vv/vvSlicer.cxx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://www.centreleonberard.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17   ===========================================================================**/
  18
  19 #include "vvSlicer.h"
  20 #include "vvImage.h"
  21 #include "vvSlicerManagerCommand.h"
  22 #include "vvGlyphSource.h"
  23 #include "vvGlyph2D.h"
  24 #include "vvImageMapToWLColors.h"
  25
  26 #include <vtkTextProperty.h>
  27 #include <vtkTextActor.h>
  28 #include <vtkTextSource.h>
  29 #include <vtkActor2D.h>
  30 #include <vtkCursor2D.h>
  31 #include <vtkPolyDataMapper2D.h>
  32 #include <vtkProperty2D.h>
  33 #include <vtkCornerAnnotation.h>
  34 #include <vtkImageMapToWindowLevelColors.h>
  35 #include <vtkImageData.h>
  36 #include <vtkImageActor.h>
  37 #include <vvBlendImageActor.h>
  38 #include <vtkToolkits.h>
  39 #include <vtkObjectFactory.h>
  40 #include <vtkPointData.h>
  41 #include <vtkDataArray.h>
  42 #include <vtkFloatArray.h>
  43 #include <vtkClipPolyData.h>
  44 #include <vtkGlyph3D.h>
  45 #include <vtkMath.h>
  46 #include <vtkCursor3D.h>
  47 #include <vtkProperty.h>
  48 #include <vtkLight.h>
  49 #include <vtkLightCollection.h>
  50 #include <vtkScalarBarActor.h>
  51 #include <vtkLookupTable.h>
  52
  53 #include <vtkRenderer.h>
  54 #include <vtkRendererCollection.h>
  55 #include <vtkRenderWindow.h>
  56 #include <vtkRenderWindowInteractor.h>
  57 #include <vtkCamera.h>
  58 #include <vtkCallbackCommand.h>
  59 #include <vtkCommand.h>
  60 #include <vtkPolyDataMapper.h>
  61 #include <vtkBox.h>
  62
  63 #include <vtkExtractVOI.h>
  64 #include <vtkSphereSource.h>
  65 #include <vtkCutter.h>
  66 #include <vtkAssignAttribute.h>
  67 #include <vtkImageAccumulate.h>
  68 #include <vtkImageReslice.h>
  69 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
  70 #  include <vtkImageMapper3D.h>
  71 #endif
  72
  73 vtkCxxRevisionMacro(vvSlicer, "DummyRevision");
  74 vtkStandardNewMacro(vvSlicer);
  75 static void copyExtent(int* in, int* to){
  76  for(int i=0; i<6; ++i) to[i]=in[i];
  77 }
  78 //------------------------------------------------------------------------------
  79 vvSlicer::vvSlicer()
  80 {
  81   this->UnInstallPipeline();
  82   mImage = NULL;
  83   mReducedExtent = new int[6];
  84   mCurrentTSlice = 0;
  85   mCurrentFusionTSlice = 0;
  86   mCurrentOverlayTSlice = 0;
  87   mUseReducedExtent = false;
  88
  89   mCurrent[0] = -VTK_DOUBLE_MAX;
  90   mCurrent[1] = -VTK_DOUBLE_MAX;
  91   mCurrent[2] = -VTK_DOUBLE_MAX;
  92
  93   mCursor[0] = 0;//-VTK_DOUBLE_MAX;
  94   mCursor[1] = 0;//-VTK_DOUBLE_MAX;
  95   mCursor[2] = 0;//-VTK_DOUBLE_MAX;
  96   mCursor[3] = 0;//-VTK_DOUBLE_MAX;
  97
  98   mSubSampling = 5;
  99   mScale = 1;
 100   mVFLog = 0;
 101   mVFWidth = 1;
 102   mVFColor[0] = 0;
 103   mVFColor[1] = 1;
 104   mVFColor[2] = 0;
 105
 106   crossCursor = vtkSmartPointer<vtkCursor2D>::New();
 107   crossCursor->AllOff();
 108   crossCursor->AxesOn();
 109   crossCursor->SetTranslationMode(1);
 110   crossCursor->SetRadius(2);
 111
 112   pdm = vtkSmartPointer<vtkPolyDataMapper2D>::New();
 113   pdm->SetInput(crossCursor->GetOutput());
 114
 115   pdmA = vtkSmartPointer<vtkActor2D>::New();
 116   pdmA->SetMapper(pdm);
 117   pdmA->GetProperty()->SetColor(255,10,212);
 118   pdmA->SetVisibility(0);
 119   pdmA->SetPickable(0);
 120
 121   ca = vtkSmartPointer<vtkCornerAnnotation>::New();
 122   ca->GetTextProperty()->SetColor(255,10,212);
 123   ca->SetVisibility(1);
 124   mFileName = "";
 125
 126   mVF = NULL;
 127   mOverlay = NULL;
 128   mFusion = NULL;
 129   mLandmarks = NULL;
 130
 131   legend = vtkSmartPointer<vtkScalarBarActor>::New();
 132   //legend->SetTitle("test!");
 133   legend->SetPosition(0.82,0.18);
 134   legend->SetWidth(0.1);
 135   legend->SetVisibility(0);
 136   legend->SetLabelFormat("%.1f");
 137   this->GetRenderer()->AddActor(legend);
 138   showFusionLegend = false;
 139
 140   this->WindowLevel->Delete();
 141   this->WindowLevel = vvImageMapToWLColors::New();
 142
 143   this->InstallPipeline();
 144
 145   mLinkOverlayWindowLevel = true;
 146
 147 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 148   this->GetImageActor()->GetMapper()->BorderOn();
 149 #endif
 150
 151   mSlicingTransform = vtkSmartPointer<vtkTransform>::New();
 152   mConcatenatedTransform = vtkSmartPointer<vtkTransform>::New();
 153   mConcatenatedFusionTransform = vtkSmartPointer<vtkTransform>::New();
 154   mConcatenatedOverlayTransform = vtkSmartPointer<vtkTransform>::New();
 155 }
 156 //------------------------------------------------------------------------------
 157
 158
 159 //------------------------------------------------------------------------------
 160 vtkImageMapToWindowLevelColors* vvSlicer::GetOverlayMapper()
 161 {
 162   return mOverlayMapper.GetPointer();
 163 }
 164 //------------------------------------------------------------------------------
 165
 166
 167 //------------------------------------------------------------------------------
 168 vvBlendImageActor* vvSlicer::GetOverlayActor()
 169 {
 170   return mOverlayActor.GetPointer();
 171 }
 172 //------------------------------------------------------------------------------
 173
 174
 175 //------------------------------------------------------------------------------
 176 vtkImageMapToColors* vvSlicer::GetFusionMapper()
 177 {
 178   return mFusionMapper.GetPointer();
 179 }
 180 //------------------------------------------------------------------------------
 181
 182
 183 //------------------------------------------------------------------------------
 184 vtkImageActor* vvSlicer::GetFusionActor()
 185 {
 186   return mFusionActor.GetPointer();
 187 }
 188 //------------------------------------------------------------------------------
 189
 190
 191 //------------------------------------------------------------------------------
 192 vtkActor* vvSlicer::GetVFActor()
 193 {
 194   return mVFActor.GetPointer();
 195 }
 196 //------------------------------------------------------------------------------
 197
 198
 199 //------------------------------------------------------------------------------
 200 vtkCornerAnnotation* vvSlicer::GetAnnotation()
 201 {
 202   return ca.GetPointer();
 203 }
 204 //------------------------------------------------------------------------------
 205
 206
 207 //------------------------------------------------------------------------------
 208 void vvSlicer::EnableReducedExtent(bool b)
 209 {
 210   mUseReducedExtent = b;
 211 }
 212 //------------------------------------------------------------------------------
 213
 214
 215 //------------------------------------------------------------------------------
 216 void vvSlicer::SetReducedExtent(int * ext)
 217 {
 218   copyExtent(ext, mReducedExtent);
 219 }
 220 //------------------------------------------------------------------------------
 221
 222
 223 //------------------------------------------------------------------------------
 224 void vvSlicer::AddContour(vvMesh::Pointer contour,bool propagate)
 225 {
 226
 227   mSurfaceCutActors.push_back(new vvMeshActor());
 228   if (propagate)
