# Encountering undefined Behavior when writing DICOM images

**URL:** <https://discourse.itk.org/t/encountering-undefined-behavior-when-writing-dicom-images/4587>\
**Category:** Beginner Questions\
**Tags:** gdcm, cpp\
**Created:** [November 17, 2021, 11:38am UTC](https://discourse.itk.org/t/encountering-undefined-behavior-when-writing-dicom-images/4587 "2021-11-17T11:38:46Z")\
**Posts on this page:** 5\
**Page:** 1

<div class="post-metadata">

**Author:** ![Keyn34](https://discourse.itk.org/letter_avatar_proxy/v4/letter/k/9fc29f/32.png) [@Keyn34](https://discourse.itk.org/u/Keyn34)\
**Post date:** [November 17, 2021, 11:38am UTC](https://discourse.itk.org/t/encountering-undefined-behavior-when-writing-dicom-images/4587/1 "2021-11-17T11:38:47Z")

</div>

Hello everyone,

I am currently encountering undefined behavior when trying to write a DICOM series with headers taken from another series. I use only the gdcmIO and loop through all files to read the header with `ReadImageInformation()` and modify the slope and intercept of the header because it appears to be faster than the regular series reader.

```auto
    // Sorting input DICOM files with gdcm IO 
	std::cout << "Sorting all DICOM files with gdcm IO...:";
	NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();
	nameGenerator->SetInputDirectory(inputDICOMDir);
	FileNamesContainer fileNames = nameGenerator->GetInputFileNames();

	// MetaDataDictionary Array
	std::vector<itk::MetaDataDictionary*> fullMetaDataDictionaryArray;
	std::vector<itk::MetaDataDictionary> allDictionaries;

	std::cout << "Reading all Headers with gdcm IO...:";

	// DICOM IO for Single file
	ImageIOType::Pointer dcmIOsingleFiles = ImageIOType::New();

	// Read files one by one
	// Read all headers of all DICOM files in fileNames
	for (std::string filename : fileNames) {
		dcmIOsingleFiles->SetFileName(filename);
		dcmIOsingleFiles->ReadImageInformation();

		// Slope and Intercept fix
		itk::MetaDataDictionary& sliceDictionary = dcmIOsingleFiles->GetMetaDataDictionary();
		itk::EncapsulateMetaData<std::string>(sliceDictionary, DICOMTag_slope, "1");
		itk::EncapsulateMetaData<std::string>(sliceDictionary, DICOMTag_intercept, "0");

		allDictionaries.push_back(sliceDictionary);
	}

```

Now, I prepare the vector for providing it to the writer, where all pointers to the `itk::MetaDataDictionary`s are stored. Everything works fine, till i reach the `Update()` call of the writer, where the program just closes without any further info. Both vectors are not empty either, I checked them before. Also they don’t go out of scope, so that should not be an issue i suppose?

```auto
    for (int dictonary = 0; dictonary < allDictionaries.size(); dictonary++)
	{
		fullMetaDataDictionaryArray.push_back(&allDictionaries[dictonary]);
	}

	// Write Series
	Series4DWriterType::Pointer seriesWriter = Series4DWriterType::New();
	seriesWriter->SetInput(reader->GetOutput());
	seriesWriter->SetImageIO(dcmIOsingleFiles);
	seriesWriter->SetFileNames(namesGenerator->GetFileNames());
	seriesWriter->SetMetaDataDictionaryArray(&fullMetaDataDictionaryArray);

	try {
		seriesWriter->Update();
	}
	catch (const itk::ExceptionObject& err) {
		std::cerr << "ExceptionObject caught!" << std::endl;
		std::cerr << err << std::endl;
		return EXIT_FAILURE;
	}

```

Can anybody tell me what the problem may be? Am I using the header reading of the GDCM object wrong? Should i stick to read the series via a regular series reader and transfer the header?

I am using ITK 5.2.1 with Visual Studio 2019.

