vv/vvSlicerManager.cxx

   1 /*=========================================================================
   2
   3 Program:   vv
   4 Language:  C++
   5 Author :   Pierre Seroul (pierre.seroul@gmail.com)
   6
   7 Copyright (C) 2008
   8 Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
   9 CREATIS-LRMN http://www.creatis.insa-lyon.fr
  10
  11 This program is free software: you can redistribute it and/or modify
  12 it under the terms of the GNU General Public License as published by
  13 the Free Software Foundation, version 3 of the License.
  14
  15 This program is distributed in the hope that it will be useful,
  16 but WITHOUT ANY WARRANTY; without even the implied warranty of
  17 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  18 GNU General Public License for more details.
  19
  20 You should have received a copy of the GNU General Public License
  21 along with this program.  If not, see <http://www.gnu.org/licenses/>.
  22
  23 =========================================================================*/
  24 #include "vvSlicerManager.h"
  25
  26 #include "vvSlicer.h"
  27 #include "vvImage.h"
  28 #include "vvSlicerManagerCommand.h"
  29 #include "vvInteractorStyleNavigator.h"
  30 #include "vvLandmarks.h"
  31 #include "vvImageReader.h"
  32 #include "vvImageReader.h"
  33 #include "vvMesh.h"
  34 #include "vvImageMapToWLColors.h"
  35
  36 #include "vtkImageActor.h"
  37 #include "vtkImageData.h"
  38 #include "vtkRenderWindow.h"
  39 #include "vtkRendererCollection.h"
  40 #include "vtkRenderWindowInteractor.h"
  41 #include "vtkImageMapToWindowLevelColors.h"
  42 #include "vtkWindowLevelLookupTable.h"
  43 #include "vtkColorTransferFunction.h"
  44 #include "vtkImageClip.h"
  45 #include <vtkLODActor.h>
  46 #include <vtkPointData.h>
  47
  48 #include <vtksys/SystemTools.hxx>
  49 //----------------------------------------------------------------------------
  50
  51 vvSlicerManager::vvSlicerManager(int numberOfSlicers)
  52 {
  53     mFileName = "";
  54     mId = "";
  55     mVFName = "";
  56     mOverlayName = "";
  57     mFusionName = "";
  58     mVFId = "";
  59     mLastError = "";
  60     mType = UNDEFINEDIMAGETYPE;
  61     mColorMap = 0;
  62     mPreset = 0;
  63     mOverlayColor = 130;
  64
  65     mFusionOpacity = 70;
  66     mFusionColorMap = 3;
  67     mFusionWindow = 1000;
  68     mFusionLevel = 1000;
  69
  70     mReader = NULL;
  71     mImage = NULL;
  72     mVF=NULL;
  73     mVectorReader = NULL;
  74     mOverlayReader = NULL;
  75     mFusionReader = NULL;
  76     mLandmarks = NULL;
  77     mLinkedId.resize(0);
  78
  79     for ( int i = 0; i < numberOfSlicers; i++)
  80     {
  81         vvSlicer *slicer = vvSlicer::New();
  82         mSlicers.push_back(slicer);
  83     }
  84 }
  85
  86 vvSlicerManager::~vvSlicerManager()
  87 {
  88     for ( unsigned int i = 0; i < mSlicers.size(); i++)
  89     {
  90         if (mSlicers[i] != NULL)
  91             mSlicers[i]->Delete();
  92     }
  93     if (mReader)
  94     {
  95         delete mReader;
  96     }
  97     if (mVectorReader)
  98     {
  99         delete mVectorReader;
 100     }
 101     if (mOverlayReader)
 102     {
 103         delete mOverlayReader;
 104     }
 105     if (mFusionReader)
 106     {
 107         delete mFusionReader;
 108     }
 109     if (mLandmarks)
 110         delete mLandmarks;
 111 }
 112
 113 void vvSlicerManager::AddContour(vvMesh::Pointer contour,bool propagate)
 114 {
 115     for ( unsigned int i = 0; i < mSlicers.size(); i++)
 116     {
 117         mSlicers[i]->AddContour(contour,propagate);
 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 bool vvSlicerManager::SetImage(std::string filename,LoadedImageType type)
 128 {
 129     mFileName = filename;
 130     mType = type;
 131     if (mReader == NULL)
 132         mReader = new vvImageReader;
 133     std::vector<std::string> filenames;
 134     filenames.push_back(filename);
 135     mReader->SetInputFilenames(filenames);
 136     mReader->Update(type);
 137     if (mReader->GetLastError().size() == 0)
 138     {
 139         mImage=mReader->GetOutput();
 140         for ( unsigned int i = 0; i < mSlicers.size(); i++)
 141         {
 142             mSlicers[i]->SetFileName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename));
 143             mSlicers[i]->SetImage(mReader->GetOutput());
 144         }
 145     }
 146     else
 147     {
 148         mLastError = mReader->GetLastError();
 149         return false;
 150     }
 151     return true;
 152 }
 153
 154 void vvSlicerManager::SetImage(vvImage::Pointer image)
 155 {
 156     mImage=image;
 157     for (unsigned int i = 0; i < mSlicers.size();i++)
 158     {
 159         mSlicers[i]->SetImage(image);
 160     }
 161 }
 162
 163 bool vvSlicerManager::SetImages(std::vector<std::string> filenames,LoadedImageType type)
 164 {
 165     mType = type;
