bool TestIsClosedLoop()
{
std::cout << "TestIsClosedLoop()" << std::endl;
// Open loop
{
typedef itk::Image<unsigned char, 2> ImageType;
ImageType::Pointer image = ImageType::New();
itk::Index<2> corner = {{0,0}};
itk::Size<2> size = {{100,100}};
itk::ImageRegion<2> region(corner, size);
image->SetRegions(region);
image->Allocate();
image->FillBuffer(0);
for(itk::Index<2>::IndexValueType i = 20; i < 30; ++i)
{
itk::Index<2> pixel = {{i, 50}};
image->SetPixel(pixel, 255);
}
itk::Index<2> start = {{25, 50}};
bool isClosedLoop = ITKHelpers::IsClosedLoop(image.GetPointer(), start);
std::cout << "Is closed loop? " << isClosedLoop << std::endl;
}
// Closed loop
{
typedef itk::Image<unsigned char, 2> ImageType;
ImageType::Pointer image = ImageType::New();
itk::Index<2> corner = {{0,0}};
itk::Size<2> size = {{100,100}};
itk::ImageRegion<2> region(corner, size);
image->SetRegions(region);
image->Allocate();
image->FillBuffer(0);
itk::Index<2> corner0 = {{10,10}};
itk::Index<2> corner1 = {{30,30}};
ITKHelpers::DrawRectangle(image.GetPointer(), 255,
corner0, corner1);
itk::Index<2> start = {{10, 10}};
bool isClosedLoop = ITKHelpers::IsClosedLoop(image.GetPointer(), start);
std::cout << "Is closed loop? " << isClosedLoop << std::endl;
}
return true;
}
bool TestBreadthFirstOrderingNonZeroPixels()
{
std::cout << "TestBreadthFirstOrderingNonZeroPixels()" << std::endl;
typedef itk::Image<unsigned char, 2> ImageType;
ImageType::Pointer image = ImageType::New();
itk::Index<2> corner = {{0,0}};
itk::Size<2> size = {{100,100}};
itk::ImageRegion<2> region(corner, size);
image->SetRegions(region);
image->Allocate();
image->FillBuffer(0);
for(itk::Index<2>::IndexValueType i = 20; i < 30; ++i)
{
itk::Index<2> pixel = {{i, 50}};
image->SetPixel(pixel, 255);
}
itk::Index<2> start = {{25, 50}};
std::vector<itk::Index<2> > breadthFirstOrdering =
ITKHelpers::BreadthFirstOrderingNonZeroPixels(image.GetPointer(), start);
for(unsigned int i = 0; i < breadthFirstOrdering.size(); ++i)
{
//std::cout << breadthFirstOrdering[i] << " ";
std::cout << breadthFirstOrdering[i] << std::endl;
}
std::cout << std::endl;
return true;
}
void TestGetOpenContourOrdering()
{
typedef itk::Image<unsigned char, 2> ImageType;
ImageType::Pointer image = ImageType::New();
itk::Index<2> corner = {{0,0}};
itk::Size<2> size = {{100,100}};
itk::ImageRegion<2> region(corner, size);
image->SetRegions(region);
image->Allocate();
image->FillBuffer(0);
for(unsigned int i = 20; i < 30; ++i)
{
itk::Index<2> pixel = {{i, 50}};
image->SetPixel(pixel, 255);
}
itk::Index<2> start = {{25, 50}};
std::vector<itk::Index<2> > contourOrdering = ITKHelpers::GetOpenContourOrdering(image.GetPointer(), start);
for(unsigned int i = 0; i < contourOrdering.size(); ++i)
{
//std::cout << breadthFirstOrdering[i] << " ";
std::cout << contourOrdering[i] << std::endl;
}
std::cout << std::endl;
}
void TestGetClosedContourOrdering()
{
typedef itk::Image<unsigned char, 2> ImageType;
ImageType::Pointer image = ImageType::New();
itk::Index<2> corner = {{0,0}};
itk::Size<2> size = {{100,100}};
itk::ImageRegion<2> region(corner, size);
image->SetRegions(region);
image->Allocate();
image->FillBuffer(0);
itk::Index<2> corner0 = {{10,10}};
itk::Index<2> corner1 = {{30,30}};
ITKHelpers::DrawRectangle(image.GetPointer(), 255,
corner0, corner1);
itk::Index<2> start = {{10, 10}};
std::vector<itk::Index<2> > ordering = ITKHelpers::GetClosedContourOrdering(image.GetPointer(), start);
for(unsigned int i = 0; i < ordering.size(); ++i)
{
std::cout << ordering[i] << std::endl;
}
std::cout << std::endl;
}
int main(int, char* [] )
{
typedef itk::Image<unsigned char, 2> ImageType;
ImageType::Pointer image = ImageType::New();
itk::Index<2> corner={{0,0}};
itk::Size<2> size = {{10,10}};
itk::ImageRegion<2> region(corner,size);
image->SetRegions(region);
image->Allocate();
image->FillBuffer(0);
unsigned char searchValue = 255; // This value does not appear in the image, so both functions
// will have to search the entire image.
