlice)
 719       mFusionReslice->SetInput( mFusion->GetVTKImages()[mCurrentTSlice]);
 720   }
 721   if (mSurfaceCutActors.size() > 0)
 722     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 723          i!=mSurfaceCutActors.end(); i++)
 724       (*i)->SetTimeSlice(mCurrentTSlice);
 725   UpdateDisplayExtent();
 726 }
 727 //------------------------------------------------------------------------------
 728
 729
 730 //------------------------------------------------------------------------------
 731 int vvSlicer::GetTSlice()
 732 {
 733   return mCurrentTSlice;
 734 }
 735 //------------------------------------------------------------------------------
 736
 737 //------------------------------------------------------------------------------
 738 void vvSlicer::SetSliceOrientation(int orientation)
 739 {
 740   //if 2D image, force to watch in Axial View
 741   int extent[6];
 742   this->GetInput()->GetWholeExtent(extent);
 743   if (extent[5]-extent[4] <= 2)
 744     orientation = vtkImageViewer2::SLICE_ORIENTATION_XY;
 745
 746   if (orientation < vtkImageViewer2::SLICE_ORIENTATION_YZ ||
 747       orientation > vtkImageViewer2::SLICE_ORIENTATION_XY) {
 748     vtkErrorMacro("Error - invalid slice orientation " << orientation);
 749     return;
 750   }
 751
 752   this->SliceOrientation = orientation;
 753
 754   if(mFusion)
 755     AdjustResliceToSliceOrientation(mFusionReslice);
 756
 757   if(mOverlay)
 758     AdjustResliceToSliceOrientation(mOverlayReslice);
 759
 760   // Update the viewer
 761   int *range = this->GetSliceRange();
 762   if (range)
 763     this->Slice = static_cast<int>((range[0] + range[1]) * 0.5);
 764
 765   // Go to current cursor position
 766   // double* cursorPos = GetCursorPosition();
 767   // DDV(cursorPos, 3);
 768   // SetCurrentPosition(cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
 769
 770   this->UpdateOrientation();
 771   this->UpdateDisplayExtent();
 772
 773   if (this->Renderer && this->GetInput()) {
 774     double scale = this->Renderer->GetActiveCamera()->GetParallelScale();
 775     this->Renderer->ResetCamera();
 776     this->Renderer->GetActiveCamera()->SetParallelScale(scale);
 777   }
 778
 779   SetContourSlice();
 780 }
 781 //----------------------------------------------------------------------------
 782
 783 //------------------------------------------------------------------------------
 784 // This function ensures that we sample the slices of a vtkImageReslice filter
 785 // in the direction of the slicer (SliceOrientation) similarly as mImageReslice.
 786 // In other words, we change the grid of the reslice in the same way as the grid
 787 // of the displayed image in the slicing direction.
