void WholeCellSeg::RemoveSmallObjs(){
typedef itk::LabelGeometryImageFilter< UShortImageType, UShortImageType > GeometryFilterType;
typedef itk::LabelStatisticsImageFilter< UShortImageType,UShortImageType > StatisticsFilterType;
typedef itk::CastImageFilter< UShortImageType, UShortImageType > CastUSUSType;
typedef itk::ImageRegionIteratorWithIndex< UShortImageType > IteratorType;
typedef GeometryFilterType::LabelIndicesType labelindicestype;
std::vector< unsigned short > labelsList;
GeometryFilterType::Pointer geomfilt1 = GeometryFilterType::New();
geomfilt1->SetInput( seg_im_out );
geomfilt1->SetCalculatePixelIndices( true );
geomfilt1->Update();
labelsList = geomfilt1->GetLabels();
StatisticsFilterType::Pointer statsfilt = StatisticsFilterType::New();
statsfilt->UseHistogramsOn();
statsfilt->SetInput( intermediate_bin_im_out );
statsfilt->SetLabelInput( seg_im_out );
statsfilt->Update();
CastUSUSType::Pointer castUSUSfilter = CastUSUSType::New();
if( draw_real_bounds && draw_synth_bounds ){
castUSUSfilter->SetInput( nuclab_inp );
castUSUSfilter->Update();
nuclab_inp_cpy = castUSUSfilter->GetOutput();
}
for( unsigned short i=0; i<labelsList.size(); ++i ){
if( !labelsList[i] ) continue;
labelindicestype indices1;
indices1 = geomfilt1->GetPixelIndices( labelsList[i] );
if( !(statsfilt->GetSum( labelsList[i] )) ){
IteratorType iterator ( seg_im_out, seg_im_out->GetRequestedRegion() );
for( labelindicestype::const_iterator itPixind = indices1.begin(); itPixind != indices1.end(); ++itPixind ){
iterator.SetIndex( *itPixind );
iterator.Set( 0 );
}
}
else if( draw_real_bounds && draw_synth_bounds ){
IteratorType iterator1 ( nuclab_inp_cpy, nuclab_inp_cpy->GetRequestedRegion() );
for( labelindicestype::const_iterator itPixind = indices1.begin(); itPixind != indices1.end(); ++itPixind ){
iterator1.SetIndex( *itPixind );
if( iterator1.Get()==labelsList[i] )
iterator1.Set( 0 );
}
}
}
if( !draw_synth_bounds && draw_real_bounds )
seg_done = 1;
}
/// return key of the iterator
const std::string& key() const
{
assert(anchor.m_object != nullptr);
switch (anchor.m_object->type())
{
// use integer array index as key
case value_t::array:
{
if (array_index != array_index_last)
{
array_index_str = std::to_string(array_index);
array_index_last = array_index;
}
return array_index_str;
}
// use key from the object
case value_t::object:
return anchor.key();
// use an empty key for all primitive types
default:
return empty_str;
}
}
/// return value of the iterator
typename IteratorType::reference value() const
{
return anchor.value();
}
vtkSmartPointer<vtkPolyData> getVTKPolyDataPrecise(LabelImageType::Pointer label)
{
LabelIteratorType liter = LabelIteratorType(label,label->GetLargestPossibleRegion());
liter.GoToBegin();
//find the maximum number of cells
unsigned short max1 = 0;
for(liter.GoToBegin();!liter.IsAtEnd();++liter)
max1 = MAX(max1,liter.Get());
//find all the cubes in which cells lie
cubecoord* carray = new cubecoord[max1+1];
for(int counter=0; counter<=max1; counter++)
{
carray[counter].sx=60000; carray[counter].sy=60000;carray[counter].sz=60000;
carray[counter].ex=0;carray[counter].ey=0;carray[counter].ez=0;
}
typedef itk::ImageRegionConstIteratorWithIndex<LabelImageType> ConstLabelIteratorWithIndex;