int counter = 0;
for(unsigned int i = 0; i < 1e7; ++i)
{
// counter += HasValue(image.GetPointer(), searchValue); // About 3 seconds
counter += HasValueConditional(image.GetPointer(), searchValue); // About 3.3 seconds
}
std::cout << "counter " << counter << std::endl;
return 0;
}
void NRRDTools::saveNRRDFile(const cleaver::FloatField *field, const std::string &name) {
auto dims = field->dataBounds().size;
ImageType::Pointer img = ImageType::New();
itk::Index<3> start; start.Fill(0);
ImageType::SizeType size;
size[0] = static_cast<size_t>(dims[0]);
size[1] = static_cast<size_t>(dims[1]);
size[2] = static_cast<size_t>(dims[2]);
ImageType::RegionType region(start, size);
img->SetRegions(region);
img->Allocate();
img->FillBuffer(0);
for (size_t i = 0; i < dims[0]; i++) {
for (size_t j = 0; j < dims[1]; j++) {
for (size_t k = 0; k < dims[2]; k++) {
ImageType::IndexType pixelIndex;
pixelIndex[0] = i;
pixelIndex[1] = j;
pixelIndex[2] = k;
auto data = ((cleaver::FloatField*)field)->data();
img->SetPixel(pixelIndex, data[i + size[0] * j + size[0] * size[1] * k]);
}
}
}
WriterType::Pointer write = WriterType::New();
write->SetFileName(name + ((name.find_first_of(".nrrd") == std::string::npos) ? ".nrrd" : ""));
write->SetInput(img);
write->Update();
}
// ------------------------------------------------------------------------
void createOutput(const ImageType::Pointer &input, ImageType::Pointer &output)
{
output->SetDirection(input->GetDirection());
output->SetSpacing(input->GetSpacing());
output->SetRegions(input->GetLargestPossibleRegion());
output->SetOrigin(input->GetOrigin());
output->Allocate();
output->FillBuffer(0);
}
// ------------------------------------------------------------------------
void buildShortAxisVolume(const SeriesTransform::Map &transforms,
const unsigned int seriesNumber, ImageType::Pointer &saVolume)
{
// get the short axis transforms
SeriesTransform::Map::const_iterator mapIt = transforms.begin();
std::vector<SeriesTransform> saSlices;
while(mapIt != transforms.end())
{
if(mapIt->second.series == seriesNumber)
{
unsigned int sliceNum = mapIt->second.slice;
if(saSlices.size() < (sliceNum+1))
saSlices.resize(sliceNum+1);
saSlices[sliceNum] = mapIt->second;
}
++mapIt;
}
// get the dimensions of the output image
ImageType::Pointer reference = saSlices[0].images[0];
unsigned int x,y,z;
x = reference->GetLargestPossibleRegion().GetSize()[0];
y = reference->GetLargestPossibleRegion().GetSize()[1];
z = saSlices.size();
ImageType::RegionType region;
ImageType::SizeType size;
ImageType::IndexType index;
size[0] = x;
size[1] = y;
size[2] = z;
index.Fill(0);
region.SetSize(size);
region.SetIndex(index);
// get the other parts
ImageType::SpacingType spacing = reference->GetSpacing();
spacing[2] = saSlices[0].sliceThickness;
ImageType::DirectionType direction = reference->GetDirection();
ImageType::PointType origin = reference->GetOrigin();
saVolume->SetOrigin(origin);
saVolume->SetDirection(direction);
saVolume->SetSpacing(spacing);
saVolume->SetRegions(region);
saVolume->Allocate();
saVolume->FillBuffer(0);
}
ComposeImageFilter::ImageType::Pointer ComposeImageFilter::ComposeIt()
{
ImageType::Pointer outputImage = ImageType::New();
outputImage->SetRegions(m_imageLR->GetLargestPossibleRegion());
outputImage->SetOrigin(m_imageLR->GetOrigin());
outputImage->SetSpacing(m_imageLR->GetSpacing());
outputImage->SetDirection(m_imageLR->GetDirection());
outputImage->Allocate();
outputImage->FillBuffer(0.0);
std::cout << "outputImage" << std::endl;
ImageType::IndexType testIndex;
testIndex[0] = 0; testIndex[1]=0; testIndex[2]=0;
std::cout << m_matrix.rows() << " " << m_matrix.cols() << std::endl;
for (int i=0; i< m_matrix.rows() ; i++ )
{
vcl_vector<int> rowIndices;
vcl_vector<float> rowValues;
vcl_vector<pair_t> rowM = m_matrix.get_row(i);
float sum_vox =0;
ImageType::IndexType outputIndex;
outputIndex = ComputeImageIndex(i, m_imageLR);
// std::cout << "ImageLR " << " " << i << " " << outputIndex << std::endl;
for (vcl_vector<pair_t>::const_iterator it = rowM.begin(); it != rowM.end(); ++it)
{
ImageType::IndexType HRIndex;
HRIndex = ComputeImageIndex(it->first, m_imageHR);
sum_vox += (it->second)* (m_imageHR->GetPixel(HRIndex));
// std::cout << HRIndex << " " << it->second << std::endl;
}
// std::cout << sum_vox << std::endl;
outputImage->SetPixel(outputIndex, sum_vox);
//
}
return outputImage;
}
bool TestRandomImage()
{
typedef itk::Image<unsigned char, 2> ImageType;
ImageType::Pointer image = ImageType::New();
itk::Index<2> corner = {{0,0}};
itk::Size<2> size = {{100,100}};
itk::ImageRegion<2> region(corner, size);
image->SetRegions(region);
image->Allocate();
image->FillBuffer(0);
ITKHelpers::RandomImage(image.GetPointer());
ITKHelpers::WriteImage(image.GetPointer(), "random.png");
return true;
}
void snapshot_beta_points(Nodes const& nodes)
{
// clear it
g_snapshot_image->FillBuffer(0);
for (Nodes::const_iterator it = nodes.begin(), end = nodes.end();
it != end; ++it) {
// &&& Hmm, maybe we can do better than this; make it truly sparse.
ImageType::IndexType index;
g_snapshot_image->TransformPhysicalPointToIndex((*it)->pos(), index);
PixelType density = g_snapshot_image->GetPixel(index);
// There is no natural beta intensity (except maybe beta-like-ness,
// which we don't keep)
density += constants::BetaPointDisplayFakeDensity;
g_snapshot_image->SetPixel(index, density);
}
}
bool VolumeProcess:: RunFillingZeroOnBouandary(int Bx,int By,int Bz)
{
ImageType::Pointer tempImg = ImageType::New();
tempImg->SetRegions( m_outputImage->GetLargestPossibleRegion() );