 166     std::string fileWithoutExtension = vtksys::SystemTools::GetFilenameWithoutExtension(filenames[0]);
 167     if (type == DICOM)
 168         fileWithoutExtension += "_dicom";
 169     else if (type == MERGED)
 170         fileWithoutExtension += "_merged";
 171     else if (type == MERGEDWITHTIME)
 172         fileWithoutExtension += "_merged_wt";
 173
 174     mFileName = fileWithoutExtension + vtksys::SystemTools::GetFilenameExtension(filenames[0]);
 175     if (mReader == NULL)
 176         mReader = new vvImageReader;
 177     mReader->SetInputFilenames(filenames);
 178     mReader->Update(type);
 179
 180
 181     if (mReader->GetLastError().size() == 0)
 182     {
 183         mImage=mReader->GetOutput();
 184         for ( unsigned int i = 0; i < mSlicers.size(); i++)
 185         {
 186             mSlicers[i]->SetFileName(fileWithoutExtension);
 187             mSlicers[i]->SetImage(mReader->GetOutput());
 188         }
 189     }
 190     else
 191     {
 192         mLastError = mReader->GetLastError();
 193         return false;
 194     }
 195     return true;
 196 }
 197
 198 bool vvSlicerManager::SetOverlay(std::string filename,int dim, std::string component)
 199 {
 200     mOverlayName = filename;
 201     mOverlayComponent = component;
 202     if (dim > mImage->GetNumberOfDimensions())
 203     {
 204         mLastError = " Overlay dimension cannot be greater then reference image!";
 205         return false;
 206     }
 207     if (mOverlayReader == NULL)
 208         mOverlayReader = new vvImageReader;
 209     std::vector<std::string> filenames;
 210     filenames.push_back(filename);
 211     mOverlayReader->SetInputFilenames(filenames);
 212     mOverlayReader->Update(mImage->GetNumberOfDimensions(),component.c_str(),mType);
 213     if (mOverlayReader->GetLastError().size() == 0)
 214     {
 215         for ( unsigned int i = 0; i < mSlicers.size(); i++)
 216         {
 217             mSlicers[i]->SetOverlay(mOverlayReader->GetOutput());
 218         }
 219     }
 220     else
 221     {
 222         mLastError = mOverlayReader->GetLastError();
 223         return false;
 224     }
 225     return true;
 226 }
 227
 228 bool vvSlicerManager::SetFusion(std::string filename,int dim, std::string component)
 229 {
 230     mFusionName = filename;
 231     mFusionComponent = component;
 232     if (dim > mImage->GetNumberOfDimensions())
 233     {
 234         mLastError = " Overlay dimension cannot be greater then reference image!";
 235         return false;
 236     }
 237     if (mFusionReader == NULL)
 238         mFusionReader = new vvImageReader;
 239     std::vector<std::string> filenames;
 240     filenames.push_back(filename);
 241     mFusionReader->SetInputFilenames(filenames);
 242     mFusionReader->Update(mImage->GetNumberOfDimensions(),component.c_str(),mType);
 243     if (mFusionReader->GetLastError().size() == 0)
 244     {
 245         for ( unsigned int i = 0; i < mSlicers.size(); i++)
 246         {
 247             mSlicers[i]->SetFusion(mFusionReader->GetOutput());
 248         }
 249     }
 250     else
 251     {
 252         mLastError = mFusionReader->GetLastError();
 253         return false;
 254     }
 255     double *fusRange = mFusionReader->GetOutput()->GetVTKImages()[0]->GetScalarRange();
 256     mFusionLevel = (fusRange[0]+fusRange[1])/2;
 257     mFusionWindow = fusRange[1]-fusRange[0];
 258     return true;
 259 }
 260
 261 bool vvSlicerManager::SetVF(std::string filename)
 262 {
 263     if (mVectorReader == NULL)
 264         mVectorReader = new vvImageReader;
 265     mVectorReader->SetInputFilename(filename);
 266     mVectorReader->Update(VECTORFIELD);
 267     if (mVectorReader->GetLastError().size() != 0)
 268     {
 269         mLastError = mVectorReader->GetLastError();
 270         return false;
 271     }
 272     else
 273         return SetVF(mVectorReader->GetOutput(),filename);
 274 }
 275
 276 bool vvSlicerManager::SetVF(vvImage::Pointer vf,std::string filename)
 277 {
 278     if (vf->GetNumberOfDimensions() > mImage->GetNumberOfDimensions())
 279     {
 280         mLastError = " Vector field dimension cannot be greater then reference image!";
 281         return false;
 282     }
 283     mVF=vf;
 284     mVFName = filename;
 285     for ( unsigned int i = 0; i < mSlicers.size(); i++)
 286     {
 287         mSlicers[i]->SetVF(vf);
 288     }
 289     return true;
 290 }
 291
 292 void vvSlicerManager::SetExtractedImage(std::string filename,vvImage::Pointer image, int slice)
 293 {
 294     mFileName = filename;
 295     mImage = vvImage::New();
 296     if (image->GetNumberOfDimensions() == 4)
 297     {
 298         mImage->AddImage(image->GetVTKImages()[slice]);
 299         for ( unsigned int i = 0; i < mSlicers.size(); i++)
 300         {
 301             mSlicers[i]->SetFileName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename));