 788 void vvSlicer::AdjustResliceToSliceOrientation(vtkImageReslice *reslice)
 789 {
 790   // Reset autocrop and update output information
 791   reslice->SetOutputOriginToDefault();
 792   reslice->SetOutputSpacingToDefault();
 793   reslice->GetOutput()->UpdateInformation();
 794
 795   // Ge new origin / spacing
 796   double origin[3];
 797   double spacing[3];
 798   reslice->GetOutput()->GetOrigin(origin);
 799   reslice->GetOutput()->GetSpacing(spacing);
 800
 801   // Use similar spacing as the image in the direction SliceOrientation
 802   spacing[this->SliceOrientation] = mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
 803
 804   // Modify origin to be on the image grid in the direction SliceOrientation in 3 steps
 805   // Step 1: from world coordinates to image coordinates
 806   origin[this->SliceOrientation] -= mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
 807   origin[this->SliceOrientation] /= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
 808   // Step 2: round to superior grid positionInc
 809   origin[this->SliceOrientation] = itk::Math::Ceil<double>(origin[this->SliceOrientation]);
 810   // Step 3: back to world coordinates
 811   origin[this->SliceOrientation] *= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
 812   origin[this->SliceOrientation] += mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
 813
 814   // Set new spacing and origin
 815   reslice->SetOutputOrigin(origin);
 816   reslice->SetOutputSpacing(spacing);
 817   reslice->UpdateInformation();
 818   reslice->GetOutput()->UpdateInformation();
 819 }
 820 //------------------------------------------------------------------------------
 821
 822 //----------------------------------------------------------------------------
 823 int * vvSlicer::GetExtent(){
 824   int *w_ext;
 825   if (mUseReducedExtent) {
 826     w_ext = mReducedExtent;
 827   } else w_ext = GetInput()->GetWholeExtent();
 828   return w_ext;
 829 }
 830 //----------------------------------------------------------------------------
 831
 832
 833 //----------------------------------------------------------------------------
 834 int vvSlicer::GetOrientation()
 835 {
 836   return this->SliceOrientation;
 837 }
 838 //----------------------------------------------------------------------------
 839
 840
 841 //----------------------------------------------------------------------------
 842 void vvSlicer::UpdateDisplayExtent()
 843 {
 844   vtkImageData *input = this->GetInput();
 845   if (!input || !this->ImageActor) {
 846     return;
 847   }
 848   input->UpdateInformation();
 849
 850   // Local copy of extent
 851   int w_ext[6];
 852   int* ext = GetExtent();
 853   copyExtent(ext, w_ext);
 854   // Set slice value
 855   int s = this->Slice > ext[this->SliceOrientation*2+1] ? ext[this->SliceOrientation*2 + 1] : this->Slice;
 856   w_ext[ this->SliceOrientation*2   ] = s;
 857   w_ext[ this->SliceOrientation*2+1 ] = s;
 858
 859   // Image actor
 860   this->ImageActor->SetDisplayExtent(w_ext);
 861
 862   // Overlay image actor
 863   if (mOverlay && mOverlayActor->GetVisibility()) {
 864     AdjustResliceToSliceOrientation(mOverlayReslice);
 865     int overExtent[6];
 866     this->ConvertImageToImageDisplayExtent(input, w_ext, mOverlayReslice->GetOutput(), overExtent);
 867     ClipDisplayedExtent(overExtent, mOverlayMapper->GetInput()->GetWholeExtent());
 868     mOverlayActor->SetDisplayExtent( overExtent );
 869   }
 870
 871   // Fusion image actor
 872   if (mFusion && mFusionActor->GetVisibility()) {
 873     AdjustResliceToSliceOrientation(mFusionReslice);
 874     int fusExtent[6];
 875     this->ConvertImageToImageDisplayExtent(input, w_ext, mFusionReslice->GetOutput(), fusExtent);
 876     ClipDisplayedExtent(fusExtent, mFusionMapper->GetInput()->GetWholeExtent());
 877     mFusionActor->SetDisplayExtent(fusExtent);
 878   }
 879
 880   // Vector field actor
 881   double* camera = Renderer->GetActiveCamera()->GetPosition();
 882   double* image_bounds = ImageActor->GetBounds();
 883   double position[3] = {0, 0, 0};
 884   position[this->SliceOrientation] = image_bounds[this->SliceOrientation*2];
 885
 886   //print_vector<double, 6>("camera", camera);
 887   //print_vector<double, 6>("image_bounds", image_bounds);
 888   //print_vector<double, 3>("position", position);
 889
 890   // find where to place the VF actor. to deal with
 891   // z-buffer issues, the VF is placed right in front of the image,
 892   // subject to a small offset. the position actually depends on the
 893   // the location of the camera relative to the image.