 229     mSurfaceCutActors.back()->Init(contour,mCurrentTSlice,mVF);
 230   else
 231     mSurfaceCutActors.back()->Init(contour,mCurrentTSlice);
 232   mSurfaceCutActors.back()->SetSlicingOrientation(SliceOrientation);
 233   this->GetRenderer()->AddActor(mSurfaceCutActors.back()->GetActor());
 234
 235   SetContourSlice();
 236 }
 237 //------------------------------------------------------------------------------
 238
 239
 240 //------------------------------------------------------------------------------
 241 void vvSlicer::ToggleContourSuperposition()
 242 {
 243   for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 244        i!=mSurfaceCutActors.end(); i++)
 245     (*i)->ToggleSuperposition();
 246 }
 247 //------------------------------------------------------------------------------
 248
 249
 250 //------------------------------------------------------------------------------
 251 void vvSlicer::SetCursorColor(int r,int g, int b)
 252 {
 253   pdmA->GetProperty()->SetColor(r,g,b);
 254 }
 255 //------------------------------------------------------------------------------
 256
 257
 258 //------------------------------------------------------------------------------
 259 void vvSlicer::SetCursorVisibility(bool s)
 260 {
 261   pdmA->SetVisibility(s);
 262 }
 263 //------------------------------------------------------------------------------
 264
 265
 266 //------------------------------------------------------------------------------
 267 bool vvSlicer::GetCursorVisibility()
 268 {
 269   return pdmA->GetVisibility();
 270 }
 271 //------------------------------------------------------------------------------
 272
 273
 274 //------------------------------------------------------------------------------
 275 void vvSlicer::SetCornerAnnotationVisibility(bool s)
 276 {
 277   ca->SetVisibility(s);
 278 }
 279 //------------------------------------------------------------------------------
 280
 281
 282 //------------------------------------------------------------------------------
 283 bool vvSlicer::GetCornerAnnotationVisibility()
 284 {
 285   return ca->GetVisibility();
 286 }
 287 //------------------------------------------------------------------------------
 288
 289
 290 //------------------------------------------------------------------------------
 291 vvSlicer::~vvSlicer()
 292 {
 293   for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 294        i!=mSurfaceCutActors.end(); i++)
 295     delete (*i);
 296   delete [] mReducedExtent;
 297 }
 298 //------------------------------------------------------------------------------
 299
 300 //------------------------------------------------------------------------------
 301 double* vvSlicer::GetCurrentPosition()
 302 {
 303   return mCurrentBeforeSlicingTransform;
 304 }
 305 //------------------------------------------------------------------------------
 306
 307 //------------------------------------------------------------------------------
 308 void vvSlicer::SetCurrentPosition(double x, double y, double z, int t)
 309 {
 310   mCurrentBeforeSlicingTransform[0]=x;
 311   mCurrentBeforeSlicingTransform[1]=y;
 312   mCurrentBeforeSlicingTransform[2]=z;
 313   mSlicingTransform->GetInverse()->TransformPoint(mCurrentBeforeSlicingTransform,mCurrent);
 314   SetTSlice(t);
 315 }
 316 //------------------------------------------------------------------------------
 317
 318
 319 //------------------------------------------------------------------------------
 320 void vvSlicer::SetImage(vvImage::Pointer image)
 321 {
 322   if (image->GetVTKImages().size()) {
 323     mImage = image;
 324
 325     if (!mImageReslice) {
 326       mImageReslice = vtkSmartPointer<vtkImageReslice>::New();
 327       mImageReslice->SetInterpolationModeToLinear();
 328       mImageReslice->AutoCropOutputOn();
 329       mImageReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 330     }
 331
 332     mConcatenatedTransform->Identity();
 333     mConcatenatedTransform->Concatenate(mImage->GetTransform()[0]);
 334     mConcatenatedTransform->Concatenate(mSlicingTransform);
 335     mImageReslice->SetResliceTransform(mConcatenatedTransform);
 336     mImageReslice->SetInput(0, mImage->GetFirstVTKImageData());
 337     mImageReslice->UpdateInformation();
 338
 339     this->Superclass::SetInput(mImageReslice->GetOutput());
 340
 341     int extent[6];
 342     this->GetInput()->GetWholeExtent(extent);
 343
 344     // Prevent crash when reload -> change slice if outside extent
 345     if (Slice < extent[SliceOrientation*2] || Slice>=extent[SliceOrientation*2+1]) {
 346       Slice = (extent[SliceOrientation*2+1]+extent[SliceOrientation*2])/2.0;
 347     }
 348
 349     // Make sure that the required part image has been computed
 350     extent[SliceOrientation*2] = Slice;
 351     extent[SliceOrientation*2+1] = Slice;
 352     mImageReslice->GetOutput()->SetUpdateExtent(extent);
 353     mImageReslice->GetOutput()->Update();
 354
 355     this->UpdateDisplayExtent();
 356
 357     mCurrentTSlice = 0;
 358     ca->SetText(0,mFileName.c_str());
 359   }
 360 }
 361 //------------------------------------------------------------------------------
 362
 363
 364 //------------------------------------------------------------------------------
 365 void vvSlicer::SetOverlay(vvImage::Pointer overlay)
 366 {
 367   if (overlay->GetVTKImages().size()) {
 368     mOverlay = overlay;
 369
 370     if (!mOverlayReslice) {
 371       mOverlayReslice = vtkSmartPointer<vtkImageReslice>::New();
 372       mOverlayReslice->SetInterpolationModeToLinear();
 373       mOverlayReslice->AutoCropOutputOn();
 374       mOverlayReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 375     }
 376
 377     mConcatenatedOverlayTransform->Identity();
 378     mConcatenatedOverlayTransform->Concatenate(mOverlay->GetTransform()[0]);
 379     mConcatenatedOverlayTransform->Concatenate(mSlicingTransform);
 380     mOverlayReslice->SetResliceTransform(mConcatenatedOverlayTransform);
 381     mOverlayReslice->SetInput(0, mOverlay->GetFirstVTKImageData());
 382     mImageReslice->UpdateInformation();
 383
 384     if (!mOverlayMapper)
 385       mOverlayMapper = vtkSmartPointer<vtkImageMapToWindowLevelColors>::New();
 386     mOverlayMapper->SetInput(mOverlayReslice->GetOutput());
 387
 388     if (!mOverlayActor) {
 389       mOverlayActor = vtkSmartPointer<vvBlendImageActor>::New();
 390       mOverlayActor->SetInput(mOverlayMapper->GetOutput());
 391       mOverlayActor->SetPickable(0);
 392       mOverlayActor->SetVisibility(true);
 393       mOverlayActor->SetOpacity(0.5);
 394 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 395       mOverlayActor->GetMapper()->BorderOn();
 396 #endif
 397       }
 398
 399     //stupid but necessary : the Overlay need to be rendered before fusion
 400     if (mFusionActor) {
 401       this->GetRenderer()->RemoveActor(mFusionActor);
 402       this->GetRenderer()->AddActor(mOverlayActor);
 403       this->GetRenderer()->AddActor(mFusionActor);
 404     } else
 405       this->GetRenderer()->AddActor(mOverlayActor);
 406
 407     //Synchronize orientation and slice
 408     AdjustResliceToSliceOrientation(mOverlayReslice);
