I only test it on this version. <div><br></div><div>I modify the class itkGDCMImageIO on line 711 replacing this code :</div><div><br></div><div>image.SetOrigin(2, 0);</div><div><br></div><div>by the following :</div><div>
<br></div><div><div> if( header.FindDataElement( gdcm::Tag(0x0020, 0x0032 ) )){</div><div> <span class="Apple-tab-span" style="white-space:pre"> </span> const gdcm::DataElement &de = header.GetDataElement( gdcm::Tag(0x0020, 0x0032) );</div>
<div> <span class="Apple-tab-span" style="white-space:pre"> </span> std::pair<std::string, std::string> s = sf.ToStringPair( de.GetTag() );</div><div> <span class="Apple-tab-span" style="white-space:pre"> </span> std::string value= s.second;</div>
<div> <span class="Apple-tab-span" style="white-space:pre"> </span> sscanf( value.c_str(), "%lf\\%lf\\%lf", &(m_Origin[0]), &(m_Origin[1]), &(m_Origin[2]) );</div><div> <span class="Apple-tab-span" style="white-space:pre"> </span> image.SetOrigin(2, m_Origin[2]);</div>
<div> }</div></div><div><br></div><div>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?</div><div><br></div><div>Thank you.</div><div>
<br></div><div><div class="gmail_quote">2011/4/15 Bill Lorensen <span dir="ltr"><<a href="mailto:bill.lorensen@gmail.com">bill.lorensen@gmail.com</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
I realize that. I was asking Mical.<br>
<br>
Did your code work properly with earlier versions of itk?<br>
<font color="#888888"><br>
Bill<br>
</font><div><div></div><div class="h5"><br>
On Fri, Apr 15, 2011 at 12:30 PM, Alberto <<a href="mailto:bertorey@gmail.com">bertorey@gmail.com</a>> wrote:<br>
> The git version of ITK<br>
><br>
> 2011/4/15 Bill Lorensen <<a href="mailto:bill.lorensen@gmail.com">bill.lorensen@gmail.com</a>><br>
>><br>
>> What version of itk are you using?<br>
>><br>
>> On Thu, Apr 14, 2011 at 5:16 AM, Bc. Michal Srna <<a href="mailto:michal@srna.info">michal@srna.info</a>> wrote:<br>
>> > Hello,<br>
>> ><br>
>> > I have used part of this code to generate MetaDataDictionary:<br>
>> ><br>
>> > <a href="http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM" target="_blank">http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM</a><br>
>> ><br>
>> > Everything works, as I need, but I have just one problem in part<br>
>> > regarding<br>
>> > saving Image Position (origin) for "z" axis. "x,y" are stored well, but<br>
>> > "z"<br>
>> > value of Image Position is 0.<br>
>> ><br>
>> > Here is that part of the code for saving the Image position:<br>
>> ><br>
>> > ImageType::PointType position;<br>
>> > ImageType::IndexType index;<br>
>> > index[0] = 0;<br>
>> > index[1] = 0;<br>
>> > index[2] = f;<br>
>> ><br>
>> > reader->GetOutput()->TransformIndexToPhysicalPoint(index, position);<br>
>> ><br>
>> > value.str("");<br>
>> > value << position[0] << "\\" << position[1] <<<br>
>> > "\\"<br>
>> > << position[2];<br>
>> ><br>
>> ><br>
>> > itk::EncapsulateMetaData<std::string>(*dict,"0020|0032", value.str());<br>
>> > //WHY<br>
>> > NOT WORKING??<br>
>> ><br>
>> > position[2] contains the correct value, but I don't know, why is that<br>
>> > value<br>
>> > not saved and instead of that value is stored just 0?<br>
>> ><br>
>> > I think I should add also the whole code for generating my<br>
>> > MetaDataDictionary for see my problem in context.<br>
>> ><br>
>> > At first it opens original data, from which I read original meta data.<br>
