vv/vvSegmentationDialog.cxx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://www.centreleonberard.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17 ===========================================================================**/
  18 #ifndef _vvSegmentationDialog_CXX
  19 #define _vvSegmentationDialog_CXX
  20 #include <QtGui>
  21 #include <Qt>
  22
  23 #include "vvSegmentationDialog.h"
  24 #include "vvProgressDialog.h"
  25 #include "vvImageWriter.h"
  26 #include "vvLandmarks.h"
  27 #include "vvInteractorStyleNavigator.h"
  28 #include "vvSlicer.h"
  29
  30 #include <vtkVersion.h>
  31 #include <vtkStreamingDemandDrivenPipeline.h>
  32 #include <vtkInformation.h>
  33 #include "vtkMarchingCubes.h"
  34 #include "vtkMarchingSquares.h"
  35 #include "vtkImageClip.h"
  36 #include "vtkCamera.h"
  37 #include "vtkRenderer.h"
  38 #include "vtkProperty.h"
  39 #include "vtkLookupTable.h"
  40 #include "vtkClipPolyData.h"
  41 #include "vtkImageToPolyDataFilter.h"
  42 #include "vtkLookupTable.h"
  43 #include "vtkDoubleArray.h"
  44 #include "vtkPointData.h"
  45 #include "vtkCellData.h"
  46 #include "vtkImageMapToWindowLevelColors.h"
  47 #include "vtkImageContinuousErode3D.h"
  48 #include "vtkImageContinuousDilate3D.h"
  49 #include "vtkImageLogic.h"
  50 #include "vtkInteractorStyleTrackballCamera.h"
  51 #include "vtkImageSeedConnectivity.h"
  52 #include "vtkConnectivityFilter.h"
  53 #include "vtkPolyData.h"
  54 #include <vtkPolyDataMapper.h>
  55 #include <vtkImageData.h>
  56 #include "vtkInformation.h"
  57 #include "vtkInformationVector.h"
  58 #include "vtkStreamingDemandDrivenPipeline.h"
  59 #include <vtkPolyDataWriter.h>
  60
  61 #include <QMessageBox>
  62 #include <QFileDialog>
  63
  64 //====================================================================
  65 vvSegmentationDialog::vvSegmentationDialog(QWidget * parent, Qt::WindowFlags f)
  66   :QDialog(parent,f), Ui::vvSegmentationDialog()
  67 {
  68
  69   // initialization
  70   setupUi(this);
  71   mManager = new vvSlicerManager(1);
  72
  73   mClipper = vtkImageClip::New();
  74   mSquares1 = vtkMarchingSquares::New();
  75   mSquaresMapper1 = vtkPolyDataMapper::New();
  76   mSquaresActor1 = vtkActor::New();
  77
  78   mSquares2 = vtkMarchingSquares::New();
  79   mSquaresMapper2 = vtkPolyDataMapper::New();
  80   mSquaresActor2 = vtkActor::New();
  81
  82   //m3DMapper = vtkPolyDataMapper::New();
  83   //m3DActor = vtkActor::New();
  84   m3DExtractor = vtkMarchingCubes::New();
  85   m3DExtractor->ComputeScalarsOff();
  86   m3DMappers.clear();
  87   m3DActors.clear();
  88
  89   mBinaireImages.clear();
  90   mKernelValue = 2;
  91
  92   connect(clipping1Slider,SIGNAL(valueChanged(int)),this,SLOT(clippingvaluechanged(int)));
  93   connect(clipping2Slider,SIGNAL(valueChanged(int)),this,SLOT(clippingvaluechanged(int)));
  94   connect(binaryButton,SIGNAL(clicked()),this,SLOT(BinariseSurface()));
  95   connect(saveButton,SIGNAL(clicked()),this,SLOT(Save()));
  96   connect(erodeButton,SIGNAL(clicked()),this,SLOT(Erode()));
  97   connect(dilateButton,SIGNAL(clicked()),this,SLOT(Dilate()));
  98   connect(dimButton,SIGNAL(clicked()),this,SLOT(ChangeDimRendering()));
  99   connect(kernelSpinBox,SIGNAL(valueChanged(int)),this,SLOT(KernelValueChanged(int)));
 100
 101   binaryButton->setEnabled(0);
 102   erodeButton->setEnabled(0);
 103   dilateButton->setEnabled(0);
 104   infoLabel->setText("Select Up and Down threshold before clicking binarise !");
 105 }
 106
 107 vvSegmentationDialog::~vvSegmentationDialog()
 108 {
 109   mClipper->Delete();
 110
 111   mSquaresActor1->Delete();
 112   mSquaresMapper1->Delete();
 113   mSquares1->Delete();
 114
 115   mSquaresActor2->Delete();
 116   mSquaresMapper2->Delete();
 117   mSquares2->Delete();
 118
 119   //m3DMapper->Delete();
 120   //m3DActor->Delete();
 121   m3DExtractor->Delete();
 122
 123   for (unsigned int i = 0; i < mBinaireImages.size(); i++)
 124     mBinaireImages[i]->Delete();
 125
 126   for (unsigned int i = 0; i < m3DActors.size(); i++)
 127     m3DActors[i]->Delete();
 128
 129   for (unsigned int i = 0; i < m3DMappers.size(); i++)
 130     m3DMappers[i]->Delete();
 131
 132   delete mManager;
 133 }
 134
 135 //----------------------------------------------------------------------------
 136 // This templated function executes the filter for any type of data.