 409     this->UpdateDisplayExtent();
 410     this->SetTSlice(mCurrentTSlice);
 411   }
 412 }
 413 //------------------------------------------------------------------------------
 414
 415
 416 //------------------------------------------------------------------------------
 417 void vvSlicer::SetFusion(vvImage::Pointer fusion)
 418 {
 419   if (fusion->GetVTKImages().size()) {
 420     mFusion = fusion;
 421
 422     if (!mFusionReslice) {
 423       mFusionReslice = vtkSmartPointer<vtkImageReslice>::New();
 424       mFusionReslice->SetInterpolationModeToLinear();
 425       mFusionReslice->AutoCropOutputOn();
 426       mFusionReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 427     }
 428
 429     mConcatenatedFusionTransform->Identity();
 430     mConcatenatedFusionTransform->Concatenate(mFusion->GetTransform()[0]);
 431     mConcatenatedFusionTransform->Concatenate(mSlicingTransform);
 432     mFusionReslice->SetResliceTransform(mConcatenatedFusionTransform);
 433     mFusionReslice->SetInput(0, mFusion->GetFirstVTKImageData());
 434     mFusionReslice->UpdateInformation();
 435
 436     if (!mFusionMapper)
 437       mFusionMapper = vtkSmartPointer<vtkImageMapToColors>::New();
 438
 439     vtkSmartPointer<vtkLookupTable> lut = vtkLookupTable::New();
 440     lut->SetRange(0, 1);
 441     lut->SetValueRange(0, 1);
 442     lut->SetSaturationRange(0, 0);
 443     lut->Build();
 444     mFusionMapper->SetLookupTable(lut);
 445     mFusionMapper->SetInput(mFusionReslice->GetOutput());
 446
 447     if (!mFusionActor) {
 448       mFusionActor = vtkSmartPointer<vtkImageActor>::New();
 449       mFusionActor->SetInput(mFusionMapper->GetOutput());
 450       mFusionActor->SetPickable(0);
 451       mFusionActor->SetVisibility(true);
 452       mFusionActor->SetOpacity(0.7);
 453 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 454       mFusionActor->GetMapper()->BorderOn();
 455 #endif
 456       this->GetRenderer()->AddActor(mFusionActor);
 457     }
 458
 459     //Synchronize orientation and slice
 460     AdjustResliceToSliceOrientation(mFusionReslice);
 461     this->UpdateDisplayExtent();
 462     this->SetTSlice(mCurrentTSlice);
 463   }
 464 }
 465 //------------------------------------------------------------------------------
 466
 467
 468 //------------------------------------------------------------------------------
 469 bool vvSlicer::GetActorVisibility(const std::string& actor_type, int overlay_index)
 470 {
 471   bool vis = false;
 472   if (actor_type == "image") {
 473     vis = this->ImageActor->GetVisibility();
 474   }
 475   else if (actor_type == "vector") {
 476     vis = this->mVFActor->GetVisibility();
 477   }
 478   else if (actor_type == "overlay") {
 479     vis = this->mOverlayActor->GetVisibility();
 480   }
 481   else if (actor_type == "fusion") {
 482     vis = this->mFusionActor->GetVisibility();
 483   }
 484   else if (actor_type == "contour")
 485     vis = this->mSurfaceCutActors[overlay_index]->GetActor()->GetVisibility();
 486
 487   return vis;
 488 }
 489 //------------------------------------------------------------------------------
 490
 491 //------------------------------------------------------------------------------
 492 void vvSlicer::SetActorVisibility(const std::string& actor_type, int overlay_index ,bool vis)
 493 {
 494   if (actor_type == "image") {
 495     this->ImageActor->SetVisibility(vis);
 496   }
 497   else if (actor_type == "vector") {
 498     this->mVFActor->SetVisibility(vis);
 499   }
 500   else if (actor_type == "overlay") {
 501     this->mOverlayActor->SetVisibility(vis);
 502   }
 503   else if (actor_type == "fusion") {
 504     this->mFusionActor->SetVisibility(vis);
 505   }
 506   else if (actor_type == "contour")
 507     this->mSurfaceCutActors[overlay_index]->GetActor()->SetVisibility(vis);
 508   UpdateDisplayExtent();
 509 }
 510 //------------------------------------------------------------------------------
 511
 512 //------------------------------------------------------------------------------
 513 void vvSlicer::SetVF(vvImage::Pointer vf)
 514 {
 515   if (vf->GetVTKImages().size()) {
 516     mVF = vf;
 517
 518     if (!mAAFilter) {
 519       mAAFilter= vtkSmartPointer<vtkAssignAttribute>::New();
 520       mVOIFilter = vtkSmartPointer<vtkExtractVOI>::New();
 521       mVOIFilter->SetSampleRate(mSubSampling,mSubSampling,mSubSampling);
 522     }
 523     mVOIFilter->SetInput(vf->GetFirstVTKImageData());
 524     mAAFilter->SetInput(mVOIFilter->GetOutput());
 525     ///This tells VTK to use the scalar (pixel) data of the image to draw the little arrows
 526     mAAFilter->Assign(vtkDataSetAttributes::SCALARS, vtkDataSetAttributes::VECTORS, vtkAssignAttribute::POINT_DATA);
 527
 528     if (!mArrow)
 529       mArrow = vtkSmartPointer<vvGlyphSource>::New();
 530     mArrow->SetGlyphTypeToSpecificArrow();
 531     mArrow->SetScale(mScale);
 532     mArrow->FilledOff();
 533
 534     // Glyph the gradient vector (with arrows)
 535     if (!mGlyphFilter)
 536       mGlyphFilter = vtkSmartPointer<vvGlyph2D>::New();
 537     mGlyphFilter->SetInput(mAAFilter->GetOutput());
 538     mGlyphFilter->SetSource(mArrow->GetOutput());
 539     mGlyphFilter->ScalingOn();
 540     mGlyphFilter->SetScaleModeToScaleByVector();
 541     mGlyphFilter->OrientOn();
 542     mGlyphFilter->SetVectorModeToUseVector();
 543     mGlyphFilter->SetColorModeToColorByVector();
 544
 545     if (!mVFColorLUT)
 546       mVFColorLUT = vtkSmartPointer<vtkLookupTable>::New();
 547
 548     double mVFColorHSV[3];
 549     vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
 550     mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
 551     mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
 552     mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
 553
 554     if (!mVFMapper)
 555       mVFMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
 556     mVFMapper->SetInput(mGlyphFilter->GetOutput());
 557     mVFMapper->ImmediateModeRenderingOn();
 558     mVFMapper->SetLookupTable(mVFColorLUT);
 559
 560     if (!mVFActor)
 561       mVFActor = vtkSmartPointer<vtkActor>::New();
 562     mVFActor->SetMapper(mVFMapper);
 563     mVFActor->SetPickable(0);
 564     mVFActor->GetProperty()->SetLineWidth(mVFWidth);
 565     this->UpdateDisplayExtent();
 566     this->GetRenderer()->AddActor(mVFActor);
 567
 568     //Synchronize slice
 569     SetTSlice(mCurrentTSlice);
 570   }
 571 }
 572 //------------------------------------------------------------------------------
 573
 574
 575 //------------------------------------------------------------------------------
 576 void vvSlicer::SetLandmarks(vvLandmarks* landmarks)
 577 {
 578   mLandmarks = landmarks;
 579   if (landmarks) {
 580
 581     if (!mCross)
 582       mCross = vtkSmartPointer<vtkCursor3D>::New();
 583     mCross->SetFocalPoint(0.0,0.0,0.0);
 584     mCross->SetModelBounds(-10,10,-10,10,-10,10);
 585     mCross->AllOff();
 586     mCross->AxesOn();
 587
 588     if (!mLandGlyph)
 589       mLandGlyph = vtkSmartPointer<vtkGlyph3D>::New();
 590     mLandGlyph->SetSource(mCross->GetOutput());
 591     mLandGlyph->SetInput(landmarks->GetOutput());
