void WholeCellSeg::BinarizationForRealBounds(){
if( !nuc_im_set || !cyt_im_set ){
std::cerr<<"Complete segmenting nuclei and set input imge before starting segmentation\n";
return;
}
itk::SizeValueType size1=cyt_im_inp->GetLargestPossibleRegion().GetSize()[0];
itk::SizeValueType size2=cyt_im_inp->GetLargestPossibleRegion().GetSize()[1];
if( ( size1 != nuclab_inp->GetLargestPossibleRegion().GetSize()[0] ) ||
( size2 != nuclab_inp->GetLargestPossibleRegion().GetSize()[1] ) )
{
std::cerr<<"The input images must be of the same size\n";
return;
}
typedef unsigned short int UShortPixelType;
typedef itk::ImageRegionIteratorWithIndex< UShortImageType > IteratorType;
typedef itk::ImageRegionConstIterator< UShortImageType > ConstIteratorType;
typedef itk::Statistics::ScalarImageToHistogramGenerator< IntImageType > ScalarImageToHistogramGeneratorType;
typedef ScalarImageToHistogramGeneratorType::HistogramType HistogramType;
typedef itk::OtsuMultipleThresholdsCalculator< HistogramType > CalculatorType;
typedef itk::RescaleIntensityImageFilter< UShortImageType, IntImageType > RescaleUsIntType;
typedef itk::RescaleIntensityImageFilter< UShortImageType, UShortImageType > RescaleUsUsType;
typedef itk::BinaryThresholdImageFilter< IntImageType, UShortImageType > ThreshFilterType;
typedef itk::BinaryThresholdImageFilter< UShortImageType, UShortImageType > ThresholdFilterType;
typedef itk::OrImageFilter< UShortImageType, UShortImageType, UShortImageType > OrFilterType;
typedef itk::BinaryBallStructuringElement< UShortPixelType, 2 > StructuringElementType;
typedef itk::BinaryErodeImageFilter< UShortImageType, UShortImageType, StructuringElementType > ErodeFilterType;
typedef itk::BinaryDilateImageFilter< UShortImageType, UShortImageType, StructuringElementType > DilateFilterType;
unsigned char *in_Image;
itk::SizeValueType ind=0;
//Call Yousef's binarization method if the number of bin levels is < 2
if( num_levels < 2 ){
bin_Image = (unsigned short *) malloc (size1*size2*sizeof(unsigned short));
for(itk::SizeValueType j=0; j<size2; ++j)
for(itk::SizeValueType i=0; i<size1; ++i)
BIN_Image(i,j)=255;
in_Image = (unsigned char *) malloc (size1*size2);
if( ( in_Image == NULL ) || ( bin_Image == NULL ) ){
std::cerr << "Memory allocation for binarization of image failed\n";
return;
}
RescaleUsUsType::Pointer rescaleususfilter = RescaleUsUsType::New();
rescaleususfilter->SetInput( cyt_im_inp );
rescaleususfilter->SetOutputMaximum( itk::NumericTraits<unsigned char>::max() );
rescaleususfilter->SetOutputMinimum( 0 );
rescaleususfilter->Update();
UShortImageType::Pointer resc_cyt_im = UShortImageType::New();
resc_cyt_im = rescaleususfilter->GetOutput();
ConstIteratorType pix_buf1( resc_cyt_im, resc_cyt_im->GetRequestedRegion() );
for ( pix_buf1.GoToBegin(); !pix_buf1.IsAtEnd(); ++pix_buf1, ++ind )
in_Image[ind]=(unsigned char)(pix_buf1.Get());
int ok = 0;
ok = Cell_Binarization_2D(in_Image,bin_Image, size1, size2, shift_bin);
free( in_Image );
if( !ok ){
std::cerr<<"Binarization Failed\n";
return;
}
//copy the output binary image into the ITK image
intermediate_bin_im_out = UShortImageType::New();
UShortImageType::PointType origin;
origin[0] = 0;
origin[1] = 0;
intermediate_bin_im_out->SetOrigin( origin );
UShortImageType::IndexType start;
start[0] = 0; // first index on X
start[1] = 0; // first index on Y
UShortImageType::SizeType size;
size[0] = size1; // size along X
size[1] = size2; // size along Y
UShortImageType::RegionType region;
region.SetSize( size );
region.SetIndex( start );
intermediate_bin_im_out->SetRegions( region );
intermediate_bin_im_out->Allocate();
intermediate_bin_im_out->FillBuffer(0);
intermediate_bin_im_out->Update();
itk::SizeValueType dum,dum1;
dum = 0;
dum1 = USHRT_MAX;
//unsigned int asd,asd1; asd=0; asd1=0;
IteratorType iterator ( intermediate_bin_im_out, intermediate_bin_im_out->GetRequestedRegion() );
for(itk::SizeValueType i=0; i < (size1*size2); ++i){
if( bin_Image[i] )
iterator.Set( dum1 );
else