 302             mSlicers[i]->SetImage(mImage);
 303         }
 304     }
 305     else
 306     {
 307         vtkImageClip* clipper = vtkImageClip::New();
 308         int extent[6];
 309         image->GetVTKImages()[0]->GetWholeExtent(extent);
 310         clipper->SetInput(image->GetVTKImages()[0]);
 311         clipper->SetOutputWholeExtent(extent[0],extent[1],extent[2],extent[3],slice,slice);
 312         clipper->Update();
 313         mImage->AddImage(clipper->GetOutput());
 314         for ( unsigned int i = 0; i < mSlicers.size(); i++)
 315         {
 316             mSlicers[i]->SetFileName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename));
 317             mSlicers[i]->SetImage(mImage);
 318         }
 319         clipper->Delete();
 320     }
 321 }
 322
 323 vvSlicer* vvSlicerManager::GetSlicer(int i)
 324 {
 325     return mSlicers[i];
 326 }
 327
 328 void vvSlicerManager::UpdateSlicer(int num, bool state)
 329 {
 330     if (mSlicers[num]->GetImage())
 331             mSlicers[num]->SetDisplayMode(state);
 332 }
 333
 334 void vvSlicerManager::SetSlicerWindow(int i, vtkRenderWindow* RW)
 335 {
 336     mSlicers[i]->SetRenderWindow(i,RW);
 337 }
 338
 339 void vvSlicerManager::SetInteractorStyleNavigator(int i, vtkInteractorStyle* style)
 340 {
 341     vvSlicerManagerCallback *smc = vvSlicerManagerCallback::New();
 342     smc->SM = this;
 343     mSlicers[i]->GetRenderWindow()->GetInteractor()->SetInteractorStyle(style);
 344
 345     mSlicers[i]->GetRenderWindow()->GetInteractor()->
 346     GetInteractorStyle()->AddObserver(vtkCommand::KeyPressEvent, smc);
 347     mSlicers[i]->GetRenderWindow()->GetInteractor()->
 348     GetInteractorStyle()->AddObserver(vtkCommand::WindowLevelEvent, smc);
 349     mSlicers[i]->GetRenderWindow()->GetInteractor()->
 350     GetInteractorStyle()->AddObserver(vtkCommand::EndWindowLevelEvent, smc);
 351     mSlicers[i]->GetRenderWindow()->GetInteractor()->
 352     GetInteractorStyle()->AddObserver(vtkCommand::StartWindowLevelEvent, smc);
 353     mSlicers[i]->GetRenderWindow()->GetInteractor()->
 354     GetInteractorStyle()->AddObserver(vtkCommand::PickEvent, smc);
 355     mSlicers[i]->GetRenderWindow()->GetInteractor()->
 356     GetInteractorStyle()->AddObserver(vtkCommand::StartPickEvent, smc);
 357     mSlicers[i]->GetRenderWindow()->GetInteractor()->
 358     GetInteractorStyle()->AddObserver(vtkCommand::LeaveEvent, smc);
 359     mSlicers[i]->GetRenderWindow()->GetInteractor()->
 360     GetInteractorStyle()->AddObserver(vtkCommand::UserEvent, smc);
 361     mSlicers[i]->GetRenderWindow()->GetInteractor()->
 362     GetInteractorStyle()->AddObserver(vtkCommand::MouseWheelForwardEvent, smc);
 363     mSlicers[i]->GetRenderWindow()->GetInteractor()->
 364     GetInteractorStyle()->AddObserver(vtkCommand::MouseWheelBackwardEvent, smc);
 365     smc->Delete();
 366 }
 367
 368 void vvSlicerManager::SetTSlice(int slice)
 369 {
 370     if (slice < 0)
 371         slice = 0;
 372     else if (slice > mSlicers[0]->GetTMax())
 373         slice = mSlicers[0]->GetTMax();
 374     if (mLandmarks)
 375         mLandmarks->SetTime(slice);
 376     for ( unsigned int i = 0; i < mSlicers.size(); i++)
 377     {
 378         mSlicers[i]->SetTSlice(slice);
 379         if (mSlicers[i]->GetImageActor()->GetVisibility())
 380             UpdateTSlice(i);
 381     }
 382 }
 383
 384 void vvSlicerManager::SetNextTSlice(int originating_slicer)
 385 {
 386     int t = mSlicers[0]->GetTSlice();
 387     t++;
 388     if (t > mSlicers[0]->GetTMax())
 389         t = 0;
 390     emit UpdateTSlice(originating_slicer,t);
 391 }
 392
 393 void vvSlicerManager::SetPreviousTSlice(int originating_slicer)
 394 {
 395     int t = mSlicers[0]->GetTSlice();
 396     t--;
 397     if (t < 0)
 398         t = mSlicers[0]->GetTMax();
 399     emit UpdateTSlice(originating_slicer,t);
 400 }
 401
 402 void vvSlicerManager::ToggleInterpolation()
 403 {
 404     bool interpolate=!(mSlicers[0]->GetImageActor()->GetInterpolate());
 405     for ( unsigned int i = 0; i < mSlicers.size(); i++)
 406     {
 407         mSlicers[i]->GetImageActor()->SetInterpolate(interpolate);
 408     }
 409 }
 410
 411
 412 void vvSlicerManager::SetTSliceInSlicer(int tslice, int slicer)
 413 {
 414     if (tslice < 0)
 415         tslice = 0;
 416     else if (tslice > mSlicers[slicer]->GetTMax())
 417         tslice = mSlicers[slicer]->GetTMax();
 418     if (mLandmarks)
 419         mLandmarks->SetTime(tslice);
 420     mSlicers[slicer]->SetTSlice(tslice);
 421     if (mSlicers[slicer]->GetImageActor()->GetVisibility())
 422         UpdateTSlice(slicer);
 423 }
 424
 425 void vvSlicerManager::SetColorWindow(double s)
 426 {
 427     for ( unsigned int i = 0; i < mSlicers.size(); i++)
 428     {
 429         mSlicers[i]->SetColorWindow(s);
 430     }
 431 }
 432
 433 void vvSlicerManager::SetColorLevel(double s)
