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   mCurrentTSlice = t;
 675   mImageReslice->SetInput( mImage->GetVTKImages()[mCurrentTSlice] );
 676   if (mVF && mVFActor->GetVisibility()) {
 677     if (mVF->GetVTKImages().size() > (unsigned int)mCurrentTSlice)
 678       mVOIFilter->SetInput(mVF->GetVTKImages()[mCurrentTSlice]);
 679   }
 680   if (mOverlay && mOverlayActor->GetVisibility()) {
 681     if (mOverlay->GetVTKImages().size() > (unsigned int)mCurrentTSlice)
 682       mOverlayReslice->SetInput( mOverlay->GetVTKImages()[mCurrentTSlice] );
 683   }
 684   if (mFusion && mFusionActor->GetVisibility()) {
 685     if (mFusion->GetVTKImages().size() > (unsigned int)mCurrentTSlice)
 686       mFusionReslice->SetInput( mFusion->GetVTKImages()[mCurrentTSlice]);
 687   }
 688   if (mSurfaceCutActors.size() > 0)
 689     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 690          i!=mSurfaceCutActors.end(); i++)
 691       (*i)->SetTimeSlice(mCurrentTSlice);
 692   UpdateDisplayExtent();
 693 }
 694 //------------------------------------------------------------------------------
 695
 696
 697 //------------------------------------------------------------------------------
 698 int vvSlicer::GetTSlice()
 699 {
 700   return mCurrentTSlice;
 701 }
 702 //------------------------------------------------------------------------------
 703
 704 //------------------------------------------------------------------------------
 705 void vvSlicer::SetSliceOrientation(int orientation)
 706 {
 707   //if 2D image, force to watch in Axial View
 708   int extent[6];
 709   this->GetInput()->GetWholeExtent(extent);
 710   if (extent[5]-extent[4] <= 2)
 711     orientation = vtkImageViewer2::SLICE_ORIENTATION_XY;
 712
 713   if (orientation < vtkImageViewer2::SLICE_ORIENTATION_YZ ||
 714       orientation > vtkImageViewer2::SLICE_ORIENTATION_XY) {
 715     vtkErrorMacro("Error - invalid slice orientation " << orientation);
 716     return;
 717   }
 718
 719   this->SliceOrientation = orientation;
 720
 721   if(mFusion)
 722     AdjustResliceToSliceOrientation(mFusionReslice);
 723
 724   if(mOverlay)
 725     AdjustResliceToSliceOrientation(mOverlayReslice);
 726
 727   // Update the viewer
 728   int *range = this->GetSliceRange();
 729   if (range)
 730     this->Slice = static_cast<int>((range[0] + range[1]) * 0.5);
 731
 732   // Go to current cursor position
 733   // double* cursorPos = GetCursorPosition();
 734   // DDV(cursorPos, 3);
 735   // SetCurrentPosition(cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
 736
 737   this->UpdateOrientation();
 738   this->UpdateDisplayExtent();
 739
 740   if (this->Renderer && this->GetInput()) {
 741     double scale = this->Renderer->GetActiveCamera()->GetParallelScale();
 742     this->Renderer->ResetCamera();
 743     this->Renderer->GetActiveCamera()->SetParallelScale(scale);
 744   }
 745
 746   SetContourSlice();
 747 }
 748 //----------------------------------------------------------------------------
 749
 750 //------------------------------------------------------------------------------
 751 // This function ensures that we sample the slices of a vtkImageReslice filter
 752 // in the direction of the slicer (SliceOrientation) similarly as mImageReslice.
 753 // In other words, we change the grid of the reslice in the same way as the grid
 754 // of the displayed image in the slicing direction.
