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
  70 vtkCxxRevisionMacro(vvSlicer, "DummyRevision");
  71 vtkStandardNewMacro(vvSlicer);
  72 static void copyExtent(int* in, int* to){
  73  for(int i=0; i<6; ++i) to[i]=in[i];
  74 }
  75 //------------------------------------------------------------------------------
  76 vvSlicer::vvSlicer()
  77 {
  78   this->UnInstallPipeline();
  79   mImage = NULL;
  80   mReducedExtent = new int[6];
  81   mCurrentTSlice = 0;
  82   mUseReducedExtent = false;
  83
  84   mCurrent[0] = -VTK_DOUBLE_MAX;
  85   mCurrent[1] = -VTK_DOUBLE_MAX;
  86   mCurrent[2] = -VTK_DOUBLE_MAX;
  87
  88   mCursor[0] = -VTK_DOUBLE_MAX;
  89   mCursor[1] = -VTK_DOUBLE_MAX;
  90   mCursor[2] = -VTK_DOUBLE_MAX;
  91   mCursor[3] = -VTK_DOUBLE_MAX;
  92
  93   mSubSampling = 5;
  94   mScale = 1;
  95   mVFLog = 0;
  96   mVFWidth = 1;
  97   mVFColor[0] = 0;
  98   mVFColor[1] = 1;
  99   mVFColor[2] = 0;
 100
 101   crossCursor = vtkSmartPointer<vtkCursor2D>::New();
 102   crossCursor->AllOff();
 103   crossCursor->AxesOn();
 104   crossCursor->SetTranslationMode(1);
 105   crossCursor->SetRadius(2);
 106
 107   pdm = vtkSmartPointer<vtkPolyDataMapper2D>::New();
 108   pdm->SetInput(crossCursor->GetOutput());
 109
 110   pdmA = vtkSmartPointer<vtkActor2D>::New();
 111   pdmA->SetMapper(pdm);
 112   pdmA->GetProperty()->SetColor(255,10,212);
 113   pdmA->SetVisibility(0);
 114   pdmA->SetPickable(0);
 115
 116   ca = vtkSmartPointer<vtkCornerAnnotation>::New();
 117   ca->GetTextProperty()->SetColor(255,10,212);
 118   ca->SetVisibility(1);
 119   mFileName = "";
 120
 121   mVF = NULL;
 122   mOverlay = NULL;
 123   mFusion = NULL;
 124   mLandmarks = NULL;
 125
 126   legend = vtkSmartPointer<vtkScalarBarActor>::New();
 127   //legend->SetTitle("test!");
 128   legend->SetPosition(0.82,0.18);
 129   legend->SetWidth(0.1);
 130   legend->SetVisibility(0);
 131   legend->SetLabelFormat("%.1f");
 132   this->GetRenderer()->AddActor(legend);
 133   showFusionLegend = false;
 134
 135   this->WindowLevel->Delete();
 136   this->WindowLevel = vvImageMapToWLColors::New();
 137
 138   this->InstallPipeline();
 139
 140   mLinkOverlayWindowLevel = true;
 141 }
 142 //------------------------------------------------------------------------------
 143
 144
 145 //------------------------------------------------------------------------------
 146 vtkImageMapToWindowLevelColors* vvSlicer::GetOverlayMapper()
 147 {
 148   return mOverlayMapper.GetPointer();
 149 }
 150 //------------------------------------------------------------------------------
 151
 152
 153 //------------------------------------------------------------------------------
 154 vvBlendImageActor* vvSlicer::GetOverlayActor()
 155 {
 156   return mOverlayActor.GetPointer();
 157 }
 158 //------------------------------------------------------------------------------
 159
 160
 161 //------------------------------------------------------------------------------
 162 vtkImageMapToColors* vvSlicer::GetFusionMapper()
 163 {
 164   return mFusionMapper.GetPointer();
 165 }
 166 //------------------------------------------------------------------------------
 167
 168
 169 //------------------------------------------------------------------------------
 170 vtkImageActor* vvSlicer::GetFusionActor()
 171 {
 172   return mFusionActor.GetPointer();
 173 }
 174 //------------------------------------------------------------------------------
 175
 176
 177 //------------------------------------------------------------------------------
 178 vtkActor* vvSlicer::GetVFActor()
 179 {
 180   return mVFActor.GetPointer();
 181 }
 182 //------------------------------------------------------------------------------
 183
 184
 185 //------------------------------------------------------------------------------
 186 vtkCornerAnnotation* vvSlicer::GetAnnotation()
 187 {
 188   return ca.GetPointer();
 189 }
 190 //------------------------------------------------------------------------------
 191
 192
 193 //------------------------------------------------------------------------------
 194 void vvSlicer::EnableReducedExtent(bool b)
 195 {
 196   mUseReducedExtent = b;
 197 }
 198 //------------------------------------------------------------------------------
 199
 200
 201 //------------------------------------------------------------------------------
 202 void vvSlicer::SetReducedExtent(int * ext)
 203 {
 204   copyExtent(ext, mReducedExtent);
 205 }
 206 //------------------------------------------------------------------------------
 207
 208
 209 //------------------------------------------------------------------------------
 210 void vvSlicer::AddContour(vvMesh::Pointer contour,bool propagate)
 211 {
 212
 213   mSurfaceCutActors.push_back(new vvMeshActor());
 214   if (propagate)
 215     mSurfaceCutActors.back()->Init(contour,mCurrentTSlice,mVF);
 216   else
 217     mSurfaceCutActors.back()->Init(contour,mCurrentTSlice);
 218   mSurfaceCutActors.back()->SetSlicingOrientation(SliceOrientation);
 219   this->GetRenderer()->AddActor(mSurfaceCutActors.back()->GetActor());
 220
 221   SetContourSlice();
 222 }
 223 //------------------------------------------------------------------------------
 224
 225
 226 //------------------------------------------------------------------------------
 227 void vvSlicer::ToggleContourSuperposition()
 228 {
 229   for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 230        i!=mSurfaceCutActors.end(); i++)
 231     (*i)->ToggleSuperposition();
 232 }
 233 //------------------------------------------------------------------------------
 234
 235
 236 //------------------------------------------------------------------------------
 237 void vvSlicer::SetCursorColor(int r,int g, int b)
 238 {
 239   pdmA->GetProperty()->SetColor(r,g,b);
 240 }
 241 //------------------------------------------------------------------------------
 242
 243
 244 //------------------------------------------------------------------------------
 245 void vvSlicer::SetCursorVisibility(bool s)
 246 {
 247   pdmA->SetVisibility(s);
 248 }
 249 //------------------------------------------------------------------------------
 250
 251
 252 //------------------------------------------------------------------------------
 253 bool vvSlicer::GetCursorVisibility()
 254 {
 255   return pdmA->GetVisibility();