tempImg->Allocate();
tempImg->FillBuffer(0);
ImageType::RegionType fullRegion = m_outputImage->GetBufferedRegion();
int numColumns = fullRegion.GetSize(0);
int numRows = fullRegion.GetSize(1);
int numStacks = fullRegion.GetSize(2);
int i, j,k;
itk::ImageRegionIteratorWithIndex< ImageType > itr( m_outputImage, fullRegion );
for(itr.GoToBegin(); !itr.IsAtEnd(); ++itr)
{
ImageType::IndexType index = itr.GetIndex();
ImageType::PixelType pix = m_outputImage->GetPixel(index);
i = index[0];
j = index[1];
k = index[2];
if (i < Bx || i > numColumns -Bx || j < By || j > numRows-By ||k <Bz ||k > numStacks-Bz )
tempImg->SetPixel(itr.GetIndex(), 0);
else
tempImg->SetPixel(itr.GetIndex(), pix);
}
//Copy temp img back to image
itk::ImageRegionIterator< ImageType > itr1( tempImg, tempImg->GetLargestPossibleRegion());
itk::ImageRegionIterator< ImageType > itr2( m_outputImage, m_outputImage->GetLargestPossibleRegion());
for(itr1.GoToBegin(), itr2.GoToBegin() ; !itr1.IsAtEnd(); ++itr1, ++itr2)
{
itr2.Set( itr1.Get() );
}
if(debug)
std::cerr << "RunFillingZero Done" << std::endl;
return true;
}
void TestDrawRectangle()
{
typedef itk::Image<unsigned char, 2> ImageType;
ImageType::Pointer image = ImageType::New();
itk::Index<2> corner = {{0,0}};
itk::Size<2> size = {{100,100}};
itk::ImageRegion<2> region(corner, size);
image->SetRegions(region);
image->Allocate();
image->FillBuffer(0);
itk::Index<2> corner0 = {{10,10}};
itk::Index<2> corner1 = {{30,30}};
ITKHelpers::DrawRectangle(image.GetPointer(), 255,
corner0, corner1);
ITKHelpers::WriteImage(image.GetPointer(), "rectangle.png");
}
int main(int, char* [] )
{
typedef itk::Image<unsigned char, 2> ImageType;
ImageType::Pointer image = ImageType::New();
itk::Index<2> corner = {{0, 0}};
itk::Size<2> size = {{31, 31}}; // Both dimensions of the size must be odd for the logic in this code to work
itk::ImageRegion<2> region(corner, size);
image->SetRegions(region);
image->Allocate();
image->FillBuffer(1);
// This is the pixel we will repeatedly query
itk::Index<2> queryIndex = {{size[0]/2, size[0]/2}};
// Create a list of all of the offsets relative to the queryIndex
std::vector<itk::Offset<2> > offsets;
itk::ImageRegionConstIteratorWithIndex<ImageType> imageIterator(image, region);
while(!imageIterator.IsAtEnd())
{
offsets.push_back(imageIterator.GetIndex() - queryIndex);
++imageIterator;
}
// Call these functions many times for timing stability
int totalSum = 0; // This variable is used so the compiler doesn't optimize away the loop
for(unsigned int i = 0; i < 1e4; ++i)
{
// ImageType::PixelType pixelSum = SumPixelsManual(image.GetPointer(), queryIndex, offsets); // about 2 seconds
ImageType::PixelType pixelSum = SumPixelsIterator(image.GetPointer(), queryIndex, offsets);
totalSum += pixelSum;
}
std::cout << "totalSum " << totalSum << std::endl;
return 0;
}
void TestGetAllPatchesContainingPixel()
{
typedef itk::Image<float, 2> ImageType;
ImageType::Pointer image = ImageType::New();
itk::Index<2> corner = {{0,0}};
itk::Size<2> size = {{10,10}};
itk::ImageRegion<2> imageRegion(corner,size);
image->SetRegions(imageRegion);
image->Allocate();
image->FillBuffer(0.0f);
itk::Index<2> queryPixel = {{5,5}};
std::vector<itk::ImageRegion<2> > allPatches =
ITKHelpers::GetAllPatchesContainingPixel(queryPixel, 1, imageRegion);
std::cout << "Number of patches " << allPatches.size() << std::endl;
}
int main(int argc, char ** argv){
typedef itk::Image<float,3> ImageType;
typedef itk::ImageFileReader<ImageType> ReaderType;
typedef itk::ImageFileWriter<ImageType> WriterType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(argv[1]);
typedef itk::HessianRecursiveGaussianImageFilter<ImageType> HessianFilterType;
typedef HessianFilterType::OutputImageType HessianImageType;
typedef HessianImageType::PixelType HessianType;
HessianFilterType::Pointer hessianFilter = HessianFilterType::New();
hessianFilter->SetSigma(0.05);
hessianFilter->SetInput(reader->GetOutput());
hessianFilter->Update();
HessianImageType::Pointer hessianImage = hessianFilter->GetOutput();
hessianImage->DisconnectPipeline();
typedef itk::ImageRegionConstIteratorWithIndex<HessianImageType> IteratorType;
IteratorType hessianIterator(hessianImage,hessianImage->GetLargestPossibleRegion());
typedef HessianType::EigenValuesArrayType EigenvalueArrayType;
EigenvalueArrayType expectation;
expectation.Fill(0.0);
unsigned count=0;
ImageType::Pointer small = ImageType::New();
small->CopyInformation(reader->GetOutput());
small->SetRegions(reader->GetOutput()->GetLargestPossibleRegion());
small->Allocate();
small->FillBuffer(0.0);
ImageType::Pointer medium = ImageType::New();
medium->CopyInformation(reader->GetOutput());
medium->SetRegions(reader->GetOutput()->GetLargestPossibleRegion());
medium->Allocate();
medium->FillBuffer(0.0);
ImageType::Pointer large = ImageType::New();
large->CopyInformation(reader->GetOutput());
large->SetRegions(reader->GetOutput()->GetLargestPossibleRegion());
large->Allocate();
large->FillBuffer(0.0);
while(!hessianIterator.IsAtEnd()){
auto hessian = hessianIterator.Get();
EigenvalueArrayType eigenValues;
hessian.ComputeEigenValues(eigenValues);
std::sort(eigenValues.Begin(),eigenValues.End(),[](double & a, double &b){
return std::abs(a) > std::abs(b);
});
//std::cout << eigenValues[0] << "\t"<< eigenValues[1] << "\t" << eigenValues[2] <<std::endl;
if(eigenValues[0]<0){
expectation[0]+=eigenValues[0];
expectation[1]+=eigenValues[1];
expectation[2]+=eigenValues[2];
count++;
large->SetPixel(hessianIterator.GetIndex(),std::abs(eigenValues[0]));