 434 {
 435     for ( unsigned int i = 0; i < mSlicers.size(); i++)
 436     {
 437         mSlicers[i]->SetColorLevel(s);
 438     }
 439 }
 440
 441 void vvSlicerManager::SetCursorVisibility(int s)
 442 {
 443     for ( unsigned int i = 0; i < mSlicers.size(); i++)
 444     {
 445         mSlicers[i]->SetCursorVisibility(s);
 446     }
 447 }
 448
 449 void vvSlicerManager::SetOpacity(int i, double factor)
 450 {
 451     mSlicers[i]->SetOpacity(1/factor);
 452 }
 453
 454 void vvSlicerManager::UpdateViews(int current,int slicer)
 455 {
 456     double x = (mSlicers[slicer]->GetCurrentPosition()[0] - mSlicers[slicer]->GetInput()->GetOrigin()[0])
 457                /mSlicers[slicer]->GetInput()->GetSpacing()[0];
 458     double y = (mSlicers[slicer]->GetCurrentPosition()[1] - mSlicers[slicer]->GetInput()->GetOrigin()[1])
 459                /mSlicers[slicer]->GetInput()->GetSpacing()[1];
 460     double z = (mSlicers[slicer]->GetCurrentPosition()[2] - mSlicers[slicer]->GetInput()->GetOrigin()[2])
 461                /mSlicers[slicer]->GetInput()->GetSpacing()[2];
 462
 463     if (x >= mSlicers[slicer]->GetInput()->GetWholeExtent()[0] &&
 464             x <= mSlicers[slicer]->GetInput()->GetWholeExtent()[1] &&
 465             y >= mSlicers[slicer]->GetInput()->GetWholeExtent()[2] &&
 466             y <= mSlicers[slicer]->GetInput()->GetWholeExtent()[3] &&
 467             z >= mSlicers[slicer]->GetInput()->GetWholeExtent()[4] &&
 468             z <= mSlicers[slicer]->GetInput()->GetWholeExtent()[5])
 469     {
 470         mSlicers[slicer]->UpdateCursorPosition();
 471         mSlicers[slicer]->SetCursorColor(10,212,255);
 472
 473         switch (mSlicers[slicer]->GetSliceOrientation())
 474         {
 475         case vtkImageViewer2::SLICE_ORIENTATION_XY:
 476             if (mSlicers[slicer]->GetSlice() == (int)floor(z))
 477                 mSlicers[slicer]->Render();
 478             else
 479                 mSlicers[slicer]->SetSlice((int)floor(z));
 480             break;
 481
 482         case vtkImageViewer2::SLICE_ORIENTATION_XZ:
 483             if (mSlicers[slicer]->GetSlice() == (int)floor(y))
 484                 mSlicers[slicer]->Render();
 485             else
 486                 mSlicers[slicer]->SetSlice((int)floor(y));
 487             break;
 488
 489         case vtkImageViewer2::SLICE_ORIENTATION_YZ:
 490             if (mSlicers[slicer]->GetSlice() == (int)floor(x))
 491                 mSlicers[slicer]->Render();
 492             else
 493                 mSlicers[slicer]->SetSlice((int)floor(x));
 494             break;
 495         }
 496
 497         for ( unsigned int i = 0; i < mSlicers.size(); i++)
 498         {
 499             if (i != (unsigned int)slicer && mSlicers[i]->GetImageActor()->GetVisibility()
 500                     && mSlicers[i]->GetRenderWindow()->GetSize()[0] > 2
 501                     && mSlicers[i]->GetRenderWindow()->GetSize()[1] > 2)
 502             {
 503                 mSlicers[i]->SetCurrentPosition(mSlicers[slicer]->GetCurrentPosition()[0],
 504                                                 mSlicers[slicer]->GetCurrentPosition()[1],
 505                                                 mSlicers[slicer]->GetCurrentPosition()[2],
 506                                                 mSlicers[slicer]->GetTSlice());
 507                 mSlicers[i]->UpdateCursorPosition();
 508                 if (current) //do not display corner annotation if image is the one picked
 509                 {
 510                     mSlicers[i]->SetCurrentPosition(-VTK_DOUBLE_MAX,-VTK_DOUBLE_MAX,
 511                                                     -VTK_DOUBLE_MAX, mSlicers[slicer]->GetTSlice());
 512                     mSlicers[i]->SetCursorColor(255,10,212);
 513                 }
 514                 else
 515                 {
 516                     mSlicers[i]->SetCursorColor(150,10,282);
 517                 }
 518                 switch (mSlicers[i]->GetSliceOrientation())
 519                 {
 520                 case vtkImageViewer2::SLICE_ORIENTATION_XY:
 521                     if (mSlicers[i]->GetSlice() == (int)floor(z))
 522                         mSlicers[i]->Render();
 523                     else
 524                         mSlicers[i]->SetSlice((int)floor(z));
 525                     break;
 526
 527                 case vtkImageViewer2::SLICE_ORIENTATION_XZ:
 528                     if (mSlicers[i]->GetSlice() == (int)floor(y))
 529                         mSlicers[i]->Render();
 530                     else
 531                         mSlicers[i]->SetSlice((int)floor(y));
 532                     break;
 533
 534                 case vtkImageViewer2::SLICE_ORIENTATION_YZ:
 535                     if (mSlicers[i]->GetSlice() == (int)floor(x))
 536                         mSlicers[i]->Render();
 537                     else