 256 }
 257 //------------------------------------------------------------------------------
 258
 259
 260 //------------------------------------------------------------------------------
 261 void vvSlicer::SetCornerAnnotationVisibility(bool s)
 262 {
 263   ca->SetVisibility(s);
 264 }
 265 //------------------------------------------------------------------------------
 266
 267
 268 //------------------------------------------------------------------------------
 269 bool vvSlicer::GetCornerAnnotationVisibility()
 270 {
 271   return ca->GetVisibility();
 272 }
 273 //------------------------------------------------------------------------------
 274
 275
 276 //------------------------------------------------------------------------------
 277 vvSlicer::~vvSlicer()
 278 {
 279   for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 280        i!=mSurfaceCutActors.end(); i++)
 281     delete (*i);
 282   delete [] mReducedExtent;
 283 }
 284 //------------------------------------------------------------------------------
 285
 286
 287 //------------------------------------------------------------------------------
 288 void vvSlicer::SetCurrentPosition(double x, double y, double z, int t)
 289 {
 290   mCurrent[0] = x;
 291   mCurrent[1] = y;
 292   mCurrent[2] = z;
 293   mCurrentTSlice = t;
 294 }
 295 //------------------------------------------------------------------------------
 296
 297
 298 //------------------------------------------------------------------------------
 299 void vvSlicer::SetImage(vvImage::Pointer image)
 300 {
 301   if (image->GetVTKImages().size()) {
 302     mImage = image;
 303
 304     if (!mImageReslice) {
 305       mImageReslice = vtkSmartPointer<vtkImageReslice>::New();
 306       mImageReslice->SetInterpolationModeToLinear();
 307       mImageReslice->AutoCropOutputOn();
 308       mImageReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 309     }
 310     mImageReslice->SetResliceTransform(mImage->GetTransform());
 311     mImageReslice->SetInput(0, mImage->GetFirstVTKImageData());
 312     mImageReslice->UpdateInformation();
 313
 314     this->Superclass::SetInput(mImageReslice->GetOutput());
 315
 316     int extent[6];
 317     this->GetInput()->GetWholeExtent(extent);
 318
 319     // Prevent crash when reload -> change slice if outside extent
 320     if (Slice < extent[SliceOrientation*2] || Slice>=extent[SliceOrientation*2+1]) {
 321       Slice = (extent[SliceOrientation*2+1]+extent[SliceOrientation*2])/2.0;
 322     }
 323
 324     // Make sure that the required part image has been computed
 325     extent[SliceOrientation*2] = Slice;
 326     extent[SliceOrientation*2+1] = Slice;
 327     mImageReslice->GetOutput()->SetUpdateExtent(extent);
 328     mImageReslice->GetOutput()->Update();
 329
 330     this->UpdateDisplayExtent();
 331
 332     mCurrentTSlice = 0;
 333     ca->SetText(0,mFileName.c_str());
 334   }
 335 }
 336 //------------------------------------------------------------------------------
 337
 338
 339 //------------------------------------------------------------------------------
 340 void vvSlicer::SetOverlay(vvImage::Pointer overlay)
 341 {
 342   if (overlay->GetVTKImages().size()) {
 343     mOverlay = overlay;
 344
 345     if (!mOverlayReslice) {
 346       mOverlayReslice = vtkSmartPointer<vtkImageReslice>::New();
 347       mOverlayReslice->SetInterpolationModeToLinear();
 348       mOverlayReslice->AutoCropOutputOn();
 349       mOverlayReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 350     }
 351     mOverlayReslice->SetResliceTransform(mOverlay->GetTransform());
 352     mOverlayReslice->SetInput(0, mOverlay->GetFirstVTKImageData());
 353
 354     if (!mOverlayMapper)
 355       mOverlayMapper = vtkSmartPointer<vtkImageMapToWindowLevelColors>::New();
 356     mOverlayMapper->SetInput(mOverlayReslice->GetOutput());
 357
 358     if (!mOverlayActor) {
 359       mOverlayActor = vtkSmartPointer<vvBlendImageActor>::New();
 360       mOverlayActor->SetInput(mOverlayMapper->GetOutput());
 361       mOverlayActor->SetPickable(0);
 362       mOverlayActor->SetVisibility(true);
 363       mOverlayActor->SetOpacity(0.5);
 364     }
 365
 366     //stupid but necessary : the Overlay need to be rendered before fusion
 367     if (mFusionActor) {
 368       this->GetRenderer()->RemoveActor(mFusionActor);
 369       this->GetRenderer()->AddActor(mOverlayActor);
 370       this->GetRenderer()->AddActor(mFusionActor);
 371     } else
 372       this->GetRenderer()->AddActor(mOverlayActor);
 373
 374     //Synchronize orientation and slice
 375     AdjustResliceToSliceOrientation(mOverlayReslice);
 376     this->UpdateDisplayExtent();
 377     this->SetTSlice(mCurrentTSlice);
 378   }
 379 }
 380 //------------------------------------------------------------------------------
 381
 382
 383 //------------------------------------------------------------------------------
 384 void vvSlicer::SetFusion(vvImage::Pointer fusion)
 385 {
 386   if (fusion->GetVTKImages().size()) {
 387     mFusion = fusion;
 388
 389     if (!mFusionReslice) {
 390       mFusionReslice = vtkSmartPointer<vtkImageReslice>::New();
 391       mFusionReslice->SetInterpolationModeToLinear();
 392       mFusionReslice->AutoCropOutputOn();
 393       mFusionReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 394     }
 395     mFusionReslice->SetResliceTransform(mFusion->GetTransform());
 396     mFusionReslice->SetInput(0, mFusion->GetFirstVTKImageData());
 397
 398     if (!mFusionMapper)
 399       mFusionMapper = vtkSmartPointer<vtkImageMapToColors>::New();
 400
 401     vtkSmartPointer<vtkLookupTable> lut = vtkLookupTable::New();
 402     lut->SetRange(0, 1);
 403     lut->SetValueRange(0, 1);
 404     lut->SetSaturationRange(0, 0);
 405     lut->Build();
 406     mFusionMapper->SetLookupTable(lut);
 407     mFusionMapper->SetInput(mFusionReslice->GetOutput());
 408
 409     if (!mFusionActor) {
 410       mFusionActor = vtkSmartPointer<vtkImageActor>::New();
 411       mFusionActor->SetInput(mFusionMapper->GetOutput());
 412       mFusionActor->SetPickable(0);
 413       mFusionActor->SetVisibility(true);
 414       mFusionActor->SetOpacity(0.7);
 415       this->GetRenderer()->AddActor(mFusionActor);
 416     }
 417
 418     //Synchronize orientation and slice
 419     AdjustResliceToSliceOrientation(mFusionReslice);