 137 // Handles the one input operations
 138 template <class T>
 139 void vvImageBinarize(vtkImageData *in1Data, T *in1Ptr,
 140                      int outExt[6],int clampMin, int clampMax)
 141 {
 142   int idxR, idxY, idxZ;
 143   int maxY, maxZ;
 144   vtkIdType inIncX, inIncY, inIncZ;
 145   int rowLength;
 146
 147   // find the region to loop over
 148   rowLength =
 149     (outExt[1] - outExt[0]+1)*in1Data->GetNumberOfScalarComponents();
 150   // What a pain. Maybe I should just make another filter.
 151
 152   maxY = outExt[3] - outExt[2];
 153   maxZ = outExt[5] - outExt[4];
 154
 155   // Get increments to march through data
 156   in1Data->GetContinuousIncrements(outExt, inIncX, inIncY, inIncZ);
 157
 158   for (idxZ = 0; idxZ <= maxZ; idxZ++) {
 159     for (idxY = 0; idxY <= maxY; idxY++) {
 160       for (idxR = 0; idxR < rowLength; idxR++) {
 161         if (static_cast<double>(*in1Ptr) > clampMin && static_cast<double>(*in1Ptr) <= clampMax)
 162           *in1Ptr = static_cast<T>(1);
 163         else
 164           *in1Ptr = static_cast<T>(0);
 165         in1Ptr++;
 166       }
 167       in1Ptr += inIncY;
 168     }
 169     in1Ptr += inIncZ;
 170   }
 171 }
 172
 173 void vvSegmentationDialog::SetImage(vvImage::Pointer image)
 174 {
 175
 176   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 177   mManager->SetImage(image);
 178   mManager->SetSlicerWindow(0,viewWidget->GetRenderWindow());
 179   vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
 180   mManager->SetInteractorStyleNavigator(0,style);
 181   style->Delete();
 182
 183   double range[2];
 184   mManager->GetImage()->GetScalarRange(range);
 185   mManager->GetSlicer(0)->SetColorWindow(range[1]-range[0]);
 186   mManager->GetSlicer(0)->SetColorLevel((range[1]+range[0])/2);
 187
 188   clipping1Slider->setMinimum(range[0]);
 189   clipping1Slider->setMaximum(range[1]);
 190   clipping2Slider->setMinimum(range[0]);
 191   clipping2Slider->setMaximum(range[1]);
 192   clipping1Slider->setValue(range[0]);
 193   clipping2Slider->setValue(range[1]);
 194
 195 #if VTK_MAJOR_VERSION <= 5
 196   mClipper->SetInput(mManager->GetSlicer(0)->GetInput());
 197 #else
 198   mClipper->SetInputData(mManager->GetSlicer(0)->GetInput());
 199 #endif
 200   mSquares1->SetValue(0,clipping1Slider->value());
 201   mSquares2->SetValue(0,clipping2Slider->value());
 202
 203 #if VTK_MAJOR_VERSION <= 5
 204   mSquares1->SetInput(mClipper->GetOutput());
 205   mSquares2->SetInput(mClipper->GetOutput());
 206
 207   mSquaresMapper1->SetInput(mSquares1->GetOutput());
 208   mSquaresMapper2->SetInput(mSquares2->GetOutput());
 209 #else
 210   mSquares1->SetInputData(mClipper->GetOutput());
 211   mSquares2->SetInputData(mClipper->GetOutput());
 212
 213   mSquaresMapper1->SetInputData(mSquares1->GetOutput());
 214   mSquaresMapper2->SetInputData(mSquares2->GetOutput());
 215 #endif
 216   mSquaresMapper1->ScalarVisibilityOff();
 217   mSquaresMapper2->ScalarVisibilityOff();
 218
 219   mSquaresActor1->SetMapper(mSquaresMapper1);
 220   mSquaresActor2->SetMapper(mSquaresMapper2);
 221   mSquaresActor1->GetProperty()->SetColor(1.0,0,0);
 222   mSquaresActor2->GetProperty()->SetColor(0,0,1.0);
