GDCM Secondary Capture spatial metadata

.gitattributes

@@ -52,6 +52,7 @@ CMakeLists.txt   whitespace=tab-in-indent,no-lf-at-eof our-cmake-style
 Modules/Numerics/FEM/src/dsrc2c.c hooks-max-size=260000
 Modules/ThirdParty/** hooks-max-size=300000 hooks.style=
 Modules/ThirdParty/ZLIB/src/itkzlib-ng/crc32_braid_tbl.h hooks-max-size=700000
+Modules/ThirdParty/GDCM/src/gdcm/Source/DataDictionary/privatedicts.xml hooks-max-size=400000
 Modules/Filtering/Denoising/include/itkPatchBasedDenoisingImageFilter.hxx hooks-max-size=120000
 Documentation/docs/releases/* hooks-max-size=300000
 

Modules/IO/DCMTK/test/Baseline/itkDCMTKColorImageSpatialMetadata.nrrd.cid

@@ -0,0 +1 @@
+bafybeiai2acs4g7k6aeneziwgi3tw2i33idmnzclpyh4mt4dqvgktca7gu

Modules/IO/DCMTK/test/CMakeLists.txt

@@ -182,6 +182,18 @@ itk_add_test(
   DATA{${ITK_DATA_ROOT}/Input/RGBDicomTest.dcm}
   ${ITK_TEST_OUTPUT_DIR}/itkDCMTKColorImage.png)
 
+itk_add_test(
+  NAME
+  itkDCMTKRGBImageIOColorImageSpatialMetadataTest
+  COMMAND
+  ITKIODCMTKTestDriver
+  --compare
+  DATA{Baseline/itkDCMTKColorImageSpatialMetadata.nrrd}
+  ${ITK_TEST_OUTPUT_DIR}/itkDCMTKColorImageSpatialMetadata.nrrd
+  itkDCMTKRGBImageIOTest
+  DATA{Input/visible-male-rgb-slice.dcm}
+  ${ITK_TEST_OUTPUT_DIR}/itkDCMTKColorImageSpatialMetadata.nrrd)
+
 itk_add_test(
   NAME
   ITKDCMTKLoggerTest

Modules/IO/DCMTK/test/Input/visible-male-rgb-slice.dcm.cid

@@ -0,0 +1 @@
+bafybeiadtxwvshbmde3aywkzlzcudcoxypafxrshabby6gmdmtawapjzre

Modules/IO/GDCM/src/itkGDCMImageIO.cxx

@@ -286,6 +286,8 @@ GDCMImageIO::Read(void * pointer)
   inputFileStream.close();
 
   itkAssertInDebugAndIgnoreInReleaseMacro(gdcm::ImageHelper::GetForceRescaleInterceptSlope());
+  // Secondary capture image orientation patient and image position patient support
+  itkAssertInDebugAndIgnoreInReleaseMacro(gdcm::ImageHelper::GetSecondaryCaptureImagePlaneModule());
   gdcm::ImageReader reader;
   reader.SetFileName(m_FileName.c_str());
   if (!reader.Read())
@@ -454,6 +456,8 @@ GDCMImageIO::InternalReadImageInformation()
 
   // In general this should be relatively safe to assume
   gdcm::ImageHelper::SetForceRescaleInterceptSlope(true);
+  // Secondary capture image orientation patient and image position patient support
+  gdcm::ImageHelper::SetSecondaryCaptureImagePlaneModule(true);
 
   gdcm::ImageReader reader;
   reader.SetFileName(m_FileName.c_str());

Modules/IO/GDCM/test/Baseline/Lily.mha.cid

@@ -0,0 +1 @@
+bafkreidhatfhe2gdne5k5pyw2rfvnuu3qmedytq7mrdjckmw6zrc5x3srq

Modules/IO/GDCM/test/Baseline/itkGDCMImageReadWriteTest_SC_RGB.nrrd.cid

@@ -0,0 +1 @@
+bafybeib67xvtf44xwu4rxapchxqjflfutheq3wja47qvniz4gdwrqkqujy

Modules/IO/GDCM/test/CMakeLists.txt

@@ -278,6 +278,19 @@ itk_add_test(
   ${ITK_TEST_OUTPUT_DIR}/itkGDCMImageReadWriteTest_RGB.mha
   rgb)
 