>> > Then<br>
>> > I modify some parts of those meta data in for cycle creating meta data<br>
>> > for<br>
>> > each slice.<br>
>> ><br>
>> > I confirmed, that original data contains correct value of Image Position<br>
>> > in<br>
>> > "z" axis. But I need to recalculate that value and store new value.<br>
>> > Problem<br>
>> > is, as I told, that this value is not saved and instead of it, there is<br>
>> > just<br>
>> > 0.<br>
>> ><br>
>> > Here is the whole code, spacing[x] is derived from other part of the<br>
>> > whole<br>
>> > code, I don't want to copy here:<br>
>> ><br>
>> > /*opening original data for getting meta data dictionry for saving it<br>
>> > into<br>
>> > output 2D series files*/<br>
>> > typedef itk::GDCMImageIO ImageIOType;<br>
>> > typedef itk::GDCMSeriesFileNames NamesGeneratorType;<br>
>> > typedef itk::ImageSeriesReader< ImageType > ReaderType;<br>
>> ><br>
>> > ImageIOType::Pointer gdcmIO = ImageIOType::New();<br>
>> > ReaderType::Pointer reader = ReaderType::New();<br>
>> ><br>
>> > NamesGeneratorType::Pointer namesGenerator =<br>
>> > NamesGeneratorType::New();<br>
>> > namesGenerator->SetInputDirectory( StudyFolderName );<br>
>> > const ReaderType::FileNamesContainer & filenames =<br>
>> > namesGenerator->GetInputFileNames();<br>
>> ><br>
>> > reader->SetImageIO( gdcmIO );<br>
>> > reader->SetFileNames( filenames );<br>
>> ><br>
>> > reader->Update();<br>
>> ><br>
>> > /*creating MetaDataDictionary for each slice*/<br>
>> ><br>
>> > /*Copy the dictionary from the first image and override<br>
>> > slice<br>
>> > specific fields*/<br>
>> > ReaderType::DictionaryRawPointer inputDictionary =<br>
>> > (*(reader->GetMetaDataDictionaryArray()))[0];<br>
>> > ReaderType::DictionaryArrayType dictionaryOutputArray;<br>
>> ><br>
>> > /*To keep the new series in the same study as the original<br>
>> > we<br>
>> > need to keep the same study UID. But we need new series and frame of<br>
>> > reference UID's.*/<br>
>> > #if ITK_VERSION_MAJOR >= 4<br>
>> > gdcm::UIDGenerator suid;<br>
>> > std::string seriesUID = suid.Generate();<br>
>> > gdcm::UIDGenerator fuid;<br>
>> > std::string frameOfReferenceUID = fuid.Generate();<br>
>> > #else<br>
>> > std::string seriesUID = gdcm::Util::CreateUniqueUID(<br>
>> > gdcmIO->GetUIDPrefix());<br>
>> > std::string frameOfReferenceUID =<br>
>> > gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());<br>
>> > #endif<br>
>> > std::string studyUID;<br>
>> > std::string sopClassUID;<br>
>> > itk::ExposeMetaData<std::string>(*inputDictionary,<br>
>> > "0020|000d", studyUID);<br>
>> > itk::ExposeMetaData<std::string>(*inputDictionary,<br>
>> > "0008|0016", sopClassUID);<br>
>> > gdcmIO->KeepOriginalUIDOn();<br>
>> ><br>
>> > for (unsigned int f = 0; f < size[2]; f++)<br>
>> > {<br>
>> > // Create a new dictionary for this slice<br>
>> > ReaderType::DictionaryRawPointer dict = new<br>
>> > ReaderType::DictionaryType;<br>
>> ><br>
>> > // Copy the dictionary from the first slice<br>
>> > CopyDictionary (*inputDictionary, *dict);<br>
>> ><br>
>> > // Set the UID's for the study, series, SOP and<br>
>> > frame<br>
>> > of reference<br>
>> ><br>
>> > itk::EncapsulateMetaData<std::string>(*dict,"0020|000d", studyUID);<br>
>> ><br>
>> > itk::EncapsulateMetaData<std::string>(*dict,"0020|000e", seriesUID);<br>
>> ><br>
>> > itk::EncapsulateMetaData<std::string>(*dict,"0020|0052",<br>
>> > frameOfReferenceUID);<br>
