void Binarize(InputImageType::Pointer im)
{
IteratorType iter(im,im->GetLargestPossibleRegion());
for(iter.GoToBegin(); !iter.IsAtEnd(); ++iter)
{
iter.Set((iter.Get()!=0)?255:0);
}
}
Input2DImageType::Pointer Curvelet::getSlice(InputImageType::Pointer im, int slice)
{
Input2DImageType::Pointer out = Input2DImageType::New();
Input2DImageType::SizeType size;
size[0] = im->GetLargestPossibleRegion().GetSize()[0];
size[1] = im->GetLargestPossibleRegion().GetSize()[1];
Input2DImageType::IndexType index;
index.Fill(0);
Input2DImageType::RegionType region;
region.SetSize(size);
region.SetIndex(index);
out->SetRegions(region);
out->Allocate();
if(out->GetBufferPointer()==NULL)
printf("Could not allocate memory -1 ... I'm going to crash any moment now.. \n");
memcpy(out->GetBufferPointer(),im->GetBufferPointer()+slice*size[0]*size[1],size[0]*size[1]*sizeof(unsigned char));
return out;
}
LabelImageType::Pointer getYousefSegmented(InputImageType::Pointer im_input,std::list<Seed> &seed_list,char *filename)
{
// copy the image into a unsigned char *
char configfile[1024];
strcpy(configfile,filename);
printf("Entering YousefSeg\n");
InputImageType::SizeType size = im_input->GetLargestPossibleRegion().GetSize();
unsigned char * in_Image;
in_Image = (unsigned char*) malloc( size[0]*size[1]*(size[2]+1)*sizeof(unsigned char));
if(in_Image == NULL)
{
printf("Couldn't allocate memory\n");
}
memset(in_Image,0,size[0]*size[1]*(size[2]+1)*sizeof(unsigned char));
ConstIteratorType pix_buf(im_input,im_input->GetLargestPossibleRegion());
int ind = 0;
for ( pix_buf.GoToBegin(); !pix_buf.IsAtEnd(); ++pix_buf, ++ind )
in_Image[ind]=(pix_buf.Get());
printf("Copied input data\n");
yousef_nucleus_seg *NucleusSeg = new yousef_nucleus_seg();
NucleusSeg->readParametersFromFile(configfile);
NucleusSeg->setDataImage(in_Image,size[0],size[1],size[2]+1,"null");
unsigned short * output_img;
// int *bounds_img;
NucleusSeg->runBinarization();
output_img = NucleusSeg->getBinImage();
// getITKImage(output_img);
// getProcessedBinaryImage(
NucleusSeg->runSeedDetection();
std::vector<Seed> seeds = NucleusSeg->getSeeds();
printf("In yousef_seg Seed size = %d\n", (int)seeds.size());
std::vector<Seed>::iterator iter = seeds.begin();
for(;iter!=seeds.end();iter++)
{
seed_list.push_back(*iter);
}
NucleusSeg->runClustering();
printf("Finished Clustering\n");
if(NucleusSeg->isSegmentationFinEnabled())
{
NucleusSeg->runAlphaExpansion3D();
output_img=NucleusSeg->getSegImage();
}
else
{
output_img=NucleusSeg->getClustImage();
}
// bounds_img = NucleusSeg->getBoundsImage();
printf("Finished segmentation\n");
LabelImageType::Pointer label = LabelImageType::New();
label->SetRegions(im_input->GetLargestPossibleRegion());
label->Allocate();
LabelIteratorType liter(label,label->GetLargestPossibleRegion());
ind = 0;
for(liter.GoToBegin();!liter.IsAtEnd();++liter,++ind)
{
liter.Set(output_img[ind]);
}
delete NucleusSeg;
free(in_Image);
return label;
}
int main()
{
InputImageType::Pointer im = readImage<InputImageType>("C:/Users/arun/Research/Farsight/exe/bin/CF_1_inverted_bg_sub.tif");
FILE *fp = fopen("C:/Users/arun/Research/Farsight/exe/bin/seeds.txt","r");
//IteratorType initer(im,im->GetLargestPossibleRegion());
//initer.GoToBegin();
//
//for(;!initer.IsAtEnd(); ++initer)
//{
// initer.Set(transfer_function1(initer.Get()));
//}
//
//writeImage<InputImageType>(im,"C:/Users/arun/Research/Farsight/exe/bin/hp2_cropped2_filtered.tif");
//
//return 0;
typedef itk::SymmetricSecondRankTensor<double,3> HessianType;
typedef itk::Hessian3DToVesselnessMeasureImageFilter<float> MeasureType;
typedef itk::Image<HessianType,3> HessianImageType;
typedef itk::MultiScaleHessianBasedMeasureImageFilter< InputImageType, HessianImageType, FloatImageType> VesselnessFilterType;
std::vector<InputImageType::RegionType> in1,in2,out1,out2;
get_tiles(im->GetLargestPossibleRegion().GetSize(),1500,1500,1500,100,100,10,in1,in2,out1,out2);
InputImageType::Pointer om;
/*
om = InputImageType::New();
om->SetRegions(im->GetLargestPossibleRegion());
om->Allocate();
for(int counter = 0; counter < in1.size(); counter++)
{
InputImageType::Pointer imtile = InputImageType::New();//
imtile->SetRegions(in2[counter]);
imtile->Allocate();
in1[counter].Print(std::cout);
in2[counter].Print(std::cout);
IteratorType iter1(im,in1[counter]);
