[Insight-users] Problem with saving Image Position value in "z" axis
Bill Lorensen
bill.lorensen at gmail.com
Fri Apr 15 12:26:39 EDT 2011
What version of itk are you using?
On Thu, Apr 14, 2011 at 5:16 AM, Bc. Michal Srna <michal at srna.info> wrote:
> Hello,
>
> I have used part of this code to generate MetaDataDictionary:
>
> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM
>
> Everything works, as I need, but I have just one problem in part regarding
> saving Image Position (origin) for "z" axis. "x,y" are stored well, but "z"
> value of Image Position is 0.
>
> Here is that part of the code for saving the Image position:
>
> ImageType::PointType position;
> ImageType::IndexType index;
> index[0] = 0;
> index[1] = 0;
> index[2] = f;
>
> reader->GetOutput()->TransformIndexToPhysicalPoint(index, position);
>
> value.str("");
> value << position[0] << "\\" << position[1] << "\\"
> << position[2];
>
>
> itk::EncapsulateMetaData<std::string>(*dict,"0020|0032", value.str()); //WHY
> NOT WORKING??
>
> position[2] contains the correct value, but I don't know, why is that value
> not saved and instead of that value is stored just 0?
>
> I think I should add also the whole code for generating my
> MetaDataDictionary for see my problem in context.
>
> At first it opens original data, from which I read original meta data. Then
> I modify some parts of those meta data in for cycle creating meta data for
> each slice.
>
> I confirmed, that original data contains correct value of Image Position in
> "z" axis. But I need to recalculate that value and store new value. Problem
> is, as I told, that this value is not saved and instead of it, there is just
> 0.
>
> Here is the whole code, spacing[x] is derived from other part of the whole
> code, I don't want to copy here:
>
> /*opening original data for getting meta data dictionry for saving it into
> output 2D series files*/
> typedef itk::GDCMImageIO ImageIOType;
> typedef itk::GDCMSeriesFileNames NamesGeneratorType;
> typedef itk::ImageSeriesReader< ImageType > ReaderType;
>
> ImageIOType::Pointer gdcmIO = ImageIOType::New();
> ReaderType::Pointer reader = ReaderType::New();
>
> NamesGeneratorType::Pointer namesGenerator =
> NamesGeneratorType::New();
> namesGenerator->SetInputDirectory( StudyFolderName );
> const ReaderType::FileNamesContainer & filenames =
> namesGenerator->GetInputFileNames();
>
> reader->SetImageIO( gdcmIO );
> reader->SetFileNames( filenames );
>
> reader->Update();
>
> /*creating MetaDataDictionary for each slice*/
>
> /*Copy the dictionary from the first image and override slice
> specific fields*/
> ReaderType::DictionaryRawPointer inputDictionary =
> (*(reader->GetMetaDataDictionaryArray()))[0];
> ReaderType::DictionaryArrayType dictionaryOutputArray;
>
> /*To keep the new series in the same study as the original we
> need to keep the same study UID. But we need new series and frame of
> reference UID's.*/
> #if ITK_VERSION_MAJOR >= 4
> gdcm::UIDGenerator suid;
> std::string seriesUID = suid.Generate();
> gdcm::UIDGenerator fuid;
> std::string frameOfReferenceUID = fuid.Generate();
> #else
> std::string seriesUID = gdcm::Util::CreateUniqueUID(
> gdcmIO->GetUIDPrefix());
> std::string frameOfReferenceUID =
> gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
> #endif
> std::string studyUID;
> std::string sopClassUID;
> itk::ExposeMetaData<std::string>(*inputDictionary,
> "0020|000d", studyUID);
> itk::ExposeMetaData<std::string>(*inputDictionary,
> "0008|0016", sopClassUID);
> gdcmIO->KeepOriginalUIDOn();
>
> for (unsigned int f = 0; f < size[2]; f++)
> {
> // Create a new dictionary for this slice
> ReaderType::DictionaryRawPointer dict = new
> ReaderType::DictionaryType;
>
> // Copy the dictionary from the first slice
> CopyDictionary (*inputDictionary, *dict);
>
> // Set the UID's for the study, series, SOP and frame
> of reference
>
> itk::EncapsulateMetaData<std::string>(*dict,"0020|000d", studyUID);
>
> itk::EncapsulateMetaData<std::string>(*dict,"0020|000e", seriesUID);
>
> itk::EncapsulateMetaData<std::string>(*dict,"0020|0052",
> frameOfReferenceUID);
>
> #if ITK_VERSION_MAJOR >= 4
> gdcm::UIDGenerator sopuid;
> std::string sopInstanceUID = sopuid.Generate();
> #else
> std::string sopInstanceUID =
> gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
> #endif
>
> itk::EncapsulateMetaData<std::string>(*dict,"0008|0018", sopInstanceUID);
>
> itk::EncapsulateMetaData<std::string>(*dict,"0002|0003", sopInstanceUID);
>
> // Change fields that are slice specific
> itksys_ios::ostringstream value;
> value.str("");
> value << f + 1;
>
> // Image Number
>
> itk::EncapsulateMetaData<std::string>(*dict,"0020|0013", value.str());
>
> // Series Description - Append new description to
> current series description
> std::string oldSeriesDesc;
> itk::ExposeMetaData<std::string>(*inputDictionary,
> "0008|103e", oldSeriesDesc);
>
> value.str("");
> value << oldSeriesDesc
> << spacing[0] << ", "
> << spacing[1] << ", "
> << spacing[2];
>
> // This is an long string and there is a 64 character
> limit in the standard
> unsigned lengthDesc = value.str().length();
>
> std::string seriesDesc( value.str(), 0,
> lengthDesc > 64 ? 64
> : lengthDesc);
>
> itk::EncapsulateMetaData<std::string>(*dict,"0008|103e", seriesDesc);
>
> // Series Number
> value.str("");
> value << 1001;
>
> itk::EncapsulateMetaData<std::string>(*dict,"0020|0011", value.str());
>
> //Image Position Patient: This is calculated by
> computing the physical coordinate of the first pixel in each slice.
> ImageType::PointType position;
> ImageType::IndexType index;
> index[0] = 0;
> index[1] = 0;
> index[2] = f;
>
> reader->GetOutput()->TransformIndexToPhysicalPoint(index, position);
>
> value.str("");
> value << position[0] << "\\" << position[1] << "\\"
> << position[2];
>
>
> itk::EncapsulateMetaData<std::string>(*dict,"0020|0032", value.str()); //WHY
> NOT WORKING??
>
> // Slice Location: For now, we store the z component of
> the Image Position Patient.
> value.str("");
> value << position[2];
>
> itk::EncapsulateMetaData<std::string>(*dict,"0020|1041", value.str());
>
> // Spacing Between Slices
> value.str("");
> value << spacing[2];
>
> itk::EncapsulateMetaData<std::string>(*dict,"0018|0088", value.str());
>
> // Change specific values
> // itk::EncapsulateMetaData<std::string>(*dict,
> "0028|0100", "16" );
>
>
> // Save the dictionary
> dictionaryOutputArray.push_back(dict);
> }
>
> Thanks guys in advance...
>
> --
> S pozdravem Bc. Michal Srna
>
> Fotografické portfolio:
> http://michalsrna.cz
>
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