iterator.Set( dum );
++iterator;
}
}
//Call multi level binarization method if the number of bin levels is >= 2
else{
RescaleUsIntType::Pointer rescaleusintfilter = RescaleUsIntType::New();
ScalarImageToHistogramGeneratorType::Pointer scalarImageToHistogramGenerator = ScalarImageToHistogramGeneratorType::New();
rescaleusintfilter->SetInput( cyt_im_inp );
rescaleusintfilter->SetOutputMaximum( itk::NumericTraits<unsigned short>::max() );
rescaleusintfilter->SetOutputMinimum( 0 );
rescaleusintfilter->Update();
ThreshFilterType::Pointer threshfilter = ThreshFilterType::New();
CalculatorType::Pointer calculator = CalculatorType::New();
scalarImageToHistogramGenerator->SetNumberOfBins( 255 );
calculator->SetNumberOfThresholds( num_levels );
threshfilter->SetOutsideValue( (int)0 );
threshfilter->SetInsideValue( (int)USHRT_MAX );
scalarImageToHistogramGenerator->SetInput( rescaleusintfilter->GetOutput() );
scalarImageToHistogramGenerator->Compute();
calculator->SetInputHistogram( scalarImageToHistogramGenerator->GetOutput() );
threshfilter->SetInput( rescaleusintfilter->GetOutput() );
calculator->Update();
const CalculatorType::OutputType &thresholdVector = calculator->GetOutput();
CalculatorType::OutputType::const_iterator itNum = thresholdVector.begin();
int lowerThreshold,upperThreshold;
for( int i=0; i<(num_levels-num_levels_incl); ++i ) ++itNum;
lowerThreshold = static_cast<unsigned short>(*itNum);
upperThreshold = itk::NumericTraits<unsigned short>::max();
threshfilter->SetLowerThreshold( lowerThreshold );
threshfilter->SetUpperThreshold( upperThreshold );
threshfilter->Update();
intermediate_bin_im_out = UShortImageType::New();
intermediate_bin_im_out = threshfilter->GetOutput();
}
//Fill holes left by the nuclei
ThresholdFilterType::Pointer binarythreshfilter = ThresholdFilterType::New();
binarythreshfilter->SetInsideValue( USHRT_MAX );
binarythreshfilter->SetOutsideValue( 0 );
binarythreshfilter->SetLowerThreshold( 1 );
binarythreshfilter->SetUpperThreshold( USHRT_MAX );
binarythreshfilter->SetInput( nuclab_inp );
OrFilterType::Pointer orfilter = OrFilterType::New();
orfilter->SetInput1( binarythreshfilter->GetOutput() );
orfilter->SetInput2( intermediate_bin_im_out );
//dialate and erode
ErodeFilterType::Pointer binaryErode = ErodeFilterType::New();
DilateFilterType::Pointer binaryDilate = DilateFilterType::New();
StructuringElementType structuringElement;
structuringElement.SetRadius( 3 ); // 3x3 structuring element
structuringElement.CreateStructuringElement();
binaryErode->SetKernel( structuringElement );
binaryErode->SetErodeValue( USHRT_MAX );
binaryDilate->SetDilateValue( USHRT_MAX );
binaryDilate->SetKernel( structuringElement );
binaryErode->SetInput( binaryDilate->GetOutput() );
binaryDilate->SetInput( orfilter->GetOutput() );
//erode and dialate
ErodeFilterType::Pointer binaryErode1 = ErodeFilterType::New();
DilateFilterType::Pointer binaryDilate1 = DilateFilterType::New();
binaryErode1->SetKernel( structuringElement );
binaryErode1->SetErodeValue( USHRT_MAX );
binaryDilate1->SetDilateValue( USHRT_MAX );
binaryDilate1->SetKernel( structuringElement );
binaryErode1->SetInput( binaryErode->GetOutput() );
binaryDilate1->SetInput( binaryErode1->GetOutput() );
binaryDilate1->Update();
//Get pointer to the final binary image and return it to calling function
UShortImageType::Pointer image_bin = UShortImageType::New();
image_bin = binaryDilate1->GetOutput();
bin_im_out = image_bin;
bin_done = 1;
//Update bin array
ind=0;
if( draw_real_bounds ){
ConstIteratorType pix_buf3( bin_im_out, bin_im_out->GetRequestedRegion() );
for ( pix_buf3.GoToBegin(); !pix_buf3.IsAtEnd(); ++pix_buf3, ++ind )
bin_Image[ind]=(pix_buf3.Get());
}else
free( bin_Image );
/*
typedef itk::ImageFileWriter< UShortImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName( "bin_info.tif" );
writer->SetInput( bin_im_out );//RescaleIntIO1--finalO/P
writer->Update();
*/
return;
}
//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
}