 592     //mLandGlyph->SetIndexModeToScalar();
 593     mLandGlyph->SetRange(0,1);
 594     mLandGlyph->ScalingOff();
 595
 596     mLandGlyph->SetColorModeToColorByScalar();
 597
 598     if (!mClipBox)
 599       mClipBox = vtkSmartPointer<vtkBox>::New();
 600     if (!mLandClipper)
 601       mLandClipper = vtkSmartPointer<vtkClipPolyData>::New();
 602     mLandClipper->InsideOutOn();
 603     mLandClipper->SetInput(mLandGlyph->GetOutput());
 604     mLandClipper->SetClipFunction(mClipBox);
 605
 606     if (!mLandMapper)
 607       mLandMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
 608     mLandMapper->SetInputConnection(mLandClipper->GetOutputPort());
 609     //mLandMapper->ScalarVisibilityOff();
 610
 611     if (!mLandActor)
 612       mLandActor = vtkSmartPointer<vtkActor>::New();
 613     mLandActor->SetMapper(mLandMapper);
 614     mLandActor->GetProperty()->SetColor(255,10,212);
 615     mLandActor->SetPickable(0);
 616     mLandActor->SetVisibility(true);
 617     this->UpdateDisplayExtent();
 618     this->GetRenderer()->AddActor(mLandActor);
 619   }
 620 }
 621 //------------------------------------------------------------------------------
 622
 623 //------------------------------------------------------------------------------
 624 //FIXME: this function leaks memory, we should fix it someday :)
 625 void vvSlicer::RemoveActor(const std::string& actor_type, int overlay_index)
 626 {
 627   if (actor_type == "vector") {
 628     Renderer->RemoveActor(mVFActor);
 629     mGlyphFilter=NULL;
 630     mVF = NULL;
 631     mArrow = NULL;
 632     mAAFilter=NULL;
 633     mVOIFilter = NULL;
 634     mVFMapper = NULL;
 635     mVFActor = NULL;
 636   }
 637   if (actor_type == "overlay") {
 638     Renderer->RemoveActor(mOverlayActor);
 639     mOverlay = NULL;
 640     mOverlayActor = NULL;
 641     mOverlayMapper = NULL;
 642   }
 643   if (actor_type == "fusion") {
 644     Renderer->RemoveActor(mFusionActor);
 645     mFusion = NULL;
 646     mFusionActor = NULL;
 647     mFusionMapper = NULL;
 648   }
 649   if (actor_type == "contour") {
 650     Renderer->RemoveActor(this->mSurfaceCutActors[overlay_index]->GetActor());
 651     mSurfaceCutActors.erase(mSurfaceCutActors.begin()+overlay_index);
 652   }
 653 }
 654 //------------------------------------------------------------------------------
 655
 656
 657 //------------------------------------------------------------------------------
 658 void vvSlicer::SetVFSubSampling(int sub)
 659 {
 660   if (mVOIFilter) {
 661     mVOIFilter->SetSampleRate(mSubSampling,mSubSampling,mSubSampling);
 662     mSubSampling = sub;
 663   }
 664   UpdateDisplayExtent();
 665   Render();
 666 }
 667 //------------------------------------------------------------------------------
 668
 669
 670 //------------------------------------------------------------------------------
 671 void vvSlicer::SetVFScale(int scale)
 672 {
 673   mScale = scale;
 674   if (mArrow)
 675     mArrow->SetScale(mScale);
 676   UpdateDisplayExtent();
 677   Render();
 678 }
 679 //------------------------------------------------------------------------------
 680
 681 //------------------------------------------------------------------------------
 682 void vvSlicer::SetVFWidth(int width)
 683 {
 684   mVFWidth = width;
 685   if (mVFActor)
 686     mVFActor->GetProperty()->SetLineWidth(mVFWidth);
 687   UpdateDisplayExtent();
 688   Render();
 689 }
 690 //------------------------------------------------------------------------------
 691
 692
 693 //------------------------------------------------------------------------------
 694 void vvSlicer::SetVFLog(int log)
 695 {
 696   mVFLog = log;
 697   if (mGlyphFilter) {
 698     mGlyphFilter->SetUseLog(mVFLog);
 699     mGlyphFilter->Modified();
 700   }
 701   UpdateDisplayExtent();
 702   Render();
 703 }
 704 //------------------------------------------------------------------------------
 705
 706
 707 //------------------------------------------------------------------------------
 708 void vvSlicer::SetTSlice(int t)
 709 {
 710   if (t < 0)
 711     mCurrentTSlice = 0;
 712   else if ((unsigned int)t >= mImage->GetVTKImages().size())
 713     mCurrentTSlice = mImage->GetVTKImages().size() -1;
 714   else
 715     mCurrentTSlice = t;
 716
 717   // Update transform
 718   mConcatenatedTransform->Identity();
 719   mConcatenatedTransform->Concatenate(mImage->GetTransform()[mCurrentTSlice]);
 720   mConcatenatedTransform->Concatenate(mSlicingTransform);
 721
 722   // Update image data
 723   mImageReslice->SetInput( mImage->GetVTKImages()[mCurrentTSlice] );
 724   if (mVF && mVFActor->GetVisibility()) {
 725     if (mVF->GetVTKImages().size() > (unsigned int)mCurrentTSlice)
 726       mVOIFilter->SetInput(mVF->GetVTKImages()[mCurrentTSlice]);
 727   }
 728   if (mOverlay && mOverlayActor->GetVisibility()) {
 729     if (mOverlay->GetVTKImages().size() > (unsigned int)t) {
 730       mCurrentOverlayTSlice = t;
 731       mOverlayReslice->SetInput( mOverlay->GetVTKImages()[mCurrentOverlayTSlice] );
 732
 733       // Update overlay transform
 734       mConcatenatedOverlayTransform->Identity();
 735       mConcatenatedOverlayTransform->Concatenate(mOverlay->GetTransform()[mCurrentOverlayTSlice]);
 736       mConcatenatedOverlayTransform->Concatenate(mSlicingTransform);
 737     }
 738   }
 739   if (mFusion && mFusionActor->GetVisibility()) {
 740     if (mFusion->GetVTKImages().size() > (unsigned int)t) {
 741       mCurrentFusionTSlice = t;
 742       mFusionReslice->SetInput( mFusion->GetVTKImages()[mCurrentFusionTSlice]);
 743
 744       // Update fusion transform
 745       mConcatenatedFusionTransform->Identity();
 746       mConcatenatedFusionTransform->Concatenate(mFusion->GetTransform()[mCurrentFusionTSlice]);
 747       mConcatenatedFusionTransform->Concatenate(mSlicingTransform);
 748     }
 749   }
 750   if (mSurfaceCutActors.size() > 0)
 751     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 752          i!=mSurfaceCutActors.end(); i++)
 753       (*i)->SetTimeSlice(mCurrentTSlice);
 754   UpdateDisplayExtent();
 755 }
 756 //------------------------------------------------------------------------------
 757
 758
 759 //------------------------------------------------------------------------------
 760 int vvSlicer::GetTSlice()
 761 {
 762   return mCurrentTSlice;
 763 }
 764 //------------------------------------------------------------------------------
 765
 766 //------------------------------------------------------------------------------
 767 int vvSlicer::GetMaxCurrentTSlice()
 768 {
 769   int t = mCurrentTSlice;
 770   if(mOverlay)
 771     t = std::max(t, mCurrentOverlayTSlice);
 772   if(mFusion)
 773     t = std::max(t, mCurrentFusionTSlice);
 774   return t;
 775 }
 776 //------------------------------------------------------------------------------
 777
 778 //------------------------------------------------------------------------------
 779 int vvSlicer::GetFusionTSlice()
 780 {
 781   return mCurrentFusionTSlice;
 782 }
 783 //------------------------------------------------------------------------------
 784