ConstLabelIteratorWithIndex cliter = ConstLabelIteratorWithIndex(label,label->GetLargestPossibleRegion());
InputImageType::IndexType index;
for(cliter.GoToBegin();!cliter.IsAtEnd();++cliter)
{
int cur = cliter.Get();
if(cur!=0)
{
index = cliter.GetIndex();
carray[cur].sx= MIN(index[0],carray[cur].sx);
carray[cur].sy= MIN(index[1],carray[cur].sy);
carray[cur].sz= MIN(index[2],carray[cur].sz);
carray[cur].ex= MAX(index[0],carray[cur].ex);
carray[cur].ey= MAX(index[1],carray[cur].ey);
carray[cur].ez= MAX(index[2],carray[cur].ez);
}
}
//find the largest image size we need
unsigned short wx=0,wy=0,wz=0;
for(int counter=1; counter<=max1; counter++)
{
wx = MAX(carray[counter].ex-carray[counter].sx+1,wx);
wy = MAX(carray[counter].ey-carray[counter].sy+1,wy);
wz = MAX(carray[counter].ez-carray[counter].sz+1,wz);
}
// accommodate padding
wx = wx+2;wy = wy +2; wz = wz+2;
printf("wx wy wz %u %u %u\n",wx,wy,wz);
// create a tiny image of maximum size
//appendfilter->UserManagedInputsOn();
//appendfilter->SetNumberOfInputs(max1);
vtkSmartPointer<vtkAppendPolyData> appendfilter = vtkSmartPointer<vtkAppendPolyData>::New();
/**************/
ExportFilterType::Pointer itkexporter = ExportFilterType::New();
vtkSmartPointer<vtkImageImport> vtkimporter = vtkSmartPointer<vtkImageImport>::New();
ConnectPipelines(itkexporter,(vtkImageImport *)vtkimporter);
vtkSmartPointer<vtkMarchingCubes> contourf = vtkSmartPointer<vtkMarchingCubes>::New();
contourf->SetInputData(vtkimporter->GetOutput());
contourf->SetValue(0,127);
contourf->ComputeNormalsOff();
contourf->ComputeScalarsOff();
contourf->ComputeGradientsOff();
vtkSmartPointer<vtkSmoothPolyDataFilter> smoothf = vtkSmartPointer<vtkSmoothPolyDataFilter>::New();
smoothf->SetInputData(contourf->GetOutput());
smoothf->SetRelaxationFactor(0.3);
smoothf->SetNumberOfIterations(20);
vtkSmartPointer<vtkTransform> transform = vtkSmartPointer<vtkTransform>::New();
transform->PostMultiply();
transform->Identity();
vtkSmartPointer<vtkTransformPolyDataFilter> tf = vtkSmartPointer<vtkTransformPolyDataFilter>::New();
tf->SetTransform(transform);
tf->SetInputData(smoothf->GetOutput());
/******************/
InputImageType::Pointer t = getEmpty(wx,wy,wz);
for(int counter=1; counter<=max1; counter++)
{
//printf("Maximum tiny image size I need is [%d %d %d]\n",wx,wy,wz);
if(carray[counter].sx > 59999)
continue;
printf("Working..\n");
// scanf("%*d");
InputImageType::SizeType size;
InputImageType::RegionType region;
index.Fill(1);
region.SetIndex(index);
region.SetSize(size);
LabelImageType::SizeType lsize;
LabelImageType::IndexType lindex;
LabelImageType::RegionType lregion;
itkexporter->SetInput(t);
t->FillBuffer(0);
lsize[0] = carray[counter].ex-carray[counter].sx+1;
lsize[1] = carray[counter].ey-carray[counter].sy+1;
lsize[2] = carray[counter].ez-carray[counter].sz+1;
lindex[0] = carray[counter].sx;
lindex[1] = carray[counter].sy;
lindex[2] = carray[counter].sz;
lregion.SetIndex(lindex);
lregion.SetSize(lsize);
LabelIteratorType localiter = LabelIteratorType(label,lregion);
size = lsize;
region.SetSize(size);
IteratorType iter = IteratorType(t,region);
for(localiter.GoToBegin(),iter.GoToBegin();!localiter.IsAtEnd();++localiter,++iter)
{
if(localiter.Get()==counter)
{
iter.Set(255);
}
}
t->Modified();
vtkimporter->Modified();