 420     this->UpdateDisplayExtent();
 421     this->SetTSlice(mCurrentTSlice);
 422   }
 423 }
 424 //------------------------------------------------------------------------------
 425
 426
 427 //------------------------------------------------------------------------------
 428 bool vvSlicer::GetActorVisibility(const std::string& actor_type, int overlay_index)
 429 {
 430   bool vis = false;
 431   if (actor_type == "image") {
 432     vis = this->ImageActor->GetVisibility();
 433   }
 434   else if (actor_type == "vector") {
 435     vis = this->mVFActor->GetVisibility();
 436   }
 437   else if (actor_type == "overlay") {
 438     vis = this->mOverlayActor->GetVisibility();
 439   }
 440   else if (actor_type == "fusion") {
 441     vis = this->mFusionActor->GetVisibility();
 442   }
 443   else if (actor_type == "contour")
 444     vis = this->mSurfaceCutActors[overlay_index]->GetActor()->GetVisibility();
 445
 446   return vis;
 447 }
 448 //------------------------------------------------------------------------------
 449
 450 //------------------------------------------------------------------------------
 451 void vvSlicer::SetActorVisibility(const std::string& actor_type, int overlay_index ,bool vis)
 452 {
 453   if (actor_type == "image") {
 454     this->ImageActor->SetVisibility(vis);
 455   }
 456   else if (actor_type == "vector") {
 457     this->mVFActor->SetVisibility(vis);
 458   }
 459   else if (actor_type == "overlay") {
 460     this->mOverlayActor->SetVisibility(vis);
 461   }
 462   else if (actor_type == "fusion") {
 463     this->mFusionActor->SetVisibility(vis);
 464   }
 465   else if (actor_type == "contour")
 466     this->mSurfaceCutActors[overlay_index]->GetActor()->SetVisibility(vis);
 467   UpdateDisplayExtent();
 468 }
 469 //------------------------------------------------------------------------------
 470
 471 //------------------------------------------------------------------------------
 472 void vvSlicer::SetVF(vvImage::Pointer vf)
 473 {
 474   if (vf->GetVTKImages().size()) {
 475     mVF = vf;
 476
 477     if (!mAAFilter) {
 478       mAAFilter= vtkSmartPointer<vtkAssignAttribute>::New();
 479       mVOIFilter = vtkSmartPointer<vtkExtractVOI>::New();
 480       mVOIFilter->SetSampleRate(mSubSampling,mSubSampling,mSubSampling);
 481     }
 482     mVOIFilter->SetInput(vf->GetFirstVTKImageData());
 483     mAAFilter->SetInput(mVOIFilter->GetOutput());
 484     ///This tells VTK to use the scalar (pixel) data of the image to draw the little arrows
 485     mAAFilter->Assign(vtkDataSetAttributes::SCALARS, vtkDataSetAttributes::VECTORS, vtkAssignAttribute::POINT_DATA);
 486
 487     if (!mArrow)
 488       mArrow = vtkSmartPointer<vvGlyphSource>::New();
 489     mArrow->SetGlyphTypeToSpecificArrow();
 490     mArrow->SetScale(mScale);
 491     mArrow->FilledOff();
 492
 493     // Glyph the gradient vector (with arrows)
 494     if (!mGlyphFilter)
 495       mGlyphFilter = vtkSmartPointer<vvGlyph2D>::New();
 496     mGlyphFilter->SetInput(mAAFilter->GetOutput());
 497     mGlyphFilter->SetSource(mArrow->GetOutput());
 498     mGlyphFilter->ScalingOn();
 499     mGlyphFilter->SetScaleModeToScaleByVector();
 500     mGlyphFilter->OrientOn();
 501     mGlyphFilter->SetVectorModeToUseVector();
 502     mGlyphFilter->SetColorModeToColorByVector();
 503
 504     if (!mVFColorLUT)
 505       mVFColorLUT = vtkSmartPointer<vtkLookupTable>::New();
 506
 507     double mVFColorHSV[3];
 508     vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
 509     mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
 510     mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
 511     mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
 512
 513     if (!mVFMapper)
 514       mVFMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
 515     mVFMapper->SetInput(mGlyphFilter->GetOutput());
 516     mVFMapper->ImmediateModeRenderingOn();
 517     mVFMapper->SetLookupTable(mVFColorLUT);
 518
 519     if (!mVFActor)
 520       mVFActor = vtkSmartPointer<vtkActor>::New();
 521     mVFActor->SetMapper(mVFMapper);
 522     mVFActor->SetPickable(0);
 523     mVFActor->GetProperty()->SetLineWidth(mVFWidth);
 524     this->UpdateDisplayExtent();
 525     this->GetRenderer()->AddActor(mVFActor);
 526
 527     //Synchronize slice
 528     SetTSlice(mCurrentTSlice);
 529   }
 530 }
 531 //------------------------------------------------------------------------------
 532
 533
 534 //------------------------------------------------------------------------------
 535 void vvSlicer::SetLandmarks(vvLandmarks* landmarks)
 536 {
 537   mLandmarks = landmarks;
 538   if (landmarks) {
 539
 540     if (!mCross)
 541       mCross = vtkSmartPointer<vtkCursor3D>::New();
 542     mCross->SetFocalPoint(0.0,0.0,0.0);
 543     mCross->SetModelBounds(-10,10,-10,10,-10,10);
 544     mCross->AllOff();
 545     mCross->AxesOn();
 546
 547     if (!mLandGlyph)
 548       mLandGlyph = vtkSmartPointer<vtkGlyph3D>::New();
 549     mLandGlyph->SetSource(mCross->GetOutput());
 550     mLandGlyph->SetInput(landmarks->GetOutput());
 551     //mLandGlyph->SetIndexModeToScalar();
 552     mLandGlyph->SetRange(0,1);
 553     mLandGlyph->ScalingOff();
 554
 555     mLandGlyph->SetColorModeToColorByScalar();
 556
 557     if (!mClipBox)
 558       mClipBox = vtkSmartPointer<vtkBox>::New();
 559     if (!mLandClipper)
 560       mLandClipper = vtkSmartPointer<vtkClipPolyData>::New();
 561     mLandClipper->InsideOutOn();
 562     mLandClipper->SetInput(mLandGlyph->GetOutput());
 563     mLandClipper->SetClipFunction(mClipBox);
 564
 565     if (!mLandMapper)
 566       mLandMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
 567     mLandMapper->SetInputConnection(mLandClipper->GetOutputPort());
 568     //mLandMapper->ScalarVisibilityOff();
 569
 570     if (!mLandActor)
 571       mLandActor = vtkSmartPointer<vtkActor>::New();
 572     mLandActor->SetMapper(mLandMapper);
 573     mLandActor->GetProperty()->SetColor(255,10,212);
 574     mLandActor->SetPickable(0);
 575     mLandActor->SetVisibility(true);
 576     this->UpdateDisplayExtent();
 577     this->GetRenderer()->AddActor(mLandActor);
 578   }
 579 }
 580 //------------------------------------------------------------------------------
 581
 582 //------------------------------------------------------------------------------
