[Insight-users] Problem with saving Image Position value in "z" axis
Bill Lorensen
bill.lorensen at gmail.com
Fri Apr 15 15:43:02 EDT 2011
Alberto,
Thanks for proving the patch for review.
Bill
On Fri, Apr 15, 2011 at 1:08 PM, Alberto <bertorey at gmail.com> wrote:
> Yes, of course. I try upload the patch now.
> Thank you.
> 2011/4/15 Bill Lorensen <bill.lorensen at gmail.com>
>>
>> This is definitely a bug. And it was introduced in itk4.
>>
>> Alberto, Can you submit a patch to gerrit?
>> http://itk.org/Wiki/ITK/Gerrit/Primer
>>
>> I can help you step through this process.
>>
>> Bill
>>
>> On Fri, Apr 15, 2011 at 12:53 PM, Alberto <bertorey at gmail.com> wrote:
>> > I only test it on this version.
>> > I modify the class itkGDCMImageIO on line 711 replacing this code :
>> > image.SetOrigin(2, 0);
>> > by the following :
>> > if( header.FindDataElement( gdcm::Tag(0x0020, 0x0032 ) )){
>> > const gdcm::DataElement &de = header.GetDataElement(
>> > gdcm::Tag(0x0020,
>> > 0x0032) );
>> > std::pair<std::string, std::string> s = sf.ToStringPair( de.GetTag()
>> > );
>> > std::string value= s.second;
>> > sscanf( value.c_str(), "%lf\\%lf\\%lf", &(m_Origin[0]),
>> > &(m_Origin[1]),
>> > &(m_Origin[2]) );
>> > image.SetOrigin(2, m_Origin[2]);
>> > }
>> > and now the Image Patient Position tag is set ok with the correct value
>> > of
>> > z-axis. Could this code be a valid patch for the problem?
>> > Thank you.
>> > 2011/4/15 Bill Lorensen <bill.lorensen at gmail.com>
>> >>
>> >> I realize that. I was asking Mical.
>> >>
>> >> Did your code work properly with earlier versions of itk?
>> >>
>> >> Bill
>> >>
>> >> On Fri, Apr 15, 2011 at 12:30 PM, Alberto <bertorey at gmail.com> wrote:
>> >> > 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
>> >> >
>> >> >
>> >> > _____________________________________
>> >> > 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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