 894   double offset = 1;
 895   if (camera[this->SliceOrientation] < image_bounds[this->SliceOrientation*2])
 896     offset = -1;
 897
 898   if (mVF && mVFActor->GetVisibility()) {
 899     int vfExtent[6];
 900     mVF->GetVTKImages()[0]->UpdateInformation();
 901     this->ConvertImageToImageDisplayExtent(input, w_ext, mVF->GetVTKImages()[0], vfExtent);
 902     ClipDisplayedExtent(vfExtent, mVOIFilter->GetInput()->GetWholeExtent());
 903     mVOIFilter->SetVOI(vfExtent);
 904     int orientation[3] = {1,1,1};
 905     orientation[this->SliceOrientation] = 0;
 906     mGlyphFilter->SetOrientation(orientation[0], orientation[1], orientation[2]);
 907     mVFMapper->Update();
 908
 909     position[this->SliceOrientation] += offset;
 910     mVFActor->SetPosition(position);
 911   }
 912
 913   // Landmarks actor
 914   if (mLandActor) {
 915     if (mClipBox) {
 916       double bounds [6];
 917       for(unsigned int i=0; i<6; i++)
 918         bounds[i] = ImageActor->GetBounds()[i];
 919       bounds[ this->SliceOrientation*2   ] = ImageActor->GetBounds()[ this->SliceOrientation*2  ]-fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
 920       bounds[ this->SliceOrientation*2+1 ] = ImageActor->GetBounds()[ this->SliceOrientation*2+1 ]+fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
 921       mClipBox->SetBounds(bounds);
 922       UpdateLandmarks();
 923     }
 924
 925     position[this->SliceOrientation] = offset;
 926     mLandActor->SetPosition(position);
 927   }
 928
 929   // Figure out the correct clipping range
 930   if (this->Renderer) {
 931     if (this->InteractorStyle &&
 932         this->InteractorStyle->GetAutoAdjustCameraClippingRange()) {
 933       this->Renderer->ResetCameraClippingRange();
 934     } else {
 935       vtkCamera *cam = this->Renderer->GetActiveCamera();
 936       if (cam) {
 937         double bounds[6];
 938         this->ImageActor->GetBounds(bounds);
 939         double spos = (double)bounds[this->SliceOrientation * 2];
 940         double cpos = (double)cam->GetPosition()[this->SliceOrientation];
 941         double range = fabs(spos - cpos);
 942         double *spacing = input->GetSpacing();
 943         double sumSpacing = spacing[0] + spacing[1] + spacing[2];
 944         cam->SetClippingRange(range - sumSpacing, range + sumSpacing);
 945       }
 946     }
 947   }
 948
 949 }
 950 //----------------------------------------------------------------------------
 951
 952 //----------------------------------------------------------------------------
 953 void vvSlicer::ConvertImageToImageDisplayExtent(vtkImageData *sourceImage, const int sourceExtent[6],
 954                                                 vtkImageData *targetImage, int targetExtent[6])
 955 {
 956   double dExtents[6];
 957   for(unsigned int i=0; i<6; i++) {
 958     // From source voxel coordinates to world coordinates
 959     dExtents[i] = sourceImage->GetOrigin()[i/2] + sourceImage->GetSpacing()[i/2] * sourceExtent[i];
 960
 961     // From world coordinates to floating point target voxel coordinates
 962     dExtents[i] = (dExtents[i]- targetImage->GetOrigin()[i/2]) / targetImage->GetSpacing()[i/2];
 963
 964     // Round to nearest
 965     //targetExtent[i] = itk::Math::Round<double>(dExtents[i]);
 966     targetExtent[i] = itk::Math::Floor<double>(dExtents[i]);
 967   }
 968 }
 969 //----------------------------------------------------------------------------
 970
 971 //----------------------------------------------------------------------------
 972 void vvSlicer::ClipDisplayedExtent(int extent[6], int refExtent[6])
 973 {
 974   bool out = false;
 975   int maxBound = 6;
 976
 977   //2D overlay on 3D image specific case
 978   if (refExtent[4] == refExtent[5]) {
 979     maxBound = 4;
 980     extent[4] = refExtent[4];
 981     extent[5] = refExtent[5];
 982   }