 538                         mSlicers[i]->SetSlice((int)floor(x));
 539                     break;
 540                 }
 541                 UpdateSlice(i);
 542                 UpdateTSlice(i);
 543             }
 544         }
 545     }
 546 }
 547
 548 void vvSlicerManager::UpdateLinked(int slicer)
 549 {
 550     double x = (mSlicers[slicer]->GetCurrentPosition()[0] - mSlicers[slicer]->GetInput()->GetOrigin()[0])
 551                /mSlicers[slicer]->GetInput()->GetSpacing()[0];
 552     double y = (mSlicers[slicer]->GetCurrentPosition()[1] - mSlicers[slicer]->GetInput()->GetOrigin()[1])
 553                /mSlicers[slicer]->GetInput()->GetSpacing()[1];
 554     double z = (mSlicers[slicer]->GetCurrentPosition()[2] - mSlicers[slicer]->GetInput()->GetOrigin()[2])
 555                /mSlicers[slicer]->GetInput()->GetSpacing()[2];
 556
 557     if (x >= mSlicers[slicer]->GetInput()->GetWholeExtent()[0] &&
 558             x <= mSlicers[slicer]->GetInput()->GetWholeExtent()[1] &&
 559             y >= mSlicers[slicer]->GetInput()->GetWholeExtent()[2] &&
 560             y <= mSlicers[slicer]->GetInput()->GetWholeExtent()[3] &&
 561             z >= mSlicers[slicer]->GetInput()->GetWholeExtent()[4] &&
 562             z <= mSlicers[slicer]->GetInput()->GetWholeExtent()[5])
 563     {
 564         for (std::list<std::string>::const_iterator i = mLinkedId.begin(); i != mLinkedId.end(); i++)
 565         {
 566             emit UpdateLinkManager(*i, slicer,mSlicers[slicer]->GetCurrentPosition()[0],
 567                                    mSlicers[slicer]->GetCurrentPosition()[1],
 568                                    mSlicers[slicer]->GetCurrentPosition()[2],mSlicers[slicer]->GetTSlice());
 569         }
 570     }
 571 }
 572 double vvSlicerManager::GetColorWindow()
 573 {
 574     if (mSlicers.size())
 575         return mSlicers[0]->GetColorWindow();
 576     return -1;
 577 }
 578
 579 double vvSlicerManager::GetColorLevel()
 580 {
 581     if (mSlicers.size())
 582         return mSlicers[0]->GetColorLevel();
 583     return -1;
 584 }
 585
 586 void vvSlicerManager::Render()
 587 {
 588     for ( unsigned int i = 0; i < mSlicers.size(); i++)
 589     {
 590         mSlicers[i]->Render();
 591     }
 592 }
 593
 594 void vvSlicerManager::GenerateDefaultLookupTable()
 595 {
 596     SetPreset(mPreset);
 597     SetColorMap(mColorMap);
 598 }
 599
 600 void vvSlicerManager::Reload()
 601 {
 602     mReader->Update(mType);
 603     mImage=mReader->GetOutput();
 604     for ( unsigned int i = 0; i < mSlicers.size(); i++)
 605     {
 606         mSlicers[i]->SetImage(mImage);
 607     }
 608 }
 609
 610 void vvSlicerManager::ReloadFusion()
 611 {
 612     mFusionReader->Update();
 613     for ( unsigned int i = 0; i < mSlicers.size(); i++)
 614     {
 615         mSlicers[i]->SetFusion(mFusionReader->GetOutput());
 616         mSlicers[i]->Render();
 617     }
 618 }
 619
 620 void vvSlicerManager::ReloadOverlay()
 621 {
 622     mOverlayReader->Update();
 623     for ( unsigned int i = 0; i < mSlicers.size(); i++)
 624     {
 625         mSlicers[i]->SetOverlay(mOverlayReader->GetOutput());
 626         mSlicers[i]->Render();
 627     }
 628 }
 629
 630 void vvSlicerManager::ReloadVF()
 631 {
 632     mVectorReader->Update(VECTORFIELD); //deletes the old images through the VF::Init() function
 633     mVF=mVectorReader->GetOutput();
 634     for ( unsigned int i = 0; i < mSlicers.size(); i++)
 635     {
 636         mSlicers[i]->SetVF(mVF);
 637         mSlicers[i]->Render();
 638     }
 639 }
 640
 641 void vvSlicerManager::RemoveActor(const std::string& actor_type, int overlay_index)
 642 {
 643     for (unsigned int i = 0; i < mSlicers.size();i++)
 644     {
 645         mSlicers[i]->RemoveActor(actor_type,overlay_index);
 646     }
 647     if (actor_type=="vector")
 648     {
 649         mVF=NULL;
 650         if (mVectorReader) {
 651             delete mVectorReader;
 652             mVectorReader=NULL;
 653         }
 654     }
 655 }
 656
 657 void vvSlicerManager::RemoveActors()
 658 {
 659     ///This method leaks a few objects. See RemoveActor for what a correct implementation would look like
 660     for ( unsigned int i = 0; i < mSlicers.size(); i++)
 661     {
 662         mSlicers[i]->SetDisplayMode(0);
 663         mSlicers[i]->GetRenderer()->RemoveActor(mSlicers[i]->GetImageActor());
 664     }
 665 }
 666
 667 void vvSlicerManager::UpdateInfoOnCursorPosition(int slicer)
 668 {
 669 //  int view = mSlicers[slicer]->GetSliceOrientation();
 670 //  int slice = mSlicers[slicer]->GetSlice();
 671     double x = mSlicers[slicer]->GetCursorPosition()[0];
 672     double y = mSlicers[slicer]->GetCursorPosition()[1];
 673     double z = mSlicers[slicer]->GetCursorPosition()[2];
 674     double X = (x - mSlicers[slicer]->GetInput()->GetOrigin()[0])/
 675         mSlicers[slicer]->GetInput()->GetSpacing()[0];
 676     double Y = (y - mSlicers[slicer]->GetInput()->GetOrigin()[1])/
