[Insight-users] Problem with saving Image Position value in "z" axis
Alberto
bertorey at gmail.com
Fri Apr 15 12:30:35 EDT 2011
The git version of ITK
2011/4/15 Bill Lorensen <bill.lorensen at gmail.com>
> 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
> >
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.html
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://www.itk.org/mailman/listinfo/insight-users
> >
> >
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.html
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://www.itk.org/mailman/listinfo/insight-users
>
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