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