transform->Identity();
transform->Translate(carray[counter].sx-1,carray[counter].sy-1,carray[counter].sz-1);
tf->SetTransform(transform);
tf->Update();
vtkSmartPointer<vtkPolyData> pol=vtkSmartPointer<vtkPolyData>::New();
pol->DeepCopy(tf->GetOutput());
// tf->GetOutput()->Print(std::cout);
appendfilter->AddInputData(pol);
//appendfilter->Update();
//appendfilter->SetInputByNumber(counter-1,tf->GetOutput());
// appendfilter->Update();
// appendfilter->GetOutput()->Print(std::cout);
//if(counter>500)
// break;
printf("Completed %d/%d\r",counter,max1);
// scanf("%*d");
}
appendfilter->Update();
vtkSmartPointer<vtkDecimatePro> decimate = vtkSmartPointer<vtkDecimatePro>::New();
decimate->SetInputData(appendfilter->GetOutput());
decimate->SetTargetReduction(0.1);
//decimate->SetNumberOfDivisions(32,32,32);
printf("Decimating the contours...");
decimate->Update();
printf("Done\n");
printf("Smoothing the contours after decimation...");
vtkSmartPointer<vtkSmoothPolyDataFilter> smoothfinal = vtkSmartPointer<vtkSmoothPolyDataFilter>::New();
smoothfinal->SetRelaxationFactor(0.2);
smoothfinal->SetInputData(decimate->GetOutput());
smoothfinal->SetNumberOfIterations(0);
smoothfinal->Update();
printf("Done\n");
delete [] carray;
vtkSmartPointer<vtkPolyData> out = smoothfinal->GetOutput();
return out;
}
bool itkDataTensorImageWriterBase::write(const QString& path, PixelType dummyArgument)
{
typedef typename itk::Vector<PixelType, 6> VectorType;
typedef typename itk::Image<VectorType, 3> VectorImageType;
typedef typename itk::Tensor<PixelType, 3> TensorType;
typedef typename itk::Image<TensorType, 3> TensorImageType;
typedef typename VectorImageType::Pointer VectorImageTypePointer;
VectorImageTypePointer myTensorImage = VectorImageType::New();
typedef typename TensorImageType::Pointer TensorImageTypePointer;
TensorImageTypePointer image = dynamic_cast< TensorImageType* >( (itk::Object*)(this->data()->output()) );
typedef typename TensorImageType::RegionType TensorImageTypeRegionType;
TensorImageTypeRegionType region = image->GetLargestPossibleRegion();
myTensorImage->SetRegions (region);
myTensorImage->SetSpacing (image->GetSpacing());
myTensorImage->SetOrigin (image->GetOrigin());
myTensorImage->SetDirection (image->GetDirection());
try {
myTensorImage->Allocate();
}
catch (itk::ExceptionObject &e) {
std::cerr << e;
throw itk::ExceptionObject (__FILE__,__LINE__,"Error during memory allocation.");
}
typedef itk::ImageRegionConstIterator<TensorImageType> IteratorType;
IteratorType it (image, image->GetLargestPossibleRegion());
itk::ImageRegionIteratorWithIndex<VectorImageType> itOut(myTensorImage, myTensorImage->GetLargestPossibleRegion());
while( !it.IsAtEnd() )
{
TensorType tensor = it.Get();
VectorType vec;
for( unsigned int i=0; i<6; i++) {
vec[i] = static_cast<float>(tensor[i]);
}
itOut.Set (vec);
++it;
++itOut;
}
typedef typename itk::ImageFileWriter<VectorImageType>::Pointer ImageFileWriterPointer;
ImageFileWriterPointer myWriter = itk::ImageFileWriter<VectorImageType>::New();
myWriter->SetFileName(path.toAscii().constData());
myWriter->SetInput(myTensorImage);
try {
myWriter->Write();
}
catch(itk::ExceptionObject &e) {
qDebug() << e.GetDescription();
return false;
}
return true;
}
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;
}