 785 //------------------------------------------------------------------------------
 786 int vvSlicer::GetOverlayTSlice()
 787 {
 788   return mCurrentOverlayTSlice;
 789 }
 790 //------------------------------------------------------------------------------
 791
 792 //------------------------------------------------------------------------------
 793 void vvSlicer::SetSliceOrientation(int orientation)
 794 {
 795   //if 2D image, force to watch in Axial View
 796   int extent[6];
 797   this->GetInput()->GetWholeExtent(extent);
 798   if (extent[5]-extent[4] <= 2)
 799     orientation = vtkImageViewer2::SLICE_ORIENTATION_XY;
 800
 801   if (orientation < vtkImageViewer2::SLICE_ORIENTATION_YZ ||
 802       orientation > vtkImageViewer2::SLICE_ORIENTATION_XY) {
 803     vtkErrorMacro("Error - invalid slice orientation " << orientation);
 804     return;
 805   }
 806
 807   this->SliceOrientation = orientation;
 808
 809   if(mFusion)
 810     AdjustResliceToSliceOrientation(mFusionReslice);
 811
 812   if(mOverlay)
 813     AdjustResliceToSliceOrientation(mOverlayReslice);
 814
 815   // Update the viewer
 816
 817   // Go to current cursor position
 818   // double* cursorPos = GetCursorPosition();
 819   // DDV(cursorPos, 3);
 820   // SetCurrentPosition(cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
 821
 822   if (this->Renderer && this->GetInput()) {
 823     double s = mCursor[orientation];
 824     double sCursor = (s - this->GetInput()->GetOrigin()[orientation])/this->GetInput()->GetSpacing()[orientation];
 825     this->Slice = static_cast<int>(sCursor);
 826   }
 827
 828 //   int *range = this->GetSliceRange();
 829 //   if (range)
 830 //     this->Slice = static_cast<int>((range[0] + range[1]) * 0.5);
 831
 832   this->UpdateOrientation();
 833   this->UpdateDisplayExtent();
 834
 835   if (this->Renderer && this->GetInput()) {
 836     double scale = this->Renderer->GetActiveCamera()->GetParallelScale();
 837     this->Renderer->ResetCamera();
 838     this->Renderer->GetActiveCamera()->SetParallelScale(scale);
 839   }
 840
 841   SetContourSlice();
 842 }
 843 //----------------------------------------------------------------------------
 844
 845 //------------------------------------------------------------------------------
 846 // This function ensures that we sample the slices of a vtkImageReslice filter
 847 // in the direction of the slicer (SliceOrientation) similarly as mImageReslice.
 848 // In other words, we change the grid of the reslice in the same way as the grid
 849 // of the displayed image in the slicing direction.
 850 void vvSlicer::AdjustResliceToSliceOrientation(vtkImageReslice *reslice)
 851 {
 852   // Reset autocrop and update output information
 853   reslice->SetOutputOriginToDefault();
 854   reslice->SetOutputSpacingToDefault();
 855   reslice->GetOutput()->UpdateInformation();
 856
 857   // Ge new origin / spacing
 858   double origin[3];
 859   double spacing[3];
 860   reslice->GetOutput()->GetOrigin(origin);
 861   reslice->GetOutput()->GetSpacing(spacing);
 862
 863   // Use similar spacing as the image in the direction SliceOrientation
 864   spacing[this->SliceOrientation] = mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
 865
 866   // Modify origin to be on the image grid in the direction SliceOrientation in 3 steps
 867   // Step 1: from world coordinates to image coordinates
 868   origin[this->SliceOrientation] -= mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
 869   origin[this->SliceOrientation] /= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
 870   // Step 2: round to superior grid positionInc
 871   origin[this->SliceOrientation] = itk::Math::Ceil<double>(origin[this->SliceOrientation]);
 872   // Step 3: back to world coordinates
 873   origin[this->SliceOrientation] *= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
 874   origin[this->SliceOrientation] += mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
 875
 876   // Set new spacing and origin
 877   reslice->SetOutputOrigin(origin);
 878   reslice->SetOutputSpacing(spacing);
 879   reslice->UpdateInformation();
 880   reslice->GetOutput()->UpdateInformation();
 881 }
 882 //------------------------------------------------------------------------------
 883
 884 //----------------------------------------------------------------------------
 885 int * vvSlicer::GetExtent(){
 886   int *w_ext;
 887   if (mUseReducedExtent) {
 888     w_ext = mReducedExtent;
 889   } else w_ext = GetInput()->GetWholeExtent();
 890   return w_ext;
 891 }
 892 //----------------------------------------------------------------------------
 893
 894
 895 //----------------------------------------------------------------------------
 896 int vvSlicer::GetOrientation()
 897 {
 898   return this->SliceOrientation;
 899 }
 900 //----------------------------------------------------------------------------
 901
 902
 903 //----------------------------------------------------------------------------
 904 void vvSlicer::UpdateDisplayExtent()
 905 {
 906   vtkImageData *input = this->GetInput();
 907   if (!input || !this->ImageActor) {
 908     return;
 909   }
 910   input->UpdateInformation();
 911
 912   // Local copy of extent
 913   int w_ext[6];
 914   int* ext = GetExtent();
 915   copyExtent(ext, w_ext);
 916   // Set slice value
 917   int s = this->Slice > ext[this->SliceOrientation*2+1] ? ext[this->SliceOrientation*2 + 1] : this->Slice;
 918   w_ext[ this->SliceOrientation*2   ] = s;
 919   w_ext[ this->SliceOrientation*2+1 ] = s;
 920
 921   // Image actor
 922   this->ImageActor->SetDisplayExtent(w_ext);
 923
 924   // Overlay image actor
 925   if (mOverlay && mOverlayActor->GetVisibility()) {
 926     AdjustResliceToSliceOrientation(mOverlayReslice);
 927     int overExtent[6];
 928     this->ConvertImageToImageDisplayExtent(input, w_ext, mOverlayReslice->GetOutput(), overExtent);
 929     ClipDisplayedExtent(overExtent, mOverlayMapper->GetInput()->GetWholeExtent());
 930     mOverlayActor->SetDisplayExtent( overExtent );
 931   }
 932
 933   // Fusion image actor
 934   if (mFusion && mFusionActor->GetVisibility()) {
 935     AdjustResliceToSliceOrientation(mFusionReslice);
 936     int fusExtent[6];
 937     this->ConvertImageToImageDisplayExtent(input, w_ext, mFusionReslice->GetOutput(), fusExtent);
 938     ClipDisplayedExtent(fusExtent, mFusionMapper->GetInput()->GetWholeExtent());
 939     mFusionActor->SetDisplayExtent(fusExtent);
 940   }
 941
 942   // Vector field actor
 943   double* camera = Renderer->GetActiveCamera()->GetPosition();
 944   double* image_bounds = ImageActor->GetBounds();
 945   double position[3] = {0, 0, 0};
 946   position[this->SliceOrientation] = image_bounds[this->SliceOrientation*2];
 947
 948   //print_vector<double, 6>("camera", camera);
 949   //print_vector<double, 6>("image_bounds", image_bounds);
 950   //print_vector<double, 3>("position", position);
 951
 952   // find where to place the VF actor. to deal with
 953   // z-buffer issues, the VF is placed right in front of the image,
 954   // subject to a small offset. the position actually depends on the
 955   // the location of the camera relative to the image.