 755 void vvSlicer::AdjustResliceToSliceOrientation(vtkImageReslice *reslice)
 756 {
 757   // Reset autocrop and update output information
 758   reslice->SetOutputOriginToDefault();
 759   reslice->SetOutputSpacingToDefault();
 760   reslice->GetOutput()->UpdateInformation();
 761
 762   // Ge new origin / spacing
 763   double origin[3];
 764   double spacing[3];
 765   reslice->GetOutput()->GetOrigin(origin);
 766   reslice->GetOutput()->GetSpacing(spacing);
 767
 768   // Use similar spacing as the image in the direction SliceOrientation
 769   spacing[this->SliceOrientation] = mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
 770
 771   // Modify origin to be on the image grid in the direction SliceOrientation in 3 steps
 772   // Step 1: from world coordinates to image coordinates
 773   origin[this->SliceOrientation] -= mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
 774   origin[this->SliceOrientation] /= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
 775   // Step 2: round to superior grid positionInc
 776   origin[this->SliceOrientation] = itk::Math::Ceil<double>(origin[this->SliceOrientation]);
 777   // Step 3: back to world coordinates
 778   origin[this->SliceOrientation] *= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
 779   origin[this->SliceOrientation] += mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
 780
 781   // Set new spacing and origin
 782   reslice->SetOutputOrigin(origin);
 783   reslice->SetOutputSpacing(spacing);
 784   reslice->UpdateInformation();
 785   reslice->GetOutput()->UpdateInformation();
 786 }
 787 //------------------------------------------------------------------------------
 788
 789 //----------------------------------------------------------------------------
 790 int * vvSlicer::GetExtent(){
 791   int *w_ext;
 792   if (mUseReducedExtent) {
 793     w_ext = mReducedExtent;
 794   } else w_ext = GetInput()->GetWholeExtent();
 795   return w_ext;
 796 }
 797 //----------------------------------------------------------------------------
 798
 799
 800 //----------------------------------------------------------------------------
 801 int vvSlicer::GetOrientation()
 802 {
 803   return this->SliceOrientation;
 804 }
 805 //----------------------------------------------------------------------------
 806
 807
 808 //----------------------------------------------------------------------------
 809 void vvSlicer::UpdateDisplayExtent()
 810 {
 811   vtkImageData *input = this->GetInput();
 812   if (!input || !this->ImageActor) {
 813     return;
 814   }
 815   input->UpdateInformation();
 816
 817   // Local copy of extent
 818   int w_ext[6];
 819   int* ext = GetExtent();
 820   copyExtent(ext, w_ext);
 821   // Set slice value
 822   int s = this->Slice > ext[this->SliceOrientation*2+1] ? ext[this->SliceOrientation*2 + 1] : this->Slice;
 823   w_ext[ this->SliceOrientation*2   ] = s;
 824   w_ext[ this->SliceOrientation*2+1 ] = s;
 825
 826   // Image actor
 827   this->ImageActor->SetDisplayExtent(w_ext);
 828
 829   // Overlay image actor
 830   if (mOverlay && mOverlayActor->GetVisibility()) {
 831     AdjustResliceToSliceOrientation(mOverlayReslice);
 832     int overExtent[6];
 833     this->ConvertImageToImageDisplayExtent(input, w_ext, mOverlayReslice->GetOutput(), overExtent);
 834     ClipDisplayedExtent(overExtent, mOverlayMapper->GetInput()->GetWholeExtent());
 835     mOverlayActor->SetDisplayExtent( overExtent );
 836   }
 837
 838   // Fusion image actor
 839   if (mFusion && mFusionActor->GetVisibility()) {
 840     AdjustResliceToSliceOrientation(mFusionReslice);
 841     int fusExtent[6];
 842     this->ConvertImageToImageDisplayExtent(input, w_ext, mFusionReslice->GetOutput(), fusExtent);
 843     ClipDisplayedExtent(fusExtent, mFusionMapper->GetInput()->GetWholeExtent());
 844     mFusionActor->SetDisplayExtent(fusExtent);
 845   }
 846
 847   // Vector field actor
 848   double* camera = Renderer->GetActiveCamera()->GetPosition();
 849   double* image_bounds = ImageActor->GetBounds();
 850   double position[3] = {0, 0, 0};
 851   position[this->SliceOrientation] = image_bounds[this->SliceOrientation*2];
 852
 853   //print_vector<double, 6>("camera", camera);
 854   //print_vector<double, 6>("image_bounds", image_bounds);
 855   //print_vector<double, 3>("position", position);
 856
 857   // find where to place the VF actor. to deal with
 858   // z-buffer issues, the VF is placed right in front of the image,
 859   // subject to a small offset. the position actually depends on the
 860   // the location of the camera relative to the image.
