[Gdcm-hackers] gdcm-git:Grassroots DICOM branch master updated. 8a1e906ccc4bb681657633cdbcea48cb129
Cross-platform DICOM implementation
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[Gdcm-hackers] gdcm-git:Grassroots DICOM branch master updated. 8a1e906ccc4bb681657633cdbcea48cb12989100
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From: Mathieu M. <ma...@us...> - 2011-01-27 16:35:43
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This is an automated email from the git hooks/post-receive script. It was
generated because a ref change was pushed to the repository containing
the project "Grassroots DICOM".
The branch, master has been updated
via 8a1e906ccc4bb681657633cdbcea48cb12989100 (commit)
from 69bba8110ce32bf61b987c0388a81278bb23ba94 (commit)
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- Log -----------------------------------------------------------------
http://gdcm.git.sourceforge.net/git/gitweb.cgi?p=gdcm/gdcm;a=commit;h=8a1e906ccc4bb681657633cdbcea48cb12989100
commit 8a1e906ccc4bb681657633cdbcea48cb12989100
Author: Mathieu Malaterre <mat...@gm...>
Date: Thu Jan 27 17:35:34 2011 +0100
More work on --unenhance mode
diff --git a/Applications/Cxx/gdcmtar.cxx b/Applications/Cxx/gdcmtar.cxx
index 270ec76..8ee0044 100644
--- a/Applications/Cxx/gdcmtar.cxx
+++ b/Applications/Cxx/gdcmtar.cxx
@@ -515,6 +515,146 @@ int MakeImageEnhanced( std::string const & filename, std::string const &outfilen
return 0;
}
+namespace gdcm
+{
+
+const DataElement &GetNestedDataElement( const DataSet &ds, const Tag & t1, const Tag & t2 )
+{
+ assert( ds.FindDataElement( t1 ) );
+ SmartPointer<SequenceOfItems> sqi1 = ds.GetDataElement( t1 ).GetValueAsSQ();
+ assert( sqi1 );
+ const Item &item1 = sqi1->GetItem(1);
+ const DataSet & ds1 = item1.GetNestedDataSet();
+ assert( ds1.FindDataElement( t2 ) );
+ return ds1.GetDataElement( t2 );
+}
+
+static bool RemapSharedIntoOld( gdcm::DataSet & ds,
+ SequenceOfItems *sfgs,
+ SequenceOfItems *pffgs,
+ unsigned int index )
+{
+ assert( sfgs );
+ assert( pffgs );
+
+ assert( sfgs->GetNumberOfItems() == 1 );
+ Item const &item1 = sfgs->GetItem( 1 );
+ const DataSet & sfgs_ds = item1.GetNestedDataSet();
+#if 1
+ // Repetition Time
+ ds.Replace( GetNestedDataElement(sfgs_ds, Tag(0x0018,0x9112), Tag(0x0018,0x0080) ) );
+ // Echo Train Length
+ ds.Replace( GetNestedDataElement(sfgs_ds, Tag(0x0018,0x9112), Tag(0x0018,0x0091) ) );
+ // Flip Angle
+ ds.Replace( GetNestedDataElement(sfgs_ds, Tag(0x0018,0x9112), Tag(0x0018,0x1314) ) );
+ // Number of Averages
+ ds.Replace( GetNestedDataElement(sfgs_ds, Tag(0x0018,0x9119), Tag(0x0018,0x0083) ) );
+
+ // Percent Sampling
+ ds.Replace( GetNestedDataElement(sfgs_ds, Tag(0x0018,0x9125), Tag(0x0018,0x0093) ) );
+ // Percent Phase Field of View
+ ds.Replace( GetNestedDataElement(sfgs_ds, Tag(0x0018,0x9125), Tag(0x0018,0x0094) ) );
+ // Receive Coil Name
+ ds.Replace( GetNestedDataElement(sfgs_ds, Tag(0x0018,0x9042), Tag(0x0018,0x1250) ) );
+ // Transmit Coil Name