 223   mSquaresActor1->SetPickable(0);
 224   mSquaresActor2->SetPickable(0);
 225
 226   mManager->GetSlicer(0)->GetRenderer()->AddActor(mSquaresActor1);
 227   mManager->GetSlicer(0)->GetRenderer()->AddActor(mSquaresActor2);
 228
 229   mSquares1->Update();
 230   mSquares2->Update();
 231
 232   UpdateSlice(0,mManager->GetSlicer(0)->GetSlice());
 233
 234   connect(mManager,SIGNAL(UpdateTSlice(int,int)),this,SLOT(UpdateSlice(int, int)));
 235   connect(mManager,SIGNAL(UpdateSlice(int,int)),this,SLOT(UpdateSlice(int, int)));
 236   connect(mManager,SIGNAL(UpdateSliceRange(int,int,int,int,int)),this,SLOT(UpdateSlice(int, int)));
 237   connect(mManager,SIGNAL(LandmarkAdded()),this,SLOT(InsertSeed()));
 238   QApplication::restoreOverrideCursor();
 239 }
 240
 241 void vvSegmentationDialog::UpdateSlice(int slicer,int slices)
 242 {
 243   int slice = mManager->GetSlicer(0)->GetSlice();
 244   int tslice = mManager->GetSlicer(0)->GetTSlice();
 245 #if VTK_MAJOR_VERSION <= 5
 246   mClipper->SetInput(mManager->GetSlicer(0)->GetInput());
 247 #else
 248   mClipper->SetInputData(mManager->GetSlicer(0)->GetInput());
 249 #endif
 250   int* extent = mManager->GetSlicer(0)->GetImageActor()->GetDisplayExtent();
 251   mClipper->SetOutputWholeExtent(extent[0],extent[1],extent[2],extent[3],extent[4],extent[5]);
 252   int i;
 253   for (i = 0; i < 6; i = i+2) {
 254     if (extent[i] == extent[i+1]) {
 255       break;
 256     }
 257   }
 258
 259   switch (i) {
 260   case 0:
 261     if (mManager->GetSlicer(0)->GetRenderer()->GetActiveCamera()->GetPosition()[0] > slice) {
 262       mSquaresActor1->SetPosition(1,0,0);
 263       mSquaresActor2->SetPosition(1,0,0);
 264     } else {
 265       mSquaresActor1->SetPosition(-1,0,0);
 266       mSquaresActor2->SetPosition(-1,0,0);
 267     }
 268     break;
 269   case 2:
 270     if (mManager->GetSlicer(0)->GetRenderer()->GetActiveCamera()->GetPosition()[1] > slice) {
 271       mSquaresActor1->SetPosition(0,1,0);
 272       mSquaresActor2->SetPosition(0,1,0);
 273     } else {
 274       mSquaresActor1->SetPosition(0,-1,0);
 275       mSquaresActor2->SetPosition(0,-1,0);
 276     }
 277     break;
 278   case 4:
 279     if (mManager->GetSlicer(0)->GetRenderer()->GetActiveCamera()->GetPosition()[2] > slice) {
 280       mSquaresActor1->SetPosition(0,0,1);
 281       mSquaresActor2->SetPosition(0,0,1);
 282     } else {
 283       mSquaresActor1->SetPosition(0,0,-1);
 284       mSquaresActor2->SetPosition(0,0,-1);
 285     }
 286     break;
 287   }
 288   mSquares1->Update();
 289   mSquares2->Update();
 290
 291   if (m3DActors.size()) {
 292     for (unsigned int i =0; i < m3DActors.size(); i++) {
 293       if (m3DActors[i]->GetVisibility()) {
 294         m3DActors[i]->VisibilityOff();
 295       }
 296     }
 297     std::cout << "display " << tslice << " on " << m3DActors.size()  << std::endl;
 298     m3DActors[tslice]->VisibilityOn();
 299   }
 300
 301   mManager->Render();
 302 }
 303
 304
 305 void vvSegmentationDialog::clippingvaluechanged(int value)
 306 {
 307   binaryButton->setEnabled(1);
 308   int min = (clipping1Slider->value() < clipping2Slider->value() ) ?