 983
 984   for (int i = 0; i < maxBound; i = i+2) {
 985     //if we are totally outside the image
 986     if ( extent[i] > refExtent[i+1] || extent[i+1] < refExtent[i] ) {
 987       out = true;
 988       break;
 989     }
 990     //crop to the limit of the image
 991     extent[i] = (extent[i] > refExtent[i]) ? extent[i] : refExtent[i];
 992     extent[i] = (extent[i] < refExtent[i+1]) ? extent[i] : refExtent[i+1];
 993     extent[i+1] = (extent[i+1] > refExtent[i]) ? extent[i+1] : refExtent[i];
 994     extent[i+1] = (extent[i+1] < refExtent[i+1]) ? extent[i+1] : refExtent[i+1];
 995   }
 996   if (out)
 997     for (int i = 0; i < maxBound; i = i+2) {
 998       extent[i] = refExtent[i];
 999       extent[i+1] = refExtent[i];
1000     }
1001 }
1002 //----------------------------------------------------------------------------
1003
1004
1005 //----------------------------------------------------------------------------
1006 void vvSlicer::UpdateOrientation()
1007 {
1008   // Set the camera position
1009   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1010   if (cam) {
1011     switch (this->SliceOrientation) {
1012     case vtkImageViewer2::SLICE_ORIENTATION_XY:
1013       cam->SetFocalPoint(0,0,0);
1014       cam->SetPosition(0,0,-1); // -1 if medical ?
1015       cam->SetViewUp(0,-1,0);
1016       break;
1017
1018     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
1019       cam->SetFocalPoint(0,0,0);
1020       cam->SetPosition(0,-1,0); // 1 if medical ?
1021       cam->SetViewUp(0,0,1);
1022       break;
1023
1024     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1025       cam->SetFocalPoint(0,0,0);
1026       cam->SetPosition(-1,0,0); // -1 if medical ?
1027       cam->SetViewUp(0,0,1);
1028       break;
1029     }
1030   }
1031 }
1032 //----------------------------------------------------------------------------
1033
1034
1035 //----------------------------------------------------------------------------
1036 void vvSlicer::SetOpacity(double s)
1037 {
1038   this->GetImageActor()->SetOpacity(s);
1039 }
1040 //----------------------------------------------------------------------------
1041
1042
1043 //----------------------------------------------------------------------------
1044 void vvSlicer::SetRenderWindow(int orientation, vtkRenderWindow * rw)
1045 {
1046   this->Superclass::SetRenderWindow(rw);
1047   this->SetupInteractor(rw->GetInteractor());
1048   ca->SetImageActor(this->GetImageActor());
1049   ca->SetWindowLevel(this->GetWindowLevel());
1050   ca->SetText(2, "<slice>");
1051   ca->SetText(3, "<window>\n<level>");
1052
1053   double bounds[6];
1054   double max = 65000;
1055
1056   bounds[0] = -max;
1057   bounds[1] = max;
1058   bounds[2] = -max;
1059   bounds[3] = max;
1060   bounds[4] = -max;
1061   bounds[5] = max;
1062
1063   crossCursor->SetModelBounds(bounds);
1064   this->GetRenderer()->AddActor(pdmA);
1065   this->GetRenderer()->AddActor(ca);
1066   this->GetRenderer()->ResetCamera();
1067
1068   //this is just a mapping between the labeling of the orientations presented to the user and
1069   //the one used by vtk
1070   SetSliceOrientation(2-(orientation%3));
1071   ResetCamera();
1072 }
1073 //----------------------------------------------------------------------------
1074
1075
1076 //----------------------------------------------------------------------------
1077 void vvSlicer::ResetCamera()
1078 {
1079   this->GetRenderer()->ResetCamera();
1080 }
1081 //----------------------------------------------------------------------------
1082
1083
1084 //----------------------------------------------------------------------------
1085 void vvSlicer::SetDisplayMode(bool i)
1086 {
1087   this->GetRenderer()->SetDraw(i);
1088   if (i)
1089     UpdateDisplayExtent();
1090 }
1091 //----------------------------------------------------------------------------