 861   double offset = 1;
 862   if (camera[this->SliceOrientation] < image_bounds[this->SliceOrientation*2])
 863     offset = -1;
 864
 865   if (mVF && mVFActor->GetVisibility()) {
 866     int vfExtent[6];
 867     mVF->GetVTKImages()[0]->UpdateInformation();
 868     this->ConvertImageToImageDisplayExtent(input, w_ext, mVF->GetVTKImages()[0], vfExtent);
 869     ClipDisplayedExtent(vfExtent, mVOIFilter->GetInput()->GetWholeExtent());
 870     mVOIFilter->SetVOI(vfExtent);
 871     int orientation[3] = {1,1,1};
 872     orientation[this->SliceOrientation] = 0;
 873     mGlyphFilter->SetOrientation(orientation[0], orientation[1], orientation[2]);
 874     mVFMapper->Update();
 875
 876     position[this->SliceOrientation] += offset;
 877     mVFActor->SetPosition(position);
 878   }
 879
 880   // Landmarks actor
 881   if (mLandActor) {
 882     if (mClipBox) {
 883       double bounds [6];
 884       for(unsigned int i=0; i<6; i++)
 885         bounds[i] = ImageActor->GetBounds()[i];
 886       bounds[ this->SliceOrientation*2   ] = ImageActor->GetBounds()[ this->SliceOrientation*2  ]-fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
 887       bounds[ this->SliceOrientation*2+1 ] = ImageActor->GetBounds()[ this->SliceOrientation*2+1 ]+fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
 888       mClipBox->SetBounds(bounds);
 889       UpdateLandmarks();
 890     }
 891
 892     position[this->SliceOrientation] = offset;
 893     mLandActor->SetPosition(position);
 894   }
 895
 896   // Figure out the correct clipping range
 897   if (this->Renderer) {
 898     if (this->InteractorStyle &&
 899         this->InteractorStyle->GetAutoAdjustCameraClippingRange()) {
 900       this->Renderer->ResetCameraClippingRange();
 901     } else {
 902       vtkCamera *cam = this->Renderer->GetActiveCamera();
 903       if (cam) {
 904         double bounds[6];
 905         this->ImageActor->GetBounds(bounds);
 906         double spos = (double)bounds[this->SliceOrientation * 2];
 907         double cpos = (double)cam->GetPosition()[this->SliceOrientation];
 908         double range = fabs(spos - cpos);
 909         double *spacing = input->GetSpacing();
 910         double avg_spacing =
 911           ((double)spacing[0] + (double)spacing[1] + (double)spacing[2]) / 3.0;
 912         cam->SetClippingRange(range - avg_spacing * 3.0, range + avg_spacing * 3.0);
 913       }
 914     }
 915   }
 916
 917 }
 918 //----------------------------------------------------------------------------
 919
 920 //----------------------------------------------------------------------------
 921 void vvSlicer::ConvertImageToImageDisplayExtent(vtkImageData *sourceImage, const int sourceExtent[6],
 922                                                 vtkImageData *targetImage, int targetExtent[6])
 923 {
 924   double dExtents[6];
 925   for(unsigned int i=0; i<6; i++) {
 926     // From source voxel coordinates to world coordinates
 927     dExtents[i] = sourceImage->GetOrigin()[i/2] + sourceImage->GetSpacing()[i/2] * sourceExtent[i];
 928
 929     // From world coordinates to floating point target voxel coordinates
 930     dExtents[i] = (dExtents[i]- targetImage->GetOrigin()[i/2]) / targetImage->GetSpacing()[i/2];
 931
 932     // Round to nearest
 933     //targetExtent[i] = itk::Math::Round<double>(dExtents[i]);
 934     targetExtent[i] = itk::Math::Floor<double>(dExtents[i]);
 935   }
 936 }
 937 //----------------------------------------------------------------------------
 938
 939 //----------------------------------------------------------------------------
 940 void vvSlicer::ClipDisplayedExtent(int extent[6], int refExtent[6])
 941 {
 942   bool out = false;
 943   int maxBound = 6;
 944
 945   //2D overlay on 3D image specific case
 946   if (refExtent[4] == refExtent[5]) {
 947     maxBound = 4;
 948     extent[4] = refExtent[4];
 949     extent[5] = refExtent[5];