 309             clipping1Slider->value():clipping2Slider->value();
 310   int max = (clipping1Slider->value() > clipping2Slider->value() ) ?
 311             clipping1Slider->value():clipping2Slider->value();
 312   mSquares1->SetValue(0,min);
 313   mSquares2->SetValue(0,max);
 314
 315   QString textMin = "<b> Min : </b>";
 316   textMin += QString::number(min);
 317   QString textMax = "\n <b> Max : </b>";
 318   textMax += QString::number(max);
 319   minLabel->setText(textMin);
 320   maxLabel->setText(textMax);
 321
 322   if (mSquares1->GetInput()) {
 323     mSquares1->Update();
 324     mSquares2->Update();
 325     mManager->Render();
 326   }
 327 }
 328
 329
 330 void vvSegmentationDialog::BinariseSurface()
 331 {
 332   infoLabel->setText("Click erode then space on desired organ !");
 333
 334   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 335   int clampMin = (clipping1Slider->value() < clipping2Slider->value() ) ?
 336                  clipping1Slider->value():clipping2Slider->value();
 337   int clampMax = (clipping1Slider->value() > clipping2Slider->value() ) ?
 338                  clipping1Slider->value():clipping2Slider->value();
 339   vtkImageData* outputImage = vtkImageData::New();
 340
 341   for (unsigned int numImage = 0; numImage < mManager->GetSlicer(0)->GetImage()->GetVTKImages().size(); numImage++) {
 342     vtkImageData* image = mManager->GetSlicer(0)->GetImage()->GetVTKImages()[numImage];
 343     int ext[6];
 344 #if VTK_MAJOR_VERSION <= 5
 345     image->GetWholeExtent(ext);
 346 #else
 347     image->GetExtent(ext);
 348 #endif
 349     void *in1Ptr;
 350     in1Ptr = image->GetScalarPointerForExtent(ext);
 351
 352     switch (image->GetScalarType()) {
 353       vtkTemplateMacro(
 354         vvImageBinarize(image, static_cast<VTK_TT *>(in1Ptr),
 355                         ext,clampMin,clampMax));
 356     default:
 357       std::cerr << "Error, unknown pixel format : " << image->GetScalarTypeAsString() << std::endl;
 358       return;
 359     }
 360
 361     outputImage->Initialize();
 362     outputImage->SetExtent(ext);
 363     outputImage->SetOrigin(image->GetOrigin());
 364     outputImage->SetSpacing(image->GetSpacing());
 365 #if VTK_MAJOR_VERSION <= 5
 366     outputImage->SetScalarTypeToUnsignedChar();
 367 #else
 368     outputImage->AllocateScalars(VTK_UNSIGNED_CHAR, 1);
 369 #endif
 370     outputImage->CopyAndCastFrom(image,ext);
 371 #if VTK_MAJOR_VERSION <= 5
 372     outputImage->Update();
 373 #else
 374     //outputImage->Update();
 375 #endif
 376
 377     image->DeepCopy(outputImage);
 378 #if VTK_MAJOR_VERSION <= 5
 379     image->UpdateInformation();
 380     image->PropagateUpdateExtent();
 381 #else
 382     //image->UpdateInformation();
 383     //image->PropagateUpdateExtent();
 384 #endif
 385
 386     vtkImageData* imageBin = vtkImageData::New();
 387     imageBin->DeepCopy(image);
 388 #if VTK_MAJOR_VERSION <= 5
 389     imageBin->Update();
 390 #else
 391     //imageBin->Update();
 392 #endif
 393     mBinaireImages.push_back(imageBin);
 394   }
 395
 396   outputImage->Delete();
 397   erodeButton->setEnabled(1);
 398   QApplication::restoreOverrideCursor();
 399   mManager->SetColorWindow(2);
 400   mManager->SetColorLevel(0.5);
 401   mManager->Render();
 402 }
 403
 404 void vvSegmentationDialog::Erode()
 405 {
 406   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 407   vtkImageContinuousErode3D* erode = vtkImageContinuousErode3D::New();