1092
1093
1094 //----------------------------------------------------------------------------
1095 void vvSlicer::FlipHorizontalView()
1096 {
1097   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1098   if (cam) {
1099     double *position = cam->GetPosition();
1100     double factor[3] = {1, 1, 1};
1101     factor[this->SliceOrientation] = -1;
1102     cam->SetPosition(factor[0]*position[0],factor[1]*position[1],factor[2]*position[2]);
1103
1104 /*    switch (this->SliceOrientation) {
1105     case vtkImageViewer2::SLICE_ORIENTATION_XY:
1106       cam->SetPosition(position[0],position[1],-position[2]);
1107       break;
1108
1109     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
1110       cam->SetPosition(position[0],-position[1],position[2]);
1111       break;
1112
1113     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1114       cam->SetPosition(-position[0],position[1],position[2]);
1115       break;
1116     }*/
1117
1118     this->Renderer->ResetCameraClippingRange();
1119     this->UpdateDisplayExtent();
1120   }
1121 }
1122 //----------------------------------------------------------------------------
1123
1124
1125 //----------------------------------------------------------------------------
1126 void vvSlicer::FlipVerticalView()
1127 {
1128   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1129   if (cam) {
1130     FlipHorizontalView();
1131     double *viewup = cam->GetViewUp();
1132     cam->SetViewUp(-viewup[0],-viewup[1],-viewup[2]);
1133     this->UpdateDisplayExtent();
1134   }
1135 }
1136 //----------------------------------------------------------------------------
1137
1138
1139 //----------------------------------------------------------------------------
1140 void vvSlicer::SetColorWindow(double window)
1141 {
1142   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1143   if ( LUT ) {
1144     double level = this->GetWindowLevel()->GetLevel();
1145     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1146     LUT->Build();
1147   }
1148   this->vtkImageViewer2::SetColorWindow(window);
1149 }
1150 //----------------------------------------------------------------------------
1151
1152 //----------------------------------------------------------------------------
1153 void vvSlicer::SetColorLevel(double level)
1154 {
1155   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1156   if ( LUT ) {
1157     double window = this->GetWindowLevel()->GetWindow();
1158     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1159     LUT->Build();
1160   }
1161   this->vtkImageViewer2::SetColorLevel(level);
1162 }
1163 //----------------------------------------------------------------------------
1164
1165 //----------------------------------------------------------------------------
1166 double vvSlicer::GetOverlayColorWindow()
1167 {
1168   if(mOverlayMapper)
1169     return mOverlayMapper->GetWindow();
1170   else
1171     return 0.;
1172 }
1173 //----------------------------------------------------------------------------
1174
1175 //----------------------------------------------------------------------------
1176 double vvSlicer::GetOverlayColorLevel()
1177 {
1178   if(mOverlayMapper)
1179     return mOverlayMapper->GetLevel();
1180   else
1181     return 0.;
1182 }
1183 //----------------------------------------------------------------------------
1184
1185 //----------------------------------------------------------------------------
1186 void vvSlicer::SetOverlayColorWindow(double window)
1187 {
1188   mOverlayMapper->SetWindow(window);
1189 }
1190 //----------------------------------------------------------------------------
1191
1192 //----------------------------------------------------------------------------
1193 void vvSlicer::SetOverlayColorLevel(double level)
1194 {
1195   mOverlayMapper->SetLevel(level);
1196 }