medium->SetPixel(hessianIterator.GetIndex(),std::abs(eigenValues[1]));
small->SetPixel(hessianIterator.GetIndex(),std::abs(eigenValues[2]));
}
++hessianIterator;
}
expectation[0]=expectation[0]/count;
expectation[1]=expectation[1]/count;
expectation[2]=expectation[2]/count;
WriterType::Pointer smallWriter = WriterType::New();
smallWriter->SetInput(small);
smallWriter->SetFileName("small.mha");
smallWriter->Update();
WriterType::Pointer mediumWriter = WriterType::New();
mediumWriter->SetInput(medium);
mediumWriter->SetFileName("medium.mha");
mediumWriter->Update();
WriterType::Pointer largeWriter = WriterType::New();
largeWriter->SetInput(large);
largeWriter->SetFileName("large.mha");
largeWriter->Update();
std::cout << "Expectation: \t" << expectation<< std::endl;
}
void CCropDialog::DoCrop(int nStartX, int nStartY, int nWidth, int nLength,
QString strInputFileName, QString strOutputFileName)
{
if(QFile::exists(strOutputFileName))
{
return; //
}
ImageType::IndexType start;
start[0] = nStartX;
start[1] = nStartY;
ImageType::SizeType size;
size[0] = nWidth;
size[1] = nLength;
ImageType::RegionType desiredRegion;
desiredRegion.SetSize( size );
desiredRegion.SetIndex( start );
FilterType::Pointer filter = FilterType::New();
filter->SetRegionOfInterest( desiredRegion );
ReaderType::Pointer reader = ReaderType::New();
const char * inputFilename = strInputFileName.toStdString().c_str();
reader->SetFileName( inputFilename );
filter->SetInput( reader->GetOutput() );
//bool bbErrorInSourceImage = false;
try
{
filter->Update();
}
catch( itk::ExceptionObject & err )
{
std::cerr << "ExceptionObject caught !" << std::endl;
std::cerr << err << std::endl;
return; // EXIT_FAILURE;
}
////////////////////////////////////
// prepare the output
ImageType::Pointer pOutputImage = ImageType::New();
pOutputImage->SetRegions( filter->GetOutput()->GetRequestedRegion() );
//pOutputImage->CopyInformation(pReader->GetOutput());
pOutputImage->Allocate();
///////////////////////////////////
// fill buffer with initial value
ImageType::PixelType InitialValue = 255;
pOutputImage->FillBuffer( InitialValue );
//if(bErrorInSourceImage != true)
{
ConstIteratorType InputItX(filter->GetOutput(), filter->GetOutput()->GetRequestedRegion());
IteratorType OutputItX(pOutputImage, filter->GetOutput()->GetRequestedRegion());
DoRelight(0, InputItX, OutputItX);
ConstIteratorType InputItY(pOutputImage, filter->GetOutput()->GetRequestedRegion());
IteratorType OutputItY(pOutputImage, filter->GetOutput()->GetRequestedRegion());
DoRelight(1, InputItY, OutputItY);
}
WriterType::Pointer pWriter = WriterType::New();
const char * outputFilename = strOutputFileName.toStdString().c_str();
pWriter->SetFileName(outputFilename);
pWriter->SetInput( pOutputImage );
try
{
pWriter->Update();
}
catch ( itk::ExceptionObject &err)
{
std::cerr << "ExceptionObject caught !" << std::endl;
std::cerr << err << std::endl;
return; // -1;
}
}
void
DistanceMapFilter::applyDistanceMapFilter(QString flnm,
QList<Vec> clipPos,
QList<Vec> clipNormal,
QList<CropObject> crops,
QList<PathObject> paths,
uchar *lut,
int chan)
{
int bpv = 1;
if (m_voxelType > 0) bpv = 2;
int nbytes = bpv*m_nY*m_nZ;
bool trim = (qRound(m_dataSize.x) < m_height ||
qRound(m_dataSize.y) < m_width ||
qRound(m_dataSize.z) < m_depth);
bool clipPresent = (clipPos.count() > 0);
m_cropPresent = false;
m_tearPresent = false;
m_blendPresent = false;
for(int ci=0; ci<m_crops.count(); ci++)
{
if (crops[ci].cropType() < CropObject::Tear_Tear)
m_cropPresent = true;
else if (crops[ci].cropType() < CropObject::View_Tear)
m_tearPresent = true;
else if (m_crops[ci].cropType() > CropObject::Displace_Displace &&
m_crops[ci].cropType() < CropObject::Glow_Ball)
m_blendPresent = true;
}
m_pathCropPresent = false;
m_pathBlendPresent = false;
for (int i=0; i<m_paths.count(); i++)
{
if (m_paths[i].blend()) m_pathBlendPresent = true;
if (m_paths[i].crop()) m_pathCropPresent = true;
}
m_meshLog->moveCursor(QTextCursor::End);
int d0 = 0;
int d1 = m_nX-1;
int d0z = d0 + qRound(m_dataMin.z);
int d1z = d1 + qRound(m_dataMin.z);
uchar *opacityVol = new uchar[m_nX*m_nY*m_nZ];
uchar *cropped = new uchar[nbytes];
uchar *tmp = new uchar[nbytes];
int i0 = 0;
for(int i=d0z; i<=d1z; i++)
{
m_meshProgress->setValue((int)(100.0*(float)i0/(float)m_nX));
qApp->processEvents();
int iv = qBound(0, i, m_depth-1);
uchar *vslice = m_vfm->getSlice(iv);
memset(cropped, 0, nbytes);
if (!trim)
memcpy(tmp, vslice, nbytes);
else
{
int wmin = qRound(m_dataMin.y);
int hmin = qRound(m_dataMin.x);
if (m_voxelType == 0)
{
for(int w=0; w<m_nY; w++)
for(int h=0; h<m_nZ; h++)
tmp[w*m_nZ + h] = vslice[(wmin+w)*m_height + (hmin+h)];
}
else
{
for(int w=0; w<m_nY; w++)
for(int h=0; h<m_nZ; h++)
((ushort*)tmp)[w*m_nZ + h] = ((ushort*)vslice)[(wmin+w)*m_height + (hmin+h)];
}
}
int jk = 0;
for(int j=0; j<m_nY; j++)
for(int k=0; k<m_nZ; k++)
{
Vec po = Vec(m_dataMin.x+k, m_dataMin.y+j, iv);
bool ok = true;
// we don't want to scale before pruning
int mop = 0;
{
Vec pp = po - m_dataMin;
int ppi = pp.x/m_pruneLod;
int ppj = pp.y/m_pruneLod;
int ppk = pp.z/m_pruneLod;
ppi = qBound(0, ppi, m_pruneX-1);
ppj = qBound(0, ppj, m_pruneY-1);
ppk = qBound(0, ppk, m_pruneZ-1);
int mopidx = ppk*m_pruneY*m_pruneX + ppj*m_pruneX + ppi;
mop = m_pruneData[3*mopidx + chan];
ok = (mop > 0);
}
po *= m_samplingLevel;
if (ok && clipPresent)
ok = StaticFunctions::getClip(po, clipPos, clipNormal);
if (ok && m_cropPresent)
ok = checkCrop(po);
if (ok && m_pathCropPresent)
ok = checkPathCrop(po);
if (ok && m_blendPresent)
{
ushort v;
if (m_voxelType == 0)
v = tmp[j*m_nZ + k];
else