 583 //FIXME: this function leaks memory, we should fix it someday :)
 584 void vvSlicer::RemoveActor(const std::string& actor_type, int overlay_index)
 585 {
 586   if (actor_type == "vector") {
 587     Renderer->RemoveActor(mVFActor);
 588     mGlyphFilter=NULL;
 589     mVF = NULL;
 590     mArrow = NULL;
 591     mAAFilter=NULL;
 592     mVOIFilter = NULL;
 593     mVFMapper = NULL;
 594     mVFActor = NULL;
 595   }
 596   if (actor_type == "overlay") {
 597     Renderer->RemoveActor(mOverlayActor);
 598     mOverlay = NULL;
 599     mOverlayActor = NULL;
 600     mOverlayMapper = NULL;
 601   }
 602   if (actor_type == "fusion") {
 603     Renderer->RemoveActor(mFusionActor);
 604     mFusion = NULL;
 605     mFusionActor = NULL;
 606     mFusionMapper = NULL;
 607   }
 608   if (actor_type == "contour") {
 609     Renderer->RemoveActor(this->mSurfaceCutActors[overlay_index]->GetActor());
 610     mSurfaceCutActors.erase(mSurfaceCutActors.begin()+overlay_index);
 611   }
 612 }
 613 //------------------------------------------------------------------------------
 614
 615
 616 //------------------------------------------------------------------------------
 617 void vvSlicer::SetVFSubSampling(int sub)
 618 {
 619   if (mVOIFilter) {
 620     mVOIFilter->SetSampleRate(mSubSampling,mSubSampling,mSubSampling);
 621     mSubSampling = sub;
 622   }
 623   UpdateDisplayExtent();
 624   Render();
 625 }
 626 //------------------------------------------------------------------------------
 627
 628
 629 //------------------------------------------------------------------------------
 630 void vvSlicer::SetVFScale(int scale)
 631 {
 632   mScale = scale;
 633   if (mArrow)
 634     mArrow->SetScale(mScale);
 635   UpdateDisplayExtent();
 636   Render();
 637 }
 638 //------------------------------------------------------------------------------
 639
 640 //------------------------------------------------------------------------------
 641 void vvSlicer::SetVFWidth(int width)
 642 {
 643   mVFWidth = width;
 644   if (mVFActor)
 645     mVFActor->GetProperty()->SetLineWidth(mVFWidth);
 646   UpdateDisplayExtent();
 647   Render();
 648 }
 649 //------------------------------------------------------------------------------
 650
 651
 652 //------------------------------------------------------------------------------
 653 void vvSlicer::SetVFLog(int log)
 654 {
 655   mVFLog = log;
 656   if (mGlyphFilter) {
 657     mGlyphFilter->SetUseLog(mVFLog);
 658     mGlyphFilter->Modified();
 659   }
 660   UpdateDisplayExtent();
 661   Render();
 662 }
 663 //------------------------------------------------------------------------------
 664
 665
 666 //------------------------------------------------------------------------------
 667 void vvSlicer::SetTSlice(int t)
 668 {
 669   if (t < 0)
 670     t = 0;
 671   else if ((unsigned int)t >= mImage->GetVTKImages().size())
 672     t = mImage->GetVTKImages().size() -1;
 673
 674   if (mCurrentTSlice == t) return;
 675
 676   mCurrentTSlice = t;
 677   mImageReslice->SetInput( mImage->GetVTKImages()[mCurrentTSlice] );
 678   if (mVF && mVFActor->GetVisibility()) {
 679     if (mVF->GetVTKImages().size() > (unsigned int)mCurrentTSlice)
 680       mVOIFilter->SetInput(mVF->GetVTKImages()[mCurrentTSlice]);
 681   }
 682   if (mOverlay && mOverlayActor->GetVisibility()) {
 683     if (mOverlay->GetVTKImages().size() > (unsigned int)mCurrentTSlice)
 684       mOverlayReslice->SetInput( mOverlay->GetVTKImages()[mCurrentTSlice] );
 685   }
 686   if (mFusion && mFusionActor->GetVisibility()) {
 687     if (mFusion->GetVTKImages().size() > (unsigned int)mCurrentTSlice)
 688       mFusionReslice->SetInput( mFusion->GetVTKImages()[mCurrentTSlice]);
 689   }
 690   if (mSurfaceCutActors.size() > 0)
 691     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 692          i!=mSurfaceCutActors.end(); i++)
 693       (*i)->SetTimeSlice(mCurrentTSlice);
 694   UpdateDisplayExtent();
 695 }
 696 //------------------------------------------------------------------------------
 697
 698
 699 //------------------------------------------------------------------------------
 700 int vvSlicer::GetTSlice()
 701 {
 702   return mCurrentTSlice;
 703 }
 704 //------------------------------------------------------------------------------
 705
 706 //------------------------------------------------------------------------------
 707 void vvSlicer::SetSliceOrientation(int orientation)
 708 {
 709   //if 2D image, force to watch in Axial View
 710   int extent[6];
 711   this->GetInput()->GetWholeExtent(extent);
 712   if (extent[5]-extent[4] <= 2)
 713     orientation = vtkImageViewer2::SLICE_ORIENTATION_XY;
 714
 715   if (orientation < vtkImageViewer2::SLICE_ORIENTATION_YZ ||
 716       orientation > vtkImageViewer2::SLICE_ORIENTATION_XY) {
 717     vtkErrorMacro("Error - invalid slice orientation " << orientation);
 718     return;
 719   }
 720
 721   this->SliceOrientation = orientation;
 722
 723   if(mFusion)
 724     AdjustResliceToSliceOrientation(mFusionReslice);
 725
 726   if(mOverlay)
 727     AdjustResliceToSliceOrientation(mOverlayReslice);
 728
 729   // Update the viewer
 730   int *range = this->GetSliceRange();
 731   if (range)
 732     this->Slice = static_cast<int>((range[0] + range[1]) * 0.5);
 733
 734   // Go to current cursor position
 735   // double* cursorPos = GetCursorPosition();
 736   // DDV(cursorPos, 3);
 737   // SetCurrentPosition(cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
 738
 739   this->UpdateOrientation();
 740   this->UpdateDisplayExtent();
 741
 742   if (this->Renderer && this->GetInput()) {
 743     double scale = this->Renderer->GetActiveCamera()->GetParallelScale();
 744     this->Renderer->ResetCamera();
 745     this->Renderer->GetActiveCamera()->SetParallelScale(scale);
 746   }
 747
 748   SetContourSlice();
 749 }
 750 //----------------------------------------------------------------------------
 751
 752 //------------------------------------------------------------------------------
 753 // This function ensures that we sample the slices of a vtkImageReslice filter
 754 // in the direction of the slicer (SliceOrientation) similarly as mImageReslice.
 755 // In other words, we change the grid of the reslice in the same way as the grid
 756 // of the displayed image in the slicing direction.
