[ITK-users] Lost Patient, Study and Series DICOM tags

[Piotr Piasecki]

Hello Again

I found the information, that in SimpleITK the MetaDataDictionary interface
is only part of the Image class. Currently it provides a read only
interface, with the GetMetaDataKeys(), and GetMetaData(key) methods. This
get method only returns the type of data in the dictionary converted to a
string.

The required method would be Image::SetMetaData(key,value). But
unfortunately I do not see this method, so I think that this is still not
implemented. The only what I need is to keep information that my files
belong to one series of images, which belongs to one patient and study (
not necessarily the same study or series as the original).

Regards.

Peter.


2016-07-07 14:45 GMT+02:00 Dženan Zukić <dzenanz at gmail.com>:

> Hi Piotr,
>
> instead of ImageReader->GetMetaDataDictionary() call
> ImageSeriesReader->GetMetaDataDictionary(). Also, the image format you are
> writing to needs to be able to support metadata (e.g. .mha, .nrrd, DICOM),
> otherwise the metadata is lost (.nii, .jpg, .bmp etc).
>
> But for writing DICOM, the process might be somewhat different from what I
> described in the first email. Definitely different if you want metadata
> copied slice for slice from input to output - in this case some metadata
> needs to be changed anyway, such as flag that this is a derived image and
> not an original image coming out of a scanner.
>
> I suppose that MetaDataDictionary class is not wrapped. You can then loop
> through all the keys and copy them and their content one by one.
>
> Regards
>
> On Thu, Jul 7, 2016 at 8:35 AM, Piotr Piasecki <
> piotpia124 at student.polsl.pl> wrote:
>
>> Hi Dženan,
>>
>> thank you for your help and for this example. Unfortunately, I have not
>> found method GetMetaDataDictionary() in SimpleITK in C# (I found only
>> GetMetaDataKeys() and GetMetaData(string key)). Also, I have not found a
>> method SetMetaDataDictionary or any other that allows me to assign DICOM
>> tags.
>>
>> My short piece of code looks like this:
>>
>> static public void ReadImage()
>>         {
>>             sitk.ImageFileReader reader = new sitk.ImageFileReader();
>>             reader.SetFileName(@".\DICOM_TEST\original.dcm");
>>             var image = reader.Execute();
>>
>>             sitk.ImageFileWriter writer = new sitk.ImageFileWriter();
>>             writer.SetFileName(@".\DICOM_TEST\modified.dcm");
>>             writer.Execute(image);
>>         }
>>
>> Another problem is that your example describes only loading and saving a
>> single .dcm file. What if I have to process a whole series of files
>> using sitk.ImageSeriesReader and sitk.ImageSeriesWriter?
>>
>> Regards,
>>
>> Peter.
>>
>> 2016-07-05 15:45 GMT+02:00 Dženan Zukić <dzenanz at gmail.com>:
>>
>>> Hi Piotr,
>>>
>>> if you want to carry over metadata from input image to output image, you
>>> should save the metadata dictionary in a way similar to this:
>>>
>>> itk::MetaDataDictionary metadata;
>>>
>>> template< typename TImage >
>>> itk::SmartPointer<TImage> readImage(std::string fileName)
>>> {
>>>     typedef itk::ImageFileReader<TImage> ReaderType;
>>>     typename ReaderType::Pointer reader = ReaderType::New();
>>>     reader->SetFileName(fileName.c_str());
>>>     try
>>>     {
>>>         reader->Update();
>>>         metadata = reader->GetMetaDataDictionary();
>>>         return reader->GetOutput();
>>>     }
>>>     catch (itk::ExceptionObject & error)
>>>     {
>>>         std::cerr << "Error: " << error << std::endl;
>>>         return NULL;
>>>     }
>>> }
>>>
>>> template< typename TImage >
>>> void writeImage(itk::SmartPointer<TImage> image, std::string fileName)
>>> {
>>>     image->SetMetaDataDictionary(metadata); //full metadata
>>>     typedef itk::ImageFileWriter<TImage> WriterType;
>>>     typename WriterType::Pointer writer = WriterType::New();
>>>     writer->SetFileName(fileName.c_str());
>>>     writer->SetInput(image);
>>>     try
>>>     {
>>>         writer->Update();
>>>     }
>>>     catch (itk::ExceptionObject & error)
>>>     {
>>>         std::cerr << "Error: " << error << std::endl;
>>>     }
>>> }
>>>
>>> On Tue, Jul 5, 2016 at 2:46 AM, Piotr Piasecki <
>>> piotpia124 at student.polsl.pl> wrote:
>>>
>>>> Dear Sir or Madam.
>>>>
>>>> I am a student in Biomedical Engineering at the Silesian University of
>>>> Technology. During my studies I worked with ITK and SimpleITK in C#. I want
>>>> to use them in my current project, but I have an important question. After
>>>> loading and processing a series of .dcm files I lost information about the
>>>> patient and study to which they belong, and that they belong to one series.
>>>> How can I keep this information?
>>>>
>>>> I will be very grateful for any answer.
>>>>
>>>> Best regards.
>>>>
>>>> Peter.
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>>>
>>
>
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