vv/vvSlicerManager.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://oncora1.lyon.fnclcc.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 "vvSlicerManager.h"
  20 #include "vvSlicer.h"
  21 #include "vvImage.h"
  22 #include "vvSlicerManagerCommand.h"
  23 #include "vvInteractorStyleNavigator.h"
  24 #include "vvLandmarks.h"
  25 #include "vvMesh.h"
  26 #include "vvImageMapToWLColors.h"
  27 #include "vvBlendImageActor.h"
  28
  29 #include <vtkImageActor.h>
  30 #include <vtkImageData.h>
  31 #include <vtkRenderWindow.h>
  32 #include <vtkRendererCollection.h>
  33 #include <vtkRenderWindowInteractor.h>
  34 #include <vtkImageMapToWindowLevelColors.h>
  35 #include <vtkWindowLevelLookupTable.h>
  36 #include <vtkColorTransferFunction.h>
  37 #include <vtkImageClip.h>
  38 #include <vtkLODActor.h>
  39 #include <vtkPointData.h>
  40 #include <vtksys/SystemTools.hxx>
  41 #include <vtkCamera.h>
  42
  43 #include <qfileinfo.h>
  44
  45 //----------------------------------------------------------------------------
  46 vvSlicerManager::vvSlicerManager(int numberOfSlicers)
  47 {
  48   mFileName = "";
  49   mId = "";
  50   mVFName = "";
  51   mOverlayName = "";
  52   mFusionName = "";
  53   mVFId = "";
  54   mLastError = "";
  55   mType = vvImageReader::UNDEFINEDIMAGETYPE;
  56   mColorMap = 0;
  57   mPreset = 0;
  58   mOverlayColor = 130;
  59
  60   mFusionOpacity = 30;
  61   mFusionThresOpacity = 1;
  62   mFusionColorMap = 3;
  63   mFusionWindow = 1000;
  64   mFusionLevel = 1000;
  65   mFusionShowLegend = true;
  66
  67   mLandmarks = NULL;
  68   mLinkedId.resize(0);
  69
  70   for ( int i = 0; i < numberOfSlicers; i++)
  71     mSlicers.push_back(vtkSmartPointer<vvSlicer>::New());
  72
  73   mPreviousSlice.resize(numberOfSlicers);
  74   mPreviousTSlice.resize(numberOfSlicers);
  75 }
  76 //----------------------------------------------------------------------------
  77
  78
  79 //----------------------------------------------------------------------------
  80 vvSlicerManager::~vvSlicerManager()
  81 {
  82   if (mLandmarks)
  83     delete mLandmarks;
  84 }
  85 //----------------------------------------------------------------------------
  86
  87
  88 //------------------------------------------------------------------------------
  89 void vvSlicerManager::SetFilename(std::string filename, int number)
  90 {
  91   mFileName = filename;
  92   mFileName = vtksys::SystemTools::GetFilenameName(mFileName);
  93   mBaseFileName = vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(mFileName));
  94   mBaseFileNameNumber = number;
  95
  96   mFileName = mBaseFileName;
  97   if (number != 0) {
  98     mFileName.append("_"+clitk::toString(number));
  99   }
 100   mFileName.append(vtksys::SystemTools::GetFilenameLastExtension(filename));
 101
 102   for(unsigned int i=0; i<mSlicers.size(); i++) {
 103     mSlicers[i]->SetFileName(mFileName);//vtksys::SystemTools::GetFilenameWithoutLastExtension(filename));
 104   }
 105
 106 }
 107 //------------------------------------------------------------------------------
 108
 109
 110 //----------------------------------------------------------------------------
 111 void vvSlicerManager::AddContour(vvMesh::Pointer contour,bool propagate)
 112 {
 113   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 114     mSlicers[i]->AddContour(contour,propagate);
 115   }
 116 }
 117 //----------------------------------------------------------------------------
 118
 119
 120 //----------------------------------------------------------------------------
 121 void vvSlicerManager::ToggleContourSuperposition()
 122 {
 123   for ( unsigned int i = 0; i < mSlicers.size(); i++)
 124     mSlicers[i]->ToggleContourSuperposition();
 125 }
 126 //----------------------------------------------------------------------------
 127
 128 //----------------------------------------------------------------------------
 129 std::string vvSlicerManager::GetListOfAbsoluteFilePathInOneString(const std::string &actorType)
 130 {
 131   vvImageReader *reader = NULL;
 132
 133   if(actorType=="image")
 134     reader = mReader;
 135   else if(actorType=="overlay")
 136     reader = mOverlayReader;
 137   else if(actorType=="fusion")
 138     reader = mFusionReader;
 139   else if(actorType=="vector")
 140     reader = mVectorReader;
 141
 142   if(!reader)
 143     return "";
 144
 145   std::string list;
 146   for(unsigned int i=0; i<reader->GetInputFilenames().size(); i++){
 147     QFileInfo fileinfo(reader->GetInputFilenames()[i].c_str()); //Do not show the path
 148     if(i)
 149       list += '\n';
 150     list += fileinfo.absoluteFilePath().toStdString();
 151   }
 152   return list;
 153 }
 154 //----------------------------------------------------------------------------
 155
 156
 157 //----------------------------------------------------------------------------
 158 bool vvSlicerManager::SetImage(std::string filename, vvImageReader::LoadedImageType type, int n, unsigned int slice)
 159 {
 160   mType = type;
 161   if (mReader.IsNull())
 162     mReader = vvImageReader::New();
 163   std::vector<std::string> filenames;
 164   filenames.push_back(filename);
 165   mReader->SetInputFilenames(filenames);
 166   mReader->SetSlice(slice); // Only used for SLICED type
 167   mReader->Update(type);
 168
 169   SetFilename(filename, n);
 170   //  mFileName = vtksys::SystemTools::GetFilenameName(mFileName);
 171   //mBaseFileName = vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(mFileName));
 172   //mBaseFileNameNumber = n;
 173
 174   if (mReader->GetLastError().size() == 0) {
 175     mImage=mReader->GetOutput();
 176     for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 177       mSlicers[i]->SetFileName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename));
 178       mSlicers[i]->SetImage(mReader->GetOutput());
 179     }
 180   } else {
 181     mLastError = mReader->GetLastError();
 182     return false;
 183   }
 184   // if (n!=0) {
 185   //   mFileName.append("_"+clitk::toString(n));
 186   // }
 187   return true;
 188 }
 189 //----------------------------------------------------------------------------
 190
 191
 192 //----------------------------------------------------------------------------
 193 void vvSlicerManager::SetImage(vvImage::Pointer image)
 194 {
 195   mImage=image;
 196   for (unsigned int i = 0; i < mSlicers.size(); i++) {
 197     mSlicers[i]->SetImage(image);
 198   }
 199 }
 200 //----------------------------------------------------------------------------
 201
 202
 203 //----------------------------------------------------------------------------
 204 bool vvSlicerManager::SetImages(std::vector<std::string> filenames, vvImageReader::LoadedImageType type, int n)
 205 {
 206   mType = type;
 207   std::string fileWithoutExtension = vtksys::SystemTools::GetFilenameWithoutExtension(filenames[0]);
 208   if (type == vvImageReader::DICOM)
 209     fileWithoutExtension += "_dicom";
 210   else if (type == vvImageReader::MERGED)