+itk_add_test(
+  NAME
+  itkGDCMImageReadWriteTest_SC_RGB
+  COMMAND
+  ITKIOGDCMTestDriver
+  --compare
+  DATA{Baseline/itkGDCMImageReadWriteTest_SC_RGB.nrrd}
+  ${ITK_TEST_OUTPUT_DIR}/itkGDCMImageReadWriteTest_SC_RGB.nrrd
+  itkGDCMImageReadWriteTest
+  DATA{Input/visible-male-rgb-slice.dcm}
+  ${ITK_TEST_OUTPUT_DIR}/itkGDCMImageReadWriteTest_SC_RGB.nrrd
+  rgb)
+
 itk_add_test(
   NAME
   itkGDCM_ComplianceTestRGB_JPEG2000ICT
@@ -397,7 +410,7 @@ function(AddComplianceTest fileName)
     --compareCoordinateTolerance
     0.001
     --compare
-    DATA{Baseline/Lily.png}
+    DATA{Baseline/Lily.mha}
     ${ITK_TEST_OUTPUT_DIR}/itkGDCM_ComplianceTestRGB_${fileName}.mha
     itkGDCMImageReadWriteTest
     DATA{Input/Lily/${fileName}.dcm}

Modules/IO/GDCM/test/Input/visible-male-rgb-slice.dcm.cid

@@ -0,0 +1 @@
+bafybeiadtxwvshbmde3aywkzlzcudcoxypafxrshabby6gmdmtawapjzre

Modules/IO/ImageBase/src/itkIOConfigure.h.in

@@ -21,6 +21,7 @@
 #cmakedefine ITK_SUPPORTS_WCHAR_T_FILENAME_CSTYLEIO
 #cmakedefine ITK_SUPPORTS_WCHAR_T_FILENAME_IOSTREAMS_CONSTRUCTORS
 #cmakedefine ITK_SUPPORTS_FDSTREAM_HPP
+#cmakedefine ITK_USE_SYSTEM_GDCM
 
 /*
  *  Enable the pre-registration of factories for specific image file formats

Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt

@@ -17,7 +17,7 @@ endif()
 #----------------------------------------------------------------------------
 
 project(GDCM
-  VERSION 3.0.22
+  VERSION 3.0.23
   LANGUAGES CXX C
 )
 ## NOTE: the "DESCRIPTION" feature of project() was introduced in cmake 3.10.0

Modules/ThirdParty/GDCM/src/gdcm/Source/DataStructureAndEncodingDefinition/gdcmCSAHeader.cxx

@@ -910,7 +910,8 @@ bool check_mapping(uint32_t syngodt, const char *vr)
 {
   static const unsigned int max = sizeof(mapping) / sizeof(equ);
   const equ *p = mapping;
-  assert( syngodt <= mapping[max-1].syngodt ); (void)max;
+  if( syngodt > mapping[max-1].syngodt ) return false;
+  assert( syngodt <= mapping[max-1].syngodt );
   while(p->syngodt < syngodt )
     {
     //std::cout << "mapping:" << p->vr << std::endl;
@@ -1098,6 +1099,11 @@ bool CSAHeader::LoadFromDataElement(DataElement const &de)
     char vr[4];
     ss.read(vr, 4);
     // In dataset without magic signature (OLD FORMAT) vr[3] is garbage...
+    if( vr[2] != 0 )
+    {
+      gdcmErrorMacro( "Garbage data. Stopping CSA parsing." );
+      return false;
+    }
     assert( /*vr[3] == 0 &&*/ vr[2] == 0 );
     csael.SetVR( VR::GetVRTypeFromFile(vr) );
     //std::cout << "VR " << vr << ", ";
@@ -1131,8 +1137,10 @@ bool CSAHeader::LoadFromDataElement(DataElement const &de)
       uint32_t item_xx[4];
       ss.read((char*)&item_xx, 4*sizeof(uint32_t));
       SwapperNoOp::SwapArray(item_xx,4);
+      if( item_xx[2] != 77 && item_xx[2] != 205 ) return false;
       assert( item_xx[2] == 77 || item_xx[2] == 205 );
       uint32_t len = item_xx[1]; // 2nd element
+      if( item_xx[0] != item_xx[1] || item_xx[1] != item_xx[3] ) return false;
       assert( item_xx[0] == item_xx[1] && item_xx[1] == item_xx[3] );
       if( len )
         {