+ ds.Replace( GetNestedDataElement(sfgs_ds, Tag(0x0018,0x9049), Tag(0x0018,0x1251) ) );
+ // InPlanePhaseEncodingDirection
+ ds.Replace( GetNestedDataElement(sfgs_ds, Tag(0x0018,0x9125), Tag(0x0018,0x1312) ) );
+ // TransmitterFrequency
+ ds.Replace( GetNestedDataElement(sfgs_ds, Tag(0x0018,0x9006), Tag(0x0018,0x9098) ) );
+ // InversionRecovery
+ ds.Replace( GetNestedDataElement(sfgs_ds, Tag(0x0018,0x9115), Tag(0x0018,0x9009) ) );
+ // FlowCompensation
+ ds.Replace( GetNestedDataElement(sfgs_ds, Tag(0x0018,0x9115), Tag(0x0018,0x9010) ) );
+ // ReceiveCoilType
+ ds.Replace( GetNestedDataElement(sfgs_ds, Tag(0x0018,0x9042), Tag(0x0018,0x9043) ) );
+ // QuadratureReceiveCoil
+ ds.Replace( GetNestedDataElement(sfgs_ds, Tag(0x0018,0x9042), Tag(0x0018,0x9044) ) );
+ // SlabThickness
+ ds.Replace( GetNestedDataElement(sfgs_ds, Tag(0x0018,0x9107), Tag(0x0018,0x9104) ) );
+ // MultiCoilDefinitionSequence
+ ds.Replace( GetNestedDataElement(sfgs_ds, Tag(0x0018,0x9042), Tag(0x0018,0x9045) ) );
+ // SlabOrientation
+ ds.Replace( GetNestedDataElement(sfgs_ds, Tag(0x0018,0x9107), Tag(0x0018,0x9105) ) );
+ // MidSlabPosition
+ ds.Replace( GetNestedDataElement(sfgs_ds, Tag(0x0018,0x9107), Tag(0x0018,0x9106) ) );
+ // OperatingModeSequence
+ ds.Replace( GetNestedDataElement(sfgs_ds, Tag(0x0018,0x9112), Tag(0x0018,0x9176) ) );
+ // MRAcquisitionPhaseEncodingStepsOutOf
+ ds.Replace( GetNestedDataElement(sfgs_ds, Tag(0x0018,0x9125), Tag(0x0018,0x9232) ) );
+ // SpecificAbsorptionRateSequence
+ ds.Replace( GetNestedDataElement(sfgs_ds, Tag(0x0018,0x9112), Tag(0x0018,0x9239) ) );
+ // AnatomicRegionSequence
+ ds.Replace( GetNestedDataElement(sfgs_ds, Tag(0x0020,0x9071), Tag(0x0008,0x2218) ) );
+ // Purpose of Reference Code Sequence
+ // FIXME what if there is multiple purpose of rcs ?
+ ds.Replace( GetNestedDataElement(sfgs_ds, Tag(0x0008,0x1140), Tag(0x0040,0xa170) ) );
+#else
+ for(
+ DataSet::ConstIterator it = sfgs_ds.Begin();
+ it != sfgs_ds.End(); ++it )
+ {
+ ds.Replace( *it );
+ }
+#endif
+
+ Item const &item2 = pffgs->GetItem( index + 1 );
+ const DataSet & pffgs_ds = item2.GetNestedDataSet();
+
+#if 1
+ // Effective Echo Time
+ ds.Replace( GetNestedDataElement(pffgs_ds, Tag(0x0018,0x9114), Tag(0x0018,0x9082) ) );
+ // -> should also be Echo Time
+ // Nominal Cardiac Trigger Delay Time
+ ds.Replace( GetNestedDataElement(pffgs_ds, Tag(0x0018,0x9118), Tag(0x0020,0x9153) ) );
+ // Metabolite Map Description
+ ds.Replace( GetNestedDataElement(pffgs_ds, Tag(0x0018,0x9152), Tag(0x0018,0x9080) ) );
+ // IPP
+ ds.Replace( GetNestedDataElement(pffgs_ds, Tag(0x0020,0x9113), Tag(0x0020,0x0032) ) );
+ // IOP
+ ds.Replace( GetNestedDataElement(pffgs_ds, Tag(0x0020,0x9116), Tag(0x0020,0x0037) ) );
+ // Slice Thickness
+ ds.Replace( GetNestedDataElement(pffgs_ds, Tag(0x0028,0x9110), Tag(0x0018,0x0050) ) );
+ // Pixel Spacing
+ ds.Replace( GetNestedDataElement(pffgs_ds, Tag(0x0028,0x9110), Tag(0x0028,0x0030) ) );
+
+ // window level