 211     fileWithoutExtension += "_merged";
 212   else if (type == vvImageReader::MERGEDWITHTIME)
 213     fileWithoutExtension += "_merged_wt";
 214
 215   mFileName = vtksys::SystemTools::GetFilenameName(mFileName);
 216   mFileName = fileWithoutExtension + vtksys::SystemTools::GetFilenameExtension(filenames[0]);
 217   if (mReader.IsNull())
 218     mReader = vvImageReader::New();
 219   mReader->SetInputFilenames(filenames);
 220   mReader->Update(type);
 221
 222   mBaseFileName = vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(mFileName));
 223   mBaseFileNameNumber = n;
 224
 225   if (mReader->GetLastError().size() == 0) {
 226     mImage=mReader->GetOutput();
 227     for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 228       mSlicers[i]->SetFileName(fileWithoutExtension);
 229       mSlicers[i]->SetImage(mReader->GetOutput());
 230     }
 231   } else {
 232     mLastError = mReader->GetLastError();
 233     return false;
 234   }
 235   if (n!=0) {
 236     mFileName.append("_"+clitk::toString(n));
 237   }
 238   return true;
 239 }
 240 //----------------------------------------------------------------------------
 241
 242
 243 //----------------------------------------------------------------------------
 244 bool vvSlicerManager::SetOverlay(std::string filename,int dim, std::string component)
 245 {
 246   mOverlayName = filename;
 247   mOverlayComponent = component;
 248   if (dim > mImage->GetNumberOfDimensions()) {
 249     mLastError = " Overlay dimension cannot be greater then reference image!";
 250     return false;
 251   }
 252   if (mOverlayReader.IsNull())
 253     mOverlayReader = vvImageReader::New();
 254   std::vector<std::string> filenames;
 255   filenames.push_back(filename);
 256   mOverlayReader->SetInputFilenames(filenames);
 257   mOverlayReader->Update(mImage->GetNumberOfDimensions(),component.c_str(),mType);
 258   if (mOverlayReader->GetLastError().size() == 0) {
 259     for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 260       mSlicers[i]->SetOverlay(mOverlayReader->GetOutput());
 261     }
 262   } else {
 263     mLastError = mOverlayReader->GetLastError();
 264     return false;
 265   }
 266   return true;
 267 }
 268 //----------------------------------------------------------------------------
 269
 270
 271 //----------------------------------------------------------------------------
 272 bool vvSlicerManager::SetFusion(std::string filename,int dim, std::string component)
 273 {
 274   mFusionName = filename;
 275   mFusionComponent = component;
 276   if (dim > mImage->GetNumberOfDimensions()) {
 277     mLastError = " Overlay dimension cannot be greater then reference image!";
 278     return false;
 279   }
 280   if (mFusionReader.IsNull())
 281     mFusionReader = vvImageReader::New();
 282   std::vector<std::string> filenames;
 283   filenames.push_back(filename);
 284   mFusionReader->SetInputFilenames(filenames);
 285   mFusionReader->Update(mImage->GetNumberOfDimensions(),component.c_str(),mType);
 286   if (mFusionReader->GetLastError().size() == 0) {
 287     for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 288       mSlicers[i]->SetFusion(mFusionReader->GetOutput());
 289     }
 290   } else {
 291     mLastError = mFusionReader->GetLastError();
 292     return false;
 293   }
 294   double *fusRange = mFusionReader->GetOutput()->GetVTKImages()[0]->GetScalarRange();
 295   mFusionLevel = (fusRange[0]+fusRange[1])/2;
 296   mFusionWindow = fusRange[1]-fusRange[0];
 297
 298   return true;
 299 }
 300 //----------------------------------------------------------------------------
 301
 302
 303 //----------------------------------------------------------------------------
 304 bool vvSlicerManager::SetVF(std::string filename)
 305 {
 306   if (mVectorReader.IsNull())
 307     mVectorReader = vvImageReader::New();
 308   mVectorReader->SetInputFilename(filename);
 309
 310   if (mType == vvImageReader::IMAGEWITHTIME)
 311     mVectorReader->Update(vvImageReader::VECTORFIELDWITHTIME);
 312   else
 313     mVectorReader->Update(vvImageReader::VECTORFIELD);
 314   if (mVectorReader->GetLastError().size() != 0) {
 315     mLastError = mVectorReader->GetLastError();
 316     return false;
 317   } else
 318     return SetVF(mVectorReader->GetOutput(),filename);
 319 }
 320 //----------------------------------------------------------------------------
 321
 322
 323 //----------------------------------------------------------------------------
 324 bool vvSlicerManager::SetVF(vvImage::Pointer vf,std::string filename)
 325 {
 326   if (vf->GetNumberOfDimensions() > mImage->GetNumberOfDimensions()) {
 327     mLastError = "Sorry, vector field dimension cannot be greater then reference image.";
 328     return false;
 329   }
 330   if (vf->GetNumberOfDimensions() == 4) {
 331     if (vf->GetSpacing()[3] != mImage->GetSpacing()[3]) {
 332       mLastError = "Sorry, vector field time spacing cannot be different from time spacing of the reference image.";
 333       return false;
 334     }
 335     if (vf->GetOrigin()[3] != mImage->GetOrigin()[3]) {
 336       mLastError = "Sorry, vector field time origin cannot be different from time origin of the reference image.";
 337       return false;
 338     }
 339   }
 340   mVF=vf;
 341   mVFName = filename;
 342   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 343     mSlicers[i]->SetVF(vf);
 344   }
 345   return true;
 346 }
 347 //----------------------------------------------------------------------------
 348
 349
 350 //----------------------------------------------------------------------------
 351 vvSlicer* vvSlicerManager::GetSlicer(int i)
 352 {
 353   return mSlicers[i];
 354 }
 355 //----------------------------------------------------------------------------
 356
 357
 358 //----------------------------------------------------------------------------
 359 void vvSlicerManager::UpdateSlicer(int num, bool state)
 360 {
 361   if (mSlicers[num]->GetImage())
 362     mSlicers[num]->SetDisplayMode(state);
 363 }
 364 //----------------------------------------------------------------------------
 365
 366
 367 //----------------------------------------------------------------------------
 368 void vvSlicerManager::SetSlicerWindow(int i, vtkRenderWindow* RW)
 369 {
 370   mSlicers[i]->SetRenderWindow(i,RW);
 371 }
 372 //----------------------------------------------------------------------------
 373
 374
 375 //----------------------------------------------------------------------------
 376 void vvSlicerManager::SetInteractorStyleNavigator(int i, vtkInteractorStyle* style)
 377 {
 378   vvSlicerManagerCommand *smc = vvSlicerManagerCommand::New();
 379   smc->SM = this;
 380   smc->SetSlicerNumber(i);
 381   mSlicers[i]->GetRenderWindow()->GetInteractor()->SetInteractorStyle(style);
 382
 383   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 384     GetInteractorStyle()->AddObserver(vtkCommand::KeyPressEvent, smc);