IteratorType iter2(imtile,in2[counter]);
for(iter1.GoToBegin(),iter2.GoToBegin();!iter1.IsAtEnd(); ++iter1,++iter2)
{
iter2.Set(iter1.Get());
}
VesselnessFilterType::Pointer vfilt = VesselnessFilterType::New();
MeasureType::Superclass::Pointer measure = MeasureType::New();
vfilt->SetInput(imtile);
vfilt->SetHessianToMeasureFilter((VesselnessFilterType::HessianToMeasureFilterType *)measure);
vfilt->SetSigmaMinimum(3.0);
vfilt->SetSigmaMaximum(5.0);
vfilt->SetNumberOfSigmaSteps(3);
vfilt->SetSigmaStepMethod(VesselnessFilterType::EquispacedSigmaSteps);
vfilt->Update();
FloatImageType::Pointer omtile = vfilt->GetOutput();
typedef itk::ImageRegionIterator<FloatImageType> FloatIteratorType;
FloatIteratorType iter3;
iter1 = IteratorType(om,out1[counter]);
iter3 = FloatIteratorType(omtile,out2[counter]);
for(iter1.GoToBegin(),iter3.GoToBegin();!iter1.IsAtEnd();++iter1,++iter3)
{
iter1.Set(iter3.Get());
}
}
writeImage<InputImageType>(om,"C:/Users/arun/Research/Farsight/exe/bin/vesselnesstest.tif");
*/
om = readImage<InputImageType>("C:/Users/arun/Research/Farsight/exe/bin/vesselnesstest.tif");
typedef itk::BinaryBallStructuringElement<InputImageType::PixelType,3> StructElementType;
typedef itk::GrayscaleDilateImageFilter<InputImageType,InputImageType,StructElementType> FilterType1;
FilterType1::Pointer minfilt = FilterType1::New();
minfilt->SetInput(om);
FilterType1::RadiusType radius;
radius[0] = 1;
radius[1] = 1;
radius[2] = 1;
StructElementType strel;
strel.SetRadius(radius);
minfilt->SetKernel(strel);
minfilt->Update();
InputImageType::Pointer seed_out = InputImageType::New();
seed_out->SetRegions(om->GetLargestPossibleRegion());
seed_out->Allocate();
seed_out->FillBuffer(0);
int thresh_value = 6;
int number_of_seeds = 200;
int tnum_seeds = 0;
typedef itk::ImageRegionIteratorWithIndex<InputImageType> IndexIteratorType;
IndexIteratorType it1(minfilt->GetOutput(),minfilt->GetOutput()->GetLargestPossibleRegion());
IteratorType it2(om,om->GetLargestPossibleRegion());
for(it2.GoToBegin();!it2.IsAtEnd(); ++it2)
{
if(it2.Get()>thresh_value)
tnum_seeds++;
}
printf("tnum_seeds = %d\n",tnum_seeds);
IteratorType it3(seed_out,seed_out->GetLargestPossibleRegion());
IteratorType it4(im,im->GetLargestPossibleRegion());
std::vector<mdl::fPoint3D> seeds;
seeds.clear();
/*for(it1.GoToBegin(),it2.GoToBegin(),it3.GoToBegin(),it4.GoToBegin();!it1.IsAtEnd();++it1,++it2,++it3,++it4)
{
if(it1.Get()==it2.Get() && it4.Get() > 150)
{
it3.Set(255);
InputImageType::IndexType index = it1.GetIndex();
mdl::fPoint3D seed1;
seed1.x = index[0];
seed1.y = index[1];
seed1.z = index[2];
seeds.push_back(seed1);
}
}*/
seeds.clear();
while(!feof(fp))
{
mdl::fPoint3D seed1;
fscanf(fp,"%f %f %f",&seed1.x,&seed1.y,&seed1.z);
if(feof(fp))
break;
seed1.x*=1;
seed1.y*=1;
seeds.push_back(seed1);
}
fclose(fp);
printf("Seeds.size = %d\n",seeds.size());
//scanf("%*d");
mdl::vtkFileHandler * fhd1 = new mdl::vtkFileHandler();
fhd1->SetNodes(&seeds);
std::vector<mdl::pairE> nullpairs;
fhd1->SetLines(&nullpairs);
std::string outFilename1 = "C:/Users/arun/Research/Farsight/exe/bin/mst_input.vtk";
fhd1->Write(outFilename1.c_str());
delete fhd1;
int edgeRange = 50;
int morphStrength = 0;
mdl::MST *mst = new mdl::MST( im );
mst->SetDebug(false);
mst->SetUseVoxelRounding(false);
mst->SetEdgeRange(edgeRange);
mst->SetPower(1);
mst->SetSkeletonPoints( &seeds );
// can choose different weight
//mst->CreateGraphAndMST(1);
mst->CreateGraphAndMST(5);
mst->ErodeAndDialateNodeDegree(morphStrength);
std::vector<mdl::fPoint3D> nodes = mst->GetNodes();
std::vector<mdl::pairE> bbpairs = mst->BackboneExtract();
delete mst;
std::cerr << "Saving\n";
//****************************************************************
// TREE WRITER
mdl::vtkFileHandler * fhd2 = new mdl::vtkFileHandler();
fhd2->SetNodes(&nodes);
fhd2->SetLines(&bbpairs);
std::string outFilename2 = "C:/Users/arun/Research/Farsight/exe/bin/mst_tree.vtk";
fhd2->Write(outFilename2.c_str());
delete fhd2;
scanf("%*d");
writeImage<InputImageType>(seed_out,"C:/Users/arun/Research/Farsight/exe/bin/seedimage.tif");
}
static mitk::Image::Pointer ResampleBySpacing(mitk::Image *input, float *spacing, bool useLinInt = true, bool useNN = false)
{
if (!useNN)
{
InputImageType::Pointer itkImage = InputImageType::New();
CastToItkImage(input,itkImage);
/**
* 1) Resampling
*
*/
// Identity transform.