 956   double offset = 1;
 957   if (camera[this->SliceOrientation] < image_bounds[this->SliceOrientation*2])
 958     offset = -1;
 959
 960   if (mVF && mVFActor->GetVisibility()) {
 961     int vfExtent[6];
 962     mVF->GetVTKImages()[0]->UpdateInformation();
 963     this->ConvertImageToImageDisplayExtent(input, w_ext, mVF->GetVTKImages()[0], vfExtent);
 964     ClipDisplayedExtent(vfExtent, mVOIFilter->GetInput()->GetWholeExtent());
 965     mVOIFilter->SetVOI(vfExtent);
 966     int orientation[3] = {1,1,1};
 967     orientation[this->SliceOrientation] = 0;
 968     mGlyphFilter->SetOrientation(orientation[0], orientation[1], orientation[2]);
 969     mVFMapper->Update();
 970
 971     position[this->SliceOrientation] += offset;
 972     mVFActor->SetPosition(position);
 973   }
 974
 975   // Landmarks actor
 976   if (mLandActor) {
 977     if (mClipBox) {
 978       double bounds [6];
 979       for(unsigned int i=0; i<6; i++)
 980         bounds[i] = ImageActor->GetBounds()[i];
 981       bounds[ this->SliceOrientation*2   ] = ImageActor->GetBounds()[ this->SliceOrientation*2  ]-fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
 982       bounds[ this->SliceOrientation*2+1 ] = ImageActor->GetBounds()[ this->SliceOrientation*2+1 ]+fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
 983       mClipBox->SetBounds(bounds);
 984       UpdateLandmarks();
 985     }
 986
 987     position[this->SliceOrientation] = offset;
 988     mLandActor->SetPosition(position);
 989   }
 990
 991   // Figure out the correct clipping range
 992   if (this->Renderer) {
 993     if (this->InteractorStyle &&
 994         this->InteractorStyle->GetAutoAdjustCameraClippingRange()) {
 995       this->Renderer->ResetCameraClippingRange();
 996     } else {
 997       vtkCamera *cam = this->Renderer->GetActiveCamera();
 998       if (cam) {
 999         double bounds[6];
1000         this->ImageActor->GetBounds(bounds);
1001         double spos = (double)bounds[this->SliceOrientation * 2];
1002         double cpos = (double)cam->GetPosition()[this->SliceOrientation];
1003         double range = fabs(spos - cpos);
1004         double *spacing = input->GetSpacing();
1005         double sumSpacing = spacing[0] + spacing[1] + spacing[2];
1006         cam->SetClippingRange(range - sumSpacing, range + sumSpacing);
1007       }
1008     }
1009   }
1010
1011 }
1012 //----------------------------------------------------------------------------
1013
1014 //----------------------------------------------------------------------------
1015 void vvSlicer::ConvertImageToImageDisplayExtent(vtkImageData *sourceImage, const int sourceExtent[6],
1016                                                 vtkImageData *targetImage, int targetExtent[6])
1017 {
1018   double dExtents[6];
1019   for(unsigned int i=0; i<6; i++) {
1020     // From source voxel coordinates to world coordinates
1021     dExtents[i] = sourceImage->GetOrigin()[i/2] + sourceImage->GetSpacing()[i/2] * sourceExtent[i];
1022
1023     // From world coordinates to floating point target voxel coordinates
1024     dExtents[i] = (dExtents[i]- targetImage->GetOrigin()[i/2]) / targetImage->GetSpacing()[i/2];
1025
1026     // Round to nearest
1027     //targetExtent[i] = itk::Math::Round<double>(dExtents[i]);
1028     targetExtent[i] = itk::Math::Floor<double>(dExtents[i]);
1029   }
1030 }
1031 //----------------------------------------------------------------------------
1032
1033 //----------------------------------------------------------------------------
1034 void vvSlicer::ClipDisplayedExtent(int extent[6], int refExtent[6])
1035 {
1036   bool out = false;
1037   int maxBound = 6;
1038
1039   //2D overlay on 3D image specific case
1040   if (refExtent[4] == refExtent[5]) {
1041     maxBound = 4;
1042     extent[4] = refExtent[4];
1043     extent[5] = refExtent[5];
1044   }
1045
1046   for (int i = 0; i < maxBound; i = i+2) {
1047     //if we are totally outside the image
1048     if ( extent[i] > refExtent[i+1] || extent[i+1] < refExtent[i] ) {
1049       out = true;
1050       break;
1051     }
1052     //crop to the limit of the image
1053     extent[i] = (extent[i] > refExtent[i]) ? extent[i] : refExtent[i];
1054     extent[i] = (extent[i] < refExtent[i+1]) ? extent[i] : refExtent[i+1];
1055     extent[i+1] = (extent[i+1] > refExtent[i]) ? extent[i+1] : refExtent[i];
1056     extent[i+1] = (extent[i+1] < refExtent[i+1]) ? extent[i+1] : refExtent[i+1];
1057   }
1058   if (out)
1059     for (int i = 0; i < maxBound; i = i+2) {
1060       extent[i] = refExtent[i];
1061       extent[i+1] = refExtent[i];
1062     }
1063 }
1064 //----------------------------------------------------------------------------
1065
1066
1067 //----------------------------------------------------------------------------
1068 void vvSlicer::UpdateOrientation()
1069 {
1070   // Set the camera position
1071   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1072   if (cam) {
1073     switch (this->SliceOrientation) {
1074     case vtkImageViewer2::SLICE_ORIENTATION_XY:
1075       cam->SetFocalPoint(0,0,0);
1076       cam->SetPosition(0,0,-1); // -1 if medical ?
1077       cam->SetViewUp(0,-1,0);
1078       break;
1079
1080     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
1081       cam->SetFocalPoint(0,0,0);
1082       cam->SetPosition(0,-1,0); // 1 if medical ?
1083       cam->SetViewUp(0,0,1);
1084       break;
1085
1086     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1087       cam->SetFocalPoint(0,0,0);
1088       cam->SetPosition(-1,0,0); // -1 if medical ?