+ ds.Replace( GetNestedDataElement(pffgs_ds, Tag(0x0028,0x9132), Tag(0x0028,0x1050) ) );
+ ds.Replace( GetNestedDataElement(pffgs_ds, Tag(0x0028,0x9132), Tag(0x0028,0x1051) ) );
+
+ // rescale slope/intercept
+ ds.Replace( GetNestedDataElement(pffgs_ds, Tag(0x0028,0x9145), Tag(0x0028,0x1052) ) );
+ ds.Replace( GetNestedDataElement(pffgs_ds, Tag(0x0028,0x9145), Tag(0x0028,0x1053) ) );
+ ds.Replace( GetNestedDataElement(pffgs_ds, Tag(0x0028,0x9145), Tag(0x0028,0x1054) ) );
+
+ // FrameReferenceDateTime
+ ds.Replace( GetNestedDataElement(pffgs_ds, Tag(0x0020,0x9111), Tag(0x0018,0x9151) ) );
+ // FrameAcquisitionDuration
+ ds.Replace( GetNestedDataElement(pffgs_ds, Tag(0x0020,0x9111), Tag(0x0018,0x9220) ) );
+ // TemporalPositionIndex
+ ds.Replace( GetNestedDataElement(pffgs_ds, Tag(0x0020,0x9111), Tag(0x0020,0x9128) ) );
+ // InStackPositionNumber
+ ds.Replace( GetNestedDataElement(pffgs_ds, Tag(0x0020,0x9111), Tag(0x0020,0x9057) ) );
+ // FrameType
+ ds.Replace( GetNestedDataElement(pffgs_ds, Tag(0x0018,0x9226), Tag(0x0008,0x9007) ) );
+ // DimensionIndexValues
+ ds.Replace( GetNestedDataElement(pffgs_ds, Tag(0x0020,0x9111), Tag(0x0020,0x9157) ) );
+ // FrameAcquisitionDateTime
+ ds.Replace( GetNestedDataElement(pffgs_ds, Tag(0x0020,0x9111), Tag(0x0018,0x9074) ) );
+ // Nominal Cardiac Trigger Delay Time -> Trigger Time
+ //const DataElement &NominalCardiacTriggerDelayTime =
+ // GetNestedDataElement(pffgs_ds, Tag(0x0018,0x9226), Tag(0x0008,0x9007) );
+#endif
+
+ // (0020,9228) UL 158 # 4, 1 ConcatenationFrameOffsetNumber
+ gdcm::Attribute<0x0020,0x9228> at = { index };
+ ds.Replace( at.GetAsDataElement() );
+
+ return true;
+}
+
+} // namespace gdcm
+
int main (int argc, char *argv[])
{
int c;
@@ -908,17 +1048,15 @@ int main (int argc, char *argv[])
de.SetByteValue( msstr, strlen(msstr) );
de.SetVR( gdcm::Attribute<0x0008, 0x0016>::GetVR() );
ds.Replace( de );
- // Remove SharedFunctionalGroupsSequence
- ds.Remove( gdcm::Tag( 0x5200,0x9229 ) );
- // Remove PerFrameFunctionalGroupsSequence
- ds.Remove( gdcm::Tag( 0x5200,0x9230 ) );
const gdcm::Image &image = reader.GetImage();
const unsigned int *dims = image.GetDimensions();
//std::cout << image << std::endl;
const gdcm::DataElement &pixeldata = image.GetDataElement();
- const gdcm::ByteValue *bv = pixeldata.GetByteValue();
+ //const gdcm::ByteValue *bv = pixeldata.GetByteValue();
+ gdcm::SmartPointer<gdcm::ByteValue> bv = (gdcm::ByteValue*)pixeldata.GetByteValue();
unsigned long slice_len = image.GetBufferLength() / dims[2];
+ assert( slice_len * dims[2] == image.GetBufferLength() );
//assert( image.GetBufferLength() == bv->GetLength() );
gdcm::FilenameGenerator fg;
@@ -937,6 +1075,32 @@ int main (int argc, char *argv[])
const double *origin = image.GetOrigin();
double zspacing = image.GetSpacing(2);
+ // Remove SharedFunctionalGroupsSequence
+ gdcm::SmartPointer<gdcm::SequenceOfItems> sfgs =
+ ds.GetDataElement( gdcm::Tag( 0x5200,0x9229 ) ).GetValueAsSQ();
+ ds.Remove( gdcm::Tag( 0x5200,0x9229 ) );