// We don't want any transform on our image except rescaling which is not
// specified by a transform but by the input/output spacing as we will see
// later.
// So no transform will be specified.
typedef itk::IdentityTransform<double, 3> T_Transform;
// The resampler type itself.
typedef itk::ResampleImageFilter<InputImageType, InputImageType> T_ResampleFilter;
// Prepare the resampler.
// Instantiate the transform and specify it should be the id transform.
T_Transform::Pointer _pTransform = T_Transform::New();
_pTransform->SetIdentity();
// Instantiate the resampler. Wire in the transform and the interpolator.
T_ResampleFilter::Pointer _pResizeFilter = T_ResampleFilter::New();
// Specify the input.
_pResizeFilter->SetInput(itkImage);
_pResizeFilter->SetTransform(_pTransform);
// Set the output origin.
_pResizeFilter->SetOutputOrigin(itkImage->GetOrigin());
// Compute the size of the output.
// The size (# of pixels) in the output is recomputed using
// the ratio of the input and output sizes.
InputImageType::SpacingType inputSpacing = itkImage->GetSpacing();
InputImageType::SpacingType outputSpacing;
const InputImageType::RegionType& inputSize = itkImage->GetLargestPossibleRegion();
InputImageType::SizeType outputSize;
typedef InputImageType::SizeType::SizeValueType SizeValueType;
// Set the output spacing.
outputSpacing[0] = spacing[0];
outputSpacing[1] = spacing[1];
outputSpacing[2] = spacing[2];
outputSize[0] = static_cast<SizeValueType>(inputSize.GetSize()[0] * inputSpacing[0] / outputSpacing[0] + .5);
outputSize[1] = static_cast<SizeValueType>(inputSize.GetSize()[1] * inputSpacing[1] / outputSpacing[1] + .5);
outputSize[2] = static_cast<SizeValueType>(inputSize.GetSize()[2] * inputSpacing[2] / outputSpacing[2] + .5);
_pResizeFilter->SetOutputSpacing(outputSpacing);
_pResizeFilter->SetSize(outputSize);
typedef itk::LinearInterpolateImageFunction< InputImageType > LinearInterpolatorType;
LinearInterpolatorType::Pointer lin_interpolator = LinearInterpolatorType::New();
typedef itk::WindowedSincInterpolateImageFunction< InputImageType, 4> WindowedSincInterpolatorType;
WindowedSincInterpolatorType::Pointer sinc_interpolator = WindowedSincInterpolatorType::New();
if (useLinInt)
_pResizeFilter->SetInterpolator(lin_interpolator);
else
_pResizeFilter->SetInterpolator(sinc_interpolator);
_pResizeFilter->Update();
mitk::Image::Pointer image = mitk::Image::New();
image->InitializeByItk(_pResizeFilter->GetOutput());
mitk::GrabItkImageMemory( _pResizeFilter->GetOutput(), image);
return image;
}
BinaryImageType::Pointer itkImage = BinaryImageType::New();
CastToItkImage(input,itkImage);
/**
* 1) Resampling
*
*/
// Identity transform.
// We don't want any transform on our image except rescaling which is not
// specified by a transform but by the input/output spacing as we will see
// later.
// So no transform will be specified.
typedef itk::IdentityTransform<double, 3> T_Transform;
// The resampler type itself.
typedef itk::ResampleImageFilter<BinaryImageType, BinaryImageType> T_ResampleFilter;
// Prepare the resampler.
// Instantiate the transform and specify it should be the id transform.
T_Transform::Pointer _pTransform = T_Transform::New();
_pTransform->SetIdentity();
// Instantiate the resampler. Wire in the transform and the interpolator.
T_ResampleFilter::Pointer _pResizeFilter = T_ResampleFilter::New();
// Specify the input.