1197 //----------------------------------------------------------------------------
1198
1199 //----------------------------------------------------------------------------
1200 // Returns the min an the max value in a 41x41 region around the mouse pointer
1201 void vvSlicer::GetExtremasAroundMousePointer(double & min, double & max, vtkImageData *image, vtkTransform *transform)
1202 {
1203   //Get mouse pointer position in view coordinates
1204   double corner1[3];
1205   double corner2[3];
1206   for(int i=0; i<3; i++) {
1207     corner1[i] = mCurrent[i];
1208     corner2[i] = mCurrent[i];
1209   }
1210
1211   this->Renderer->WorldToView(corner1[0], corner1[1], corner1[2]);
1212   this->Renderer->WorldToView(corner2[0], corner2[1], corner2[2]);
1213
1214   // In view coordinates, x is the slicer width and y is the slicer height are the in-plane axis
1215   int w, h;
1216   this->Renderer->GetTiledSize(&w, &h);
1217   corner1[0] -= 0.2*h/(double)w;
1218   corner2[0] += 0.2*h/(double)w;
1219   corner1[1] -= 0.2;
1220   corner2[1] += 0.2;
1221   this->Renderer->ViewToWorld(corner1[0], corner1[1], corner1[2]);
1222   this->Renderer->ViewToWorld(corner2[0], corner2[1], corner2[2]);
1223
1224   //Convert to image pixel coordinates (rounded)
1225   transform->TransformPoint(corner1, corner1);
1226   transform->TransformPoint(corner2, corner2);
1227   int iLocalExtents[6];
1228   for(int i=0; i<3; i++) {
1229     corner1[i] = (corner1[i] - image->GetOrigin()[i])/image->GetSpacing()[i];
1230     corner2[i] = (corner2[i] - image->GetOrigin()[i])/image->GetSpacing()[i];
1231
1232     iLocalExtents[i*2  ] = lrint(corner1[i]);
1233     iLocalExtents[i*2+1] = lrint(corner2[i]);
1234
1235     if(iLocalExtents[i*2  ]>iLocalExtents[i*2+1])
1236       std::swap(iLocalExtents[i*2], iLocalExtents[i*2+1]);
1237   }
1238
1239   vtkSmartPointer<vtkExtractVOI> voiFilter = vtkSmartPointer<vtkExtractVOI>::New();
1240   voiFilter->SetInput(image);
1241   voiFilter->SetVOI(iLocalExtents);
1242   voiFilter->Update();
1243   if (!voiFilter->GetOutput()->GetNumberOfPoints()) {
1244     min = 0;
1245     max = 0;
1246     return;
1247   }
1248
1249   vtkSmartPointer<vtkImageAccumulate> accFilter = vtkSmartPointer<vtkImageAccumulate>::New();
1250   accFilter->SetInput(voiFilter->GetOutput());
1251   accFilter->Update();
1252
1253   min = *(accFilter->GetMin());
1254   max = *(accFilter->GetMax());
1255 }
1256 //----------------------------------------------------------------------------
1257
1258 //----------------------------------------------------------------------------
1259 double vvSlicer::GetScalarComponentAsDouble(vtkImageData *image, double X, double Y, double Z, int &ix, int &iy, int &iz, int component)
1260 {
1261   ix = lrint(X);
1262   iy = lrint(Y);
1263   iz = lrint(Z);
1264   if (ix < image->GetWholeExtent()[0] ||
1265       ix > image->GetWholeExtent()[1] ||
1266       iy < image->GetWholeExtent()[2] ||
1267       iy > image->GetWholeExtent()[3] ||
1268       iz < image->GetWholeExtent()[4] ||
1269       iz > image->GetWholeExtent()[5] )
1270     return std::numeric_limits<double>::quiet_NaN();
1271
1272   image->SetUpdateExtent(ix, ix, iy, iy, iz, iz);
1273   image->Update();
1274   return image->GetScalarComponentAsDouble(ix, iy, iz, component);
1275 }
1276 //----------------------------------------------------------------------------
1277
1278 //----------------------------------------------------------------------------
1279 void vvSlicer::Render()
1280 {
1281   if (this->mFusion && mFusionActor->GetVisibility() && showFusionLegend) {
1282     legend->SetLookupTable(this->GetFusionMapper()->GetLookupTable());
1283     legend->UseOpacityOn();
1284     legend->SetVisibility(1);
1285   }
1286   else if (this->GetWindowLevel()->GetLookupTable() && !this->mOverlay)  {
1287     legend->SetLookupTable(this->GetWindowLevel()->GetLookupTable());