 385   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 386     GetInteractorStyle()->AddObserver(vtkCommand::WindowLevelEvent, smc);
 387   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 388     GetInteractorStyle()->AddObserver(vtkCommand::EndWindowLevelEvent, smc);
 389   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 390     GetInteractorStyle()->AddObserver(vtkCommand::StartWindowLevelEvent, smc);
 391   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 392     GetInteractorStyle()->AddObserver(vtkCommand::PickEvent, smc);
 393   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 394     GetInteractorStyle()->AddObserver(vtkCommand::StartPickEvent, smc);
 395   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 396     GetInteractorStyle()->AddObserver(vtkCommand::LeaveEvent, smc);
 397   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 398     GetInteractorStyle()->AddObserver(vtkCommand::UserEvent, smc);
 399   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 400     GetInteractorStyle()->AddObserver(vtkCommand::MouseWheelForwardEvent, smc);
 401   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 402     GetInteractorStyle()->AddObserver(vtkCommand::MouseWheelBackwardEvent, smc);
 403   // mSlicers[i]->GetRenderWindow()->GetInteractor()->
 404   //   GetInteractorStyle()->AddObserver(vtkCommand::LeftButtonReleaseEvent, smc);
 405   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 406     GetInteractorStyle()->AddObserver(vtkCommand::EndPickEvent, smc);
 407   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 408     GetInteractorStyle()->AddObserver(vtkCommand::EndInteractionEvent, smc);
 409   smc->Delete();
 410 }
 411 //----------------------------------------------------------------------------
 412
 413
 414 //----------------------------------------------------------------------------
 415 void vvSlicerManager::LeftButtonReleaseEvent(int slicer)
 416 {
 417   emit LeftButtonReleaseSignal(slicer);
 418 }
 419 //----------------------------------------------------------------------------
 420
 421
 422 //----------------------------------------------------------------------------
 423 void vvSlicerManager::EmitMousePositionUpdated(int slicer)
 424 {
 425   emit MousePositionUpdatedSignal(slicer);
 426 }
 427 //----------------------------------------------------------------------------
 428
 429
 430 //----------------------------------------------------------------------------
 431 void vvSlicerManager::SetSliceOrientation(int slicer, int orientation)
 432 {
 433   mSlicers[slicer]->SetSliceOrientation(orientation);
 434   emit UpdateOrientation(slicer, orientation);
 435 }
 436 //----------------------------------------------------------------------------
 437
 438 //----------------------------------------------------------------------------
 439 void vvSlicerManager::SetTSlice(int slice)
 440 {
 441   if (slice < 0)
 442     slice = 0;
 443   else if (slice > mSlicers[0]->GetTMax())
 444     slice = mSlicers[0]->GetTMax();
 445   if (mLandmarks)
 446     mLandmarks->SetTime(slice);
 447   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 448     if (slice != mSlicers[i]->GetTSlice()) {
 449       mSlicers[i]->SetTSlice(slice);
 450         UpdateTSlice(i);
 451     }
 452   }
 453 }
 454 //----------------------------------------------------------------------------
 455
 456
 457 //----------------------------------------------------------------------------
 458 void vvSlicerManager::SetNextTSlice(int originating_slicer)
 459 {
 460   int t = mSlicers[0]->GetTSlice();
 461   t++;
 462   if (t > mSlicers[0]->GetTMax())
 463     t = 0;
 464   //std::cout << "vvSlicerManager::SetNextTSlice" << std::endl;
 465   emit UpdateTSlice(originating_slicer,t);
 466 }
 467 //----------------------------------------------------------------------------
 468
 469
 470 //----------------------------------------------------------------------------
 471 void vvSlicerManager::SetPreviousTSlice(int originating_slicer)
 472 {
 473   int t = mSlicers[0]->GetTSlice();
 474   t--;
 475   if (t < 0)
 476     t = mSlicers[0]->GetTMax();
 477   //std::cout << "vvSlicerManager::SetPreviousTSlice" << std::endl;
 478   emit UpdateTSlice(originating_slicer,t);
 479 }
 480 //----------------------------------------------------------------------------
 481
 482
 483 //----------------------------------------------------------------------------
 484 void vvSlicerManager::ToggleInterpolation()
 485 {
 486   bool interpolate=!(mSlicers[0]->GetImageActor()->GetInterpolate());
 487   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 488     mSlicers[i]->GetImageActor()->SetInterpolate(interpolate);
 489     if (mSlicers[i]->GetOverlayActor())
 490       mSlicers[i]->GetOverlayActor()->SetInterpolate(interpolate);
 491     if (mSlicers[i]->GetFusionActor())
 492       mSlicers[i]->GetFusionActor()->SetInterpolate(interpolate);
 493   }
 494 }
 495 //----------------------------------------------------------------------------
 496
 497
 498 //----------------------------------------------------------------------------
 499 void vvSlicerManager::SetTSliceInSlicer(int tslice, int slicer)
 500 {
 501   if (tslice < 0)
 502     tslice = 0;
 503   else if (tslice > mSlicers[slicer]->GetTMax())
 504     tslice = mSlicers[slicer]->GetTMax();
 505   if (mLandmarks)
 506     mLandmarks->SetTime(tslice);
 507
 508   if (mSlicers[slicer]->GetTSlice() == tslice) return;
 509
 510   mSlicers[slicer]->SetTSlice(tslice);
 511   UpdateTSlice(slicer);
 512 }
 513 //----------------------------------------------------------------------------
 514
 515
 516 //----------------------------------------------------------------------------
 517 void vvSlicerManager::SetColorWindow(double s)
 518 {
 519   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 520     mSlicers[i]->SetColorWindow(s);
 521   }
 522 }
 523 //----------------------------------------------------------------------------
 524
 525 //----------------------------------------------------------------------------
 526 void vvSlicerManager::SetColorLevel(double s)
 527 {
 528   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 529     mSlicers[i]->SetColorLevel(s);
 530   }
 531 }
 532 //----------------------------------------------------------------------------
 533
 534 //----------------------------------------------------------------------------
 535 void vvSlicerManager::SetOverlayColorWindow(double s)
 536 {
 537   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 538     mSlicers[i]->SetOverlayColorWindow(s);
 539   }
 540 }
 541 //----------------------------------------------------------------------------
 542
 543 //----------------------------------------------------------------------------
 544 void vvSlicerManager::SetOverlayColorLevel(double s)
 545 {
 546   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 547     mSlicers[i]->SetOverlayColorLevel(s);
 548   }
 549 }
 550 //----------------------------------------------------------------------------
 551