_pResizeFilter->SetInput(itkImage);
_pResizeFilter->SetTransform(_pTransform);
// Set the output origin.
_pResizeFilter->SetOutputOrigin(itkImage->GetOrigin());
// Compute the size of the output.
// The size (# of pixels) in the output is recomputed using
// the ratio of the input and output sizes.
BinaryImageType::SpacingType inputSpacing = itkImage->GetSpacing();
BinaryImageType::SpacingType outputSpacing;
const BinaryImageType::RegionType& inputSize = itkImage->GetLargestPossibleRegion();
BinaryImageType::SizeType outputSize;
typedef BinaryImageType::SizeType::SizeValueType SizeValueType;
// Set the output spacing.
outputSpacing[0] = spacing[0];
outputSpacing[1] = spacing[1];
outputSpacing[2] = spacing[2];
outputSize[0] = static_cast<SizeValueType>(inputSize.GetSize()[0] * inputSpacing[0] / outputSpacing[0] + .5);
outputSize[1] = static_cast<SizeValueType>(inputSize.GetSize()[1] * inputSpacing[1] / outputSpacing[1] + .5);
outputSize[2] = static_cast<SizeValueType>(inputSize.GetSize()[2] * inputSpacing[2] / outputSpacing[2] + .5);
_pResizeFilter->SetOutputSpacing(outputSpacing);
_pResizeFilter->SetSize(outputSize);
typedef itk::NearestNeighborInterpolateImageFunction< BinaryImageType> NearestNeighborInterpolateImageType;
NearestNeighborInterpolateImageType::Pointer nn_interpolator = NearestNeighborInterpolateImageType::New();
_pResizeFilter->SetInterpolator(nn_interpolator);
_pResizeFilter->Update();
mitk::Image::Pointer image = mitk::Image::New();
image->InitializeByItk(_pResizeFilter->GetOutput());
mitk::GrabItkImageMemory( _pResizeFilter->GetOutput(), image);
return image;
}
static void TestOverlay(mitk::Image::Pointer original,
mitk::Image::Pointer truth,
const double lower,
const double upper)
{
mitk::Image::Pointer overlayImage;
const double th[] = {lower, upper};
typedef itk::Image<unsigned int, 3> ImageType;
ImageType::Pointer itkOverlayImage = ImageType::New();
AccessByItk_2(original, InternalThreshold, overlayImage, th);
/*
AccessFixedDimensionByItk_2( original, InternalThreshold2,
3, itkOverlayImage,
th );
overlayImage = mitk::ImportItkImage( itkOverlayImage );
*/
// mitk::IOUtil::Save(truth, "/tmp/truth_TestOverlay.nii");
try
{
// mitk::Image::Pointer temp = overlayImage;
mitk::IOUtil::Save(overlayImage, "/tmp/overlayImage_TestOverlay.nrrd");
}
catch (const itk::ExceptionObject &e)
{
MITK_ERROR << "Save image: exception : " << e.what();
}
typedef itk::Image<unsigned int, 3> InputImageType;
InputImageType::Pointer overlayItk;
try
{
mitk::CastToItkImage(overlayImage, overlayItk);
}
catch (const mitk::Exception &e)
{
MITK_ERROR << "(CAST) Catched exception while creating accessor " << e.what();
// MITK_TEST_FAILED_MSG("Exception for ouverlay image");
}
/*
typedef itk::ImageFileWriter< InputImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName("/tmp/overlayITK_TestOverlay.nii");
writer->SetInput(overlayItk);
writer->Update();
*/
InputImageType::Pointer truthItk;
mitk::CastToItkImage(truth, truthItk);
bool difference = false;
/*
try
{
typedef unsigned int TPixel;
itk::ImageRegionConstIteratorWithIndex< InputImageType > iter( truthItk, truthItk->GetLargestPossibleRegion()
);
iter.GoToBegin();
mitk::ImagePixelReadAccessor< TPixel, 3 > readAccessor( overlayImage, overlayImage->GetVolumeData(0),
mitk::ImageAccessorBase::ExceptionIfLocked );
while( !iter.IsAtEnd() )
{
TPixel ref = iter.Get();
TPixel val = readAccessor.GetPixelByIndex( iter.GetIndex() );
difference |= ( ref != val );
//if( difference )
//{
std::cout << iter.GetIndex() << ":" << ref << " ? " << val << "\n";
//}
++iter;
}
}
catch( const mitk::Exception &e)
{
MITK_ERROR << "Catched exception while creating accessor "<< e.what();
//MITK_TEST_FAILED_MSG("Exception for ouverlay image");
}
*/
/*
typedef itk::Testing::ComparisonImageFilter
<InputImageType, InputImageType> ComparisonImageFilterType;
ComparisonImageFilterType::Pointer comp =
ComparisonImageFilterType::New();
comp->SetValidInput(truthItk);
comp->SetTestInput(overlayItk);
try
{
comp->Update();
}
catch( const itk::ExceptionObject& e)
{
MITK_ERROR << "ITK Exception: " << e.what();