v = ((ushort*)tmp)[j*m_nZ + k];
ok = checkBlend(po, v, lut);
}
if (ok && m_pathBlendPresent)
{
ushort v;
if (m_voxelType == 0)
v = tmp[j*m_nZ + k];
else
v = ((ushort*)tmp)[j*m_nZ + k];
ok = checkPathBlend(po, v, lut);
}
if (ok)
cropped[jk] = mop;
else
cropped[jk] = 0;
jk ++;
}
if (m_voxelType == 0)
{
for(int j=0; j<m_nY*m_nZ; j++)
{
if (cropped[j] == 0)
tmp[j] = 0;
}
}
else
{
for(int j=0; j<m_nY*m_nZ; j++)
{
if (cropped[j] == 0)
((ushort*)tmp)[j] = 0;
}
}
applyOpacity(iv, cropped, lut, tmp);
memcpy(opacityVol + i0*m_nY*m_nZ, tmp, m_nY*m_nZ);
i0++;
}
delete [] tmp;
delete [] cropped;
m_meshProgress->setValue(100);
qApp->processEvents();
//------------
if (m_tearPresent)
{
uchar *data0 = new uchar[m_nX*m_nY*m_nZ];
memcpy(data0, opacityVol, m_nX*m_nY*m_nZ);
applyTear(d0, d1, 0,
data0, opacityVol, false);
delete [] data0;
}
typedef uchar PixelType;
const unsigned int Dimension = 3;
typedef itk::Image< PixelType, Dimension > ImageType;
ImageType::IndexType start;
start.Fill(0);
ImageType::SizeType size;
size[0] = m_nZ;
size[1] = m_nY;
size[2] = m_nX;
ImageType::RegionType region(start, size);
ImageType::Pointer image = ImageType::New();
image->SetRegions(region);
image->Allocate();
image->FillBuffer(0);
uchar *iptr = (uchar*)image->GetBufferPointer();
memcpy(iptr, opacityVol, m_nX*m_nY*m_nZ);
typedef itk::Image< float, 3 > OutputImageType;
typedef itk::SignedMaurerDistanceMapImageFilter<ImageType, OutputImageType> DistanceMapFilter;
DistanceMapFilter::Pointer filter = DistanceMapFilter::New();
filter->SetInput( image );
filter->SetSquaredDistance(0);
filter->SetUseImageSpacing(0);
filter->SetInsideIsPositive(1);
filter->Update();
QFile fp;
fp.setFileName(flnm);
fp.open(QFile::WriteOnly);
uchar vt = 8;
fp.write((char*)&vt, 1);
fp.write((char*)&m_nX, 4);
fp.write((char*)&m_nY, 4);
fp.write((char*)&m_nZ, 4);
OutputImageType *dimg = filter->GetOutput();
char *tdata = (char*)(dimg->GetBufferPointer());
fp.write(tdata, 4*m_nX*m_nY*m_nZ);
fp.close();
m_meshLog->moveCursor(QTextCursor::End);
m_meshLog->insertPlainText("Signed Distance Map data saved in "+flnm);
QMessageBox::information(0, "", QString("Signed Distance Map saved in "+flnm));
}
void CUnitVolumeMakerDlg::GetImage(int iWidth, int iLength, int iHeight, int iZ,
EZoomOut eZoomOutLevel)
{
int nCol;
int nX, nY, nZ;
int nRibbonWidth;
int nImageWidth;
int nRightWidth;
int nTotalWidth;
QString strPathName, strImageFileName, strImageVolPathName, strImage4VolFileName;
nRibbonWidth = qRound(float(m_TissueBlock.m_Ribbon.m_nWidth)/eZoomOutLevel);
nCol = (int)((m_TissueBlock.m_UnitCube.m_nWidth*iWidth)/nRibbonWidth);
nX = nRibbonWidth - (nRibbonWidth*(nCol+1)-(iWidth*m_TissueBlock.m_UnitCube.m_nWidth));
nY = iLength*m_TissueBlock.m_UnitCube.m_nLength;
nZ = iHeight*m_TissueBlock.m_UnitCube.m_nHeight;
strPathName = QString(tr("%1%2%3/%4/")
.arg(sINIT_DATA_DIR).arg(sZOOM_OUT_DIR_PREFIX).arg(eZoomOutLevel).arg(nCol));
strImageFileName.sprintf("%05d%s", nZ+eZoomOutLevel*iZ, sDATA_FILE_FORMAT);
nRightWidth = nRibbonWidth - nX;
if(nRightWidth > m_TissueBlock.m_UnitCube.m_nWidth)
{
nImageWidth = qMin(m_TissueBlock.m_UnitCube.m_nWidth, nRibbonWidth);
}
else
{
nImageWidth = nRightWidth;
}
// extract nX, nY, nImageWidth, m_TissueBlock.m_UnitCube.m_nLength
//...
qDebug() << "nX: " << nX << ", nY: " << nY << ", nImageWidth: " << nImageWidth << "\n";
ui.listWidgetResult->addItem(tr("nCol: %1, nX: %2, nY: %3, nImageWidth: %4").arg(nCol).arg(nX).arg(nY).arg(nImageWidth));
ui.listWidgetResult->addItem(strPathName);
ui.listWidgetResult->addItem(strImageFileName);
// source image filename (full path)
QString strFileName = strPathName + strImageFileName;
/////////////////////////
// read an image
// typedef
typedef unsigned char PixelType;
const unsigned int nDimension = 2;
typedef itk::Image<PixelType, nDimension> ImageType;
typedef itk::ImageFileReader<ImageType> ReaderType;
typedef itk::ImageFileWriter<ImageType> WriterType;
//typedef itk::RegionOfInterestImageFilter<ImageType, ImageType> ROIFilterType;
typedef itk::ImageRegionConstIterator< ImageType > ConstIteratorType;
typedef itk::ImageRegionIterator< ImageType> IteratorType;
/////////////////////////////////////
// input: a region of a source image
ImageType::RegionType InputRegion;
ImageType::RegionType::IndexType InputStart;
ImageType::RegionType::SizeType InputSize;
InputStart[0] = nX;
InputStart[1] = nY;
InputSize[0] = nImageWidth;
InputSize[1] = m_TissueBlock.m_UnitCube.m_nLength;
InputRegion.SetSize( InputSize );
InputRegion.SetIndex( InputStart );
/////////////////////////////////////
// output: a region of a output image
ImageType::RegionType OutputRegion, OutputSubRegion;
ImageType::RegionType::IndexType OutputStart;
ImageType::RegionType::SizeType OutputSize;
OutputStart[0] = 0;
OutputStart[1] = 0;
OutputSize[0] = m_TissueBlock.m_UnitCube.m_nWidth; //InputSize[0];
OutputSize[1] = m_TissueBlock.m_UnitCube.m_nLength; //InputSize[1];
OutputRegion.SetSize( OutputSize );
OutputRegion.SetIndex( OutputStart );
OutputSize[0] = InputSize[0];
OutputSize[1] = InputSize[1];
OutputSubRegion.SetSize( OutputSize );
OutputSubRegion.SetIndex( OutputStart );
bool bErrorInSourceImage = false;
/////////////////////////////////////
// read the source image
ReaderType::Pointer pReader = ReaderType::New();
pReader->SetFileName(strFileName.toStdString());
try
{
pReader->Update();
}
catch ( itk::ExceptionObject &err)
{
std::cerr << "ExceptionObject caught !" << std::endl;
std::cerr << err << std::endl;
bErrorInSourceImage = true;
//return; // -1;
}
// Check that the region is contained within the input image.