 677         mSlicers[slicer]->GetInput()->GetSpacing()[1];
 678     double Z = (z - mSlicers[slicer]->GetInput()->GetOrigin()[2])/
 679         mSlicers[slicer]->GetInput()->GetSpacing()[2];
 680     double value = -VTK_DOUBLE_MAX;
 681     int displayVec = 0;
 682     double xVec=0, yVec=0, zVec=0, valueVec=0;
 683     int displayOver = 0;
 684     int displayFus = 0;
 685     double valueOver=0, valueFus=0;
 686     if (X >= mSlicers[slicer]->GetInput()->GetWholeExtent()[0] &&
 687             X <= mSlicers[slicer]->GetInput()->GetWholeExtent()[1] &&
 688             Y >= mSlicers[slicer]->GetInput()->GetWholeExtent()[2] &&
 689             Y <= mSlicers[slicer]->GetInput()->GetWholeExtent()[3] &&
 690             Z >= mSlicers[slicer]->GetInput()->GetWholeExtent()[4] &&
 691             Z <= mSlicers[slicer]->GetInput()->GetWholeExtent()[5])
 692     {
 693         value = mSlicers[slicer]->GetInput()->GetScalarComponentAsDouble(
 694                 (int)floor(X),
 695                 (int)floor(Y),
 696                 (int)floor(Z),0);
 697         if (mSlicers[slicer]->GetVFActor() && mSlicers[slicer]->GetVFActor()->GetVisibility())
 698         {
 699             displayVec = 1;
 700             unsigned int currentTime = mSlicers[slicer]->GetTSlice();
 701             vtkImageData *vf = NULL;
 702
 703             if (mSlicers[slicer]->GetVF()->GetVTKImages().size() > currentTime)
 704                 vf = mSlicers[slicer]->GetVF()->GetVTKImages()[currentTime];
 705             else
 706                 vf = mSlicers[slicer]->GetVF()->GetVTKImages()[0];
 707
 708             if (vf)
 709             {
 710                 double Xvf = (x - vf->GetOrigin()[0])/ vf->GetSpacing()[0];
 711                 double Yvf = (y - vf->GetOrigin()[1])/ vf->GetSpacing()[1];
 712                 double Zvf = (z - vf->GetOrigin()[2])/ vf->GetSpacing()[2];
 713                 xVec = vf->GetScalarComponentAsDouble( (int)floor(Xvf), (int)floor(Yvf), (int)floor(Zvf),0);
 714                 yVec = vf->GetScalarComponentAsDouble( (int)floor(Xvf), (int)floor(Yvf), (int)floor(Zvf),1);
 715                 zVec = vf->GetScalarComponentAsDouble( (int)floor(Xvf), (int)floor(Yvf), (int)floor(Zvf),2);
 716                 valueVec = sqrt(xVec*xVec + yVec*yVec + zVec*zVec);
 717             }
 718         }
 719         if (mSlicers[slicer]->GetOverlayActor() && mSlicers[slicer]->GetOverlayActor()->GetVisibility())
 720         {
 721             displayOver = 1;
 722             double Xover = (x - mSlicers[slicer]->GetOverlay()->GetOrigin()[0])
 723                 /mSlicers[slicer]->GetOverlay()->GetSpacing()[0];
 724             double Yover = (y - mSlicers[slicer]->GetOverlay()->GetOrigin()[1])
 725                 /mSlicers[slicer]->GetOverlay()->GetSpacing()[1];
 726             double Zover = (z - mSlicers[slicer]->GetOverlay()->GetOrigin()[2])
 727                 /mSlicers[slicer]->GetOverlay()->GetSpacing()[2];
 728             if (Xover >= mSlicers[slicer]->GetOverlayMapper()->GetInput()->GetWholeExtent()[0] &&
 729                     Xover <= mSlicers[slicer]->GetOverlayMapper()->GetInput()->GetWholeExtent()[1] &&
 730                     Yover >= mSlicers[slicer]->GetOverlayMapper()->GetInput()->GetWholeExtent()[2] &&
 731                     Yover <= mSlicers[slicer]->GetOverlayMapper()->GetInput()->GetWholeExtent()[3] &&
 732                     Zover >= mSlicers[slicer]->GetOverlayMapper()->GetInput()->GetWholeExtent()[4] &&
 733                     Zover <= mSlicers[slicer]->GetOverlayMapper()->GetInput()->GetWholeExtent()[5])
 734             {
 735                 valueOver = static_cast<vtkImageData*>(mSlicers[slicer]->GetOverlayMapper()->GetInput())->
 736                     GetScalarComponentAsDouble(
 737                             (int)floor(Xover),
 738                             (int)floor(Yover),
 739                             (int)floor(Zover),0);
 740             }
 741         }
 742         if (mSlicers[slicer]->GetFusionActor() && mSlicers[slicer]->GetFusionActor()->GetVisibility())
 743         {
 744             displayFus = 1;
 745             double Xfus = (x - mSlicers[slicer]->GetFusion()->GetOrigin()[0])
 746                 /mSlicers[slicer]->GetFusion()->GetSpacing()[0];
 747             double Yfus = (y - mSlicers[slicer]->GetFusion()->GetOrigin()[1])
 748                 /mSlicers[slicer]->GetFusion()->GetSpacing()[1];
 749             double Zfus = (z - mSlicers[slicer]->GetFusion()->GetOrigin()[2])
 750                 /mSlicers[slicer]->GetFusion()->GetSpacing()[2];
 751             if (Xfus >= mSlicers[slicer]->GetFusionMapper()->GetInput()->GetWholeExtent()[0] &&
 752                     Xfus <= mSlicers[slicer]->GetFusionMapper()->GetInput()->GetWholeExtent()[1] &&
 753                     Yfus >= mSlicers[slicer]->GetFusionMapper()->GetInput()->GetWholeExtent()[2] &&