}
*/
typedef unsigned int TPixel;
itk::ImageRegionConstIteratorWithIndex<InputImageType> iter(truthItk, truthItk->GetLargestPossibleRegion());
itk::ImageRegionConstIteratorWithIndex<InputImageType> iter2(overlayItk, overlayItk->GetLargestPossibleRegion());
iter.GoToBegin();
unsigned int counter = 0;
while (!iter.IsAtEnd() && !iter2.IsAtEnd())
{
TPixel ref = iter.Get();
TPixel val = iter2.Get();
if (ref != val)
{
counter++;
// std::cout << iter.GetIndex() << ":" << ref << " ? " << val << "\n";
}
++iter;
++iter2;
}
std::cout << "Differs in " << counter << "voxels" << std::endl;
MITK_TEST_CONDITION_REQUIRED(
// comp->GetNumberOfPixelsWithDifferences() == 0,
counter == 0,
"Comparing overlay with ground truth")
}
void segmentation::on_retinalLayerSegButton_clicked()
{
fstream fin1, fin7, fin11, fin12;
char* s1Txt = ("../data/ped/txt/15715_1.txt");//s1.txt
char* s7Txt = ("../data/ped/txt/15715_7.txt");
char* s11Txt = ("../data/ped/txt/15715_11.txt");
char* s12Txt = ("../data/ped/txt/15715_12.txt");
//这样开辟内存容易出现堆栈溢出问题, 选择new & delete
//int s1[64][512], s7[64][512], s11[64][512], s12[64][512];
int (*s1)[512] = new int [64][512];
int (*s7)[512] = new int [64][512];
int (*s11)[512] = new int [64][512];
int (*s12)[512] = new int [64][512];
fin1.open(s1Txt, ios::in);
fin7.open(s7Txt, ios::in);
fin11.open(s11Txt, ios::in);
fin12.open(s12Txt, ios::in);
for(int z=0; z<64; z++)
{
for(int x=0; x<512; x++)
{
fin1>>s1[z][x];
fin7>>s7[z][x];
fin11>>s11[z][x];
fin12>>s12[z][x];
}
}
fin1.close();
fin7.close();
fin11.close();
fin12.close();
typedef itk::Image<unsigned short,3>InputImageType;
typedef itk::Image<unsigned short,3>OutputImageType;
InputImageType::Pointer inputImage = InputImageType::New();
InputImageType::Pointer outputImage = InputImageType::New();
typedef itk::ImageFileReader<InputImageType>ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(inputFileName);
reader->Update();
inputImage = reader->GetOutput();
InputImageType::IndexType voxelIndex;
InputImageType::SizeType imgSize = inputImage->GetLargestPossibleRegion().GetSize();
OutputImageType::IndexType index;
index[0]=0;
index[1]=0;
index[2]=0;
OutputImageType::SizeType size;
size[0]=imgSize[0];
size[1]=imgSize[1];
size[2]=imgSize[2];
//create a region for enhance result
OutputImageType::RegionType region;
region.SetIndex(index);
region.SetSize(size);
outputImage->SetRegions(region);
outputImage->Allocate();
//make four surfaces into a MHD file
for(int z = 0; z < imgSize[2]; z++)
for(int y = 0; y < imgSize[1]; y++)
for(int x = 0; x < imgSize[0]; x++)
{
voxelIndex[0] = x;
voxelIndex[1] = y;
voxelIndex[2] = z;
if(y == s1[z][x])
{
inputImage->SetPixel(voxelIndex, 65535);
}
if(y == s7[z][x])
{
inputImage->SetPixel(voxelIndex, 65535);
}
if(y == s11[z][x])
{
inputImage->SetPixel(voxelIndex, 65535);
}
if(y == s12[z][x])
{
inputImage->SetPixel(voxelIndex, 65535);
}
}
delete []s1;//释放内存
delete []s7;
delete []s11;
delete []s12;
//文件前缀名
filePrefix = inputFileName;//char* to string
filePrefix = filePrefix.substr(0, filePrefix.length() - 4);
filePrefix = filePrefix + "_layerSeg.mhd";
strcpy(outputFileName, filePrefix.c_str());//string to char*
typedef itk::ImageFileWriter<OutputImageType>WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName(outputFileName);
writer->SetInput(inputImage);
writer->Update();
emit returnOutputFileName(outputFileName);//发出信号
}
//腐蚀操作
void segmentation::erosionOperation()//未用到
{
const unsigned int Dimension = 3;
typedef unsigned char InputPixelType;
typedef unsigned char OutputPixelType;
typedef itk::Image< InputPixelType, Dimension > InputImageType;
typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
typedef itk::ImageFileReader< InputImageType > ReaderType;
typedef itk::ImageFileWriter< OutputImageType > WriterType;
typedef itk::BinaryThresholdImageFilter< InputImageType, InputImageType > ThresholdFilterType;
typedef itk::BinaryBallStructuringElement<
InputPixelType,
Dimension > StructuringElementType;
typedef itk::BinaryErodeImageFilter<
InputImageType,
OutputImageType,
StructuringElementType > ErodeFilterType;