 552 //----------------------------------------------------------------------------
 553 void vvSlicerManager::SetLinkOverlayWindowLevel(bool b)
 554 {
 555   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 556     mSlicers[i]->SetLinkOverlayWindowLevel(b);
 557   }
 558 }
 559 //----------------------------------------------------------------------------
 560
 561 //----------------------------------------------------------------------------
 562 void vvSlicerManager::SetCursorAndCornerAnnotationVisibility(int s)
 563 {
 564   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 565     mSlicers[i]->SetCursorVisibility(s);
 566     mSlicers[i]->SetCornerAnnotationVisibility(s);
 567   }
 568 }
 569 //----------------------------------------------------------------------------
 570
 571 //----------------------------------------------------------------------------
 572 void vvSlicerManager::SetOpacity(int i, double factor)
 573 {
 574   mSlicers[i]->SetOpacity(1/factor);
 575 }
 576 //----------------------------------------------------------------------------
 577
 578
 579 //----------------------------------------------------------------------------
 580 void vvSlicerManager::UpdateViews(int current,int slicer)
 581 {
 582   double x = (mSlicers[slicer]->GetCurrentPosition()[0] - mSlicers[slicer]->GetInput()->GetOrigin()[0])
 583     /mSlicers[slicer]->GetInput()->GetSpacing()[0];
 584   double y = (mSlicers[slicer]->GetCurrentPosition()[1] - mSlicers[slicer]->GetInput()->GetOrigin()[1])
 585     /mSlicers[slicer]->GetInput()->GetSpacing()[1];
 586   double z = (mSlicers[slicer]->GetCurrentPosition()[2] - mSlicers[slicer]->GetInput()->GetOrigin()[2])
 587     /mSlicers[slicer]->GetInput()->GetSpacing()[2];
 588
 589   if (x >= mSlicers[slicer]->GetInput()->GetWholeExtent()[0] &&
 590       x <= mSlicers[slicer]->GetInput()->GetWholeExtent()[1] &&
 591       y >= mSlicers[slicer]->GetInput()->GetWholeExtent()[2] &&
 592       y <= mSlicers[slicer]->GetInput()->GetWholeExtent()[3] &&
 593       z >= mSlicers[slicer]->GetInput()->GetWholeExtent()[4] &&
 594       z <= mSlicers[slicer]->GetInput()->GetWholeExtent()[5]) {
 595     mSlicers[slicer]->UpdateCursorPosition();
 596     mSlicers[slicer]->SetCursorColor(10,212,255);
 597
 598     switch (mSlicers[slicer]->GetSliceOrientation()) {
 599     case vtkImageViewer2::SLICE_ORIENTATION_XY:
 600       if (mSlicers[slicer]->GetSlice() != (int)floor(z))
 601         mSlicers[slicer]->SetSlice((int)floor(z));
 602       break;
 603
 604     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
 605       if (mSlicers[slicer]->GetSlice() != (int)floor(y))
 606         mSlicers[slicer]->SetSlice((int)floor(y));
 607       break;
 608
 609     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
 610       if (mSlicers[slicer]->GetSlice() != (int)floor(x))
 611         mSlicers[slicer]->SetSlice((int)floor(x));
 612       break;
 613     }
 614     mSlicers[slicer]->Render();
 615
 616     for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 617       if (i != (unsigned int)slicer
 618           && mSlicers[i]->GetRenderer()->GetDraw()
 619           && mSlicers[i]->GetRenderWindow()->GetSize()[0] > 2
 620           && mSlicers[i]->GetRenderWindow()->GetSize()[1] > 2) {
 621         mSlicers[i]->SetCurrentPosition(mSlicers[slicer]->GetCurrentPosition()[0],
 622                                         mSlicers[slicer]->GetCurrentPosition()[1],
 623                                         mSlicers[slicer]->GetCurrentPosition()[2],
 624                                         mSlicers[slicer]->GetTSlice());
 625         mSlicers[i]->UpdateCursorPosition();
 626         if (current) { //do not display corner annotation if image is the one picked
 627           mSlicers[i]->SetCurrentPosition(-VTK_DOUBLE_MAX,-VTK_DOUBLE_MAX,
 628                                           -VTK_DOUBLE_MAX, mSlicers[slicer]->GetTSlice());
 629           mSlicers[i]->SetCursorColor(255,10,212);
 630         } else {
 631           mSlicers[i]->SetCursorColor(150,10,282);
 632         }
 633         switch (mSlicers[i]->GetSliceOrientation()) {
 634         case vtkImageViewer2::SLICE_ORIENTATION_XY:
 635           if (mSlicers[i]->GetSlice() != (int)floor(z))
 636             mSlicers[i]->SetSlice((int)floor(z));
 637           break;
 638
 639         case vtkImageViewer2::SLICE_ORIENTATION_XZ:
 640           if (mSlicers[i]->GetSlice() != (int)floor(y))
 641             mSlicers[i]->SetSlice((int)floor(y));
 642           break;
 643
 644         case vtkImageViewer2::SLICE_ORIENTATION_YZ:
 645           if (mSlicers[i]->GetSlice() != (int)floor(x))
 646             mSlicers[i]->SetSlice((int)floor(x));
 647           break;
 648         }
 649
 650         mSlicers[i]->Render();
 651
 652         UpdateSlice(i);
 653         UpdateTSlice(i);
 654       }
 655     }
 656   }
 657 }
 658 //----------------------------------------------------------------------------
 659
 660
 661 //----------------------------------------------------------------------------
 662 void vvSlicerManager::UpdateLinked(int slicer)
 663 {
 664   double x = (mSlicers[slicer]->GetCurrentPosition()[0] - mSlicers[slicer]->GetInput()->GetOrigin()[0])
 665     /mSlicers[slicer]->GetInput()->GetSpacing()[0];
 666   double y = (mSlicers[slicer]->GetCurrentPosition()[1] - mSlicers[slicer]->GetInput()->GetOrigin()[1])
 667     /mSlicers[slicer]->GetInput()->GetSpacing()[1];
 668   double z = (mSlicers[slicer]->GetCurrentPosition()[2] - mSlicers[slicer]->GetInput()->GetOrigin()[2])
 669     /mSlicers[slicer]->GetInput()->GetSpacing()[2];
 670
 671   if (x >= mSlicers[slicer]->GetInput()->GetWholeExtent()[0] &&
 672       x <= mSlicers[slicer]->GetInput()->GetWholeExtent()[1] &&
 673       y >= mSlicers[slicer]->GetInput()->GetWholeExtent()[2] &&
 674       y <= mSlicers[slicer]->GetInput()->GetWholeExtent()[3] &&
 675       z >= mSlicers[slicer]->GetInput()->GetWholeExtent()[4] &&
 676       z <= mSlicers[slicer]->GetInput()->GetWholeExtent()[5]) {
 677     for (std::list<std::string>::const_iterator i = mLinkedId.begin(); i != mLinkedId.end(); i++) {
 678       emit UpdateLinkManager(*i, slicer,mSlicers[slicer]->GetCurrentPosition()[0],
 679                              mSlicers[slicer]->GetCurrentPosition()[1],
 680                              mSlicers[slicer]->GetCurrentPosition()[2],mSlicers[slicer]->GetTSlice());
 681     }
 682   }
 683 }
 684 //----------------------------------------------------------------------------
 685
 686 //----------------------------------------------------------------------------
 687 void vvSlicerManager::UpdateLinkedNavigation(vvSlicer *refSlicer, bool bPropagate)
 688 {
 689   vtkCamera *refCam = refSlicer->GetRenderer()->GetActiveCamera();
 690   double refPosition[3], refFocal[3];
 691   refCam->GetPosition(refPosition);
 692   refCam->GetFocalPoint(refFocal);
 693
 694   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 695     vtkCamera *camera = mSlicers[i]->GetRenderer()->GetActiveCamera();