1089       cam->SetViewUp(0,0,1);
1090       break;
1091     }
1092   }
1093 }
1094 //----------------------------------------------------------------------------
1095
1096
1097 //----------------------------------------------------------------------------
1098 void vvSlicer::SetOpacity(double s)
1099 {
1100   this->GetImageActor()->SetOpacity(s);
1101 }
1102 //----------------------------------------------------------------------------
1103
1104
1105 //----------------------------------------------------------------------------
1106 void vvSlicer::SetRenderWindow(int orientation, vtkRenderWindow * rw)
1107 {
1108   this->Superclass::SetRenderWindow(rw);
1109   this->SetupInteractor(rw->GetInteractor());
1110   ca->SetImageActor(this->GetImageActor());
1111   ca->SetWindowLevel(this->GetWindowLevel());
1112   ca->SetText(2, "<slice>");
1113   ca->SetText(3, "<window>\n<level>");
1114
1115   double bounds[6];
1116   double max = 65000;
1117
1118   bounds[0] = -max;
1119   bounds[1] = max;
1120   bounds[2] = -max;
1121   bounds[3] = max;
1122   bounds[4] = -max;
1123   bounds[5] = max;
1124
1125   crossCursor->SetModelBounds(bounds);
1126   this->GetRenderer()->AddActor(pdmA);
1127   this->GetRenderer()->AddActor(ca);
1128   this->GetRenderer()->ResetCamera();
1129
1130   //this is just a mapping between the labeling of the orientations presented to the user and
1131   //the one used by vtk
1132   SetSliceOrientation(2-(orientation%3));
1133   ResetCamera();
1134 }
1135 //----------------------------------------------------------------------------
1136
1137
1138 //----------------------------------------------------------------------------
1139 void vvSlicer::ResetCamera()
1140 {
1141   this->GetRenderer()->ResetCamera();
1142 }
1143 //----------------------------------------------------------------------------
1144
1145
1146 //----------------------------------------------------------------------------
1147 void vvSlicer::SetDisplayMode(bool i)
1148 {
1149   this->GetRenderer()->SetDraw(i);
1150   if (i)
1151     UpdateDisplayExtent();
1152 }
1153 //----------------------------------------------------------------------------
1154
1155
1156 //----------------------------------------------------------------------------
1157 void vvSlicer::FlipHorizontalView()
1158 {
1159   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1160   if (cam) {
1161     double *position = cam->GetPosition();
1162     double factor[3] = {1, 1, 1};
1163     factor[this->SliceOrientation] = -1;
1164     cam->SetPosition(factor[0]*position[0],factor[1]*position[1],factor[2]*position[2]);
1165
1166 /*    switch (this->SliceOrientation) {
1167     case vtkImageViewer2::SLICE_ORIENTATION_XY:
1168       cam->SetPosition(position[0],position[1],-position[2]);
1169       break;
1170
1171     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
1172       cam->SetPosition(position[0],-position[1],position[2]);
1173       break;
1174
1175     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1176       cam->SetPosition(-position[0],position[1],position[2]);
1177       break;
1178     }*/
1179
1180     this->Renderer->ResetCameraClippingRange();
1181     this->UpdateDisplayExtent();
1182   }
1183 }
1184 //----------------------------------------------------------------------------
1185
1186
1187 //----------------------------------------------------------------------------
1188 void vvSlicer::FlipVerticalView()
1189 {
1190   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1191   if (cam) {
1192     FlipHorizontalView();
1193     double *viewup = cam->GetViewUp();
1194     cam->SetViewUp(-viewup[0],-viewup[1],-viewup[2]);
1195     this->UpdateDisplayExtent();
1196   }
1197 }
1198 //----------------------------------------------------------------------------
1199
1200
1201 //----------------------------------------------------------------------------
1202 void vvSlicer::SetColorWindow(double window)
1203 {
1204   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1205   if ( LUT ) {
1206     double level = this->GetWindowLevel()->GetLevel();
1207     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1208     LUT->Build();
1209   }
1210   this->vtkImageViewer2::SetColorWindow(window);
1211 }
1212 //----------------------------------------------------------------------------
1213
1214 //----------------------------------------------------------------------------
1215 void vvSlicer::SetColorLevel(double level)
1216 {
1217   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1218   if ( LUT ) {
1219     double window = this->GetWindowLevel()->GetWindow();
1220     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1221     LUT->Build();
1222   }
1223   this->vtkImageViewer2::SetColorLevel(level);
1224 }
1225 //----------------------------------------------------------------------------
1226
1227 //----------------------------------------------------------------------------
1228 double vvSlicer::GetOverlayColorWindow()
1229 {
1230   if(mOverlayMapper)
1231     return mOverlayMapper->GetWindow();
1232   else
1233     return 0.;
1234 }
1235 //----------------------------------------------------------------------------
1236
1237 //----------------------------------------------------------------------------
1238 double vvSlicer::GetOverlayColorLevel()
1239 {
1240   if(mOverlayMapper)
1241     return mOverlayMapper->GetLevel();
1242   else
1243     return 0.;
1244 }
1245 //----------------------------------------------------------------------------
1246
1247 //----------------------------------------------------------------------------
1248 void vvSlicer::SetOverlayColorWindow(double window)
1249 {
1250   mOverlayMapper->SetWindow(window);
1251 }
1252 //----------------------------------------------------------------------------
1253
1254 //----------------------------------------------------------------------------
1255 void vvSlicer::SetOverlayColorLevel(double level)
1256 {
1257   mOverlayMapper->SetLevel(level);
1258 }
1259 //----------------------------------------------------------------------------
1260
1261 //----------------------------------------------------------------------------
1262 // Returns the min an the max value in a 20%x20% region around the mouse pointer
1263 void vvSlicer::GetExtremasAroundMousePointer(double & min, double & max, vtkImageData *image, vtkTransform *transform)
1264 {
1265   //Get mouse pointer position in view coordinates
1266   double corner1[3];
1267   double corner2[3];
1268   for(int i=0; i<3; i++) {
1269     corner1[i] = mCurrent[i];
1270     corner2[i] = mCurrent[i];
1271   }
1272
1273   this->Renderer->WorldToView(corner1[0], corner1[1], corner1[2]);
1274   this->Renderer->WorldToView(corner2[0], corner2[1], corner2[2]);
1275
1276   // In view coordinates, x is the slicer width and y is the slicer height are the in-plane axis
1277   int w, h;
1278   this->Renderer->GetTiledSize(&w, &h);
1279   corner1[0] -= 0.2*h/(double)w;
1280   corner2[0] += 0.2*h/(double)w;
1281   corner1[1] -= 0.2;
1282   corner2[1] += 0.2;
1283   this->Renderer->ViewToWorld(corner1[0], corner1[1], corner1[2]);
1284   this->Renderer->ViewToWorld(corner2[0], corner2[1], corner2[2]);
1285
1286   //Convert to image pixel coordinates (rounded)
1287   transform->TransformPoint(corner1, corner1);
1288   transform->TransformPoint(corner2, corner2);
1289   int iLocalExtents[6];
1290   for(int i=0; i<3; i++) {
1291     corner1[i] = (corner1[i] - image->GetOrigin()[i])/image->GetSpacing()[i];
1292     corner2[i] = (corner2[i] - image->GetOrigin()[i])/image->GetSpacing()[i];
1293
1294     iLocalExtents[i*2  ] = lrint(corner1[i]);
1295     iLocalExtents[i*2+1] = lrint(corner2[i]);
1296
1297     if(iLocalExtents[i*2  ]>iLocalExtents[i*2+1])
1298       std::swap(iLocalExtents[i*2], iLocalExtents[i*2+1]);
1299   }
1300
1301   vtkSmartPointer<vtkExtractVOI> voiFilter = vtkSmartPointer<vtkExtractVOI>::New();
1302   voiFilter->SetInput(image);
1303   voiFilter->SetVOI(iLocalExtents);
1304   voiFilter->Update();
1305   if (!voiFilter->GetOutput()->GetNumberOfPoints()) {
1306     min = 0;
1307     max = 0;
1308     return;
1309   }
1310
1311   vtkSmartPointer<vtkImageAccumulate> accFilter = vtkSmartPointer<vtkImageAccumulate>::New();
1312   accFilter->SetInput(voiFilter->GetOutput());
1313   accFilter->Update();
1314
1315   min = *(accFilter->GetMin());
1316   max = *(accFilter->GetMax());
1317 }
1318 //----------------------------------------------------------------------------
1319
1320 //----------------------------------------------------------------------------
1321 double vvSlicer::GetScalarComponentAsDouble(vtkImageData *image, double X, double Y, double Z, int &ix, int &iy, int &iz, int component)
1322 {
1323   ix = lrint(X);
1324   iy = lrint(Y);
1325   iz = lrint(Z);
1326   if (ix < image->GetWholeExtent()[0] ||
1327       ix > image->GetWholeExtent()[1] ||
1328       iy < image->GetWholeExtent()[2] ||
1329       iy > image->GetWholeExtent()[3] ||