ReaderType::Pointer reader = ReaderType::New();
WriterType::Pointer writerErosion = WriterType::New();
ThresholdFilterType::Pointer thresholder = ThresholdFilterType::New();
ErodeFilterType::Pointer binaryErode = ErodeFilterType::New();
StructuringElementType structuringElementErosion;
reader->SetFileName( initFileName );//读入二值图
reader->Update();
InputImageType::Pointer inputImage = InputImageType::New();
InputImageType::IndexType voxelIndex;
inputImage = reader->GetOutput();
InputImageType::SizeType imgSize = inputImage->GetLargestPossibleRegion().GetSize();
long vol = 0;
unsigned char temp;
float r;
for(int z = 0; z < imgSize[2]; z++)
for(int y = 0; y < imgSize[1]; y++)
for(int x = 0; x < imgSize[0]; x++)
{
voxelIndex[0] = x;
voxelIndex[1] = y;
voxelIndex[2] = z;
temp = inputImage->GetPixel(voxelIndex);
if(temp == 255)// 255 for PED
vol += 1;
}
r = pow((3 * vol) / (4 * PI), (1.0 / 3)) ;
r = r / 20;//experiment data
structuringElementErosion.SetRadius( r ); // 3x3 structuring element
structuringElementErosion.CreateStructuringElement();
binaryErode->SetKernel( structuringElementErosion );
//文件前缀名
filePrefix = inputFileName;//char* to string
filePrefix = filePrefix.substr(0, filePrefix.length() - 4);
string erosionFileName;
erosionFileName = filePrefix + "_erosionResult.mhd";
strcpy(outputFileName, erosionFileName.c_str());//string to char*
writerErosion->SetFileName(outputFileName);
const InputPixelType lowerThreshold = 255;
const InputPixelType upperThreshold = 255;
thresholder->SetInput( reader->GetOutput() );
InputPixelType background = 0;
InputPixelType foreground = 255;
thresholder->SetOutsideValue( background );
thresholder->SetInsideValue( foreground );
thresholder->SetLowerThreshold( lowerThreshold );
thresholder->SetUpperThreshold( upperThreshold );
binaryErode->SetInput( thresholder->GetOutput() );
binaryErode->SetErodeValue( foreground );
writerErosion->SetInput( binaryErode->GetOutput() );
writerErosion->Update();
//binaryErode->GetOutput()->GetPixel(index);//获取像素值失败
//腐蚀结果叠加到原图
typedef itk::Image< unsigned short, Dimension > OriginalImageType;
typedef itk::ImageFileReader<OriginalImageType>OriginalReaderType;
OriginalReaderType::Pointer orignalImgreader = OriginalReaderType::New();
OriginalImageType::Pointer originalImage = OriginalImageType::New();
OriginalReaderType::IndexType originalImgVoxelIndex;
reader->SetFileName(outputFileName);//读入腐蚀结果图像
reader->Update();
inputImage = reader->GetOutput();
orignalImgreader->SetFileName(inputFileName);//读入原图像
orignalImgreader->Update();
originalImage = orignalImgreader->GetOutput();
for(int z = 0; z < imgSize[2]; z++)
for(int y = 0; y < imgSize[1]; y++)
for(int x = 0; x < imgSize[0]; x++)
{
voxelIndex[0] = x;
voxelIndex[1] = y;
voxelIndex[2] = z;
originalImgVoxelIndex[0] = x;
originalImgVoxelIndex[1] = y;
originalImgVoxelIndex[2] = z;
temp = inputImage->GetPixel(voxelIndex);
if(temp == 255)
originalImage->SetPixel(originalImgVoxelIndex, 65535);
}
//输出结果
typedef itk::ImageFileWriter<OriginalImageType>NewWriterType;
NewWriterType::Pointer writer = NewWriterType::New();
//文件前缀名
filePrefix = inputFileName;//char* to string
filePrefix = filePrefix.substr(0, filePrefix.length() - 4);
filePrefix = filePrefix + "_refinedResult.mhd";
strcpy(outputFileName, filePrefix.c_str());//string to char*
writer->SetFileName(outputFileName);
writer->SetInput(originalImage);
writer->Update();
emit returnInternalFileName(initResultFileName);//更新原视图
emit returnOutputFileName(outputFileName);//显示结果图
}
void segmentation::on_abnormalRegionSegButton_clicked()
{
fstream fin11, fin12;
char* s11Txt = ("../data/ped/txt/15715_11.txt");//s11.txt
char* s12Txt = ("../data/ped/txt/15715_12.txt");
int (*s11)[512] = new int[64][512];
int (*s12)[512] = new int[64][512];
int (*p)[512] = new int[64][512];
//read TXT
fin11.open(s11Txt, ios::in);
fin12.open(s12Txt, ios::in);
//get the p matrix
for(int z = 0; z < 64; z++)
{
for(int x = 0; x < 512; x++)
{
fin11>>s11[z][x];
fin12>>s12[z][x];
if(s12[z][x] - s11[z][x] > 5) //5 threshold
p[z][x] = 1;
else
p[z][x] = 0;
}
}
fin11.close();