Thank you so much in advance, as usual. 🙂

---

<div class="post-metadata">

**Author:** ![dzenanz](https://discourse.itk.org/user_avatar/discourse.itk.org/dzenanz/32/1093_2.png) [@dzenanz](https://discourse.itk.org/u/dzenanz)\
**Post date:** [November 17, 2021, 3:05pm UTC](https://discourse.itk.org/t/encountering-undefined-behavior-when-writing-dicom-images/4587/2 "2021-11-17T15:05:39Z")

</div>

Have you tried also catching `std::runtime_error`? An example here:

> <https://github.com/InsightSoftwareConsortium/ITKMontage/blob/v0.7.3/examples/RefineMontage.cxx#L187-L198>

Problem might be reading too. Have you called `reader->Update();`? Does that go smoothly?

---

<div class="post-metadata">

**Author:** ![Keyn34](https://discourse.itk.org/letter_avatar_proxy/v4/letter/k/9fc29f/32.png) [@Keyn34](https://discourse.itk.org/u/Keyn34)\
**Post date:** [November 17, 2021, 3:20pm UTC](https://discourse.itk.org/t/encountering-undefined-behavior-when-writing-dicom-images/4587/3 "2021-11-17T15:20:43Z")

</div>

Thank you for the rapid response.

Yes, i update the reader explicitly:

```auto
    ReaderType::Pointer reader = ReaderType::New();
	reader->SetFileName(inputFilename);
	std::cout << "Reading input data: <" << inputFilename << ">...";
	try {
		reader->Update();
	}
	catch (const itk::ExceptionObject& excp) {
		std::cerr << "Exception thrown while reading the image" << std::endl;
		std::cerr << excp << std::endl;
		return EXIT_FAILURE;
	}

```

This works perfectly without any issues and errors.

I just added the `runtimer_error` exception block but still, without any error the program closes…

```auto
   try {
   	seriesWriter->Update();
   }
   catch (const itk::ExceptionObject& err) {
   	std::cerr << "ExceptionObject caught!" << std::endl;
   	std::cerr << err << std::endl;
   	return EXIT_FAILURE;
   }
   catch (std::runtime_error& err)
   {
   	std::cerr << err.what();
   	return EXIT_FAILURE;
   }
   catch (...)
   {
   	std::cerr << "Unknown error has occurred" << std::endl;
   	return EXIT_FAILURE;
   }

```

Maybe something else to check?  
Thanks again!

---

<div class="post-metadata">

**Author:** ![dzenanz](https://discourse.itk.org/user_avatar/discourse.itk.org/dzenanz/32/1093_2.png) [@dzenanz](https://discourse.itk.org/u/dzenanz)\
**Post date:** [November 17, 2021, 3:24pm UTC](https://discourse.itk.org/t/encountering-undefined-behavior-when-writing-dicom-images/4587/4 "2021-11-17T15:24:08Z")

</div>

Search for `std::terminate()` and `exit()` function invocations in GDCM code 😃. Or step through the code using a debugger.

---

<div class="post-metadata">

**Author:** ![Keyn34](https://discourse.itk.org/letter_avatar_proxy/v4/letter/k/9fc29f/32.png) [@Keyn34](https://discourse.itk.org/u/Keyn34)\
**Post date:** [November 17, 2021, 3:26pm UTC](https://discourse.itk.org/t/encountering-undefined-behavior-when-writing-dicom-images/4587/5 "2021-11-17T15:26:05Z")

</div>

Ok, I’ll see if i find something. 😃  
And report back if I do…

Thanks 🙂

@dzenanz, and anyone curious, analyzing it with the debugger prompted following error:

```auto
HEAP CORRUPTION DETECTED: after Normal block (#133158230) at 0x000001A80A036040.
CRT detected that the application wrote to memory after end of heap buffer.

```

Apparently `dcmIOsingleFiles` is the problem. If I create and use another ImageIO besides this one, I do not get any error or crash…