1288     legend->UseOpacityOff();
1289     legend->SetVisibility(1);
1290   } else legend->SetVisibility(0);
1291
1292   if (ca->GetVisibility()) {
1293     std::stringstream worldPos;
1294     double pt[3];
1295     mConcatenatedTransform->TransformPoint(mCurrent, pt);
1296     double X = (pt[0] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[0])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[0];
1297     double Y = (pt[1] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[1])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[1];
1298     double Z = (pt[2] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[2])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[2];
1299
1300     if (X >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[0]-0.5 &&
1301         X <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[1]+0.5 &&
1302         Y >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[2]-0.5 &&
1303         Y <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[3]+0.5 &&
1304         Z >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[4]-0.5 &&
1305         Z <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[5]+0.5) {
1306
1307
1308       int ix, iy, iz;
1309       double value = this->GetScalarComponentAsDouble(mImage->GetVTKImages()[mCurrentTSlice], X, Y, Z, ix, iy, iz);
1310
1311       if(ImageActor->GetVisibility())
1312         worldPos << "data value : " << value << std::endl;
1313
1314       worldPos << "mm : " << lrint(mCurrentBeforeSlicingTransform[0]) << ' '
1315                           << lrint(mCurrentBeforeSlicingTransform[1]) << ' '
1316                           << lrint(mCurrentBeforeSlicingTransform[2]) << ' '
1317                           << mCurrentTSlice
1318                           << std::endl;
1319       worldPos << "pixel : " << ix << ' '
1320                              << iy << ' '
1321                              << iz << ' '
1322                              << mCurrentTSlice
1323                              << std::endl;
1324     }
1325     ca->SetText(1,worldPos.str().c_str());
1326   }
1327
1328   if (pdmA->GetVisibility()) {
1329     double x = mCursor[0];
1330     double y = mCursor[1];
1331     double z = mCursor[2];
1332     double xCursor = (x - this->GetInput()->GetOrigin()[0])/this->GetInput()->GetSpacing()[0];
1333     double yCursor = (y - this->GetInput()->GetOrigin()[1])/this->GetInput()->GetSpacing()[1];
1334     double zCursor = (z - this->GetInput()->GetOrigin()[2])/this->GetInput()->GetSpacing()[2];
1335
1336     if (xCursor >= this->GetImageActor()->GetDisplayExtent()[0] &&
1337         xCursor < this->GetImageActor()->GetDisplayExtent()[1]+1 &&
1338         yCursor >= this->GetImageActor()->GetDisplayExtent()[2] &&
1339         yCursor < this->GetImageActor()->GetDisplayExtent()[3]+1 &&
1340         zCursor >= this->GetImageActor()->GetDisplayExtent()[4] &&
1341         zCursor < this->GetImageActor()->GetDisplayExtent()[5]+1 ) {
1342       vtkRenderer * renderer = this->Renderer;
1343
1344       renderer->WorldToView(x,y,z);
1345       renderer->ViewToNormalizedViewport(x,y,z);
1346       renderer->NormalizedViewportToViewport(x,y);
1347       renderer->ViewportToNormalizedDisplay(x,y);
1348       renderer->NormalizedDisplayToDisplay(x,y);
1349       crossCursor->SetFocalPoint(x,y,z);
1350     } else
1351       crossCursor->SetFocalPoint(-1,-1,z);
1352   }
1353
1354
1355   if (mOverlay && mOverlayActor->GetVisibility()) {
1356     if(mLinkOverlayWindowLevel) {
1357       mOverlayMapper->SetWindow(this->GetColorWindow());
1358       mOverlayMapper->SetLevel(this->GetColorLevel());
1359     }
1360     mOverlayMapper->GetOutput()->SetUpdateExtent(mOverlayActor->GetDisplayExtent());
1361     mOverlayMapper->GetOutput()->Update();
1362     mOverlayMapper->Update();
1363   }
1364   if (mLandMapper)
