[Insight-users] Problem with saving Image Position value in "z" axis

Bill Lorensen bill.lorensen at gmail.com
Fri Apr 15 12:53:50 EDT 2011


Have either you(Michal) or Alberto seen the same problem on an earlier
version of ITK?

On Fri, Apr 15, 2011 at 12:46 PM, Bc. Michal Srna <michal at srna.info> wrote:
> Sorry for forgetting to mention it - ITKv4, latest from Git.
>
> 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
>> >
>> > _____________________________________
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>> >
>> >
>
>
>
> --
> S pozdravem Bc. Michal Srna
>
> Fotografické portfolio:
> http://michalsrna.cz
>


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