 408   erode->SetKernelSize(mKernelValue,mKernelValue,mKernelValue);
 409   for (unsigned int numImage = 0; numImage < mManager->GetSlicer(0)->GetImage()->GetVTKImages().size(); numImage++) {
 410     vtkImageData* image = mManager->GetSlicer(0)->GetImage()->GetVTKImages()[numImage];
 411 #if VTK_MAJOR_VERSION <= 5
 412     erode->SetInput(image);
 413     erode->Update();
 414 #else
 415     erode->SetInputData(image);
 416     //erode->Update();
 417 #endif
 418     image->DeepCopy(erode->GetOutput());
 419 #if VTK_MAJOR_VERSION <= 5
 420     image->Update();
 421 #else
 422     //image->Update();
 423 #endif
 424   }
 425   erode->Delete();
 426   dilateButton->setEnabled(1);
 427   mManager->Render();
 428   QApplication::restoreOverrideCursor();
 429 }
 430
 431 void vvSegmentationDialog::Dilate()
 432 {
 433   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 434   vtkImageContinuousDilate3D* dilate = vtkImageContinuousDilate3D::New();
 435   vtkImageLogic* And = vtkImageLogic::New();
 436   And->SetOperationToAnd();
 437   dilate->SetKernelSize(mKernelValue,mKernelValue,mKernelValue);
 438   for (unsigned int numImage = 0; numImage < mManager->GetSlicer(0)->GetImage()->GetVTKImages().size(); numImage++) {
 439     vtkImageData* image = mManager->GetSlicer(0)->GetImage()->GetVTKImages()[numImage];
 440 #if VTK_MAJOR_VERSION <= 5
 441     dilate->SetInput(image);
 442 #else
 443     dilate->SetInputData(image);
 444 #endif
 445     vtkImageData* mask = mBinaireImages[numImage];
 446 #if VTK_MAJOR_VERSION <= 5
 447     And->SetInput1(dilate->GetOutput());
 448     And->SetInput2(mask);
 449 #else
 450     And->SetInput1Data(dilate->GetOutput());
 451     And->SetInput2Data(mask);
 452 #endif
 453     And->Update();
 454     image->DeepCopy(And->GetOutput());
 455 #if VTK_MAJOR_VERSION <= 5
 456     image->Update();
 457 #else
 458     //image->Update();
 459 #endif
 460   }
 461   And->Delete();
 462   dilate->Delete();
 463   mManager->Render();
 464   QApplication::restoreOverrideCursor();
 465 }
 466
 467 void vvSegmentationDialog::InsertSeed()
 468 {
 469   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 470   int point4D[4];
 471   point4D[0] = mManager->GetLandmarks()->GetCoordinates(
 472                  mManager->GetLandmarks()->GetNumberOfPoints()-1)[0];
 473   point4D[1] = mManager->GetLandmarks()->GetCoordinates(
 474                  mManager->GetLandmarks()->GetNumberOfPoints()-1)[1];
 475   point4D[2] = mManager->GetLandmarks()->GetCoordinates(
 476                  mManager->GetLandmarks()->GetNumberOfPoints()-1)[2];
 477   point4D[3] = mManager->GetLandmarks()->GetCoordinates(
 478                  mManager->GetLandmarks()->GetNumberOfPoints()-1)[3];
 479
 480   point4D[0] = (point4D[0]-mManager->GetSlicer(0)->GetImage()->GetVTKImages()[0]->GetOrigin()[0])/mManager->GetSlicer(0)->GetImage()->GetVTKImages()[0]->GetSpacing()[0];
 481   point4D[1] = (point4D[1]-mManager->GetSlicer(0)->GetImage()->GetVTKImages()[0]->GetOrigin()[1])/mManager->GetSlicer(0)->GetImage()->GetVTKImages()[0]->GetSpacing()[1];
 482   point4D[2] = (point4D[2]-mManager->GetSlicer(0)->GetImage()->GetVTKImages()[0]->GetOrigin()[2])/mManager->GetSlicer(0)->GetImage()->GetVTKImages()[0]->GetSpacing()[2];
 483
 484   vtkImageSeedConnectivity* seed = vtkImageSeedConnectivity::New();
 485   seed->SetInputConnectValue(1);
 486   seed->SetOutputConnectedValue(1);