 696     camera->SetParallelScale(refCam->GetParallelScale());
 697
 698     double position[3], focal[3];
 699     camera->GetPosition(position);
 700     camera->GetFocalPoint(focal);
 701
 702     if(refSlicer->GetSliceOrientation()==mSlicers[i]->GetSliceOrientation()) {
 703       for(int i=0; i<3; i++) {
 704         position[i] = refPosition[i];
 705         focal[i]    = refFocal[i];
 706       }
 707     }
 708
 709     if(refSlicer->GetSliceOrientation()==vtkImageViewer2::SLICE_ORIENTATION_XY) {
 710       if(mSlicers[i]->GetSliceOrientation()==vtkImageViewer2::SLICE_ORIENTATION_XZ) {
 711         position[0] = refPosition[0];
 712         focal[0]    = refFocal[0];
 713       }
 714       if(mSlicers[i]->GetSliceOrientation()==vtkImageViewer2::SLICE_ORIENTATION_YZ) {
 715         position[1] = refPosition[1];
 716         focal[1]    = refFocal[1];
 717       }
 718     }
 719
 720     if(refSlicer->GetSliceOrientation()==vtkImageViewer2::SLICE_ORIENTATION_XZ) {
 721       if(mSlicers[i]->GetSliceOrientation()==vtkImageViewer2::SLICE_ORIENTATION_YZ) {
 722         position[2] = refPosition[2];
 723         focal[2]    = refFocal[2];
 724       }
 725       if(mSlicers[i]->GetSliceOrientation()==vtkImageViewer2::SLICE_ORIENTATION_XY) {
 726         position[0] = refPosition[0];
 727         focal[0]    = refFocal[0];
 728       }
 729     }
 730
 731     if(refSlicer->GetSliceOrientation()==vtkImageViewer2::SLICE_ORIENTATION_YZ) {
 732       if(mSlicers[i]->GetSliceOrientation()==vtkImageViewer2::SLICE_ORIENTATION_XY) {
 733         position[1] = refPosition[1];
 734         focal[1]    = refFocal[1];
 735       }
 736       if(mSlicers[i]->GetSliceOrientation()==vtkImageViewer2::SLICE_ORIENTATION_XZ) {
 737         position[2] = refPosition[2];
 738         focal[2]    = refFocal[2];
 739       }
 740     }
 741
 742     camera->SetFocalPoint(focal);
 743     camera->SetPosition(position);
 744
 745     //Fix for bug #243
 746     mSlicers[i]->ForceUpdateDisplayExtent();
 747   }
 748
 749   Render();
 750   if(bPropagate)
 751     for (std::list<std::string>::const_iterator i = mLinkedId.begin(); i != mLinkedId.end(); i++)
 752       emit UpdateLinkedNavigation(*i, this, refSlicer);
 753 }
 754 //----------------------------------------------------------------------------
 755
 756 //----------------------------------------------------------------------------
 757 double vvSlicerManager::GetColorWindow()
 758 {
 759   if (mSlicers.size())
 760     return mSlicers[0]->GetColorWindow();
 761   return -1;
 762 }
 763 //----------------------------------------------------------------------------
 764
 765
 766 //----------------------------------------------------------------------------
 767 double vvSlicerManager::GetColorLevel()
 768 {
 769   if (mSlicers.size())
 770     return mSlicers[0]->GetColorLevel();
 771   return -1;
 772 }
 773 //----------------------------------------------------------------------------
 774
 775 //----------------------------------------------------------------------------
 776 double vvSlicerManager::GetOverlayColorWindow() const
 777 {
 778   if (mSlicers.size())
 779     return mSlicers[0]->GetOverlayColorWindow();
 780   return -1;
 781 }
 782 //----------------------------------------------------------------------------
 783
 784 //----------------------------------------------------------------------------
 785 double vvSlicerManager::GetOverlayColorLevel() const
 786 {
 787   if (mSlicers.size())
 788     return mSlicers[0]->GetOverlayColorLevel();
 789   return -1;
 790 }
 791 //----------------------------------------------------------------------------
 792
 793 //----------------------------------------------------------------------------
 794 bool vvSlicerManager::GetLinkOverlayWindowLevel() const
 795 {
 796   if (mSlicers.size())
 797     return mSlicers[0]->GetLinkOverlayWindowLevel();
 798   return -1;
 799 }
 800 //----------------------------------------------------------------------------
 801
 802 //------------------------------------------------------------------------------
 803 void vvSlicerManager::ResetTransformationToIdentity(const std::string actorType)
 804 {
 805   if(actorType == "image")
 806     this->GetImage()->GetTransform()->Identity();
 807   else if(actorType == "overlay")
 808     this->GetSlicer(0)->GetOverlay()->GetTransform()->Identity();
 809   else if(actorType == "fusion")
 810     this->GetSlicer(0)->GetFusion()->GetTransform()->Identity();
 811   else if(actorType == "vf")
 812     this->GetVF()->GetTransform()->Identity();
 813   else
 814     return;
 815
 816   for(int i=0; i< this->GetNumberOfSlicers(); i++){
 817     this->GetSlicer(i)->ForceUpdateDisplayExtent();
 818     this->GetSlicer(i)->ResetCamera();
 819     this->GetSlicer(i)->Render();
 820   }
 821 }
 822 //------------------------------------------------------------------------------
 823
 824 //----------------------------------------------------------------------------
 825 void vvSlicerManager::Render()
 826 {
 827   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 828     mSlicers[i]->Render();
 829   }
 830 }
 831 //----------------------------------------------------------------------------
 832
 833
 834 //----------------------------------------------------------------------------
 835 void vvSlicerManager::GenerateDefaultLookupTable()
 836 {
 837   SetPreset(mPreset);
 838   SetColorMap(mColorMap);
 839 }
 840 //----------------------------------------------------------------------------
 841
 842
 843 //----------------------------------------------------------------------------
 844 void vvSlicerManager::Reload()
 845 {
 846   mReader->Update(mType);
 847   mImage=mReader->GetOutput();
 848   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 849     mSlicers[i]->SetImage(mImage);
 850   }
 851 }
 852 //----------------------------------------------------------------------------
 853
 854
 855 //----------------------------------------------------------------------------
 856 void vvSlicerManager::ReloadFusion()
 857 {
 858   mFusionReader->Update(mImage->GetNumberOfDimensions(),mFusionComponent.c_str(),mType);
 859
 860   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 861     mSlicers[i]->SetFusion(mFusionReader->GetOutput());
 862     mSlicers[i]->Render();
 863   }
 864 }
 865 //----------------------------------------------------------------------------
 866
 867
 868 //----------------------------------------------------------------------------
 869 void vvSlicerManager::ReloadOverlay()
 870 {
 871   mOverlayReader->Update(mImage->GetNumberOfDimensions(),mOverlayComponent.c_str(),mType);
 872   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 873     mSlicers[i]->SetOverlay(mOverlayReader->GetOutput());
 874     mSlicers[i]->Render();
 875   }
 876 }
 877 //----------------------------------------------------------------------------
 878
 879
 880 //----------------------------------------------------------------------------
 881 void vvSlicerManager::ReloadVF()