1330       iz < image->GetWholeExtent()[4] ||
1331       iz > image->GetWholeExtent()[5] )
1332     return std::numeric_limits<double>::quiet_NaN();
1333
1334   image->SetUpdateExtent(ix, ix, iy, iy, iz, iz);
1335   image->Update();
1336   return image->GetScalarComponentAsDouble(ix, iy, iz, component);
1337 }
1338 //----------------------------------------------------------------------------
1339
1340 //----------------------------------------------------------------------------
1341 void vvSlicer::Render()
1342 {
1343   if (this->mFusion && mFusionActor->GetVisibility() && showFusionLegend) {
1344     legend->SetLookupTable(this->GetFusionMapper()->GetLookupTable());
1345     legend->UseOpacityOn();
1346     legend->SetVisibility(1);
1347   }
1348   else if (this->GetWindowLevel()->GetLookupTable() && !this->mOverlay)  {
1349     legend->SetLookupTable(this->GetWindowLevel()->GetLookupTable());
1350     legend->UseOpacityOff();
1351     legend->SetVisibility(1);
1352   } else legend->SetVisibility(0);
1353
1354   if (ca->GetVisibility()) {
1355     std::stringstream worldPos;
1356     double pt[3];
1357     mConcatenatedTransform->TransformPoint(mCurrent, pt);
1358     double X = (pt[0] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[0])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[0];
1359     double Y = (pt[1] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[1])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[1];
1360     double Z = (pt[2] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[2])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[2];
1361
1362     if (X >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[0]-0.5 &&
1363         X <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[1]+0.5 &&
1364         Y >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[2]-0.5 &&
1365         Y <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[3]+0.5 &&
1366         Z >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[4]-0.5 &&
1367         Z <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[5]+0.5) {
1368
1369
1370       int ix, iy, iz;
1371       double value = this->GetScalarComponentAsDouble(mImage->GetVTKImages()[mCurrentTSlice], X, Y, Z, ix, iy, iz);
1372
1373       if(ImageActor->GetVisibility())
1374         worldPos << "data value : " << value << std::endl;
1375
1376       worldPos << "mm : " << lrint(mCurrentBeforeSlicingTransform[0]) << ' '
1377                           << lrint(mCurrentBeforeSlicingTransform[1]) << ' '
1378                           << lrint(mCurrentBeforeSlicingTransform[2]) << ' '
1379                           << mCurrentTSlice
1380                           << std::endl;
1381       worldPos << "pixel : " << ix << ' '
1382                              << iy << ' '
1383                              << iz << ' '
1384                              << mCurrentTSlice
1385                              << std::endl;
1386     }
1387     ca->SetText(1,worldPos.str().c_str());
1388   }
1389
1390   if (pdmA->GetVisibility()) {
1391     double x = mCursor[0];
1392     double y = mCursor[1];
1393     double z = mCursor[2];
1394     double xCursor = (x - this->GetInput()->GetOrigin()[0])/this->GetInput()->GetSpacing()[0];
1395     double yCursor = (y - this->GetInput()->GetOrigin()[1])/this->GetInput()->GetSpacing()[1];
1396     double zCursor = (z - this->GetInput()->GetOrigin()[2])/this->GetInput()->GetSpacing()[2];
1397
1398     if (xCursor >= this->GetImageActor()->GetDisplayExtent()[0] &&
1399         xCursor < this->GetImageActor()->GetDisplayExtent()[1]+1 &&
1400         yCursor >= this->GetImageActor()->GetDisplayExtent()[2] &&
1401         yCursor < this->GetImageActor()->GetDisplayExtent()[3]+1 &&
1402         zCursor >= this->GetImageActor()->GetDisplayExtent()[4] &&
1403         zCursor < this->GetImageActor()->GetDisplayExtent()[5]+1 ) {
1404       vtkRenderer * renderer = this->Renderer;
1405
1406       renderer->WorldToView(x,y,z);
1407       renderer->ViewToNormalizedViewport(x,y,z);
1408       renderer->NormalizedViewportToViewport(x,y);
1409       renderer->ViewportToNormalizedDisplay(x,y);
1410       renderer->NormalizedDisplayToDisplay(x,y);
1411       crossCursor->SetFocalPoint(x,y,z);
1412     } else
1413       crossCursor->SetFocalPoint(-1,-1,z);
1414   }
1415
1416
1417   if (mOverlay && mOverlayActor->GetVisibility()) {
1418     if(mLinkOverlayWindowLevel) {
1419       mOverlayMapper->SetWindow(this->GetColorWindow());
1420       mOverlayMapper->SetLevel(this->GetColorLevel());
1421     }
1422     mOverlayMapper->GetOutput()->SetUpdateExtent(mOverlayActor->GetDisplayExtent());
1423     mOverlayMapper->GetOutput()->Update();
1424     mOverlayMapper->Update();
1425   }
1426   if (mLandMapper)
1427     UpdateLandmarks();
1428
1429   this->GetRenderWindow()->Render();
1430 }
1431 //----------------------------------------------------------------------------
1432
1433
1434 //----------------------------------------------------------------------------
1435 void vvSlicer::UpdateCursorPosition()
1436 {
1437   pdmA->SetVisibility(true);
1438   mCursor[0] = mCurrent[0];
1439   mCursor[1] = mCurrent[1];
1440   mCursor[2] = mCurrent[2];
1441   mCursor[3] = mCurrentTSlice;
1442 }
1443 //----------------------------------------------------------------------------
1444
1445
1446 //----------------------------------------------------------------------------
1447 void vvSlicer::UpdateLandmarks()
1448 {
1449   vtkPolyData *pd = static_cast<vtkPolyData*>(mLandClipper->GetInput());
1450   if (pd->GetPoints()) {
1451     mLandGlyph->SetRange(0,1);
1452     mLandGlyph->Modified();
1453     mLandGlyph->Update();
1454
1455     mClipBox->Modified();
1456     mLandClipper->Update();
1457     mLandMapper->Update();
1458   }
1459
1460 }
1461 //----------------------------------------------------------------------------
1462
1463
1464 //----------------------------------------------------------------------------
1465 void vvSlicer::SetSlice(int slice)
1466 {
1467   int *range = this->GetSliceRange();
1468   if (range) {
1469     if (slice < range[0]) {
1470       slice = range[0];
1471     } else if (slice > range[1]) {
1472       slice = range[1];
1473     }
1474   }
1475
1476   if (this->Slice == slice) {
1477     return;
1478   }
1479
1480   this->Slice = slice;
1481   SetContourSlice();
1482   this->Modified();
1483   this->UpdateDisplayExtent();
1484
1485   // Seems to work without this line
1486   //this->Render();
1487 }
1488 //----------------------------------------------------------------------------
1489
1490 //----------------------------------------------------------------------------
1491 int vvSlicer::GetTMax() {
1492   int tmax = (int)mImage->GetVTKImages().size() - 1;
1493   if(mOverlay)
1494     tmax = std::max(tmax, (int)mOverlay->GetVTKImages().size()-1);
1495   return tmax;
1496 }
1497 //----------------------------------------------------------------------------
1498
1499 //----------------------------------------------------------------------------
1500 void vvSlicer::SetContourSlice()
1501 {
1502   if (mSurfaceCutActors.size() > 0)
1503     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
1504          i!=mSurfaceCutActors.end(); i++) {
1505
1506       (*i)->SetSlicingOrientation(this->SliceOrientation);
1507       (*i)->SetCutSlice((this->Slice)*this->GetImage()->GetSpacing()[this->SliceOrientation]+
1508                         this->GetImage()->GetOrigin()[this->SliceOrientation]);
1509     }
1510 }
1511 //----------------------------------------------------------------------------
1512
1513
1514 //----------------------------------------------------------------------------
1515 void vvSlicer::ForceUpdateDisplayExtent()
1516 {
1517   this->UpdateDisplayExtent();
1518 }
1519 //----------------------------------------------------------------------------
1520
1521
1522 //----------------------------------------------------------------------------
1523 int* vvSlicer::GetDisplayExtent()
1524 {
1525   return this->GetImageActor()->GetDisplayExtent();
1526 }
1527 //----------------------------------------------------------------------------
1528
1529
1530 //----------------------------------------------------------------------------
1531 void vvSlicer::PrintSelf(ostream& os, vtkIndent indent)
1532 {
1533   this->Superclass::PrintSelf(os, indent);
1534 }
1535 //----------------------------------------------------------------------------
1536
1537 //----------------------------------------------------------------------------
1538 void vvSlicer::SetVFColor(double r, double g, double b)
1539 {
1540   double mVFColorHSV[3];
1541   mVFColor[0] = r;
1542   mVFColor[1] = g;
1543   mVFColor[2] = b;
1544
1545   vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
1546   mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
1547   mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
1548   mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
1549
1550   this->Render();
1551 }
1552