 757 void vvSlicer::AdjustResliceToSliceOrientation(vtkImageReslice *reslice)
 758 {
 759   // Reset autocrop and update output information
 760   reslice->SetOutputOriginToDefault();
 761   reslice->SetOutputSpacingToDefault();
 762   reslice->GetOutput()->UpdateInformation();
 763
 764   // Ge new origin / spacing
 765   double origin[3];
 766   double spacing[3];
 767   reslice->GetOutput()->GetOrigin(origin);
 768   reslice->GetOutput()->GetSpacing(spacing);
 769
 770   // Use similar spacing as the image in the direction SliceOrientation
 771   spacing[this->SliceOrientation] = mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
 772
 773   // Modify origin to be on the image grid in the direction SliceOrientation in 3 steps
 774   // Step 1: from world coordinates to image coordinates
 775   origin[this->SliceOrientation] -= mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
 776   origin[this->SliceOrientation] /= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
 777   // Step 2: round to superior grid positionInc
 778   origin[this->SliceOrientation] = itk::Math::Ceil<double>(origin[this->SliceOrientation]);
 779   // Step 3: back to world coordinates
 780   origin[this->SliceOrientation] *= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
 781   origin[this->SliceOrientation] += mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
 782
 783   // Set new spacing and origin
 784   reslice->SetOutputOrigin(origin);
 785   reslice->SetOutputSpacing(spacing);
 786   reslice->UpdateInformation();
 787   reslice->GetOutput()->UpdateInformation();
 788 }
 789 //------------------------------------------------------------------------------
 790
 791 //----------------------------------------------------------------------------
 792 int * vvSlicer::GetExtent(){
 793   int *w_ext;
 794   if (mUseReducedExtent) {
 795     w_ext = mReducedExtent;
 796   } else w_ext = GetInput()->GetWholeExtent();
 797   return w_ext;
 798 }
 799 //----------------------------------------------------------------------------
 800
 801
 802 //----------------------------------------------------------------------------
 803 int vvSlicer::GetOrientation()
 804 {
 805   return this->SliceOrientation;
 806 }
 807 //----------------------------------------------------------------------------
 808
 809
 810 //----------------------------------------------------------------------------
 811 void vvSlicer::UpdateDisplayExtent()
 812 {
 813   vtkImageData *input = this->GetInput();
 814   if (!input || !this->ImageActor) {
 815     return;
 816   }
 817   input->UpdateInformation();
 818
 819   // Local copy of extent
 820   int w_ext[6];
 821   int* ext = GetExtent();
 822   copyExtent(ext, w_ext);
 823   // Set slice value
 824   int s = this->Slice > ext[this->SliceOrientation*2+1] ? ext[this->SliceOrientation*2 + 1] : this->Slice;
 825   w_ext[ this->SliceOrientation*2   ] = s;
 826   w_ext[ this->SliceOrientation*2+1 ] = s;
 827
 828   // Image actor
 829   this->ImageActor->SetDisplayExtent(w_ext);
 830
 831   // Overlay image actor
 832   if (mOverlay && mOverlayActor->GetVisibility()) {
 833     AdjustResliceToSliceOrientation(mOverlayReslice);
 834     int overExtent[6];
 835     this->ConvertImageToImageDisplayExtent(input, w_ext, mOverlayReslice->GetOutput(), overExtent);
 836     ClipDisplayedExtent(overExtent, mOverlayMapper->GetInput()->GetWholeExtent());
 837     mOverlayActor->SetDisplayExtent( overExtent );
 838   }
 839
 840   // Fusion image actor
 841   if (mFusion && mFusionActor->GetVisibility()) {
 842     AdjustResliceToSliceOrientation(mFusionReslice);
 843     int fusExtent[6];
 844     this->ConvertImageToImageDisplayExtent(input, w_ext, mFusionReslice->GetOutput(), fusExtent);
 845     ClipDisplayedExtent(fusExtent, mFusionMapper->GetInput()->GetWholeExtent());
 846     mFusionActor->SetDisplayExtent(fusExtent);
 847   }
 848
 849   // Vector field actor
 850   double* camera = Renderer->GetActiveCamera()->GetPosition();
 851   double* image_bounds = ImageActor->GetBounds();
 852   double position[3] = {0, 0, 0};
 853   position[this->SliceOrientation] = image_bounds[this->SliceOrientation*2];
 854
 855   //print_vector<double, 6>("camera", camera);
 856   //print_vector<double, 6>("image_bounds", image_bounds);
 857   //print_vector<double, 3>("position", position);
 858
 859   // find where to place the VF actor. to deal with
 860   // z-buffer issues, the VF is placed right in front of the image,
 861   // subject to a small offset. the position actually depends on the
 862   // the location of the camera relative to the image.
 863   double offset = 1;
 864   if (camera[this->SliceOrientation] < image_bounds[this->SliceOrientation*2])
 865     offset = -1;
 866
 867   if (mVF && mVFActor->GetVisibility()) {
 868     int vfExtent[6];
 869     mVF->GetVTKImages()[0]->UpdateInformation();
 870     this->ConvertImageToImageDisplayExtent(input, w_ext, mVF->GetVTKImages()[0], vfExtent);
 871     ClipDisplayedExtent(vfExtent, mVOIFilter->GetInput()->GetWholeExtent());
 872     mVOIFilter->SetVOI(vfExtent);
 873     int orientation[3] = {1,1,1};
 874     orientation[this->SliceOrientation] = 0;
 875     mGlyphFilter->SetOrientation(orientation[0], orientation[1], orientation[2]);
 876     mVFMapper->Update();
 877
 878     position[this->SliceOrientation] += offset;
 879     mVFActor->SetPosition(position);
 880   }
 881
 882   // Landmarks actor
 883   if (mLandActor) {
 884     if (mClipBox) {
 885       double bounds [6];
 886       for(unsigned int i=0; i<6; i++)
 887         bounds[i] = ImageActor->GetBounds()[i];
 888       bounds[ this->SliceOrientation*2   ] = ImageActor->GetBounds()[ this->SliceOrientation*2  ]-fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
 889       bounds[ this->SliceOrientation*2+1 ] = ImageActor->GetBounds()[ this->SliceOrientation*2+1 ]+fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
 890       mClipBox->SetBounds(bounds);
 891       UpdateLandmarks();
 892     }
 893
 894     position[this->SliceOrientation] = offset;
 895     mLandActor->SetPosition(position);
 896   }
 897
 898   // Figure out the correct clipping range
 899   if (this->Renderer) {
 900     if (this->InteractorStyle &&
 901         this->InteractorStyle->GetAutoAdjustCameraClippingRange()) {
 902       this->Renderer->ResetCameraClippingRange();
 903     } else {
 904       vtkCamera *cam = this->Renderer->GetActiveCamera();
 905       if (cam) {
 906         double bounds[6];
 907         this->ImageActor->GetBounds(bounds);
 908         double spos = (double)bounds[this->SliceOrientation * 2];
 909         double cpos = (double)cam->GetPosition()[this->SliceOrientation];
 910         double range = fabs(spos - cpos);
 911         double *spacing = input->GetSpacing();
 912         double avg_spacing =
 913           ((double)spacing[0] + (double)spacing[1] + (double)spacing[2]) / 3.0;
 914         cam->SetClippingRange(range - avg_spacing * 3.0, range + avg_spacing * 3.0);
 915       }
 916     }
 917   }
 918
 919 }
 920 //----------------------------------------------------------------------------
 921
 922 //----------------------------------------------------------------------------
 923 void vvSlicer::ConvertImageToImageDisplayExtent(vtkImageData *sourceImage, const int sourceExtent[6],
 924                                                 vtkImageData *targetImage, int targetExtent[6])
 925 {
 926   double dExtents[6];
 927   for(unsigned int i=0; i<6; i++) {
 928     // From source voxel coordinates to world coordinates
 929     dExtents[i] = sourceImage->GetOrigin()[i/2] + sourceImage->GetSpacing()[i/2] * sourceExtent[i];
 930
 931     // From world coordinates to floating point target voxel coordinates
 932     dExtents[i] = (dExtents[i]- targetImage->GetOrigin()[i/2]) / targetImage->GetSpacing()[i/2];
 933
 934     // Round to nearest
 935     //targetExtent[i] = itk::Math::Round<double>(dExtents[i]);
 936     targetExtent[i] = itk::Math::Floor<double>(dExtents[i]);
 937   }
 938 }
 939 //----------------------------------------------------------------------------
 940
 941 //----------------------------------------------------------------------------
 942 void vvSlicer::ClipDisplayedExtent(int extent[6], int refExtent[6])
 943 {
 944   bool out = false;
 945   int maxBound = 6;
 946
 947   //2D overlay on 3D image specific case
 948   if (refExtent[4] == refExtent[5]) {
 949     maxBound = 4;
 950     extent[4] = refExtent[4];
 951     extent[5] = refExtent[5];
 952   }
 953
