Problems converting binary array to ITK image

Beginner Questions
1

Dear all,

I would like to read in a binary array and convert part of this array into an ITK image. I would like to use the ITK image later on as a mask.
However, my code is not working yet, there has to be a mistake somewhere.
It always crashes in the last line:
importFilter->SetImportPointer(localBuffer, dimPET[0]*dimPET[1]*dimPET[2], importImageFilterWillOwnTheBuffer);

Here is what I have until now:

typedef unsigned char PixelType;
typedef itk::Image< PixelType, 3 > ImageTypeChar;
typedef itk::ImportImageFilter< PixelType, 3 > ImportFilterTypeChar;
ImportFilterTypeChar::Pointer importFilter = ImportFilterTypeChar::New();

ImportFilterTypeChar::SizeType size;
ImageTypeChar::Pointer maskImage;
ifstream prjfile;

//image size
unsigned int dimPET[3] = {{144,144,275}};
//voxel size
float voxelSize[3] = {{4,4,4}};

fstream voiFile;
//open binary file
voiFile.open(voiPath, ios::in | ios::binary);

if (voiFile.is_open() == false) {
std::cout << “Cannot open voi file\n”;
exit(0);
}
//opening the file worked
else {
streampos begin, end;
begin = voiFile.tellg();
voiFile.seekg(0, ios::end);
end = voiFile.tellg();
//get the total file size
int fileSize = (end - begin);
//vector to store the elements of the

vector<char> wholeFile(fileSize);
voiFile.seekg(0, std::ios::beg);
voiFile.read(&wholeFile[0], fileSize);
vector<unsigned char> mask(fileSize);
    //convert whole array to unsigned char - I do not know if this is necessary?
transform(wholeFile.begin(), wholeFile.end(), mask.begin(), [](auto& elem) {return ((unsigned char)(elem)); });
   //in the end, I only want to convert the second half of the image into an ITK image
vector< PixelType> voi(mask.begin() + (fileSize / 2), mask.end());

voiFile.close();
		
size[0]= dimPET[0];
size[1] = dimPET[1];
size[2] = dimPET[2];

ImportFilterTypeChar::IndexType start;
start.Fill(0);

ImportFilterTypeChar::RegionType region;
region.SetIndex(start);
region.SetSize(size);

importFilter->SetRegion(region);
double origin[3];
origin[0]= 0;
origin[1] = 0;
origin[2] = 0;

importFilter->SetOrigin(origin);
double spacing[3];
spacing[0] = voxelSize[0];
    spacing[1] = voxelSize[1];
spacing[2] = voxelSize[2];
importFilter->SetSpacing(spacing);

PixelType * localBuffer = &voi[0];
importFilter->SetOrigin(origin);
importFilter->SetSpacing(spacing);
const bool importImageFilterWillOwnTheBuffer = true;		                                 
    importFilter->SetImportPointer(localBuffer, dimPET[0]*dimPET[1]*dimPET[2], importImageFilterWillOwnTheBuffer);
		
	}
}
2

Is DimPET already the size of half image ? Otherwise you are overreading the buffer.

3

Dear tim,

yes, dimPET is half the size of the image…

4

The code seems good otherwise. Note that I’m not sure that letting the import filter own a vector memory block is a safe behavior. Did you try to run your code through a debugger to have information about your crash ?

5

Dear Tim,

thanks for your help. I fixed the problem. There was a problem with this
line:

transform(wholeFile.begin(), wholeFile.end(), mask.begin(), [](auto&
elem) {return ((unsigned char)(elem)); });

I changed the imageType to float (what was actually what I wanted) and
changed this line to:

transform(wholeFile.begin(), wholeFile.end(), mask.begin(), [](auto& elem)
{return ((float)(elem)); });

And now its working. I do not really know why it was not working before…

Thanks a lot anyway,

Regards

Elli

2 Likes
6

Ok, I can’t tell you what was wrong, but I’m glad you managed to get a functional code. :+1:
Maybe something about “char” / “unsigned char” (which are not strictly equivalent) ?
Thanks for reporting the fix.

1 Like