fin12.close();
//read filtered MHD data
typedef itk::Image<unsigned short, 3>InputImageType;
typedef itk::Image<unsigned short, 3>OutputImageType;
typedef itk::Image<unsigned char, 3>InitOutputImageType;
InputImageType::Pointer inputImage = InputImageType::New();
OutputImageType::Pointer outputImage = OutputImageType::New();
InitOutputImageType::Pointer initOutputImage = InitOutputImageType::New();
typedef itk::ImageFileReader<InputImageType>ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(inputFileName);//读入原图像
reader->Update();
inputImage = reader->GetOutput();
InputImageType::IndexType voxelIndex;
InitOutputImageType::IndexType initvoxelIndex;
OutputImageType::IndexType newvoxelIndex;
InputImageType::SizeType imgSize = inputImage->GetLargestPossibleRegion().GetSize();
OutputImageType::IndexType index;
index[0] = 0;
index[1] = 0;
index[2] = 0;
OutputImageType::SizeType size;
size[0] = imgSize[0];
size[1] = imgSize[1];
size[2] = imgSize[2];
//create a region for initial result
InitOutputImageType::RegionType initRegion;
initRegion.SetIndex(index);
initRegion.SetSize(size);
initOutputImage->SetRegions( initRegion);
initOutputImage->Allocate();
//create a region for enhance result
OutputImageType::RegionType region;
region.SetIndex(index);
region.SetSize(size);
outputImage->SetRegions(region);
outputImage->Allocate();
//Initial result for PED segmentation (a binary image)
for(int z = 0; z < imgSize[2]; z++)
for(int x = 0; x < imgSize[0]; x++)
{
initvoxelIndex[0] = x;
initvoxelIndex[2] = z;
for(int y = 0; y < imgSize[1]; y++)
{
//set all background a black region
initvoxelIndex[1] = y;
initOutputImage->SetPixel(initvoxelIndex, 0);
}
//set the same intensity for all PED region (empirical value)
if(p[z][x] == 1)
{
for(int y = s11[z][x]; y <= s12[z][x]; y++)
{
initvoxelIndex[1] = y;
initOutputImage->SetPixel(initvoxelIndex, 255);//亮区域
}
}
}
//输出中间分割结果
//文件前缀名
filePrefix = inputFileName;//char* to string
filePrefix = filePrefix.substr(0, filePrefix.length() - 4);
string strInitFileName;
strInitFileName = filePrefix + "_initBinaryImg.mhd";
strcpy(initFileName, strInitFileName.c_str());//string to char*
typedef itk::ImageFileWriter<InitOutputImageType>InitWriterType;
InitWriterType::Pointer initWriter = InitWriterType::New();
initWriter->SetFileName(initFileName);//生成二值图
initWriter->SetInput(initOutputImage);
initWriter->Update();
//Enhance PED region and overlay it on the original image
for(int z = 0; z < imgSize[2]; z++)
for(int x = 0; x < imgSize[0]; x++)
{
voxelIndex[0] = x;
voxelIndex[2] = z;
newvoxelIndex[0] = x;
newvoxelIndex[2] = z;
for(int y = 0; y < imgSize[1]; y++)
{
voxelIndex[1] = y;
newvoxelIndex[1] = y;
outputImage->SetPixel(newvoxelIndex, inputImage->GetPixel(voxelIndex));
}
//set the same intensity for all PED region (empirical value)
if(p[z][x] == 1)
{
for(int y = s11[z][x]; y <= s12[z][x]; y++)
{
newvoxelIndex[1] = y;
outputImage->SetPixel(newvoxelIndex, 65535);//亮区域
}
}
}
//释放内存不能缺省
delete[]s11;
delete[]s12;
delete[]p;
typedef itk::ImageFileWriter<OutputImageType>WriterType;
WriterType::Pointer writer = WriterType::New();
filePrefix = filePrefix + "_initResult.mhd";
strcpy(outputFileName, filePrefix.c_str());//string to char*
initResultFileName = outputFileName;//输出初始分割结果，二值图重叠在原图像上面
writer->SetFileName(outputFileName);
writer->SetInput(outputImage);
writer->Update();
emit returnOutputFileName(outputFileName);//发出信号
}
InputImageType::Pointer Curvelet::RunOnInputImage(InputImageType::Pointer InputImage)
{
//InputImage = NewInputImage;
slices = InputImage->GetLargestPossibleRegion().GetSize()[2];
InputImageType::Pointer outputim = InputImageType::New();
outputim->SetRegions(InputImage->GetLargestPossibleRegion());
outputim->Allocate();
FloatImageType::Pointer cosim = FloatImageType::New();
cosim->SetRegions(InputImage->GetLargestPossibleRegion());
cosim->Allocate();
FloatImageType::Pointer sinim = FloatImageType::New();
sinim->SetRegions(InputImage->GetLargestPossibleRegion());
sinim->Allocate();
if(outputim->GetBufferPointer() == NULL || cosim->GetBufferPointer() == NULL || sinim->GetBufferPointer() == NULL)