 950   }
 951
 952   for (int i = 0; i < maxBound; i = i+2) {
 953     //if we are totally outside the image
 954     if ( extent[i] > refExtent[i+1] || extent[i+1] < refExtent[i] ) {
 955       out = true;
 956       break;
 957     }
 958     //crop to the limit of the image
 959     extent[i] = (extent[i] > refExtent[i]) ? extent[i] : refExtent[i];
 960     extent[i] = (extent[i] < refExtent[i+1]) ? extent[i] : refExtent[i+1];
 961     extent[i+1] = (extent[i+1] > refExtent[i]) ? extent[i+1] : refExtent[i];
 962     extent[i+1] = (extent[i+1] < refExtent[i+1]) ? extent[i+1] : refExtent[i+1];
 963   }
 964   if (out)
 965     for (int i = 0; i < maxBound; i = i+2) {
 966       extent[i] = refExtent[i];
 967       extent[i+1] = refExtent[i];
 968     }
 969 }
 970 //----------------------------------------------------------------------------
 971
 972
 973 //----------------------------------------------------------------------------
 974 void vvSlicer::UpdateOrientation()
 975 {
 976   // Set the camera position
 977   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
 978   if (cam) {
 979     switch (this->SliceOrientation) {
 980     case vtkImageViewer2::SLICE_ORIENTATION_XY:
 981       cam->SetFocalPoint(0,0,0);
 982       cam->SetPosition(0,0,-1); // -1 if medical ?
 983       cam->SetViewUp(0,-1,0);
 984       break;
 985
 986     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
 987       cam->SetFocalPoint(0,0,0);
 988       cam->SetPosition(0,-1,0); // 1 if medical ?
 989       cam->SetViewUp(0,0,1);
 990       break;
 991
 992     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
 993       cam->SetFocalPoint(0,0,0);
 994       cam->SetPosition(-1,0,0); // -1 if medical ?
 995       cam->SetViewUp(0,0,1);
 996       break;
 997     }
 998   }
 999 }
1000 //----------------------------------------------------------------------------
1001
1002
1003 //----------------------------------------------------------------------------
1004 void vvSlicer::SetOpacity(double s)
1005 {
1006   this->GetImageActor()->SetOpacity(s);
1007 }
1008 //----------------------------------------------------------------------------
1009
1010
1011 //----------------------------------------------------------------------------
1012 void vvSlicer::SetRenderWindow(int orientation, vtkRenderWindow * rw)
1013 {
1014   this->Superclass::SetRenderWindow(rw);
1015   this->SetupInteractor(rw->GetInteractor());
1016   ca->SetImageActor(this->GetImageActor());
1017   ca->SetWindowLevel(this->GetWindowLevel());
1018   ca->SetText(2, "<slice>");
1019   ca->SetText(3, "<window>\n<level>");
1020
1021   double bounds[6];
1022   double max = 65000;
1023
1024   bounds[0] = -max;
1025   bounds[1] = max;
1026   bounds[2] = -max;
1027   bounds[3] = max;
1028   bounds[4] = -max;
1029   bounds[5] = max;
1030
1031   crossCursor->SetModelBounds(bounds);
1032   this->GetRenderer()->AddActor(pdmA);
1033   this->GetRenderer()->AddActor(ca);
1034   this->GetRenderer()->ResetCamera();
1035
1036   //this is just a mapping between the labeling of the orientations presented to the user and
1037   //the one used by vtk
1038   SetSliceOrientation(2-(orientation%3));
1039   ResetCamera();
1040 }
1041 //----------------------------------------------------------------------------
1042
1043
1044 //----------------------------------------------------------------------------
1045 void vvSlicer::ResetCamera()
1046 {
1047   this->GetRenderer()->ResetCamera();
1048 }
1049 //----------------------------------------------------------------------------
1050
1051
1052 //----------------------------------------------------------------------------
1053 void vvSlicer::SetDisplayMode(bool i)
1054 {
1055   this->GetRenderer()->SetDraw(i);
1056   if (i)
1057     UpdateDisplayExtent();
1058 }
1059 //----------------------------------------------------------------------------
1060
1061