if(!pReader->GetOutput()->GetRequestedRegion().IsInside( InputRegion ) )
{
std::cerr << "Error" << std::endl;
std::cerr << "The region " << InputRegion << "is not contained within the input image region "
<< pReader->GetOutput()->GetRequestedRegion() << std::endl;
bErrorInSourceImage = true;
//return; // -1;
}
////////////////////////////////////
// prepare the output
ImageType::Pointer pOutputImage = ImageType::New();
pOutputImage->SetRegions( OutputRegion );
pOutputImage->Allocate();
///////////////////////////////////
// fill buffer with initial value
ImageType::PixelType InitialValue = nDEF_BG_COLOR;
pOutputImage->FillBuffer( InitialValue );
/////////////////////////////////////////////////////////////////////////
// get pixels from the source image file and put them into the output image file
if(bErrorInSourceImage != true)
{
ConstIteratorType InputIt( pReader->GetOutput(), InputRegion );
IteratorType OutputIt( pOutputImage, OutputSubRegion );
for(InputIt.GoToBegin(), OutputIt.GoToBegin(); !InputIt.IsAtEnd(); ++InputIt, ++OutputIt)
{
OutputIt.Set(InputIt.Get());
}
}
nTotalWidth = nImageWidth;
while(nTotalWidth < m_TissueBlock.m_UnitCube.m_nWidth)
{
nCol++;
if(nCol == m_TissueBlock.m_nNumCol)
break;
nX = 0;
nImageWidth = m_TissueBlock.m_UnitCube.m_nWidth - nTotalWidth;
if(nImageWidth > nRibbonWidth)
{
nImageWidth = nRibbonWidth;
}
strPathName = QString(tr("%1%2%3/%4/")
.arg(sINIT_DATA_DIR).arg(sZOOM_OUT_DIR_PREFIX).arg(eZoomOutLevel).arg(nCol));
strImageFileName.sprintf("%05d%s", nZ+eZoomOutLevel*iZ, sDATA_FILE_FORMAT);
// extract nX, nY, nImageWidth, m_TissueBlock.m_UnitCube.m_nLength
// for display
qDebug() << "nX: " << nX << ", nY: " << nY << ", nImageWidth: " << nImageWidth << "\n";
ui.listWidgetResult->addItem(tr("nCol: %1, nX: %2, nY: %3, nImageWidth: %4").arg(nCol).arg(nX).arg(nY).arg(nImageWidth));
ui.listWidgetResult->addItem(strPathName);
ui.listWidgetResult->addItem(strImageFileName);
// source image filename (full path)
strFileName = strPathName + strImageFileName;
// set input size
InputStart[0] = nX;
InputStart[1] = nY;
InputSize[0] = nImageWidth;
InputSize[1] = m_TissueBlock.m_UnitCube.m_nLength;
InputRegion.SetSize( InputSize );
InputRegion.SetIndex( InputStart );
OutputSize[0] = InputSize[0];
OutputSize[1] = InputSize[1];
ImageType::RegionType::IndexType OutputStartSub;
OutputStartSub[0] = nTotalWidth;
OutputStartSub[1] = 0;
OutputSubRegion.SetSize( OutputSize );
OutputSubRegion.SetIndex( OutputStartSub );
bErrorInSourceImage = false;
/////////////////////////////////////
// read the source image
//ReaderType::Pointer pReader = ReaderType::New();
pReader->SetFileName(strFileName.toStdString());
try
{
pReader->Update();
}
catch ( itk::ExceptionObject &err)
{
std::cerr << "ExceptionObject caught !" << std::endl;
std::cerr << err << std::endl;
bErrorInSourceImage = true;
//return; // -1;
}
// Check that the region is contained within the input image.
if(!pReader->GetOutput()->GetRequestedRegion().IsInside( InputRegion ) )
{
std::cerr << "Error" << std::endl;
std::cerr << "The region " << InputRegion << "is not contained within the input image region "
<< pReader->GetOutput()->GetRequestedRegion() << std::endl;
bErrorInSourceImage = true;
//return; // -1;
}
////////////////////////////////////
// prepare the output
//ImageType::Pointer pOutputImage = ImageType::New();
//pOutputImage->SetRegions( OutputRegion );
//pOutputImage->Allocate();
if(bErrorInSourceImage != true)
{
ConstIteratorType InputIt( pReader->GetOutput(), InputRegion );
IteratorType OutputIt( pOutputImage, OutputSubRegion );
for(InputIt.GoToBegin(), OutputIt.GoToBegin(); !InputIt.IsAtEnd(); ++InputIt, ++OutputIt)
{
OutputIt.Set(InputIt.Get());
}
}
nTotalWidth += nImageWidth;
}
/////////////////////////////////////////////////////////
// get an output image file name (full path)
strImageVolPathName = QString(tr("%1%2%3/%4/")
.arg(sINIT_DATA_DIR).arg(sZOOM_OUT_DIR_PREFIX).arg(eZoomOutLevel).arg(sVOL_DIR_PREFIX));
QString strVolDir;
strVolDir.sprintf("%03d_%03d_%03d", iWidth, iLength, iHeight);
strVolDir = strImageVolPathName + strVolDir;
QDir dir;
dir.mkdir(strImageVolPathName);
dir.mkdir(strVolDir);
strImage4VolFileName.sprintf("%03d_%03d_%03d/%05d%s",
iWidth, iLength, iHeight, nZ+eZoomOutLevel*iZ, sDATA_FILE_FORMAT);
strImage4VolFileName = strImageVolPathName + strImage4VolFileName;
/////////////////////////////////
// write an output image
WriterType::Pointer pWriter = WriterType::New();
pWriter->SetFileName(strImage4VolFileName.toStdString());
pWriter->SetInput( pOutputImage );
try
{
pWriter->Update();
}
catch ( itk::ExceptionObject &err)
{
std::cerr << "ExceptionObject caught !" << std::endl;
std::cerr << err << std::endl;
return; // -1;
}
}
int main(int argc, char *argv[])
{
//check that the user specified the right number of command line arguments
if(argc < 3)
{
cerr << argv[0] << " <input file> <output file>" << endl;
cerr << argv[0] << " <raw input file> <sizeX> <sizeY> <sizeZ> <output file>"
<< endl;
return EXIT_FAILURE;
}
//check if the input image is .raw
bool rawInput = false;
string inputFileName = argv[1];
const char *outputFileName;
//double space[3]={1,1,1};
if(inputFileName.rfind(".raw") != string::npos)
{
//if so, the user is also required to pass in image dimensions
if(argc < 6)
{
cerr << "Usage: <raw input file> <sizeX> <sizeY> <sizeZ> <output file>" << endl;
return EXIT_FAILURE;
}
rawInput = true;
sizeX = atoi(argv[2]);
sizeY = atoi(argv[3]);