 954   for (int i = 0; i < maxBound; i = i+2) {
 955     //if we are totally outside the image
 956     if ( extent[i] > refExtent[i+1] || extent[i+1] < refExtent[i] ) {
 957       out = true;
 958       break;
 959     }
 960     //crop to the limit of the image
 961     extent[i] = (extent[i] > refExtent[i]) ? extent[i] : refExtent[i];
 962     extent[i] = (extent[i] < refExtent[i+1]) ? extent[i] : refExtent[i+1];
 963     extent[i+1] = (extent[i+1] > refExtent[i]) ? extent[i+1] : refExtent[i];
 964     extent[i+1] = (extent[i+1] < refExtent[i+1]) ? extent[i+1] : refExtent[i+1];
 965   }
 966   if (out)
 967     for (int i = 0; i < maxBound; i = i+2) {
 968       extent[i] = refExtent[i];
 969       extent[i+1] = refExtent[i];
 970     }
 971 }
 972 //----------------------------------------------------------------------------
 973
 974
 975 //----------------------------------------------------------------------------
 976 void vvSlicer::UpdateOrientation()
 977 {
 978   // Set the camera position
 979   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
 980   if (cam) {
 981     switch (this->SliceOrientation) {
 982     case vtkImageViewer2::SLICE_ORIENTATION_XY:
 983       cam->SetFocalPoint(0,0,0);
 984       cam->SetPosition(0,0,-1); // -1 if medical ?
 985       cam->SetViewUp(0,-1,0);
 986       break;
 987
 988     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
 989       cam->SetFocalPoint(0,0,0);
 990       cam->SetPosition(0,-1,0); // 1 if medical ?
 991       cam->SetViewUp(0,0,1);
 992       break;
 993
 994     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
 995       cam->SetFocalPoint(0,0,0);
 996       cam->SetPosition(-1,0,0); // -1 if medical ?
 997       cam->SetViewUp(0,0,1);
 998       break;
 999     }
1000   }
1001 }
1002 //----------------------------------------------------------------------------
1003
1004
1005 //----------------------------------------------------------------------------
1006 void vvSlicer::SetOpacity(double s)
1007 {
1008   this->GetImageActor()->SetOpacity(s);
1009 }
1010 //----------------------------------------------------------------------------
1011
1012
1013 //----------------------------------------------------------------------------
1014 void vvSlicer::SetRenderWindow(int orientation, vtkRenderWindow * rw)
1015 {
1016   this->Superclass::SetRenderWindow(rw);
1017   this->SetupInteractor(rw->GetInteractor());
1018   ca->SetImageActor(this->GetImageActor());
1019   ca->SetWindowLevel(this->GetWindowLevel());
1020   ca->SetText(2, "<slice>");
1021   ca->SetText(3, "<window>\n<level>");
1022
1023   double bounds[6];
1024   double max = 65000;
1025
1026   bounds[0] = -max;
1027   bounds[1] = max;
1028   bounds[2] = -max;
1029   bounds[3] = max;
1030   bounds[4] = -max;
1031   bounds[5] = max;
1032
1033   crossCursor->SetModelBounds(bounds);
1034   this->GetRenderer()->AddActor(pdmA);
1035   this->GetRenderer()->AddActor(ca);
1036   this->GetRenderer()->ResetCamera();
1037
1038   //this is just a mapping between the labeling of the orientations presented to the user and
1039   //the one used by vtk
1040   SetSliceOrientation(2-(orientation%3));
1041   ResetCamera();
1042 }
1043 //----------------------------------------------------------------------------
1044
1045
1046 //----------------------------------------------------------------------------
1047 void vvSlicer::ResetCamera()
1048 {
1049   this->GetRenderer()->ResetCamera();
1050 }
1051 //----------------------------------------------------------------------------
1052
1053
1054 //----------------------------------------------------------------------------
1055 void vvSlicer::SetDisplayMode(bool i)
1056 {
1057   this->GetRenderer()->SetDraw(i);
1058   if (i)
1059     UpdateDisplayExtent();
1060 }
1061 //----------------------------------------------------------------------------
1062
1063
1064 //----------------------------------------------------------------------------
1065 void vvSlicer::FlipHorizontalView()
1066 {
1067   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1068   if (cam) {
1069     double *position = cam->GetPosition();
1070     double factor[3] = {1, 1, 1};
1071     factor[this->SliceOrientation] = -1;
1072     cam->SetPosition(factor[0]*position[0],factor[1]*position[1],factor[2]*position[2]);
1073
1074 /*    switch (this->SliceOrientation) {
1075     case vtkImageViewer2::SLICE_ORIENTATION_XY:
1076       cam->SetPosition(position[0],position[1],-position[2]);
1077       break;
1078
1079     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
1080       cam->SetPosition(position[0],-position[1],position[2]);
1081       break;
1082
1083     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1084       cam->SetPosition(-position[0],position[1],position[2]);
1085       break;
1086     }*/
1087
1088     this->Renderer->ResetCameraClippingRange();
1089     this->UpdateDisplayExtent();
1090   }
1091 }
1092 //----------------------------------------------------------------------------
1093
1094
1095 //----------------------------------------------------------------------------
1096 void vvSlicer::FlipVerticalView()
1097 {
1098   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1099   if (cam) {
1100     FlipHorizontalView();
1101     double *viewup = cam->GetViewUp();
1102     cam->SetViewUp(-viewup[0],-viewup[1],-viewup[2]);
1103     this->UpdateDisplayExtent();
1104   }
1105 }
1106 //----------------------------------------------------------------------------
1107
1108
1109 //----------------------------------------------------------------------------
1110 void vvSlicer::SetColorWindow(double window)
1111 {
1112   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1113   if ( LUT ) {
1114     double level = this->GetWindowLevel()->GetLevel();
1115     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1116     LUT->Build();
1117   }
1118   this->vtkImageViewer2::SetColorWindow(window);
1119 }
1120 //----------------------------------------------------------------------------
1121
1122 //----------------------------------------------------------------------------
1123 void vvSlicer::SetColorLevel(double level)
1124 {
1125   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1126   if ( LUT ) {
1127     double window = this->GetWindowLevel()->GetWindow();
1128     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1129     LUT->Build();
1130   }
1131   this->vtkImageViewer2::SetColorLevel(level);
1132 }
1133 //----------------------------------------------------------------------------
1134
1135 //----------------------------------------------------------------------------
1136 double vvSlicer::GetOverlayColorWindow()
1137 {
1138   if(mOverlayMapper)
1139     return mOverlayMapper->GetWindow();
1140   else
1141     return 0.;
1142 }
1143 //----------------------------------------------------------------------------
1144
1145 //----------------------------------------------------------------------------
1146 double vvSlicer::GetOverlayColorLevel()
1147 {
1148   if(mOverlayMapper)
1149     return mOverlayMapper->GetLevel();
1150   else
1151     return 0.;
1152 }
1153 //----------------------------------------------------------------------------
1154
1155 //----------------------------------------------------------------------------
1156 void vvSlicer::SetOverlayColorWindow(double window)
1157 {
1158   mOverlayMapper->SetWindow(window);
1159 }
1160 //----------------------------------------------------------------------------
1161
1162 //----------------------------------------------------------------------------
1163 void vvSlicer::SetOverlayColorLevel(double level)
1164 {
1165   mOverlayMapper->SetLevel(level);
1166 }
1167 //----------------------------------------------------------------------------
1168
1169 //----------------------------------------------------------------------------
1170 // Returns the min an the max value in a 41x41 region around the mouse pointer
1171 void vvSlicer::GetExtremasAroundMousePointer(double & min, double & max, vtkImageData *image)
1172 {
1173   //Get mouse pointer position in view coordinates
1174   double fLocalExtents[6];
1175   for(int i=0; i<3; i++) {
1176     fLocalExtents[i*2  ] = mCurrent[i];
1177     fLocalExtents[i*2+1] = mCurrent[i];
1178   }
1179   this->Renderer->WorldToView(fLocalExtents[0], fLocalExtents[2], fLocalExtents[4]);
1180   this->Renderer->WorldToView(fLocalExtents[1], fLocalExtents[3], fLocalExtents[5]);
1181   for(int i=0; i<3; i++) {
1182     if (i!=SliceOrientation) { //SR: assumes that SliceOrientation is valid in ViewCoordinates (???)