 882 {
 883   mVectorReader->Update(vvImageReader::VECTORFIELD); //deletes the old images through the VF::Init() function
 884   mVF=mVectorReader->GetOutput();
 885   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 886     mSlicers[i]->SetVF(mVF);
 887     mSlicers[i]->Render();
 888   }
 889 }
 890 //----------------------------------------------------------------------------
 891
 892
 893 //----------------------------------------------------------------------------
 894 void vvSlicerManager::RemoveActor(const std::string& actor_type, int overlay_index)
 895 {
 896   if (actor_type =="overlay")
 897     mOverlayReader = NULL;
 898
 899   if (actor_type =="fusion")
 900     mFusionReader = NULL;
 901
 902   for (unsigned int i = 0; i < mSlicers.size(); i++)
 903     mSlicers[i]->RemoveActor(actor_type,overlay_index);
 904
 905   if (actor_type=="vector") {
 906     mVF=NULL;
 907     mVectorReader=NULL;
 908   }
 909 }
 910 //----------------------------------------------------------------------------
 911
 912
 913 //----------------------------------------------------------------------------
 914 void vvSlicerManager::RemoveActors()
 915 {
 916   ///This method leaks a few objects. See RemoveActor for what a
 917   ///correct implementation would look like
 918   //DS -> probably due to the reader (now released in the
 919   //RemoveActor() function. (I hope)
 920   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 921     mSlicers[i]->SetDisplayMode(0);
 922     mSlicers[i]->GetRenderer()->RemoveActor(mSlicers[i]->GetImageActor());
 923   }
 924 }
 925 //----------------------------------------------------------------------------
 926
 927
 928 //----------------------------------------------------------------------------
 929 void vvSlicerManager::UpdateInfoOnCursorPosition(int slicer)
 930 {
 931   //  int view = mSlicers[slicer]->GetSliceOrientation();
 932   //  int slice = mSlicers[slicer]->GetSlice();
 933   double x = mSlicers[slicer]->GetCursorPosition()[0];
 934   double y = mSlicers[slicer]->GetCursorPosition()[1];
 935   double z = mSlicers[slicer]->GetCursorPosition()[2];
 936   double X = (x - mSlicers[slicer]->GetInput()->GetOrigin()[0])/
 937     mSlicers[slicer]->GetInput()->GetSpacing()[0];
 938   double Y = (y - mSlicers[slicer]->GetInput()->GetOrigin()[1])/
 939     mSlicers[slicer]->GetInput()->GetSpacing()[1];
 940   double Z = (z - mSlicers[slicer]->GetInput()->GetOrigin()[2])/
 941     mSlicers[slicer]->GetInput()->GetSpacing()[2];
 942   double value = -VTK_DOUBLE_MAX;
 943   int displayVec = 0;
 944   double xVec=0, yVec=0, zVec=0, valueVec=0;
 945   int displayOver = 0;
 946   int displayFus = 0;
 947   double valueOver=0, valueFus=0;
 948   if (X >= mSlicers[slicer]->GetInput()->GetWholeExtent()[0] &&
 949       X <= mSlicers[slicer]->GetInput()->GetWholeExtent()[1] &&
 950       Y >= mSlicers[slicer]->GetInput()->GetWholeExtent()[2] &&
 951       Y <= mSlicers[slicer]->GetInput()->GetWholeExtent()[3] &&
 952       Z >= mSlicers[slicer]->GetInput()->GetWholeExtent()[4] &&
 953       Z <= mSlicers[slicer]->GetInput()->GetWholeExtent()[5]) {
 954     value = this->GetScalarComponentAsDouble(mSlicers[slicer]->GetInput(), X, Y, Z);
 955
 956     if (mSlicers[slicer]->GetVFActor() ) {
 957       displayVec = 1;
 958       unsigned int currentTime = mSlicers[slicer]->GetTSlice();
 959       vtkImageData *vf = NULL;
 960
 961       if (mSlicers[slicer]->GetVF()->GetVTKImages().size() > currentTime)
 962         vf = mSlicers[slicer]->GetVF()->GetVTKImages()[currentTime];
 963       else
 964         vf = mSlicers[slicer]->GetVF()->GetVTKImages()[0];
 965
 966       if (vf) {
 967         double Xvf = (x - vf->GetOrigin()[0])/ vf->GetSpacing()[0];
 968         double Yvf = (y - vf->GetOrigin()[1])/ vf->GetSpacing()[1];
 969         double Zvf = (z - vf->GetOrigin()[2])/ vf->GetSpacing()[2];
 970         xVec = this->GetScalarComponentAsDouble( vf, Xvf, Yvf, Zvf, 0);
 971         yVec = this->GetScalarComponentAsDouble( vf, Xvf, Yvf, Zvf, 1);
 972         zVec = this->GetScalarComponentAsDouble( vf, Xvf, Yvf, Zvf, 2);
 973         valueVec = sqrt(xVec*xVec + yVec*yVec + zVec*zVec);
 974       }
 975     }
 976     if (mSlicers[slicer]->GetOverlayActor() ) {
 977       displayOver = 1;
 978       vtkImageData *overlay = dynamic_cast<vtkImageData*>(mSlicers[slicer]->GetOverlayMapper()->GetInput());
 979       double Xover = (x - overlay->GetOrigin()[0]) / overlay->GetSpacing()[0];
 980       double Yover = (y - overlay->GetOrigin()[1]) / overlay->GetSpacing()[1];
 981       double Zover = (z - overlay->GetOrigin()[2]) / overlay->GetSpacing()[2];
 982       valueOver = this->GetScalarComponentAsDouble(overlay, Xover, Yover, Zover);
 983     }
 984     if (mSlicers[slicer]->GetFusionActor() ) {
 985       displayFus = 1;
 986       vtkImageData *fusion = dynamic_cast<vtkImageData*>(mSlicers[slicer]->GetFusionMapper()->GetInput());
 987       double Xover = (x - fusion->GetOrigin()[0]) / fusion->GetSpacing()[0];
 988       double Yover = (y - fusion->GetOrigin()[1]) / fusion->GetSpacing()[1];
 989       double Zover = (z - fusion->GetOrigin()[2]) / fusion->GetSpacing()[2];
 990       valueFus = this->GetScalarComponentAsDouble(fusion, Xover, Yover, Zover);
 991     }
 992     emit UpdatePosition(mSlicers[slicer]->GetCursorVisibility(),
 993                         x,y,z,X,Y,Z,value);
 994     emit UpdateVector(displayVec,xVec, yVec, zVec, valueVec);
 995     emit UpdateOverlay(displayOver,valueOver,value);
 996     emit UpdateFusion(displayFus,valueFus);
 997   }
 998 }
 999 //----------------------------------------------------------------------------
1000
1001
1002 //----------------------------------------------------------------------------
1003 void vvSlicerManager::Activated()
1004 {
1005   emit currentImageChanged(mId);
1006 }
1007 //----------------------------------------------------------------------------
1008
1009
1010 //----------------------------------------------------------------------------
1011 void vvSlicerManager::Picked()
1012 {
1013   emit currentPickedImageChanged(mId);
1014 }
1015 //----------------------------------------------------------------------------
1016
1017
1018 //----------------------------------------------------------------------------
1019 void vvSlicerManager::UpdateWindowLevel()
1020 {
1021   emit WindowLevelChanged();
1022 }
1023 //----------------------------------------------------------------------------
1024
1025
1026 //----------------------------------------------------------------------------
1027 void vvSlicerManager::UpdateSlice(int slicer)
1028 {
1029   if (mPreviousSlice[slicer] == mSlicers[slicer]->GetSlice()) {
1030     //DD("============= NOTHING");
1031     return;
1032   }
1033   //std::cout << "vvSlicerManager::UpdateSlice " << slicer << " " << mSlicers[slicer]->GetSlice() << std::endl;
1034   emit UpdateSlice(slicer, mSlicers[slicer]->GetSlice());
1035   mSlicers[slicer]->Render(); // DS <-- I add this, this could/must be the only Render ...
