How to use Image Iterators in right way

Beginner Questions
#1

Hello everyone,

i have noticed if i use for-loop across the image to get the every pixel value is time-consuming and inefficient,and that is also be mentioned in the user guide.
I read this page https://itk.org/Doxygen50/html/ImageIteratorsPage.html
but i still dont know how to get the pixel value and get its coordinates at the same time with using iterator.
Here is my code how can i rewrite them with using iterator.

ImageType::IndexType pixcelIndex;
int image_width = RegionInFilter.GetSize()[0];
int image_height = RegionInFilter.GetSize()[1];
int image_slice = RegionInFilter.GetSize()[2];
for (int k = 0; k < image_slice; ++k) //
{
for (int i = 0; i < image_height; ++i)//
{
for (int j = 0; j < image_width; ++j)//
{
pixcelIndex[0] = j;//
pixcelIndex[1] = i;//
pixcelIndex[2] = k;//
ImageType::PixelType pixel1 = image->GetPixel(pixcelIndex);
if (pixel1 !=0 ) {
slicecoordinates .push_back(pixcelIndex[2]);//
Ycoordinates .push_back(pixcelIndex[1]);//
Xcoordinates .push_back(pixcelIndex[0]);//
}
}
}
}

now the code is running good but also use too much memory so I want to optimize it .
Thanks in advance!!

#2

it.GetIndex() gives the index, e.g.:

2 Likes
#3

Thank you!! And i want to know how apply image filter on dicom series? All example is base on single image .Now i read a dicom series and i want to do the same processing on every slice,for example opening operation. But it didn`t work. i want to konw how to apply it in right way.

using ImageType = itk::Image< PixelType, 3>;
using FilterType = itk::OtsuThresholdImageFilter<
	ImageType, ImageType >;

FilterType::Pointer filter = FilterType::New();

filter->SetInput(reader->GetOutput());

try
{
	filter->Update();
}
catch (itk::ExceptionObject & excp)
{
	std::cerr << "Exception thrown " << excp << std::endl;
}
filter->SetOutsideValue(0);
filter->SetInsideValue(1000);
int threshold = filter->GetThreshold();
std::cout << "Threshold = " << threshold << std::endl;
//////////////////
using StructuringElementType = itk::BinaryBallStructuringElement<ImageType::PixelType, ImageType::ImageDimension>;
StructuringElementType structuringElement;
structuringElement.SetRadius(15);
structuringElement.CreateStructuringElement();
  using BinaryMorphologicalOpeningImageFilterType =
	itk::BinaryMorphologicalOpeningImageFilter<ImageType, ImageType, StructuringElementType>;
BinaryMorphologicalOpeningImageFilterType::Pointer openingFilter = BinaryMorphologicalOpeningImageFilterType::New();
openingFilter->SetInput(mathOperationFilter->GetOutput());
openingFilter->SetKernel(structuringElement);
try
{
	openingFilter->Update();
}
catch (itk::ExceptionObject & excp)
{
	std::cerr << "Exception thrown " << excp << std::endl;
}

Here is the code ,the otsu part works but the opening part does not work, do you have any advice?

#4

Here is my rewrite code ,now program is faster than before .

using IteratorType = itk::ImageRegionIteratorWithIndex<ImageType>;

IteratorType outputIt(image, image->GetLargestPossibleRegion());

for (outputIt.GoToBegin(); !outputIt.IsAtEnd(); ++outputIt)
{
	ImageType::IndexType idx = outputIt.GetIndex();
	//idx[0] = requestedIndex[0] + requestedSize[0] - 1 - idx[0];
	if (outputIt.Get() != 0) {
	
		slicecoordinates.push_back(idx[2]);//
		Ycoordinates .push_back(idx[1]);//
		Xcoordinates .push_back(idx[0]);//
	
}

I love Iterator

#5

This might need to be openingFilter->SetInput(filter->GetOutput());

#6

Oh sorry there is my copy mistake. Because I use a lot of filters.I pick out some of the code for the sake of simplicity.
It is indeed openingFilter->SetInput(filter->GetOutput()) in my code;
every single filter does not work except OtsuThresholdImageFilter . I have tried to apply many Morphological operation ,opening closing,Dilate… But the image hasn’t been changed.
also i have changed structuringElement.SetRadius(15); biger or smaller it does not help neither.
What’s special is that my data is a dicom series, so I think something should be changed, but I’m not sure where.

#7

That problem is unrelated to iterators. Please start a new topic, preferably providing a minimal complete example (with just one filter) which can be copy-pasted for easy reproduction.

#8

Thank you ! right that is unrelated to iterators,and my iterator problem is fixed .
i will start a new topic to ask filter problem