Modules/ThirdParty/GDCM/src/gdcm/Source/DataStructureAndEncodingDefinition/gdcmElement.h

@@ -473,7 +473,7 @@ template<> class EncodingImplementation<VR::VRBINARY> {
     assert( _is ); // Is stream valid ?
     _is.read( reinterpret_cast<char*>(data+0), type_size);
     for(unsigned long i=1; i<length; ++i) {
-      assert( _is );
+      if( _is )
       _is.read( reinterpret_cast<char*>(data+i), type_size );
     }
     //ByteSwap<T>::SwapRangeFromSwapCodeIntoSystem(data,
@@ -489,7 +489,7 @@ template<> class EncodingImplementation<VR::VRBINARY> {
     assert( _is ); // Is stream valid ?
     _is.read( reinterpret_cast<char*>(data+0), type_size);
     for(unsigned long i=1; i<length; ++i) {
-      assert( _is );
+      if( _is )
       _is.read( reinterpret_cast<char*>(data+i), type_size );
     }
     //ByteSwap<T>::SwapRangeFromSwapCodeIntoSystem(data,

Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmCleaner.cxx

@@ -538,10 +538,12 @@ struct Cleaner::impl {
   bool AllMissingPrivateCreator;
   bool AllGroupLength;
   bool AllIllegal;
+  bool WhenScrubFails;
   impl()
       : AllMissingPrivateCreator(true),
         AllGroupLength(true),
-        AllIllegal(true) {}
+        AllIllegal(true),
+        WhenScrubFails(false) {}
 
   enum ACTION { NONE, EMPTY, REMOVE, SCRUB };
   enum ACTION ComputeAction(File const &file, DataSet &ds,
@@ -668,6 +670,10 @@ struct Cleaner::impl {
   bool RemoveMissingPrivateCreator(Tag const & /*t*/) { return false; }
   void RemoveAllGroupLength(bool remove) { AllGroupLength = remove; }
   void RemoveAllIllegal(bool remove) { AllIllegal = remove; }
+  void EmptyWhenScrubFails(bool empty) { WhenScrubFails = empty; }
+
+  bool CleanCSAImage(DataSet &ds, const DataElement &de);
+  bool CleanCSASeries(DataSet &ds, const DataElement &de);
 };
 
 static VR ComputeDictVR(File &file, DataSet &ds, DataElement const &de) {
@@ -840,7 +846,7 @@ static inline bool bs_is_signature(const ByteValue *bv, const char *str) {
   return false;
 }
 
-static bool CleanCSAImage(DataSet &ds, const DataElement &de) {
+bool Cleaner::impl::CleanCSAImage(DataSet &ds, const DataElement &de) {
   const ByteValue *bv = de.GetByteValue();
   // fast path:
   if (!bv) return true;
@@ -888,6 +894,13 @@ static bool CleanCSAImage(DataSet &ds, const DataElement &de) {
       gdcmDebugMacro("Zero-out CSA header");
       return true;
     }
+    // fallback logic:
+    if (WhenScrubFails && is_signature(bv, sv10)) {
+      // so SV10 header has been identified, but we failed to 'scrub', let's
+      // empty it:
+      ds.Replace(clean);
+      return true;
+    }
     gdcmErrorMacro("Failure to call CleanCSAImage");
     return false;
   }
@@ -900,7 +913,7 @@ static bool CleanCSAImage(DataSet &ds, const DataElement &de) {
   return true;
 }
 