1062 //----------------------------------------------------------------------------
1063 void vvSlicer::FlipHorizontalView()
1064 {
1065   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1066   if (cam) {
1067     double *position = cam->GetPosition();
1068     double factor[3] = {1, 1, 1};
1069     factor[this->SliceOrientation] = -1;
1070     cam->SetPosition(factor[0]*position[0],factor[1]*position[1],factor[2]*position[2]);
1071
1072 /*    switch (this->SliceOrientation) {
1073     case vtkImageViewer2::SLICE_ORIENTATION_XY:
1074       cam->SetPosition(position[0],position[1],-position[2]);
1075       break;
1076
1077     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
1078       cam->SetPosition(position[0],-position[1],position[2]);
1079       break;
1080
1081     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1082       cam->SetPosition(-position[0],position[1],position[2]);
1083       break;
1084     }*/
1085
1086     this->Renderer->ResetCameraClippingRange();
1087     this->UpdateDisplayExtent();
1088   }
1089 }
1090 //----------------------------------------------------------------------------
1091
1092
1093 //----------------------------------------------------------------------------
1094 void vvSlicer::FlipVerticalView()
1095 {
1096   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1097   if (cam) {
1098     FlipHorizontalView();
1099     double *viewup = cam->GetViewUp();
1100     cam->SetViewUp(-viewup[0],-viewup[1],-viewup[2]);
1101     this->UpdateDisplayExtent();
1102   }
1103 }
1104 //----------------------------------------------------------------------------
1105
1106
1107 //----------------------------------------------------------------------------
1108 void vvSlicer::SetColorWindow(double window)
1109 {
1110   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1111   if ( LUT ) {
1112     double level = this->GetWindowLevel()->GetLevel();
1113     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1114     LUT->Build();
1115   }
1116   this->vtkImageViewer2::SetColorWindow(window);
1117 }
1118 //----------------------------------------------------------------------------
1119
1120 //----------------------------------------------------------------------------
1121 void vvSlicer::SetColorLevel(double level)
1122 {
1123   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1124   if ( LUT ) {
1125     double window = this->GetWindowLevel()->GetWindow();
1126     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1127     LUT->Build();
1128   }
1129   this->vtkImageViewer2::SetColorLevel(level);
1130 }
1131 //----------------------------------------------------------------------------
1132
1133 //----------------------------------------------------------------------------
1134 double vvSlicer::GetOverlayColorWindow()
1135 {
1136   if(mOverlayMapper)
1137     return mOverlayMapper->GetWindow();
1138   else
1139     return 0.;
1140 }
1141 //----------------------------------------------------------------------------
1142
1143 //----------------------------------------------------------------------------
1144 double vvSlicer::GetOverlayColorLevel()
1145 {
1146   if(mOverlayMapper)
1147     return mOverlayMapper->GetLevel();
1148   else
1149     return 0.;
1150 }
1151 //----------------------------------------------------------------------------
1152
1153 //----------------------------------------------------------------------------
1154 void vvSlicer::SetOverlayColorWindow(double window)
1155 {
1156   mOverlayMapper->SetWindow(window);
1157 }
1158 //----------------------------------------------------------------------------
1159
1160 //----------------------------------------------------------------------------
1161 void vvSlicer::SetOverlayColorLevel(double level)
1162 {
1163   mOverlayMapper->SetLevel(level);
1164 }
1165 //----------------------------------------------------------------------------
1166