 487   seed->SetOutputUnconnectedValue(0);
 488   seed->AddSeed(point4D[0],point4D[1],point4D[2]);
 489
 490   for (unsigned int numImage = 0; numImage < mManager->GetSlicer(0)->GetImage()->GetVTKImages().size(); numImage++) {
 491     vtkImageData* image = mManager->GetSlicer(0)->GetImage()->GetVTKImages()[numImage];
 492 #if VTK_MAJOR_VERSION <= 5
 493     seed->SetInput(image);
 494 #else
 495     seed->SetInputData(image);
 496 #endif
 497     seed->Update();
 498     image->DeepCopy(seed->GetOutput());
 499 #if VTK_MAJOR_VERSION <= 5
 500     image->Update();
 501 #else
 502     //image->Update();
 503 #endif
 504   }
 505
 506   seed->Delete();
 507   QApplication::restoreOverrideCursor();
 508 }
 509
 510 void vvSegmentationDialog::ChangeDimRendering()
 511 {
 512   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 513
 514   if (dimButton->text() == "3D") {
 515     if (m3DActors.size() == 0) {
 516       m3DExtractor->SetValue(0,0.5);
 517       for (unsigned int numImage = 0; numImage < mManager->GetSlicer(0)->GetImage()->GetVTKImages().size(); numImage++) {
 518         vtkActor* actor = vtkActor::New();
 519 #if VTK_MAJOR_VERSION <= 5
 520         m3DExtractor->SetInput(mManager->GetSlicer(0)->GetImage()->GetVTKImages()[numImage]);
 521 #else
 522         m3DExtractor->SetInputData(mManager->GetSlicer(0)->GetImage()->GetVTKImages()[numImage]);
 523 #endif
 524         m3DExtractor->Update();
 525
 526         vtkPolyDataMapper* mapper = vtkPolyDataMapper::New();
 527 #if VTK_MAJOR_VERSION <= 5
 528         mapper->SetInput(m3DExtractor->GetOutput());
 529 #else
 530         mapper->SetInputData(m3DExtractor->GetOutput());
 531 #endif
 532         m3DMappers.push_back(mapper);
 533
 534         actor->SetMapper(mapper);
 535         actor->GetProperty()->SetColor(1.0,0.7,0.2);
 536         actor->VisibilityOff();
 537
 538         mManager->GetSlicer(0)->GetRenderer()->AddActor(actor);
 539         m3DActors.push_back(actor);
 540       }
 541     }
 542
 543     mManager->GetSlicer(0)->GetRenderer()->SetBackground(0.5,0.6,0.9);
 544     m3DActors[0]->VisibilityOn();
 545
 546     vtkInteractorStyleTrackballCamera* style = vtkInteractorStyleTrackballCamera::New();
 547     mManager->SetInteractorStyleNavigator(0,style);
 548     style->Delete();
 549
 550     mManager->GetSlicer(0)->GetImageActor()->VisibilityOff();
 551     mSquaresActor1->VisibilityOff();
 552     mSquaresActor2->VisibilityOff();
 553     mManager->Render();
 554     dimButton->setText("2D");
 555   } else {
 556     mManager->GetSlicer(0)->GetRenderer()->SetBackground(0.0,0.0,0.0);
 557     vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
 558     mManager->SetInteractorStyleNavigator(0,style);
 559     style->Delete();
 560
 561     mManager->GetSlicer(0)->SetSliceOrientation(2);
 562     m3DActors[mManager->GetSlicer(0)->GetTSlice()]->VisibilityOff();
 563
 564     mManager->GetSlicer(0)->GetImageActor()->VisibilityOn();
 565     mSquaresActor1->VisibilityOn();
 566     mSquaresActor2->VisibilityOn();
 567     dimButton->setText("3D");
 568   }
 569   QApplication::restoreOverrideCursor();
 570 }
 571
 572 void vvSegmentationDialog::KernelValueChanged(int kernel)
 573 {
 574   mKernelValue = kernel;
 575 }
 576
 577 void vvSegmentationDialog::Save()
 578 {
 579   if (dimButton->text() == "2D") { //If in *3D* mode, save the mesh
 580     QString fileName = QFileDialog::getSaveFileName(this,