+ assert( ds.FindDataElement( gdcm::Tag( 0x5200,0x9229 ) ) == false );
+ // Remove PerFrameFunctionalGroupsSequence
+ gdcm::SmartPointer<gdcm::SequenceOfItems> pffgs =
+ ds.GetDataElement( gdcm::Tag( 0x5200,0x9230 ) ).GetValueAsSQ();
+ ds.Remove( gdcm::Tag( 0x5200,0x9230 ) );
+ assert( ds.FindDataElement( gdcm::Tag( 0x5200,0x9230 ) ) == false );
+ ds.Remove( gdcm::Tag( 0x28,0x8) );
+ ds.Remove( gdcm::Tag( 0x7fe0,0x0010) );
+ assert( ds.FindDataElement( gdcm::Tag( 0x7fe0,0x0010) ) == false );
+ //ds.Remove( gdcm::Tag( 0x0008,0x0012) );
+ //ds.Remove( gdcm::Tag( 0x0008,0x0013) );
+
+ char date[22];
+ const size_t datelen = 8;
+ int res = gdcm::System::GetCurrentDateTime(date);
+ gdcm::Attribute<0x8,0x12> instcreationdate;
+ instcreationdate.SetValue( gdcm::DTComp( date, datelen ) );
+ ds.Replace( instcreationdate.GetAsDataElement() );
+ gdcm::Attribute<0x8,0x13> instcreationtime;
+ instcreationtime.SetValue( gdcm::DTComp( date + datelen, 13 ) );
+ ds.Replace( instcreationtime.GetAsDataElement() );
+
for(unsigned int i = 0; i < dims[2]; ++i)
{
double new_origin[3];
@@ -948,33 +1112,41 @@ int main (int argc, char *argv[])
}
const char *outfilenamei = fg.GetFilename(i);
- gdcm::ImageWriter writer;
+ //gdcm::ImageWriter writer;
+ gdcm::Writer writer;
writer.SetFileName( outfilenamei );
//writer.SetFile( filter.GetFile() );
writer.SetFile( reader.GetFile() );
+ if ( !gdcm::RemapSharedIntoOld( ds, sfgs, pffgs, i ) )
+ {
+ return 1;
+ }
+
//
//writer.SetImage( filter.GetImage() );
- gdcm::Image &slice = writer.GetImage();
+ gdcm::Image & //slice = writer.GetImage();
slice = reader.GetImage();
- slice.SetOrigin( new_origin );
- slice.SetNumberOfDimensions( 2 );
- assert( slice.GetPixelFormat() == reader.GetImage().GetPixelFormat() );
- slice.SetSpacing(2, reader.GetImage().GetSpacing(2) );
+// slice.SetOrigin( new_origin );
+// slice.SetNumberOfDimensions( 2 );
+// assert( slice.GetPixelFormat() == reader.GetImage().GetPixelFormat() );
+// slice.SetSpacing(2, reader.GetImage().GetSpacing(2) );
//slice.Print( std::cout );
- gdcm::DataElement &pd = slice.GetDataElement();
+// gdcm::DataElement &pd = slice.GetDataElement();
const char *sliceptr = bv->GetPointer() + i * slice_len;
- pd.SetByteValue( sliceptr, slice_len); // slow !
+ gdcm::DataElement newpixeldata( gdcm::Tag(0x7fe0,0x0010) );
+ newpixeldata.SetByteValue( sliceptr, slice_len); // slow !
+ ds.Replace( newpixeldata );
if( !writer.Write() )
{
std::cerr << "Failed to write: " << outfilenamei << std::endl;
return 1;
}
- else
- {
- std::cout << "Success to write: " << outfilenamei << std::endl;
- }
+ //else
+ // {
+ // std::cout << "Success to write: " << outfilenamei << std::endl;
+ // }
}
return 0;
-----------------------------------------------------------------------
Summary of changes:
Applications/Cxx/gdcmtar.cxx | 206 ++++++++++++++++++++++++++++++++++++++----
1 files changed, 189 insertions(+), 17 deletions(-)
hooks/post-receive
--
Grassroots DICOM
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