1167 //----------------------------------------------------------------------------
1168 // Returns the min an the max value in a 41x41 region around the mouse pointer
1169 void vvSlicer::GetExtremasAroundMousePointer(double & min, double & max, vtkImageData *image, vtkTransform *transform)
1170 {
1171   //Get mouse pointer position in view coordinates
1172   double corner1[3];
1173   double corner2[3];
1174   for(int i=0; i<3; i++) {
1175     corner1[i] = mCurrent[i];
1176     corner2[i] = mCurrent[i];
1177   }
1178
1179   this->Renderer->WorldToView(corner1[0], corner1[1], corner1[2]);
1180   this->Renderer->WorldToView(corner2[0], corner2[1], corner2[2]);
1181
1182   // In view coordinates, x is the slicer width and y is the slicer height are the in-plane axis
1183   int w, h;
1184   this->Renderer->GetTiledSize(&w, &h);
1185   corner1[0] -= 0.2*h/(double)w;
1186   corner2[0] += 0.2*h/(double)w;
1187   corner1[1] -= 0.2;
1188   corner2[1] += 0.2;
1189   this->Renderer->ViewToWorld(corner1[0], corner1[1], corner1[2]);
1190   this->Renderer->ViewToWorld(corner2[0], corner2[1], corner2[2]);
1191
1192   //Convert to image pixel coordinates (rounded)
1193   transform->TransformPoint(corner1, corner1);
1194   transform->TransformPoint(corner2, corner2);
1195   int iLocalExtents[6];
1196   for(int i=0; i<3; i++) {
1197     corner1[i] = (corner1[i] - image->GetOrigin()[i])/image->GetSpacing()[i];
1198     corner2[i] = (corner2[i] - image->GetOrigin()[i])/image->GetSpacing()[i];
1199
1200     iLocalExtents[i*2  ] = lrint(corner1[i]);
1201     iLocalExtents[i*2+1] = lrint(corner2[i]);
1202
1203     if(iLocalExtents[i*2  ]>iLocalExtents[i*2+1])
1204       std::swap(iLocalExtents[i*2], iLocalExtents[i*2+1]);
1205   }
1206
1207   vtkSmartPointer<vtkExtractVOI> voiFilter = vtkSmartPointer<vtkExtractVOI>::New();
1208   voiFilter->SetInput(image);
1209   voiFilter->SetVOI(iLocalExtents);
1210   voiFilter->Update();
1211   if (!voiFilter->GetOutput()->GetNumberOfPoints()) {
1212     min = 0;
1213     max = 0;
1214     return;
1215   }
1216
1217   vtkSmartPointer<vtkImageAccumulate> accFilter = vtkSmartPointer<vtkImageAccumulate>::New();
1218   accFilter->SetInput(voiFilter->GetOutput());
1219   accFilter->Update();
1220
1221   min = *(accFilter->GetMin());
1222   max = *(accFilter->GetMax());
1223 }
1224 //----------------------------------------------------------------------------
1225
1226 //----------------------------------------------------------------------------
1227 double vvSlicer::GetScalarComponentAsDouble(vtkImageData *image, double X, double Y, double Z, int &ix, int &iy, int &iz, int component)
1228 {
1229   ix = lrint(X);
1230   iy = lrint(Y);
1231   iz = lrint(Z);
1232   if (ix < image->GetWholeExtent()[0] ||
1233       ix > image->GetWholeExtent()[1] ||
1234       iy < image->GetWholeExtent()[2] ||
1235       iy > image->GetWholeExtent()[3] ||
1236       iz < image->GetWholeExtent()[4] ||
1237       iz > image->GetWholeExtent()[5] )
1238     return std::numeric_limits<double>::quiet_NaN();
1239
1240   image->SetUpdateExtent(ix, ix, iy, iy, iz, iz);
1241   image->Update();
1242   return image->GetScalarComponentAsDouble(ix, iy, iz, component);
1243 }
1244 //----------------------------------------------------------------------------
1245
1246 //----------------------------------------------------------------------------
1247 void vvSlicer::Render()
1248 {
1249   if (this->mFusion && mFusionActor->GetVisibility() && showFusionLegend) {
1250     legend->SetLookupTable(this->GetFusionMapper()->GetLookupTable());
1251     legend->UseOpacityOn();
1252     legend->SetVisibility(1);
1253   }
1254   else if (this->GetWindowLevel()->GetLookupTable() && !this->mOverlay)  {
1255     legend->SetLookupTable(this->GetWindowLevel()->GetLookupTable());
1256     legend->UseOpacityOff();
1257     legend->SetVisibility(1);
1258   } else legend->SetVisibility(0);
1259