1183       fLocalExtents[i*2  ] -= 0.2;
1184       fLocalExtents[i*2+1] += 0.2;
1185     }
1186   }
1187   this->Renderer->ViewToWorld(fLocalExtents[0], fLocalExtents[2], fLocalExtents[4]);
1188   this->Renderer->ViewToWorld(fLocalExtents[1], fLocalExtents[3], fLocalExtents[5]);
1189
1190   //Convert to image pixel coordinates (rounded)
1191   int iLocalExtents[6];
1192   for(int i=0; i<3; i++) {
1193     fLocalExtents[i*2  ] = (fLocalExtents[i*2  ] - image->GetOrigin()[i])/image->GetSpacing()[i];
1194     fLocalExtents[i*2+1] = (fLocalExtents[i*2+1] - image->GetOrigin()[i])/image->GetSpacing()[i];
1195
1196     iLocalExtents[i*2  ] = lrint(fLocalExtents[i*2  ]);
1197     iLocalExtents[i*2+1] = lrint(fLocalExtents[i*2+1]);
1198
1199     if(iLocalExtents[i*2  ]>iLocalExtents[i*2+1])
1200       std::swap(iLocalExtents[i*2], iLocalExtents[i*2+1]);
1201   }
1202
1203   vtkSmartPointer<vtkExtractVOI> voiFilter = vtkSmartPointer<vtkExtractVOI>::New();
1204   voiFilter->SetInput(image);
1205   voiFilter->SetVOI(iLocalExtents);
1206   voiFilter->Update();
1207   if (!voiFilter->GetOutput()->GetNumberOfPoints()) {
1208     min = 0;
1209     max = 0;
1210     return;
1211   }
1212
1213   vtkSmartPointer<vtkImageAccumulate> accFilter = vtkSmartPointer<vtkImageAccumulate>::New();
1214   accFilter->SetInput(voiFilter->GetOutput());
1215   accFilter->Update();
1216
1217   min = *(accFilter->GetMin());
1218   max = *(accFilter->GetMax());
1219 }
1220 //----------------------------------------------------------------------------
1221
1222 //----------------------------------------------------------------------------
1223 double vvSlicer::GetScalarComponentAsDouble(vtkImageData *image, double X, double Y, double Z, int &ix, int &iy, int &iz, int component)
1224 {
1225   ix = lrint(X);
1226   iy = lrint(Y);
1227   iz = lrint(Z);
1228   if (ix < image->GetWholeExtent()[0] ||
1229       ix > image->GetWholeExtent()[1] ||
1230       iy < image->GetWholeExtent()[2] ||
1231       iy > image->GetWholeExtent()[3] ||
1232       iz < image->GetWholeExtent()[4] ||
1233       iz > image->GetWholeExtent()[5] )
1234     return std::numeric_limits<double>::quiet_NaN();
1235
1236   image->SetUpdateExtent(ix, ix, iy, iy, iz, iz);
1237   image->Update();
1238   return image->GetScalarComponentAsDouble(ix, iy, iz, component);
1239 }
1240 //----------------------------------------------------------------------------
1241
1242 //----------------------------------------------------------------------------
1243 void vvSlicer::Render()
1244 {
1245   if (this->mFusion && mFusionActor->GetVisibility() && showFusionLegend) {
1246     legend->SetLookupTable(this->GetFusionMapper()->GetLookupTable());
1247     legend->UseOpacityOn();
1248     legend->SetVisibility(1);
1249   }
1250   else if (this->GetWindowLevel()->GetLookupTable() && !this->mOverlay)  {
1251     legend->SetLookupTable(this->GetWindowLevel()->GetLookupTable());
1252     legend->UseOpacityOff();
1253     legend->SetVisibility(1);
1254   } else legend->SetVisibility(0);
1255
1256   if (ca->GetVisibility()) {
1257     std::stringstream worldPos;
1258     double X = (mCurrent[0] - this->GetInput()->GetOrigin()[0])/this->GetInput()->GetSpacing()[0];
1259     double Y = (mCurrent[1] - this->GetInput()->GetOrigin()[1])/this->GetInput()->GetSpacing()[1];
1260     double Z = (mCurrent[2] - this->GetInput()->GetOrigin()[2])/this->GetInput()->GetSpacing()[2];
1261
1262 //     if (X < this->GetInput()->GetWholeExtent()[0]) X = this->GetInput()->GetWholeExtent()[0];
1263 //     else if (X > this->GetInput()->GetWholeExtent()[1]) X = this->GetInput()->GetWholeExtent()[1];
1264 //     if (Y < this->GetInput()->GetWholeExtent()[2]) Y = this->GetInput()->GetWholeExtent()[2];
1265 //     else if (Y > this->GetInput()->GetWholeExtent()[3]) Y = this->GetInput()->GetWholeExtent()[3];
1266 //     if (Z < this->GetInput()->GetWholeExtent()[4]) Z = this->GetInput()->GetWholeExtent()[4];
1267 //     else if (Z > this->GetInput()->GetWholeExtent()[5]) Z = this->GetInput()->GetWholeExtent()[5];
1268
1269     if (X >= this->GetInput()->GetWholeExtent()[0] &&
1270         X <= this->GetInput()->GetWholeExtent()[1] &&
1271         Y >= this->GetInput()->GetWholeExtent()[2] &&
1272         Y <= this->GetInput()->GetWholeExtent()[3] &&
1273         Z >= this->GetInput()->GetWholeExtent()[4] &&
1274         Z <= this->GetInput()->GetWholeExtent()[5]) {
1275
1276
1277       int ix, iy, iz;
1278       double value = this->GetScalarComponentAsDouble(this->GetInput(), X, Y, Z, ix, iy, iz);
1279
1280       if(ImageActor->GetVisibility())
1281         worldPos << "data value : " << value << std::endl;
1282
1283       worldPos << "mm : " << lrint(mCurrent[0]) << ' '
1284                           << lrint(mCurrent[1]) << ' '
1285                           << lrint(mCurrent[2]) << ' '
1286                           << mCurrentTSlice
1287                           << std::endl;
1288       worldPos << "pixel : " << ix << ' '
1289                              << iy << ' '
1290                              << iz << ' '
1291                              << mCurrentTSlice
1292                              << std::endl;
1293     }
1294     ca->SetText(1,worldPos.str().c_str());
1295   }
1296
1297   if (pdmA->GetVisibility()) {
1298     double x = mCursor[0];
1299     double y = mCursor[1];
1300     double z = mCursor[2];
1301     double xCursor = (x - this->GetInput()->GetOrigin()[0])/this->GetInput()->GetSpacing()[0];