-static bool CleanCSASeries(DataSet &ds, const DataElement &de) {
+bool Cleaner::impl::CleanCSASeries(DataSet &ds, const DataElement &de) {
   const ByteValue *bv = de.GetByteValue();
   // fast path:
   if (!bv) return true;
@@ -944,6 +957,13 @@ static bool CleanCSASeries(DataSet &ds, const DataElement &de) {
       gdcmDebugMacro("Zero-out CSA header");
       return true;
     }
+    // fallback logic:
+    if (WhenScrubFails && is_signature(bv, sv10)) {
+      // so SV10 header has been identified, but we failed to 'scrub', let's
+      // empty it:
+      ds.Replace(clean);
+      return true;
+    }
     gdcmErrorMacro("Failure to call CleanCSASeries");
     return false;
   }
@@ -1065,8 +1085,8 @@ static bool IsDPathInSet(std::set<DPath> const &aset, DPath const dpath) {
 }
 
 Cleaner::impl::ACTION Cleaner::impl::ComputeAction(
-    File const & /*file*/, DataSet &ds, const DataElement &de, VR const &ref_dict_vr,
-    const std::string &tag_path) {
+    File const & /*file*/, DataSet &ds, const DataElement &de,
+    VR const &ref_dict_vr, const std::string &tag_path) {
   const Tag &tag = de.GetTag();
   // Group Length & Illegal cannot be preserved so it is safe to do them now:
   if (tag.IsGroupLength()) {
@@ -1302,6 +1322,9 @@ void Cleaner::RemoveAllGroupLength(bool remove) {
   pimpl->RemoveAllGroupLength(remove);
 }
 void Cleaner::RemoveAllIllegal(bool remove) { pimpl->RemoveAllIllegal(remove); }
+void Cleaner::EmptyWhenScrubFails(bool empty) {
+  pimpl->EmptyWhenScrubFails(empty);
+}
 
 bool Cleaner::Clean() {
   DataSet &ds = F->GetDataSet();

Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmCleaner.h

@@ -65,6 +65,9 @@ class GDCM_EXPORT Cleaner : public Subject {
   /// Should I remove all illegal attribute. Default: true
   void RemoveAllIllegal(bool remove);
 
+  /// Should I empty instead of scrub upon failure
+  void EmptyWhenScrubFails(bool empty);
+
   /// main loop
   bool Clean();
 

Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmDirectionCosines.cxx

@@ -98,15 +98,20 @@ double DirectionCosines::Dot() const
 }
 
 // static function is within gdcm:: namespace, so should not pollute too much on UNIX
-static inline double Norm(const double x[3])
+static inline double NormImpl(const double x[3])
 {
   return sqrt(x[0]*x[0] + x[1]*x[1] + x[2]*x[2]);
 }
 
+double DirectionCosines::Norm(const double v[3])
+{
+  return NormImpl(v);
+}
+
 void DirectionCosines::Normalize(double v[3])
 {
   double den;
-  if ( (den = Norm(v)) != 0.0 )
+  if ( (den = NormImpl(v)) != 0.0 )
     {
     for (int i=0; i < 3; i++)
       {
@@ -119,15 +124,15 @@ void DirectionCosines::Normalize()
 {
   double *x = Values;
   double den;
-  if ( (den = Norm(x)) != 0.0 )
+  if ( (den = NormImpl(x)) != 0.0 )
     {
     for (int i=0; i < 3; i++)
       {
       x[i] /= den;
       }
     }
   x = Values+3;
-  if ( (den = Norm(x)) != 0.0 )
+  if ( (den = NormImpl(x)) != 0.0 )
     {
     for (int i=0; i < 3; i++)
       {

Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmDirectionCosines.h

@@ -49,6 +49,9 @@ class GDCM_EXPORT DirectionCosines
   /// Normalize in-place
   static void Normalize(double v[3]);
 
+  /// Return norm of the vector
+  static double Norm(const double v[3]);
+
   /// Make the class behave like a const double *
   operator const double* () const { return Values; }
 

Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmEquipmentManufacturer.cxx

@@ -219,8 +219,11 @@ EquipmentManufacturer::Type EquipmentManufacturer::Compute(DataSet const& ds) {
     manu.SetFromDataSet(ds);
     manufacturer = manu.GetValue().Trim();
     // TODO: contributing equipement ?
-  } else {
+  } 
+  if( manufacturer.empty() )
+  {
     // MFSPLIT export seems to remove the attribute completely:
+    // or in some case make it empty
     manufacturer = GetPrivateTagValueOrEmpty<VR::SH, VM::VM1>(
         ds, PrivateTag(0x0021, 0x0022, "SIEMENS MR SDS 01"));
   }

Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmFileStreamer.cxx

@@ -35,7 +35,7 @@
 #include <io.h>
 typedef int64_t off64_t;
 #else
-#if defined(__APPLE__) || defined(__FreeBSD__) || defined(__OpenBSD__) || defined(__NetBSD__)
+#if defined(__APPLE__) || defined(__FreeBSD__) || defined(__OpenBSD__) || defined(__NetBSD__) || defined(__EMSCRIPTEN__)
 #  define off64_t off_t
 #endif
 #include <unistd.h> // ftruncate

Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageChangeTransferSyntax.cxx

@@ -421,6 +421,7 @@ bool ImageChangeTransferSyntax::Change()
     if( !b )
       {
       gdcmErrorMacro( "Error in getting buffer from input image." );
+      delete bv0;
       return false;
       }
     pixeldata.SetValue( *bv0 );

Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageCodec.cxx

@@ -460,7 +460,8 @@ bool ImageCodec::CleanupUnusedBits(char * data8, size_t datalen)
       smask = (uint16_t)(
         smask << ( 16 - (PF.GetBitsAllocated() - PF.GetBitsStored() + 1) ));
       // nmask : to propagate sign bit on negative values
-      int16_t nmask = (int16_t)(0x8000U >> ( PF.GetBitsAllocated() - PF.GetBitsStored() - 1 ));
+      int16_t nmask = (int16_t)0x8000;
+      nmask = (int16_t)(nmask >> ( PF.GetBitsAllocated() - PF.GetBitsStored() - 1 ));
 
       uint16_t *start = (uint16_t*)data;
       for( uint16_t *p = start ; p != start + datalen / 2; ++p )
@@ -515,7 +516,8 @@ bool ImageCodec::DoOverlayCleanup(std::istream &is, std::ostream &os)
       smask = (uint16_t)(
         smask << ( 16 - (PF.GetBitsAllocated() - PF.GetBitsStored() + 1) ));
       // nmask : to propagate sign bit on negative values
-      int16_t nmask = (int16_t)(0x8000U >> ( PF.GetBitsAllocated() - PF.GetBitsStored() - 1 ));
+      int16_t nmask = (int16_t)0x8000;
+      nmask = (int16_t)(nmask >> ( PF.GetBitsAllocated() - PF.GetBitsStored() - 1 ));
 
       uint16_t c;
       while( is.read((char*)&c,2) )
@@ -673,6 +675,7 @@ bool ImageCodec::DecodeByStreams(std::istream &is, std::ostream &os)
 
   // Do the overlay cleanup (cleanup the unused bits)
   // must be the last operation (duh!)
+  bool copySuccess = false;
   if ( PF.GetBitsAllocated() != PF.GetBitsStored()
     && PF.GetBitsAllocated() != 8 )
     {
@@ -683,21 +686,23 @@ bool ImageCodec::DecodeByStreams(std::istream &is, std::ostream &os)
     // Sigh, I finally found someone not declaring that unused bits where not zero:
     // gdcmConformanceTests/dcm4chee_unusedbits_not_zero.dcm
     if( NeedOverlayCleanup )
-      DoOverlayCleanup(*cur_is,os);
+      {
+      copySuccess = DoOverlayCleanup(*cur_is, os);
+      }
     else
       {
       // Once the issue with IMAGES/JPLY/RG3_JPLY aka gdcmData/D_CLUNIE_RG3_JPLY.dcm is solved the previous
       // code will be replace with a simple call to:
-      DoSimpleCopy(*cur_is,os);
+      copySuccess = DoSimpleCopy(*cur_is, os);
       }
     }
   else
     {
     assert( PF.GetBitsAllocated() == PF.GetBitsStored() );
-    DoSimpleCopy(*cur_is,os);
+    copySuccess = DoSimpleCopy(*cur_is, os);
     }
 
-  return true;
+  return copySuccess;
 }
 
 bool ImageCodec::IsValid(PhotometricInterpretation const &)