1260   if (ca->GetVisibility()) {
1261     std::stringstream worldPos;
1262     double X = (mCurrent[0] - this->GetInput()->GetOrigin()[0])/this->GetInput()->GetSpacing()[0];
1263     double Y = (mCurrent[1] - this->GetInput()->GetOrigin()[1])/this->GetInput()->GetSpacing()[1];
1264     double Z = (mCurrent[2] - this->GetInput()->GetOrigin()[2])/this->GetInput()->GetSpacing()[2];
1265
1266 //     if (X < this->GetInput()->GetWholeExtent()[0]) X = this->GetInput()->GetWholeExtent()[0];
1267 //     else if (X > this->GetInput()->GetWholeExtent()[1]) X = this->GetInput()->GetWholeExtent()[1];
1268 //     if (Y < this->GetInput()->GetWholeExtent()[2]) Y = this->GetInput()->GetWholeExtent()[2];
1269 //     else if (Y > this->GetInput()->GetWholeExtent()[3]) Y = this->GetInput()->GetWholeExtent()[3];
1270 //     if (Z < this->GetInput()->GetWholeExtent()[4]) Z = this->GetInput()->GetWholeExtent()[4];
1271 //     else if (Z > this->GetInput()->GetWholeExtent()[5]) Z = this->GetInput()->GetWholeExtent()[5];
1272
1273     if (X >= this->GetInput()->GetWholeExtent()[0] &&
1274         X <= this->GetInput()->GetWholeExtent()[1] &&
1275         Y >= this->GetInput()->GetWholeExtent()[2] &&
1276         Y <= this->GetInput()->GetWholeExtent()[3] &&
1277         Z >= this->GetInput()->GetWholeExtent()[4] &&
1278         Z <= this->GetInput()->GetWholeExtent()[5]) {
1279
1280
1281       int ix, iy, iz;
1282       double value = this->GetScalarComponentAsDouble(this->GetInput(), X, Y, Z, ix, iy, iz);
1283
1284       if(ImageActor->GetVisibility())
1285         worldPos << "data value : " << value << std::endl;
1286
1287       worldPos << "mm : " << lrint(mCurrent[0]) << ' '
1288                           << lrint(mCurrent[1]) << ' '
1289                           << lrint(mCurrent[2]) << ' '
1290                           << mCurrentTSlice
1291                           << std::endl;
1292       worldPos << "pixel : " << ix << ' '
1293                              << iy << ' '
1294                              << iz << ' '
1295                              << mCurrentTSlice
1296                              << std::endl;
1297     }
1298     ca->SetText(1,worldPos.str().c_str());
1299   }
1300
1301   if (pdmA->GetVisibility()) {
1302     double x = mCursor[0];
1303     double y = mCursor[1];
1304     double z = mCursor[2];
1305     double xCursor = (x - this->GetInput()->GetOrigin()[0])/this->GetInput()->GetSpacing()[0];
1306     double yCursor = (y - this->GetInput()->GetOrigin()[1])/this->GetInput()->GetSpacing()[1];
1307     double zCursor = (z - this->GetInput()->GetOrigin()[2])/this->GetInput()->GetSpacing()[2];
1308
1309     if (xCursor >= this->GetImageActor()->GetDisplayExtent()[0] &&
1310         xCursor < this->GetImageActor()->GetDisplayExtent()[1]+1 &&
1311         yCursor >= this->GetImageActor()->GetDisplayExtent()[2] &&
1312         yCursor < this->GetImageActor()->GetDisplayExtent()[3]+1 &&
1313         zCursor >= this->GetImageActor()->GetDisplayExtent()[4] &&
1314         zCursor < this->GetImageActor()->GetDisplayExtent()[5]+1 ) {
1315       vtkRenderer * renderer = this->Renderer;
1316
1317       renderer->WorldToView(x,y,z);
1318       renderer->ViewToNormalizedViewport(x,y,z);
1319       renderer->NormalizedViewportToViewport(x,y);
1320       renderer->ViewportToNormalizedDisplay(x,y);
1321       renderer->NormalizedDisplayToDisplay(x,y);
1322       crossCursor->SetFocalPoint(x,y,z);
1323     } else
1324       crossCursor->SetFocalPoint(-1,-1,z);
1325   }
1326
1327
1328   if (mOverlay && mOverlayActor->GetVisibility()) {
1329     if(mLinkOverlayWindowLevel) {
1330       mOverlayMapper->SetWindow(this->GetColorWindow());
1331       mOverlayMapper->SetLevel(this->GetColorLevel());
1332     }
1333     mOverlayMapper->GetOutput()->SetUpdateExtent(mOverlayActor->GetDisplayExtent());
1334     mOverlayMapper->GetOutput()->Update();
1335     mOverlayMapper->Update();