1036   mPreviousSlice[slicer] = mSlicers[slicer]->GetSlice();
1037 }
1038 //----------------------------------------------------------------------------
1039
1040
1041 //----------------------------------------------------------------------------
1042 void vvSlicerManager::UpdateTSlice(int slicer)
1043 {
1044   int slice = mSlicers[slicer]->GetSlice();
1045   int tslice = mSlicers[slicer]->GetTSlice();
1046   if (mPreviousSlice[slicer] == slice) {
1047     if (mPreviousTSlice[slicer] == tslice) {
1048       //      DD("************** NOTHING ***********");
1049       return;
1050     }
1051   }
1052   mPreviousSlice[slicer] = slice;
1053   mPreviousTSlice[slicer] = tslice;
1054   //std::cout << "vvSlicerManager::UpdateTSlice " << slicer << " " << tslice << std::endl;
1055   emit UpdateTSlice(slicer, tslice);
1056 }
1057 //----------------------------------------------------------------------------
1058
1059
1060 //----------------------------------------------------------------------------
1061 void vvSlicerManager::UpdateSliceRange(int slicer)
1062 {
1063   emit UpdateSliceRange(slicer,
1064                         mSlicers[slicer]->GetSliceRange()[0], mSlicers[slicer]->GetSliceRange()[1],
1065                         0,mSlicers[slicer]->GetTMax());
1066 }
1067 //----------------------------------------------------------------------------
1068
1069
1070 //----------------------------------------------------------------------------
1071 void vvSlicerManager::SetPreset(int preset)
1072 {
1073   //vtkLookupTable* LUT = static_cast<vtkLookupTable*>(mSlicers[0]->GetWindowLevel()->GetLookupTable());
1074   double window = mSlicers[0]->GetColorWindow();
1075   double level = mSlicers[0]->GetColorLevel();
1076
1077   std::string component_type=mImage->GetScalarTypeAsITKString();
1078   switch (preset) {
1079   case 0:
1080     double range[2];
1081     mImage->GetScalarRange(range);
1082     window = range[1] - range[0];
1083     level = (range[1] + range[0])* 0.5;
1084     break;
1085   case 1:
1086     window = 2000;
1087     level = 0;
1088     break;
1089   case 2:
1090     window = 400;
1091     level = 20;
1092     break;
1093   case 3:
1094     window = 1500;
1095     level = -500;
1096     break;
1097   case 4:
1098     window = 1000;
1099     level = 500;
1100     break;
1101   case 5:
1102     window = 1;
1103     level = 0.5;
1104     break;
1105   case 6:
1106     break;
1107   case 7:
1108     window=1.;
1109     level=0.;
1110     break;
1111   }
1112   mPreset = preset;
1113   this->SetColorWindow(window);
1114   this->SetColorLevel(level);
1115
1116   //if (LUT)
1117   //{
1118   //    SetColorMap(-1);
1119   //}
1120 }
1121 //----------------------------------------------------------------------------
1122
1123
1124 //----------------------------------------------------------------------------
1125 void vvSlicerManager::SetLocalColorWindowing(const int slicer, const bool bCtrlKey)
1126 {
1127   double min, max;
1128   int t = this->mSlicers[slicer]->GetTSlice();
1129   if(bCtrlKey && this->mSlicers[slicer]->GetFusion()) {
1130     this->mSlicers[slicer]->GetExtremasAroundMousePointer(min, max,
1131                                                           this->mSlicers[slicer]->GetFusion()->GetVTKImages()[t],
1132                                                           this->mSlicers[slicer]->GetFusion()->GetTransform());
1133     this->SetFusionWindow(max-min);
1134     this->SetFusionLevel(0.5*(min+max));
1135     this->SetColorMap(mColorMap);
1136   }
1137   else if(bCtrlKey && this->mSlicers[slicer]->GetOverlay()) {
1138     this->mSlicers[slicer]->GetExtremasAroundMousePointer(min, max,
1139                                                           this->mSlicers[slicer]->GetOverlay()->GetVTKImages()[t],
1140                                                           this->mSlicers[slicer]->GetOverlay()->GetTransform());
1141     if(this->mSlicers[slicer]->GetLinkOverlayWindowLevel()){
1142       this->SetColorWindow(max-min);
1143       this->SetColorLevel(0.5*(min+max));
1144     } else {
1145       this->SetOverlayColorWindow(max-min);
1146       this->SetOverlayColorLevel(0.5*(min+max));
1147     }
1148   }
1149   else {
1150     this->mSlicers[slicer]->GetExtremasAroundMousePointer(min, max,
1151                                                           this->mSlicers[slicer]->GetImage()->GetVTKImages()[t],
1152                                                           this->mSlicers[slicer]->GetImage()->GetTransform());
1153     this->SetColorWindow(max-min);
1154     this->SetColorLevel(0.5*(min+max));
1155     this->SetPreset(6);
1156   }
1157   this->Render();
1158   this->UpdateWindowLevel();
1159 }
1160 //----------------------------------------------------------------------------
1161
1162
1163 //----------------------------------------------------------------------------
1164 void vvSlicerManager::SetColorMap(int colormap)
1165 {
1166   double range[2];
1167   range[0] = mSlicers[0]->GetInput()->GetScalarRange()[0];
1168   range[1] = mSlicers[0]->GetInput()->GetScalarRange()[1];
1169
1170   double window = mSlicers[0]->GetWindowLevel()->GetWindow();
1171   double level = mSlicers[0]->GetWindowLevel()->GetLevel();
1172
1173   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(mSlicers[0]->GetWindowLevel()->GetLookupTable());
1174   switch (colormap) {
1175   case -1:
1176     break;
1177   case 0:
1178     LUT = NULL;
1179     break;
1180   case 1:
1181     if (LUT == NULL)
1182       LUT = vtkLookupTable::New();
1183     LUT->SetValueRange(0,1);
1184     LUT->SetSaturationRange(1,1);
1185     LUT->SetHueRange(0,0.18);
1186     break;
1187   case 2:
1188     if (LUT == NULL)
1189       LUT = vtkLookupTable::New();
1190     LUT->SetValueRange(0,1);
1191     LUT->SetSaturationRange(1,1);
1192     LUT->SetHueRange(0.4,0.80);
1193     break;
1194   case 3:
1195     if (LUT == NULL)
1196       LUT = vtkLookupTable::New();
1197     LUT->SetValueRange(0.5,1);
1198     LUT->SetSaturationRange(1,1);
1199     LUT->SetHueRange(0.666,0);
1200     break;
1201   case 4:
1202     if (LUT == NULL)
1203       LUT = vtkLookupTable::New();
1204     LUT->SetValueRange(1,1);
1205     LUT->SetSaturationRange(1,1);
1206     LUT->SetHueRange(0,1);
1207     LUT->SetAlphaRange(1, 1);
1208     break;
1209   case 5:
1210     if (LUT == NULL)
1211       LUT = vtkLookupTable::New();
1212     LUT->SetValueRange(1,1);
1213     LUT->SetSaturationRange(1,1);
1214     LUT->SetHueRange(1,0.1);
1215     //LUT->SetRampToLinear();
1216     break;
1217   }
1218   if (LUT) {
1219     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1220     LUT->Build();
1221   }
1222   vtkWindowLevelLookupTable* fusLUT = NULL;