{
printf("Couldnt' allocate memory - 3.. going to crash now\n");
}
int max_dim = tile_size;
int xsize = InputImage->GetLargestPossibleRegion().GetSize()[0];
int ysize = InputImage->GetLargestPossibleRegion().GetSize()[1];
int kx = 0;int ky = 0;
kx = xsize /(max_dim-this->border);
ky = ysize /(max_dim-this->border);
int remx = xsize % (max_dim-this->border);
int remy = ysize % (max_dim-this->border);
if ( remx > 0 )
kx ++;
if ( remy > 0 )
ky ++;
for(int xco = 0; xco < kx; xco++)
{
for(int yco = 0; yco < ky; yco++)
{
InputImageType::SizeType imsize = InputImage->GetLargestPossibleRegion().GetSize();
InputImageType::IndexType index;
InputImageType::SizeType size;
InputImageType::RegionType region;
index.Fill(0);
size[0] = MIN((xco)*(max_dim-this->border)+max_dim-1,imsize[0]-1) - xco * (max_dim-this->border) +1;
size[1] = MIN((yco)*(max_dim-this->border)+max_dim-1,imsize[1]-1) - yco * (max_dim-this->border) +1;
size[2] = imsize[2];
InputImageType::Pointer imtile = InputImageType::New();
region.SetIndex(index);
region.SetSize(size);
imtile->SetRegions(region);
imtile->Allocate();
if(imtile->GetBufferPointer()==NULL)
printf("Couldn't allocate memory - 4 .. going to crash now\n");
InputImageType::RegionType region1;
index[0] = xco *(max_dim-this->border);
index[1] = yco *(max_dim-this->border);
index[2] = 0;
region1.SetIndex(index);
region1.SetSize(size);
typedef itk::ImageRegionIterator<InputImageType> IteratorType;
IteratorType iter1(InputImage,region1);
IteratorType iter2(imtile,region);
//printf("xco = %d yco = %d :\n",xco,yco);
region1.Print(std::cout);
region.Print(std::cout);
iter1.GoToBegin();
iter2.GoToBegin();
for(;!iter1.IsAtEnd();++iter1,++iter2)
{
iter2.Set(iter1.Get());
}
InputImageType::Pointer outputtile = InputImageType::New();
outputtile->SetRegions(imtile->GetLargestPossibleRegion());
outputtile->Allocate();
FloatImageType::Pointer cosimtile = FloatImageType::New();
cosimtile->SetRegions(imtile->GetLargestPossibleRegion());
cosimtile->Allocate();
FloatImageType::Pointer sinimtile = FloatImageType::New();
sinimtile->SetRegions(imtile->GetLargestPossibleRegion());
sinimtile->Allocate();
if(outputtile->GetBufferPointer() == NULL || cosimtile->GetBufferPointer()==NULL || sinimtile->GetBufferPointer() == NULL )
{
printf("Couldn't allocate memory - 5 .. going to crash now ..\n");
}
{
#pragma omp parallel for shared(cosimtile,imtile,sinimtile,outputtile) num_threads(numt)
for(int counter = 0; counter < slices; counter++)
{
//printf("Counter = %d\n",counter);
Input2DImageType::Pointer im2d = getSlice(imtile,counter);
Input2DImageType::Pointer om2d;
Float2DImageType::Pointer cosim2d,sinim2d;
//call single slice 2-d curvelets function
getCurveletsForOneSlice(im2d,om2d,cosim2d,sinim2d);
copyslice<InputPixelType>(om2d,outputtile,counter);
copyslice<float>(cosim2d,cosimtile,counter);
copyslice<float>(sinim2d,sinimtile,counter);
}
}
//printf("copying the tile\n");
if(xco != 0)
{
size[0] = size[0] - border/2;
index[0] = border/2;
}
if(xco != kx-1)
{
size[0] = size[0] - border/2;
}
if(yco != 0)
{
size[1] = size[1] - border/2;
index[1] = border/2;
}
if(yco != ky-1)
{
size[1] = size[1] - border/2;
}
size[2] = slices;
index[2] = 0;
region.SetIndex(index);
region.SetSize(size);
if(xco!=0)
{
index[0] = xco *(max_dim-border)+border/2;
}
if(yco!=0)
{
index[1] = yco *(max_dim-border)+border/2;
}
index[2] = 0;
region1.SetSize(size);
region1.SetIndex(index);
iter1 = IteratorType(outputim,region1);
iter2 = IteratorType(outputtile,region);
typedef itk::ImageRegionIterator<FloatImageType> FIteratorType;
FIteratorType iter3(cosim,region1);
FIteratorType iter4(cosimtile,region);
FIteratorType iter5(sinim,region1);
FIteratorType iter6(sinimtile, region);
iter1.GoToBegin();iter2.GoToBegin();
iter3.GoToBegin();iter4.GoToBegin();
iter5.GoToBegin();iter6.GoToBegin();
for(;!iter1.IsAtEnd();++iter1,++iter2,++iter3,++iter4,++iter5,++iter6)
{
iter1.Set(iter2.Get());
iter3.Set(iter4.Get());
iter5.Set(iter6.Get());
}
//printf("Done with copying the tile to full image\n");
}
}
return outputim;
}