1336   }
1337   if (mLandMapper)
1338     UpdateLandmarks();
1339
1340   this->GetRenderWindow()->Render();
1341 }
1342 //----------------------------------------------------------------------------
1343
1344
1345 //----------------------------------------------------------------------------
1346 void vvSlicer::UpdateCursorPosition()
1347 {
1348   pdmA->SetVisibility(true);
1349   mCursor[0] = mCurrent[0];
1350   mCursor[1] = mCurrent[1];
1351   mCursor[2] = mCurrent[2];
1352   mCursor[3] = mCurrentTSlice;
1353 }
1354 //----------------------------------------------------------------------------
1355
1356
1357 //----------------------------------------------------------------------------
1358 void vvSlicer::UpdateLandmarks()
1359 {
1360   vtkPolyData *pd = static_cast<vtkPolyData*>(mLandClipper->GetInput());
1361   if (pd->GetPoints()) {
1362     mLandGlyph->SetRange(0,1);
1363     mLandGlyph->Modified();
1364     mLandGlyph->Update();
1365
1366     mClipBox->Modified();
1367     mLandClipper->Update();
1368     mLandMapper->Update();
1369   }
1370
1371 }
1372 //----------------------------------------------------------------------------
1373
1374
1375 //----------------------------------------------------------------------------
1376 void vvSlicer::SetSlice(int slice)
1377 {
1378   int *range = this->GetSliceRange();
1379   if (range) {
1380     if (slice < range[0]) {
1381       slice = range[0];
1382     } else if (slice > range[1]) {
1383       slice = range[1];
1384     }
1385   }
1386
1387   if (this->Slice == slice) {
1388     return;
1389   }
1390
1391   this->Slice = slice;
1392   SetContourSlice();
1393   this->Modified();
1394   this->UpdateDisplayExtent();
1395
1396   // Seems to work without this line
1397   //this->Render();
1398 }
1399 //----------------------------------------------------------------------------
1400
1401
1402 //----------------------------------------------------------------------------
1403 void vvSlicer::SetContourSlice()
1404 {
1405   if (mSurfaceCutActors.size() > 0)
1406     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
1407          i!=mSurfaceCutActors.end(); i++) {
1408
1409       (*i)->SetSlicingOrientation(this->SliceOrientation);
1410       (*i)->SetCutSlice((this->Slice)*this->GetImage()->GetSpacing()[this->SliceOrientation]+
1411                         this->GetImage()->GetOrigin()[this->SliceOrientation]);
1412     }
1413 }
1414 //----------------------------------------------------------------------------
1415
1416
1417 //----------------------------------------------------------------------------
1418 void vvSlicer::ForceUpdateDisplayExtent()
1419 {
1420   this->UpdateDisplayExtent();
1421 }
1422 //----------------------------------------------------------------------------
1423
1424
1425 //----------------------------------------------------------------------------
1426 int* vvSlicer::GetDisplayExtent()
1427 {
1428   return this->GetImageActor()->GetDisplayExtent();
1429 }
1430 //----------------------------------------------------------------------------
1431
1432
1433 //----------------------------------------------------------------------------
1434 void vvSlicer::PrintSelf(ostream& os, vtkIndent indent)
1435 {
1436   this->Superclass::PrintSelf(os, indent);
1437 }
1438 //----------------------------------------------------------------------------
1439
1440 //----------------------------------------------------------------------------
1441 void vvSlicer::SetVFColor(double r, double g, double b)
1442 {
1443   double mVFColorHSV[3];
1444   mVFColor[0] = r;
1445   mVFColor[1] = g;
1446   mVFColor[2] = b;
1447
1448   vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
1449   mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
1450   mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
1451   mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
1452
1453   this->Render();
1454 }
1455