>> ><br>
>> > #if ITK_VERSION_MAJOR >= 4<br>
>> > gdcm::UIDGenerator sopuid;<br>
>> > std::string sopInstanceUID = sopuid.Generate();<br>
>> > #else<br>
>> > std::string sopInstanceUID =<br>
>> > gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());<br>
>> > #endif<br>
>> ><br>
>> > itk::EncapsulateMetaData<std::string>(*dict,"0008|0018",<br>
>> > sopInstanceUID);<br>
>> ><br>
>> > itk::EncapsulateMetaData<std::string>(*dict,"0002|0003",<br>
>> > sopInstanceUID);<br>
>> ><br>
>> > // Change fields that are slice specific<br>
>> > itksys_ios::ostringstream value;<br>
>> > value.str("");<br>
>> > value << f + 1;<br>
>> ><br>
>> > // Image Number<br>
>> ><br>
>> > itk::EncapsulateMetaData<std::string>(*dict,"0020|0013", value.str());<br>
>> ><br>
>> > // Series Description - Append new description to<br>
>> > current series description<br>
>> > std::string oldSeriesDesc;<br>
>> ><br>
>> > itk::ExposeMetaData<std::string>(*inputDictionary,<br>
>> > "0008|103e", oldSeriesDesc);<br>
>> ><br>
>> > value.str("");<br>
>> > value << oldSeriesDesc<br>
>> > << spacing[0] << ", "<br>
>> > << spacing[1] << ", "<br>
>> > << spacing[2];<br>
>> ><br>
>> > // This is an long string and there is a 64<br>
>> > character<br>
>> > limit in the standard<br>
>> > unsigned lengthDesc = value.str().length();<br>
>> ><br>
>> > std::string seriesDesc( value.str(), 0,<br>
>> > lengthDesc > 64 ? 64<br>
>> > : lengthDesc);<br>
>> ><br>
>> > itk::EncapsulateMetaData<std::string>(*dict,"0008|103e", seriesDesc);<br>
>> ><br>
>> > // Series Number<br>
>> > value.str("");<br>
>> > value << 1001;<br>
>> ><br>
>> > itk::EncapsulateMetaData<std::string>(*dict,"0020|0011", value.str());<br>
>> ><br>
>> > //Image Position Patient: This is calculated by<br>
>> > computing the physical coordinate of the first pixel in each slice.<br>
>> > ImageType::PointType position;<br>
>> > ImageType::IndexType index;<br>
>> > index[0] = 0;<br>
>> > index[1] = 0;<br>
>> > index[2] = f;<br>
>> ><br>
>> > reader->GetOutput()->TransformIndexToPhysicalPoint(index, position);<br>
>> ><br>
>> > value.str("");<br>
>> > value << position[0] << "\\" << position[1] <<<br>
>> > "\\"<br>
>> > << position[2];<br>
>> ><br>
>> ><br>
>> > itk::EncapsulateMetaData<std::string>(*dict,"0020|0032", value.str());<br>
>> > //WHY<br>
>> > NOT WORKING??<br>
>> ><br>
>> > // Slice Location: For now, we store the z component<br>
>> > of<br>
>> > the Image Position Patient.<br>
>> > value.str("");<br>
>> > value << position[2];<br>
>> ><br>
>> > itk::EncapsulateMetaData<std::string>(*dict,"0020|1041", value.str());<br>
>> ><br>
>> > // Spacing Between Slices<br>
>> > value.str("");<br>
>> > value << spacing[2];<br>
>> ><br>
>> > itk::EncapsulateMetaData<std::string>(*dict,"0018|0088", value.str());<br>
>> ><br>
>> > // Change specific values<br>
>> > // itk::EncapsulateMetaData<std::string>(*dict,<br>
>> > "0028|0100", "16" );<br>
>> ><br>
>> ><br>
>> > // Save the dictionary<br>
>> > dictionaryOutputArray.push_back(dict);<br>
>> > }<br>
>> ><br>
>> > Thanks guys in advance...<br>
>> ><br>
>> > --<br>
>> > S pozdravem Bc. Michal Srna<br>
>> ><br>
>> > Fotografické portfolio:<br>
>> > <a href="http://michalsrna.cz" target="_blank">http://michalsrna.cz</a><br>
>> ><br>
>> > _____________________________________<br>
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</div></div></blockquote></div><br></div>