[ITK] How to get a vector of DICOM Series description strings in ITKv4 (GDCM 2.x)?

[Matt McCormick]

Passing along nice follow-up from Mathieu Malaterre:


You should be using gdcm::Scanner:

http://gdcm.sourceforge.net/html/classgdcm_1_1Scanner.html

See for example:
http://gdcm.sourceforge.net/html/SimpleScanner_8cxx-example.html#_a7

>From the command line, you will discover it is much *much* faster than
the very old GDCM 1.x implementation, see:

http://gdcm.sourceforge.net/html/gdcmscanner.html

On Wed, Dec 3, 2014 at 11:43 AM, Sebastian Ordas
<sebastian.ordas at gmail.com> wrote:
> Hi Matt,
> several issues: the GDCM API has changed in 2.x
> For instance,  gdcm::DirList does not exist anymore, same for
> m_GDCMHelper->AddFileName(), etc
> I would also like to know whether to put the efforts on GDCM or DCMTK (I
> have seen a gdcm::SerieHelper2 class in plastimach that is worthy to
> explore)
>
>
> ... but there should be some basic functionality / approach already
> available for such a simple and general action (i.e. explore available DICOM
> Series and/or Studies in a folder with DICOM files)
>
> let me know if you have some useful links (I don´'t want to link against CTK
> in my app)
>
> thanks
> sebastian
>
>
> On 03/12/2014 01:30 p.m., Matt McCormick wrote:
>>
>> Hi Sebastian,
>>
>> What specifically is the issue using this code with ITKv4?
>>
>> Thanks,
>> Matt
>>
>> On Wed, Dec 3, 2014 at 11:21 AM, Sebastian Ordas
>> <sebastian.ordas at gmail.com> wrote:
>>>
>>> Dear All,
>>>
>>> I used to be able with ITK 3.12 (GDCM 1.x) to populate a vector with
>>> series
>>> description strings, recursively, given the path to a folder with DICOM
>>> files.
>>> The goal is to fill in an "Open DICOM" dialog with such information, in
>>> order to let the user load a single DICOM Series.
>>> How can I do that with ITKv4 (GDCM 2.x)?
>>>
>>> thank you,
>>> sebastian
>>>
>>> Here´s my original code:
>>>
>>> typedef gdcm::FileList DICOMFileListType;
>>>
>>> m_GDCMScanner = itk::GDCMSeriesFileNames::New();
>>> m_GDCMScanner->SetUseSeriesDetails(true);
>>> m_GDCMScanner->LoadPrivateTagsOff();
>>> m_GDCMHelper = m_GDCMScanner->GetSeriesHelper();
>>>
>>> m_GDCMScanner->SetInputDirectory( m_ImageDirectoryName );
>>>
>>> if (!itksys::SystemTools::FileExists (ImageDirectoryName ))
>>>      {
>>>          return;
>>>      }
>>>
>>> // we now scan from scratch all dicom file headers
>>> try
>>> {
>>>      this->m_GDCMHelper->Clear();
>>>
>>>      unsigned long counter_im = 0;
>>>      gdcm::DirList dirlist(dirname, m_UseRecursiveScan);
>>>
>>>      gdcm::DirListType filenames_list = dirlist.GetFilenames();
>>>
>>>      unsigned long totalImages = filenames_list.size();
>>>      if (totalImages<10)
>>>          return;
>>>
>>>      for( gdcm::DirListType::const_iterator it = filenames_list.begin();
>>>          it != filenames_list.end(); ++it)
>>>      {
>>>        if (itksys::SystemTools::FileExists ((*it).c_str(), true))
>>>            m_GDCMHelper->AddFileName ((*it));
>>>        counter_im++;
>>>      }
>>> }
>>> catch (itk::ExceptionObject & excp)
>>> {
>>>    return;
>>> }
>>>
>>> std::vector<std::string> UIDs;
>>> UIDs = m_GDCMScanner->GetSeriesUIDs();
>>>
>>> if (!UIDs.size())
>>> return;
>>>
>>>      try
>>>      {
>>>          m_SeriesNames.clear();
>>>
>>>          int nSeries = 0;
>>>
>>>          for (unsigned int uid=0; uid<UIDs.size(); uid++)
>>>          {
>>>              std::string uidname = UIDs[uid];
>>>              DICOMFileListType* t_filelist =
>>> m_GDCMHelper->GetSingleSerieUIDFileSet(uidname);
>>>              this->m_GDCMHelper->OrderFileList (t_filelist);
>>>
>>>              DICOMFileListType::iterator it;
>>>              it = t_filelist.begin();
>>>
>>>              for (; it != t_filelist.end(); it++)
>>>              {
>>>                  DICOMFileListType* filelist = (*it);
>>>                  if ( !filelist->size() )
>>>                  {
>>>                  continue;
>>>                  }
>>>                  std::stringstream stream;
>>>                  stream << "series# " << nSeries << ": " <<
>>> this->GenerateName(filelist) << " (" << filelist->size() << " slices)";
>>>                  m_SeriesNames.push_back( stream.str() );
>>>                  nSeries++;
>>>              }
>>>          }
>>>      }
>>>      catch (itk::ExceptionObject & excp)
>>>      {
>>>          return;
>>>      }
>>>
>>> template <class TPixelType>
>>> std::string DICOMImageReader<TPixelType>::GenerateName
>>> (DICOMFileListType*
>>> filelist)
>>> {
>>>    std::string description = (*filelist)[0]->GetEntryValue(0x0008,
>>> 0x103E);
>>>    if (description == gdcm::GDCM_UNFOUND)
>>>    {
>>>      (*filelist)[0]->Load();
>>>      description = (*filelist)[0]->GetEntryValue(0x0008, 0x103E);
>>>    }
>>>    return description;
>>> }
>>>
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>
>