1223   if (mSlicers[0]->GetFusion()) { // && mFusionColorMap >= 0) {
1224     fusLUT = vtkWindowLevelLookupTable::New();
1225     double fusRange [2];
1226     fusRange[0] = mFusionLevel - mFusionWindow/2;
1227     fusRange[1] = mFusionLevel + mFusionWindow/2;
1228     double* frange = mFusionReader->GetOutput()->GetVTKImages()[0]->GetScalarRange();
1229     fusLUT->SetTableRange(frange);
1230     fusLUT->SetValueRange(1,1);
1231     fusLUT->SetSaturationRange(1,1);
1232     fusLUT->SetAlphaRange(1, 1);
1233     fusLUT->SetWindow(mFusionWindow);
1234     fusLUT->SetLevel(mFusionLevel);
1235     if (mFusionColorMap == 1)
1236       fusLUT->SetHueRange(0,0.18);
1237     else if (mFusionColorMap == 2)
1238       fusLUT->SetHueRange(0.4,0.80);
1239     else if (mFusionColorMap == 3)
1240     {
1241       fusLUT->SetHueRange(0.666, 0);
1242       fusLUT->SetValueRange(0.5, 1);
1243     }
1244     else if (mFusionColorMap == 4)
1245       fusLUT->SetHueRange(0,1);
1246     else if (mFusionColorMap <= 0)
1247     {
1248       fusLUT->SetValueRange(0,1);
1249       fusLUT->SetSaturationRange(0,0);
1250     }
1251
1252     fusLUT->ForceBuild();
1253     double v[4];
1254
1255     // set color table transparency
1256     //double alpha_range=(double)mFusionThresOpacity/10;
1257     double range_end = fusRange[0] + (double)mFusionThresOpacity*(fusRange[1] - fusRange[0])/100;
1258     double curr_value = fusRange[0];
1259     int nvalues = fusLUT->GetNumberOfTableValues();
1260     for (double i = 0; curr_value < range_end; i++) {
1261       fusLUT->GetTableValue(i, v);
1262       v[3] = 0;
1263       //if (curr_value >= -alpha_range && curr_value <= alpha_range) v[3] = pow(fabs(curr_value/alpha_range),2);
1264       //else v[3] = 1;
1265       fusLUT->SetTableValue(i, v);
1266       curr_value += (fusRange[1] - fusRange[0])/nvalues;
1267     }
1268   }
1269   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
1270
1271     if (mSlicers[i]->GetOverlay()) {
1272       vtkLookupTable* supLUT = vtkLookupTable::New();
1273       supLUT->SetTableRange(range[0],range[1]);
1274       supLUT->SetValueRange(1,1);
1275       supLUT->SetSaturationRange(1,1);
1276       supLUT->SetHueRange(double(mOverlayColor)/360,double(mOverlayColor)/360);
1277       supLUT->Build();
1278       vtkLookupTable* invLUT = vtkLookupTable::New();
1279       invLUT->SetTableRange(range[0],range[1]);
1280       invLUT->SetValueRange(1,1);
1281       invLUT->SetSaturationRange(1,1);
1282       invLUT->SetHueRange(double((mOverlayColor+180)%360)/360,double((mOverlayColor+180)%360)/360);
1283       invLUT->Build();
1284       dynamic_cast<vvImageMapToWLColors*>(mSlicers[i]->GetWindowLevel())
1285         ->SetWindowLevelMode(true);
1286       mSlicers[i]->GetWindowLevel()->SetLookupTable(supLUT);
1287       mSlicers[i]->GetOverlayMapper()->SetLookupTable(invLUT);
1288       invLUT->Delete();
1289       supLUT->Delete();
1290     } else if (mSlicers[i]->GetOverlay()) {
1291       //dynamic_cast<vvImageMapToWLColors*>(mSlicers[i]->GetWindowLevel())
1292       //->SetWindowLevelMode(false);
1293       mSlicers[i]->GetWindowLevel()->SetLookupTable(LUT);
1294     } else {
1295       mSlicers[i]->GetWindowLevel()->SetLookupTable(LUT);
1296     }
1297
1298     if (mSlicers[i]->GetFusion()) {
1299       mSlicers[i]->ShowFusionLegend(mFusionShowLegend);
1300       mSlicers[i]->GetFusionMapper()->SetLookupTable(fusLUT);
1301       mSlicers[i]->GetFusionActor()->SetOpacity(double(mFusionOpacity)/100);
1302     }
1303   }
1304   if (fusLUT)
1305     fusLUT->Delete();
1306   if (colormap >= 0)
1307     mColorMap = colormap;
1308 }
1309 //----------------------------------------------------------------------------
1310
1311
1312 //----------------------------------------------------------------------------
1313 vvLandmarks* vvSlicerManager::GetLandmarks()
1314 {
1315   if (mLandmarks == NULL) {
1316     mLandmarks = new vvLandmarks(mSlicers[0]->GetTMax()+1);
1317     for (unsigned int i = 0; i < mSlicers.size(); i++)
1318       mSlicers[i]->SetLandmarks(mLandmarks);
1319   }
1320   return mLandmarks;
1321 }
1322 //----------------------------------------------------------------------------
1323
1324
1325 //----------------------------------------------------------------------------
1326 void vvSlicerManager::AddLandmark(float x,float y,float z,float t)
1327 {
1328   double x_index = (x - mSlicers[0]->GetInput()->GetOrigin()[0])/mSlicers[0]->GetInput()->GetSpacing()[0];
1329   double y_index = (y - mSlicers[0]->GetInput()->GetOrigin()[1])/mSlicers[0]->GetInput()->GetSpacing()[1];
1330   double z_index = (z - mSlicers[0]->GetInput()->GetOrigin()[2])/mSlicers[0]->GetInput()->GetSpacing()[2];
1331   if (x_index >= mSlicers[0]->GetInput()->GetWholeExtent()[0] &&
1332       x_index <= mSlicers[0]->GetInput()->GetWholeExtent()[1] &&
1333       y_index >= mSlicers[0]->GetInput()->GetWholeExtent()[2] &&
1334       y_index <= mSlicers[0]->GetInput()->GetWholeExtent()[3] &&
1335       z_index >= mSlicers[0]->GetInput()->GetWholeExtent()[4] &&
1336       z_index <= mSlicers[0]->GetInput()->GetWholeExtent()[5]) {
1337     double value = this->GetScalarComponentAsDouble(mSlicers[0]->GetInput(), x_index, y_index, z_index);
1338     this->GetLandmarks()->AddLandmark(x,y,z,t,value);
1339     emit LandmarkAdded();
1340   }
1341 }
1342 //----------------------------------------------------------------------------
1343
1344 //----------------------------------------------------------------------------
1345 void vvSlicerManager::PrevImage(int slicer)
1346 {
1347   emit ChangeImageWithIndexOffset(this, slicer, -1);
1348 }
1349 //----------------------------------------------------------------------------
1350
1351 //----------------------------------------------------------------------------
1352 void vvSlicerManager::NextImage(int slicer)
1353 {
1354   emit ChangeImageWithIndexOffset(this, slicer,  1);
1355 }
1356 //----------------------------------------------------------------------------
1357
1358 //----------------------------------------------------------------------------
1359 void vvSlicerManager::VerticalSliderHasChanged(int slicer, int slice)
1360 {
1361   emit AVerticalSliderHasChanged(slicer, slice);
1362 }
1363
1364 //----------------------------------------------------------------------------
1365
1366 //----------------------------------------------------------------------------
1367 double vvSlicerManager::GetScalarComponentAsDouble(vtkImageData *image, double X, double Y, double Z, int component)
1368 {
1369   int ix, iy, iz;
1370   return mSlicers[0]->GetScalarComponentAsDouble(image, X, Y, Z, ix, iy, iz, component);
1371 }
1372 //----------------------------------------------------------------------------