 754                     Yfus <= mSlicers[slicer]->GetFusionMapper()->GetInput()->GetWholeExtent()[3] &&
 755                     Zfus >= mSlicers[slicer]->GetFusionMapper()->GetInput()->GetWholeExtent()[4] &&
 756                     Zfus <= mSlicers[slicer]->GetFusionMapper()->GetInput()->GetWholeExtent()[5])
 757             {
 758                 valueFus = static_cast<vtkImageData*>(mSlicers[slicer]->GetFusionMapper()->GetInput())->
 759                     GetScalarComponentAsDouble(
 760                             (int)floor(Xfus),
 761                             (int)floor(Yfus),
 762                             (int)floor(Zfus),0);
 763             }
 764         }
 765         emit UpdatePosition(mSlicers[slicer]->GetCursorVisibility(),
 766                 x,y,z,X,Y,Z,value);
 767         emit UpdateVector(displayVec,xVec, yVec, zVec, valueVec);
 768         emit UpdateOverlay(displayOver,valueOver,value);
 769         emit UpdateFusion(displayFus,valueFus);
 770         for (unsigned int i = 0; i < mSlicers.size(); i++)
 771         {
 772             if (mSlicers[i]->GetImageActor()->GetVisibility() == 1)
 773                 emit UpdateWindows(i,mSlicers[i]->GetSliceOrientation(),mSlicers[i]->GetSlice());
 774             else
 775                 emit UpdateWindows(i,-1,-1);
 776         }
 777     }
 778 }
 779
 780 void vvSlicerManager::Activated()
 781 {
 782     emit currentImageChanged(mId);
 783 }
 784
 785 void vvSlicerManager::UpdateWindowLevel()
 786 {
 787     emit WindowLevelChanged(mSlicers[0]->GetColorWindow(),mSlicers[0]->GetColorLevel(),mPreset,mColorMap);
 788 }
 789
 790 void vvSlicerManager::UpdateSlice(int slicer)
 791 {
 792     emit UpdateSlice(slicer, mSlicers[slicer]->GetSlice());
 793 }
 794
 795 void vvSlicerManager::UpdateTSlice(int slicer)
 796 {
 797     emit UpdateTSlice(slicer,mSlicers[0]->GetTSlice());
 798 }
 799
 800 void vvSlicerManager::UpdateSliceRange(int slicer)
 801 {
 802     emit UpdateSliceRange(slicer,
 803                           mSlicers[slicer]->GetSliceRange()[0], mSlicers[slicer]->GetSliceRange()[1],
 804                           0,mSlicers[slicer]->GetTMax());
 805 }
 806
 807 void vvSlicerManager::SetPreset(int preset)
 808 {
 809     double range[2];
 810     mImage->GetScalarRange(range);
 811     //vtkLookupTable* LUT = static_cast<vtkLookupTable*>(mSlicers[0]->GetWindowLevel()->GetLookupTable());
 812     double window = mSlicers[0]->GetColorWindow();
 813     double level = mSlicers[0]->GetColorLevel();
 814
 815     std::string component_type=mImage->GetScalarTypeAsString();
 816     switch (preset)
 817     {
 818     case 0:
 819         if (component_type == "unsigned_char")
 820         {
 821             window = 255;
 822             level = 127;
 823         }
 824         else if (component_type == "short")
 825         {
 826             window = 2000;
 827             level = 0;
 828         }
 829         else
 830         {
 831             window = range[1] - range[0];
 832             level = (range[1] + range[0])* 0.5;
 833         }
 834         break;
 835     case 1:
 836         window = 2000;
 837         level = 0;
 838         break;
 839     case 2:
 840         window = 350;
 841         level = 60;
 842         break;
 843     case 3:
 844         window = 1500;
 845         level = -500;
 846         break;
 847     case 4:
 848         window = 1000;
 849         level = 500;
 850         break;
 851     case 5:
 852         window = 1;
 853         level = 0.5;
 854         break;
 855     case 6:
 856         break;
 857     case 7:
 858         window=1.;
 859         level=1;
 860         break;
 861     }
 862     mPreset = preset;
 863     this->SetColorWindow(window);
 864     this->SetColorLevel(level);
 865
 866     //if (LUT)
 867     //{
 868     //    SetColorMap(-1);
 869     //}
 870 }
 871 void vvSlicerManager::SetColorMap()
 872 {
 873     SetColorMap(mColorMap);
 874 }
 875
 876 void vvSlicerManager::SetColorMap(int colormap)
 877 {
 878     double range[2];
 879     range[0] = mSlicers[0]->GetInput()->GetScalarRange()[0];
 880     range[1] = mSlicers[0]->GetInput()->GetScalarRange()[1];
 881
 882     double window = mSlicers[0]->GetWindowLevel()->GetWindow();
 883     double level = mSlicers[0]->GetWindowLevel()->GetLevel();
 884
 885     vtkLookupTable* LUT = static_cast<vtkLookupTable*>(mSlicers[0]->GetWindowLevel()->GetLookupTable());
 886     switch (colormap)
 887     {
 888     case -1:
 889         if (LUT)
 890             LUT->SetTableRange(level-fabs(window)/4,level+fabs(window)/4);
 891         break;
 892     case 0:
 893         LUT = NULL;
 894         break;
 895     case 1:
 896         if (LUT == NULL)
 897             LUT = vtkLookupTable::New();
 898         LUT->SetTableRange(level-fabs(window)/4,level+fabs(window)/4);
 899         LUT->SetValueRange(0,1);
 900         LUT->SetSaturationRange(1,1);