sizeZ = atoi(argv[4]);
outputFileName = argv[5];
}
else
{
outputFileName = argv[2];
}
FILE *infile = 0;
FILE *outfile;
int i,j,k;
int ii, jj, kk;
DATATYPEOUT *volout;
long idx;
int sizeExpand = 0;
DATATYPEOUT blockMax;
int timesDilate;
int border;
unsigned short *GraphcutResults;
cout << "Volume Processing..." << endl;
//make sure we can write to the output file
if((outfile=fopen(outputFileName, "wb")) == NULL)
{
cerr << "Output file open error!" << endl;
return EXIT_FAILURE;
}
typedef float PixelType;
const unsigned int Dimension = 3;
typedef itk::Image< PixelType, Dimension > ImageType;
ImageType::Pointer inputImage;
if(rawInput)
{
if((infile=fopen(inputFileName.c_str(), "rb"))==NULL)
{
cout << "Input file open error!" << endl;
return EXIT_FAILURE;
}
volin = (DATATYPEIN*)malloc(sizeX*sizeY*(sizeZ+sizeExpand*2)*sizeof(DATATYPEIN));
if (fread(volin, sizeof(DATATYPEIN), sizeX*sizeY*sizeZ, infile) < (unsigned int)(sizeX*sizeY*sizeZ))
{
cerr << "File size is not the same as volume size" << endl;
return EXIT_FAILURE;
}
inputImage = ImageType::New();
ImageType::PointType origin;
origin[0] = 0.;
origin[1] = 0.;
origin[2] = 0.;
inputImage->SetOrigin( origin );
ImageType::IndexType start;
start[0] = 0;
start[1] = 0;
start[2] = 0;
ImageType::SizeType size;
size[0] = sizeX;
size[1] = sizeY;
size[2] = sizeZ;
ImageType::RegionType region;
region.SetSize( size );
region.SetIndex( start );
inputImage->SetRegions( region );
inputImage->Allocate();
inputImage->FillBuffer(0);
inputImage->Update();
typedef itk::ImageRegionIteratorWithIndex< ImageType > IteratorType;
IteratorType iterator1(inputImage,inputImage->GetRequestedRegion());
int lng = sizeX*sizeY*sizeZ;
for(int i=0; i<lng; i++)
{
iterator1.Set((float)volin[i]);
++iterator1;
}
} // end if(rawInput)
else
{
typedef itk::ImageFileReader< ImageType > ReaderType;
ReaderType::Pointer reader = ReaderType::New();
inputImage = reader->GetOutput();
reader->SetFileName( inputFileName.c_str() );
try
{
reader->Update();
}
catch( itk::ExceptionObject & err )
{
cerr << "ExceptionObject caught!" << endl;
cerr << err << endl;
return EXIT_FAILURE;
}
} // end of itk image read
// ---------------Linear Mapping --------------------//
typedef itk::RescaleIntensityImageFilter<
ImageType, ImageType> RescaleFilterType;
RescaleFilterType::Pointer rescaleFilter = RescaleFilterType::New();
rescaleFilter->SetInput(inputImage);
rescaleFilter->SetOutputMinimum( 0 );
rescaleFilter->SetOutputMaximum( 255 );
try
{
rescaleFilter->Update();
}
catch( itk::ExceptionObject & err )
{
cerr << "ExceptionObject caught!" << endl;
cerr << err << endl;
return EXIT_FAILURE;
}
inputImage = rescaleFilter->GetOutput();
cout << "The Linear Mapping is done\n";
# if Curvature_Anistropic_Diffusion
{
cout << "The Curvature Diffusion is doing\n";
typedef itk::CurvatureAnisotropicDiffusionImageFilter<
ImageType, ImageType > MCD_FilterType;
MCD_FilterType::Pointer MCDFilter = MCD_FilterType::New();
//Initialnization, using the paper's optimal parameters
const unsigned int numberOfIterations = 5;
const double timeStep = 0.0425;
const double conductance = 3;
MCDFilter->SetNumberOfIterations(numberOfIterations);
MCDFilter->SetTimeStep( timeStep );
MCDFilter->SetConductanceParameter( conductance );
MCDFilter->SetInput(inputImage);
try
{
MCDFilter->Update();
}
catch( itk::ExceptionObject & err )
{
cerr << "ExceptionObject caught!" << endl;
cerr << err << endl;
return EXIT_FAILURE;
}
inputImage=MCDFilter->GetOutput();
cout << "The Curvature Diffusion is done\n";
}
#endif
ImageType::RegionType region = inputImage->GetBufferedRegion();
ImageType::SizeType size = region.GetSize();
cout << "input image size: " << size << endl;
sizeX = size[0];
sizeY = size[1];
sizeZ = size[2];
itk::ImageRegionIterator< ImageType >
itr( inputImage, inputImage->GetBufferedRegion() );
itr.GoToBegin();
idx = 0;
volin = (DATATYPEIN*)malloc(sizeX*sizeY*(sizeZ+sizeExpand*2)*sizeof(DATATYPEIN));
while( ! itr.IsAtEnd() )
{
volin[idx] = itr.Get();
++itr;
++idx;
}
//allocate memory for the output image
volout = (DATATYPEOUT*)malloc(sizeX*sizeY*(sizeZ+sizeExpand*2)*sizeof(DATATYPEOUT));
// one pre-processing scheme
GraphcutResults = (unsigned short*)malloc(sizeX*sizeY*(sizeZ+sizeExpand*2)*sizeof(unsigned short));
Neuron_Binarization_3D(volin,GraphcutResults,sizeX,sizeY,sizeZ,0,1);
for (k=0; k<(sizeZ+sizeExpand*2); k++)
for (j=0; j<sizeY; j++)
for (i=0; i<sizeX; i++) {
volout[k *sizeX*sizeY + j *sizeX + i] = 0;
} //initial to zeros
std::cout << "Do you think we need the distance transform to make the centerline of image become bright with higher intensity?";
char tmpAnswer = 'n';
//tmpAnswer = getchar();
if (tmpAnswer =='Y' || tmpAnswer =='y')
{
unsigned char *GraphcutResultsTmp;
GraphcutResultsTmp = (unsigned char*)malloc(sizeX*sizeY*(sizeZ+sizeExpand*2)*sizeof(unsigned char));
for (k=0; k<(sizeZ+sizeExpand*2); k++)
for (j=0; j<sizeY; j++)
for (i=0; i<sizeX; i++)
{
GraphcutResultsTmp[k *sizeX*sizeY + j *sizeX + i] = (unsigned char) GraphcutResults[k *sizeX*sizeY + j *sizeX + i];
} //initial to zeros
distTransform(GraphcutResultsTmp,sizeX,sizeY,sizeZ);
for (k=0; k<sizeZ; k++)
{
// threshold first
for (j=0; j<sizeY; j++)
{
for (i=0; i<sizeX; i++)
{
idx = k *sizeX*sizeY + j *sizeX + i;
volin[idx] = GraphcutResultsTmp [idx];
} // end for
} // end for
} // end for
free(GraphcutResultsTmp);
GraphcutResultsTmp=NULL;
} // end if
else {
for (k=0; k<sizeZ; k++)
{
// threshold first
for (j=0; j<sizeY; j++)
{
for (i=0; i<sizeX; i++)
