BUG: ImageSeriesWriter + GDCMImageIO loses info

When directional cosines are copied from 3D volume to 2D slices by ImageSeriesWriter, only the upper-left 2x2 matrix can be copied, due to the dimension of m_Direction matrix. Then GDCMImageIO sets zeros in the missing values of the first 2 lines of the matrix. This is not a problem if the directional cosines matrix is the identity matrix, otherwise DICOM tag (0020,0037) Image Orientation (Patient) of the output DICOM files is not valid. ITK-281 Change-Id: I44bac496fb1132abb85a5f9d66bd7ad469c774b2
Kitware · Jun 26, 2013 · df66144 · df66144
1 parent ec61e6e
commit df66144
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Showing 4 changed files with 32 additions and 0 deletions.
diff --git a/Modules/IO/GDCM/src/itkGDCMImageIO.cxx b/Modules/IO/GDCM/src/itkGDCMImageIO.cxx
@@ -708,6 +708,11 @@ void GDCMImageIO::Write(const void *buffer)
         m_GlobalNumberOfDimensions = numberOfDimensions;
         m_Origin.resize(m_GlobalNumberOfDimensions);
         m_Spacing.resize(m_GlobalNumberOfDimensions);
+        m_Direction.resize(m_GlobalNumberOfDimensions);
+        for (unsigned int i = 0; i < m_GlobalNumberOfDimensions; i++)
+          {
+          m_Direction[i].resize(m_GlobalNumberOfDimensions);
+          }
         }
       else if ( key == ITK_Origin )
         {
@@ -727,6 +732,19 @@ void GDCMImageIO::Write(const void *buffer)
         m_Spacing[1] = spacingArray[1];
         m_Spacing[2] = spacingArray[2];
         }
+      else if( key == ITK_ZDirection )
+        {
+        typedef Matrix< double > DoubleMatrixType;
+        DoubleMatrixType directionMatrix;
+        ExposeMetaData< DoubleMatrixType >( dict, key, directionMatrix );
+        for(int i = 0; i<3; i++)
+          {
+          for(int j = 0; j<3; j++)
+            {
+            m_Direction[i][j]=directionMatrix[i][j];
+            }
+          }
+        }
       else
         {
         itkDebugMacro(

diff --git a/Modules/IO/ImageBase/include/itkIOCommon.h b/Modules/IO/ImageBase/include/itkIOCommon.h
@@ -69,6 +69,7 @@ extern ITK_EXPORT const char *const SPM_ROI_SCALE;
 extern ITK_EXPORT const char *const ITK_FileNotes;
 extern ITK_EXPORT const char *const ITK_Origin;
 extern ITK_EXPORT const char *const ITK_Spacing;
+extern ITK_EXPORT const char *const ITK_ZDirection;
 extern ITK_EXPORT const char *const ITK_FileOriginator;
 extern ITK_EXPORT const char *const ITK_OriginationDate;
 extern ITK_EXPORT const char *const ITK_PatientID;

diff --git a/Modules/IO/ImageBase/include/itkImageSeriesWriter.hxx b/Modules/IO/ImageBase/include/itkImageSeriesWriter.hxx
@@ -352,6 +352,18 @@ ImageSeriesWriter< TInputImage, TOutputImage >
         EncapsulateMetaData< DoubleArrayType >(dictionary, ITK_Origin, originArray);
         EncapsulateMetaData< DoubleArrayType >(dictionary, ITK_Spacing, spacingArray);
         EncapsulateMetaData<  unsigned int   >(dictionary, ITK_NumberOfDimensions, inputImageDimension);
+
+        typename InputImageType::DirectionType direction2 = inputImage->GetDirection();
+        typedef Matrix< double, inputImageDimension, inputImageDimension> DoubleMatrixType;
+        DoubleMatrixType directionMatrix;
+        for( unsigned int i = 0; i < inputImageDimension; i++ )
+          {
+          for( unsigned int j = 0; j < inputImageDimension; j++ )
+            {
+            directionMatrix[j][i]  = direction2[i][j];
+            }
+          }
+        EncapsulateMetaData< DoubleMatrixType >( dictionary, ITK_ZDirection, directionMatrix );
         }
       }
 

diff --git a/Modules/IO/ImageBase/src/itkIOCommon.cxx b/Modules/IO/ImageBase/src/itkIOCommon.cxx
@@ -27,6 +27,7 @@ const char *const SPM_ROI_SCALE = "SPM_ROI_SCALE";
 const char *const ITK_FileNotes = "ITK_FileNotes";
 const char *const ITK_Origin = "ITK_Origin";
 const char *const ITK_Spacing = "ITK_Spacing";
+const char *const ITK_ZDirection = "ITK_ZDirection";
 const char *const ITK_FileOriginator = "ITK_FileOriginator";
 const char *const ITK_OriginationDate = "ITK_OriginationDate";
 const char *const ITK_PatientID = "ITK_PatientID";