 901         LUT->SetHueRange(0,0.18);
 902         break;
 903     case 2:
 904         if (LUT == NULL)
 905             LUT = vtkLookupTable::New();
 906         LUT->SetTableRange(level-fabs(window)/4,level+fabs(window)/4);
 907         LUT->SetValueRange(0,1);
 908         LUT->SetSaturationRange(1,1);
 909         LUT->SetHueRange(0.4,0.80);
 910         break;
 911     case 3:
 912         if (LUT == NULL)
 913             LUT = vtkLookupTable::New();
 914         LUT->SetTableRange(level-fabs(window)/4,level+fabs(window)/4);
 915         LUT->SetValueRange(0,1);
 916         LUT->SetSaturationRange(1,1);
 917         LUT->SetHueRange(0,1);
 918         break;
 919     case 5:
 920         if (LUT == NULL)
 921             LUT = vtkLookupTable::New();
 922         LUT->SetValueRange(0.,1);
 923         LUT->SetSaturationRange(1,1);
 924         LUT->SetHueRange(1,0.1);
 925         //LUT->SetRampToLinear();
 926         break;
 927     }
 928     if (LUT)
 929         LUT->Build();
 930     vtkLookupTable* fusLUT = NULL;
 931     if (mSlicers[0]->GetFusion())
 932     {
 933         fusLUT = vtkLookupTable::New();
 934         double fusRange [2];
 935         fusRange[0] = mFusionLevel - mFusionWindow/2;
 936         fusRange[1] = mFusionLevel + mFusionWindow/2;
 937         fusLUT->SetTableRange(fusRange[0],fusRange[1]);
 938         fusLUT->SetValueRange(1,1);
 939         fusLUT->SetSaturationRange(1,1);
 940         if (mFusionColorMap == 1)
 941             fusLUT->SetHueRange(0,0.18);
 942         else if (mFusionColorMap == 2)
 943             fusLUT->SetHueRange(0.4,0.80);
 944         else if (mFusionColorMap == 3)
 945             fusLUT->SetHueRange(0,1);
 946         fusLUT->Build();
 947         if (mFusionColorMap == 0)
 948             fusLUT = NULL;
 949     }
 950     for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 951         if (mSlicers[i]->GetOverlay() && mSlicers[i]->GetOverlayActor()->GetVisibility()) {
 952             vtkLookupTable* supLUT = vtkLookupTable::New();
 953             supLUT->SetTableRange(range[0],range[1]);
 954             supLUT->SetValueRange(1,1);
 955             supLUT->SetSaturationRange(1,1);
 956             supLUT->SetHueRange(double(mOverlayColor)/360,double(mOverlayColor)/360);
 957             supLUT->Build();
 958             vtkLookupTable* invLUT = vtkLookupTable::New();
 959             invLUT->SetTableRange(range[0],range[1]);
 960             invLUT->SetValueRange(1,1);
 961             invLUT->SetSaturationRange(1,1);
 962             invLUT->SetHueRange(double((mOverlayColor+180)%360)/360,double((mOverlayColor+180)%360)/360);
 963             invLUT->Build();
 964             dynamic_cast<vvImageMapToWLColors*>(mSlicers[i]->GetWindowLevel())
 965                 ->SetWindowLevelMode(true);
 966             mSlicers[i]->GetWindowLevel()->SetLookupTable(supLUT);
 967             mSlicers[i]->GetOverlayMapper()->SetLookupTable(invLUT);
 968             invLUT->Delete();
 969             supLUT->Delete();
 970         }
 971         else if (mSlicers[i]->GetOverlay())
 972         {
 973             //dynamic_cast<vvImageMapToWLColors*>(mSlicers[i]->GetWindowLevel())
 974                 //->SetWindowLevelMode(false);
 975             mSlicers[i]->GetWindowLevel()->SetLookupTable(LUT);
 976         }
 977         else
 978         {
 979             mSlicers[i]->GetWindowLevel()->SetLookupTable(LUT);
 980         }
 981         if (mSlicers[i]->GetFusion() && mSlicers[i]->GetFusionActor()->GetVisibility())
 982         {
 983             mSlicers[i]->GetFusionActor()->SetOpacity(double(mFusionOpacity)/100);
 984             mSlicers[i]->GetFusionMapper()->SetLookupTable(fusLUT);
 985         }
 986     }
 987     if (fusLUT)
 988         fusLUT->Delete();
 989     if (colormap >= 0)
 990         mColorMap = colormap;
 991 }
 992
 993 vvLandmarks* vvSlicerManager::GetLandmarks()
 994 {
 995     if (mLandmarks == NULL)
 996     {
 997         mLandmarks = new vvLandmarks(mSlicers[0]->GetTMax()+1);
 998         for (unsigned int i = 0; i < mSlicers.size(); i++)
 999             mSlicers[i]->SetLandmarks(mLandmarks);
1000     }
1001     return mLandmarks;
1002 }
1003
1004 void vvSlicerManager::AddLandmark(float x,float y,float z,float t)
1005 {
1006     double x_index = (x - mSlicers[0]->GetInput()->GetOrigin()[0])/mSlicers[0]->GetInput()->GetSpacing()[0];
1007     double y_index = (y - mSlicers[0]->GetInput()->GetOrigin()[1])/mSlicers[0]->GetInput()->GetSpacing()[1];
1008     double z_index = (z - mSlicers[0]->GetInput()->GetOrigin()[2])/mSlicers[0]->GetInput()->GetSpacing()[2];
1009     double value = mSlicers[0]->GetInput()->GetScalarComponentAsDouble(
1010             (int)x_index,
1011             (int)y_index,
1012             (int)z_index,0);
1013     this->GetLandmarks()->AddLandmark(x,y,z,t,value);
1014     emit LandmarkAdded();
1015 }