1302     double yCursor = (y - this->GetInput()->GetOrigin()[1])/this->GetInput()->GetSpacing()[1];
1303     double zCursor = (z - this->GetInput()->GetOrigin()[2])/this->GetInput()->GetSpacing()[2];
1304
1305     if (xCursor >= this->GetImageActor()->GetDisplayExtent()[0] &&
1306         xCursor < this->GetImageActor()->GetDisplayExtent()[1]+1 &&
1307         yCursor >= this->GetImageActor()->GetDisplayExtent()[2] &&
1308         yCursor < this->GetImageActor()->GetDisplayExtent()[3]+1 &&
1309         zCursor >= this->GetImageActor()->GetDisplayExtent()[4] &&
1310         zCursor < this->GetImageActor()->GetDisplayExtent()[5]+1 ) {
1311       vtkRenderer * renderer = this->Renderer;
1312
1313       renderer->WorldToView(x,y,z);
1314       renderer->ViewToNormalizedViewport(x,y,z);
1315       renderer->NormalizedViewportToViewport(x,y);
1316       renderer->ViewportToNormalizedDisplay(x,y);
1317       renderer->NormalizedDisplayToDisplay(x,y);
1318       crossCursor->SetFocalPoint(x,y,z);
1319     } else
1320       crossCursor->SetFocalPoint(-1,-1,z);
1321   }
1322
1323
1324   if (mOverlay && mOverlayActor->GetVisibility()) {
1325     if(mLinkOverlayWindowLevel) {
1326       mOverlayMapper->SetWindow(this->GetColorWindow());
1327       mOverlayMapper->SetLevel(this->GetColorLevel());
1328     }
1329     mOverlayMapper->GetOutput()->SetUpdateExtent(mOverlayActor->GetDisplayExtent());
1330     mOverlayMapper->GetOutput()->Update();
1331     mOverlayMapper->Update();
1332   }
1333   if (mLandMapper)
1334     UpdateLandmarks();
1335
1336   this->GetRenderWindow()->Render();
1337 }
1338 //----------------------------------------------------------------------------
1339
1340
1341 //----------------------------------------------------------------------------
1342 void vvSlicer::UpdateCursorPosition()
1343 {
1344   pdmA->SetVisibility(true);
1345   mCursor[0] = mCurrent[0];
1346   mCursor[1] = mCurrent[1];
1347   mCursor[2] = mCurrent[2];
1348   mCursor[3] = mCurrentTSlice;
1349 }
1350 //----------------------------------------------------------------------------
1351
1352
1353 //----------------------------------------------------------------------------
1354 void vvSlicer::UpdateLandmarks()
1355 {
1356   vtkPolyData *pd = static_cast<vtkPolyData*>(mLandClipper->GetInput());
1357   if (pd->GetPoints()) {
1358     mLandGlyph->SetRange(0,1);
1359     mLandGlyph->Modified();
1360     mLandGlyph->Update();
1361
1362     mClipBox->Modified();
1363     mLandClipper->Update();
1364     mLandMapper->Update();
1365   }
1366
1367 }
1368 //----------------------------------------------------------------------------
1369
1370
1371 //----------------------------------------------------------------------------
1372 void vvSlicer::SetSlice(int slice)
1373 {
1374   int *range = this->GetSliceRange();
1375   if (range) {
1376     if (slice < range[0]) {
1377       slice = range[0];
1378     } else if (slice > range[1]) {
1379       slice = range[1];
1380     }
1381   }
1382
1383   if (this->Slice == slice) {
1384     return;
1385   }
1386
1387   this->Slice = slice;
1388   SetContourSlice();
1389   this->Modified();
1390   this->UpdateDisplayExtent();
1391
1392   // Seems to work without this line
1393   //this->Render();
1394 }
1395 //----------------------------------------------------------------------------
1396
1397
1398 //----------------------------------------------------------------------------
1399 void vvSlicer::SetContourSlice()
1400 {
1401   if (mSurfaceCutActors.size() > 0)
1402     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
1403          i!=mSurfaceCutActors.end(); i++) {
1404
1405       (*i)->SetSlicingOrientation(this->SliceOrientation);
1406       (*i)->SetCutSlice((this->Slice)*this->GetImage()->GetSpacing()[this->SliceOrientation]+
1407                         this->GetImage()->GetOrigin()[this->SliceOrientation]);
1408     }
1409 }
1410 //----------------------------------------------------------------------------
1411
1412
1413 //----------------------------------------------------------------------------
1414 void vvSlicer::ForceUpdateDisplayExtent()
1415 {
1416   this->UpdateDisplayExtent();
1417 }
1418 //----------------------------------------------------------------------------
1419
1420
1421 //----------------------------------------------------------------------------
1422 int* vvSlicer::GetDisplayExtent()
1423 {
1424   return this->GetImageActor()->GetDisplayExtent();
1425 }
1426 //----------------------------------------------------------------------------
1427
1428
1429 //----------------------------------------------------------------------------
1430 void vvSlicer::PrintSelf(ostream& os, vtkIndent indent)
1431 {
1432   this->Superclass::PrintSelf(os, indent);
1433 }
1434 //----------------------------------------------------------------------------
1435
1436 //----------------------------------------------------------------------------
1437 void vvSlicer::SetVFColor(double r, double g, double b)
1438 {
1439   double mVFColorHSV[3];
1440   mVFColor[0] = r;
1441   mVFColor[1] = g;
1442   mVFColor[2] = b;
1443
1444   vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
1445   mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
1446   mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
1447   mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
1448
1449   this->Render();
1450 }
1451