 581                        tr("Save Mesh As"),
 582                        QDir::home().dirName(),
 583                        "Mesh Files (*.vtk *.vtp)");
 584     if (!fileName.isEmpty()) {
 585       vtkSmartPointer<vtkPolyDataWriter> w = vtkSmartPointer<vtkPolyDataWriter>::New();
 586 #if VTK_MAJOR_VERSION <= 5
 587       w->SetInput(m3DExtractor->GetOutput());
 588 #else
 589       w->SetInputData(m3DExtractor->GetOutput());
 590 #endif
 591       w->SetFileName(fileName.toStdString().c_str());
 592       w->Write();
 593     }
 594   } else {
 595     QStringList OutputListeFormat;
 596     OutputListeFormat.clear();
 597     int dimension = mManager->GetDimension();
 598     if (dimension == 1) {
 599       OutputListeFormat.push_back(".mhd");
 600       OutputListeFormat.push_back(".mha");
 601     }
 602     if (dimension == 2) {
 603       OutputListeFormat.push_back(".bmp");
 604       OutputListeFormat.push_back(".png");
 605       OutputListeFormat.push_back(".jpeg");
 606       OutputListeFormat.push_back(".tif");
 607       OutputListeFormat.push_back(".mha");
 608       OutputListeFormat.push_back(".mhd");
 609       OutputListeFormat.push_back(".hdr");
 610       OutputListeFormat.push_back(".vox");
 611     } else if (dimension == 3) {
 612       OutputListeFormat.push_back(".mha");
 613       OutputListeFormat.push_back(".mhd");
 614       OutputListeFormat.push_back(".hdr");
 615       OutputListeFormat.push_back(".vox");
 616     } else if (dimension == 4) {
 617       OutputListeFormat.push_back(".mha");
 618       OutputListeFormat.push_back(".mhd");
 619     }
 620     QString Extensions = "AllFiles(*.*)";
 621     for (int i = 0; i < OutputListeFormat.count(); i++) {
 622       Extensions += ";;Images ( *";
 623       Extensions += OutputListeFormat[i];
 624       Extensions += ")";
 625     }
 626     QString fileName = QFileDialog::getSaveFileName(this,
 627                        tr("Save As"),
 628                        QDir::home().dirName(),
 629                        Extensions);
 630     if (!fileName.isEmpty()) {
 631       std::string fileformat = vtksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
 632       if (OutputListeFormat.contains(
 633             fileformat.c_str())) {
 634         QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 635         vvProgressDialog progress("Saving "+fileName.toStdString());
 636         qApp->processEvents();
 637         vvImageWriter::Pointer writer = vvImageWriter::New();
 638         writer->SetOutputFileName(fileName.toStdString());
 639         writer->SetInput(mManager->GetSlicer(0)->GetImage());
 640         writer->Update(dimension,"unsigned_char");
 641         QApplication::restoreOverrideCursor();
 642         if (writer->GetLastError().size()) {
 643           QString error = "Saving did not succeed\n";
 644           error += writer->GetLastError().c_str();
 645           QMessageBox::information(this,tr("Saving Problem"),error);
 646           Save();
 647         }
 648       } else {
 649         QString error = fileformat.c_str();
 650         if (error.isEmpty())
 651           error += "no file format specified !";
 652         else
 653           error += " format unknown !!!\n";
 654         QMessageBox::information(this,tr("Saving Problem"),error);
 655         Save();
 656       }
 657     }
 658   }
 659 }
 660
 661 #endif /* end #define _vvSegmentationDialog_CXX */
 662