1365     UpdateLandmarks();
1366
1367   this->GetRenderWindow()->Render();
1368 }
1369 //----------------------------------------------------------------------------
1370
1371
1372 //----------------------------------------------------------------------------
1373 void vvSlicer::UpdateCursorPosition()
1374 {
1375   pdmA->SetVisibility(true);
1376   mCursor[0] = mCurrent[0];
1377   mCursor[1] = mCurrent[1];
1378   mCursor[2] = mCurrent[2];
1379   mCursor[3] = mCurrentTSlice;
1380 }
1381 //----------------------------------------------------------------------------
1382
1383
1384 //----------------------------------------------------------------------------
1385 void vvSlicer::UpdateLandmarks()
1386 {
1387   vtkPolyData *pd = static_cast<vtkPolyData*>(mLandClipper->GetInput());
1388   if (pd->GetPoints()) {
1389     mLandGlyph->SetRange(0,1);
1390     mLandGlyph->Modified();
1391     mLandGlyph->Update();
1392
1393     mClipBox->Modified();
1394     mLandClipper->Update();
1395     mLandMapper->Update();
1396   }
1397
1398 }
1399 //----------------------------------------------------------------------------
1400
1401
1402 //----------------------------------------------------------------------------
1403 void vvSlicer::SetSlice(int slice)
1404 {
1405   int *range = this->GetSliceRange();
1406   if (range) {
1407     if (slice < range[0]) {
1408       slice = range[0];
1409     } else if (slice > range[1]) {
1410       slice = range[1];
1411     }
1412   }
1413
1414   if (this->Slice == slice) {
1415     return;
1416   }
1417
1418   this->Slice = slice;
1419   SetContourSlice();
1420   this->Modified();
1421   this->UpdateDisplayExtent();
1422
1423   // Seems to work without this line
1424   //this->Render();
1425 }
1426 //----------------------------------------------------------------------------
1427
1428
1429 //----------------------------------------------------------------------------
1430 void vvSlicer::SetContourSlice()
1431 {
1432   if (mSurfaceCutActors.size() > 0)
1433     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
1434          i!=mSurfaceCutActors.end(); i++) {
1435
1436       (*i)->SetSlicingOrientation(this->SliceOrientation);
1437       (*i)->SetCutSlice((this->Slice)*this->GetImage()->GetSpacing()[this->SliceOrientation]+
1438                         this->GetImage()->GetOrigin()[this->SliceOrientation]);
1439     }
1440 }
1441 //----------------------------------------------------------------------------
1442
1443
1444 //----------------------------------------------------------------------------
1445 void vvSlicer::ForceUpdateDisplayExtent()
1446 {
1447   this->UpdateDisplayExtent();
1448 }
1449 //----------------------------------------------------------------------------
1450
1451
1452 //----------------------------------------------------------------------------
1453 int* vvSlicer::GetDisplayExtent()
1454 {
1455   return this->GetImageActor()->GetDisplayExtent();
1456 }
1457 //----------------------------------------------------------------------------
1458
1459
1460 //----------------------------------------------------------------------------
1461 void vvSlicer::PrintSelf(ostream& os, vtkIndent indent)
1462 {
1463   this->Superclass::PrintSelf(os, indent);
1464 }
1465 //----------------------------------------------------------------------------
1466
1467 //----------------------------------------------------------------------------
1468 void vvSlicer::SetVFColor(double r, double g, double b)
1469 {
1470   double mVFColorHSV[3];
1471   mVFColor[0] = r;
1472   mVFColor[1] = g;
1473   mVFColor[2] = b;
1474
1475   vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
1476   mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
1477   mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
1478   mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
1479
1480   this->Render();
1481 }
1482