{
idx = k *sizeX*sizeY + j *sizeX + i;
if (GraphcutResults [idx] == 0)
{
volin[idx] = 0;
}
}
}
}
} // end else
free(GraphcutResults);
GraphcutResults=NULL;
// the secpnd Pre-Processing method, corresponding to the old version MDL
/*
double threshold;
// by xiao liang, using 3 sigma theory to estimate threshold;
double meanValue =0.0, VarianceValue = 0.0;
// threshold first
for (k=0; k<sizeZ; k++)
{
for (j=0; j<sizeY; j++)
{
for (i=0; i<sizeX; i++)
{
idx = k *sizeX*sizeY + j *sizeX + i;
meanValue += volin[idx];
}
}
}
meanValue = meanValue/(double)(sizeX*sizeY*sizeZ);
// threshold first
for (k=0; k<sizeZ; k++)
{
for (j=0; j<sizeY; j++)
{
for (i=0; i<sizeX; i++)
{
idx = k *sizeX*sizeY + j *sizeX + i;
VarianceValue += (volin[idx]-meanValue)*(volin[idx]-meanValue);
}
}
}
VarianceValue = VarianceValue/(double)(sizeX*sizeY*sizeZ);
VarianceValue = sqrt(VarianceValue);
double m_threshold=OtsuThreshold (sizeX,sizeY,sizeZ);
if (m_threshold > 7 || m_threshold < 0)
{
threshold =(meanValue-VarianceValue/30);
}
else
{
threshold = m_threshold;
}
//threshold =7;
cout << "OTSU optimal threshold " << threshold << endl;
for (k=0; k<(sizeZ+sizeExpand*2); k++)
for (j=0; j<sizeY; j++)
for (i=0; i<sizeX; i++) {
volout[k *sizeX*sizeY + j *sizeX + i] = 0;
} //initial to zeros
for (k=0; k<sizeZ; k++)
{
// threshold first
for (j=0; j<sizeY; j++)
{
for (i=0; i<sizeX; i++)
{
idx = k *sizeX*sizeY + j *sizeX + i;
if (volin[idx] < threshold)
{
volin[idx] = 0;
}
}
}
}
*/
// Method 2: Dilation of the object
timesDilate = 1;
border = 3;
while (timesDilate >0 )
{
for (k=border; k<sizeZ-border; k++)
{
for (j=border; j<sizeY-border; j++)
{
for (i=border; i<sizeX-border; i++)
{
blockMax = volin[k *sizeX*sizeY + j *sizeX + i];
for (kk=-1; kk<=1; kk++)
{
for (jj=-1; jj<=1; jj++)
{
for (ii=-1; ii<=1; ii++)
{
if(volin[(k+kk)*sizeX*sizeY + (j+jj)*sizeX + (i+ii)] > blockMax)
{
blockMax = volin[(k+kk)*sizeX*sizeY + (j+jj)*sizeX + (i+ii)];
}
}
}
}
// Keep the peak of the original intensity
if (blockMax == volin[k *sizeX*sizeY + j *sizeX + i] && blockMax != 0)
{
blockMax = blockMax + 1;
//if (blockMax > 255) blockMax = 255;
}
volout[k *sizeX*sizeY + j *sizeX + i] = blockMax;
}
}
}
// copy volout back to volin for the next dilation
for (k=0; k<sizeZ; k++)
{
for (j=0; j<sizeY; j++)
{
for (i=0; i<sizeX; i++)
{
volin[k *sizeX*sizeY + j *sizeX + i] = volout[k *sizeX*sizeY + j *sizeX + i];
}
}
}
timesDilate--;
}
//----- Image write
/*
typedef itk::ImageRegionIteratorWithIndex< ImageType > IteratorType;
IteratorType iterator1(inputImage,inputImage->GetRequestedRegion());
int lng = sizeX*sizeY*sizeZ;
for(int i=0; i<lng; i++)
{
iterator1.Set((float)volin[i]);
++iterator1;
}
*/
//write the output image and free memory
fwrite(volout, sizeX*sizeY*sizeZ, sizeof(DATATYPEOUT), outfile);
FILE *mhdfile;
if((mhdfile=fopen("volume_Processed.mhd","w"))==NULL)
{
cerr << "output file open error!" << endl;
return -1;
}
fprintf (mhdfile,"ObjectType = Image\n");
fprintf (mhdfile,"NDims = 3\n");
fprintf (mhdfile,"BinaryData = True\n");
fprintf (mhdfile,"BinaryDataByteOrderMSB = False\n");
fprintf (mhdfile,"CompressedData = False\n");
fprintf (mhdfile,"TransformMatrix = 1 0 0 0 1 0 0 0 1\n");
fprintf (mhdfile,"Offset = 0 0 0\n");
fprintf (mhdfile,"CenterOfRotation = 0 0 0\n");
fprintf (mhdfile,"AnatomicalOrientation = RAI\n");
fprintf (mhdfile,"ElementSpacing = 1 1 1\n");
fprintf (mhdfile,"DimSize = %d %d %d\n",sizeX,sizeY,sizeZ);
fprintf (mhdfile,"ElementType = MET_UCHAR\n");
fprintf (mhdfile,"ElementDataFile = volume_Processed.raw\n");
fclose(mhdfile);
if (rawInput)
fclose(infile);
fclose(outfile);
free(volin); // by xiao
free(volout); // by xiao
volin=NULL;
volout=NULL;
//cout << "Done" << endl;
return 0;
}
bool VolumeProcess::DialateImage(int iterations)
{
int border = 2;
ImageType::Pointer tempImg = ImageType::New();
tempImg->SetRegions( m_outputImage->GetLargestPossibleRegion() );
tempImg->Allocate();
tempImg->FillBuffer(0);
ImageType::RegionType fullRegion = m_outputImage->GetBufferedRegion();
ImageType::RegionType borderRegion;
borderRegion.SetIndex(0, fullRegion.GetIndex(0)+border);
borderRegion.SetIndex(1, fullRegion.GetIndex(1)+border);
borderRegion.SetIndex(2, fullRegion.GetIndex(2)+border);
borderRegion.SetSize(0, fullRegion.GetSize(0)-(2*border));
borderRegion.SetSize(1, fullRegion.GetSize(1)-(2*border));
borderRegion.SetSize(2, fullRegion.GetSize(2)-(2*border));
itk::ImageRegionIteratorWithIndex< ImageType > itr( m_outputImage, borderRegion );
while(iterations > 0)
{
for(itr.GoToBegin(); !itr.IsAtEnd(); ++itr)
{
double blockMax = itr.Get();
for(int k=-1; k<=1; k++)
{
for(int j=-1; j<=1; j++)
{
for(int i=-1; i<=1; i++)
{
ImageType::IndexType index = itr.GetIndex();
index[0] += i;
index[1] += j;
index[2] += k;
ImageType::PixelType pix = m_outputImage->GetPixel(index);
if((double)pix > blockMax)
{
blockMax = (double)pix;
}
}
}
}
// Keep the peak of the original intensity
if (blockMax == itr.Get() && blockMax != 0)
{
blockMax = blockMax + 1;
}
tempImg->SetPixel(itr.GetIndex(), blockMax);
}
//Copy temp img back to image for next dialation
itk::ImageRegionIterator< ImageType > itr1( tempImg, tempImg->GetLargestPossibleRegion() );
itk::ImageRegionIterator< ImageType > itr2( m_outputImage, m_outputImage->GetLargestPossibleRegion() );
for(itr1.GoToBegin(), itr2.GoToBegin() ; !itr1.IsAtEnd(); ++itr1, ++itr2)
{
itr2.Set( itr1.Get() );
}
iterations--;
}
if(debug)
std::cerr << "Dialation Done" << std::endl;
return true;
}
