Merge branch 'upstream-GDCM' into gdcm-sc-image-metadata

# By GDCM Upstream
* upstream-GDCM:
  GDCM 2024-03-15 (a9916012)

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/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/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/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) )

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

@@ -48,6 +48,7 @@ namespace gdcm
 bool ImageHelper::ForceRescaleInterceptSlope = false;
 bool ImageHelper::PMSRescaleInterceptSlope = true;
 bool ImageHelper::ForcePixelSpacing = false;
+bool ImageHelper::SecondaryCaptureImagePlaneModule = false;
 
 static bool GetOriginValueFromSequence(const DataSet& ds, const Tag& tfgs, std::vector<double> &ori)
 {
@@ -205,6 +206,7 @@ static bool ComputeZSpacingFromIPP(const DataSet &ds, double &zspacing)
   double normal[3];
   DirectionCosines dc( cosines.data() );
   dc.Cross( normal );
+  DirectionCosines::Normalize(normal);
 
   // For each item
   SequenceOfItems::SizeType nitems = sqi->GetNumberOfItems();
@@ -577,7 +579,7 @@ std::vector<double> ImageHelper::GetOriginValue(File const & f)
 
   // else
   const Tag timagepositionpatient(0x0020, 0x0032);
-  if( ms != MediaStorage::SecondaryCaptureImageStorage && ds.FindDataElement( timagepositionpatient ) )
+  if( (ms != MediaStorage::SecondaryCaptureImageStorage || SecondaryCaptureImagePlaneModule) && ds.FindDataElement( timagepositionpatient ) )
     {
     const DataElement& de = ds.GetDataElement( timagepositionpatient );
     Attribute<0x0020,0x0032> at = {{0,0,0}}; // default value if empty
@@ -729,7 +731,7 @@ std::vector<double> ImageHelper::GetDirectionCosinesValue(File const & f)
     }
 
   dircos.resize( 6 );
-  if( ms == MediaStorage::SecondaryCaptureImageStorage || !GetDirectionCosinesFromDataSet(ds, dircos) )
+  if( (ms == MediaStorage::SecondaryCaptureImageStorage && !SecondaryCaptureImagePlaneModule) || !GetDirectionCosinesFromDataSet(ds, dircos) )
     {
     dircos[0] = 1;
     dircos[1] = 0;
@@ -773,6 +775,16 @@ bool ImageHelper::GetForcePixelSpacing()
   return ForcePixelSpacing;
 }
 
+void ImageHelper::SetSecondaryCaptureImagePlaneModule(bool b)
+{
+  SecondaryCaptureImagePlaneModule = b;
+}
+
+bool ImageHelper::GetSecondaryCaptureImagePlaneModule()
+{
+  return SecondaryCaptureImagePlaneModule;
+}
+
 bool GetRescaleInterceptSlopeValueFromDataSet(const DataSet& ds, std::vector<double> & interceptslope)
 {
   Attribute<0x0028,0x1052> at1;
@@ -1388,6 +1400,7 @@ std::vector<double> ImageHelper::GetSpacingValue(File const & f)
   MediaStorage ms;
   ms.SetFromFile(f);
   const DataSet& ds = f.GetDataSet();
+  Tag spacingtag(0xffff,0xffff);
 
   if( ms == MediaStorage::EnhancedCTImageStorage
     || ms == MediaStorage::EnhancedMRImageStorage
@@ -1450,8 +1463,24 @@ std::vector<double> ImageHelper::GetSpacingValue(File const & f)
       return sp;
       }
     }
+  else if( ms == MediaStorage::SecondaryCaptureImageStorage )
+    {
+      if( ds.FindDataElement( Tag(0x0028,0x0030) ) )
+        {
+        // Type 1C in 'SC Image' (for calibrated images)
+        spacingtag = Tag(0x0028,0x0030);
+        }
+      else if( ds.FindDataElement( Tag(0x0018,0x2010) ) )
+        {
+        // Type 3 in 'SC Image'
+        spacingtag = Tag(0x0018,0x2010);
+        }
+    }
+  else
+    {
+    spacingtag = GetSpacingTagFromMediaStorage(ms);
+    }
 
-  Tag spacingtag = GetSpacingTagFromMediaStorage(ms);
   if( spacingtag != Tag(0xffff,0xffff) && ds.FindDataElement( spacingtag ) && !ds.GetDataElement( spacingtag ).IsEmpty() )
     {
     const DataElement& de = ds.GetDataElement( spacingtag );
@@ -2027,6 +2056,7 @@ void ImageHelper::SetOriginValue(DataSet & ds, const Image & image)
 
     double normal[3];
     dc.Cross( normal );
+    DirectionCosines::Normalize(normal);
 
     for(unsigned int i = 0; i < dimz; ++i )
       {
@@ -2896,6 +2926,7 @@ MediaStorage ImageHelper::ComputeMediaStorageFromModality(const char *modality,
       || pi == PhotometricInterpretation::YBR_RCT
       || pi == PhotometricInterpretation::YBR_ICT
       || pi == PhotometricInterpretation::YBR_PARTIAL_420
+      || pi == PhotometricInterpretation::YBR_FULL /* PI when coming from other gdcm filter */
       || pi == PhotometricInterpretation::YBR_FULL_422 ) &&
       pixeltype.GetBitsAllocated() == 8 &&
       pixeltype.GetBitsStored() == 8 &&

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

@@ -85,6 +85,12 @@ class GDCM_EXPORT ImageHelper
   static void SetForcePixelSpacing(bool);
   static bool GetForcePixelSpacing();
 
+  /// Opt into Image Plane Module for Secondary Capture Image Storage
+  /// Enable reading Image Position Patient (IPP) and Image Orientation Patient (IOP)
+  /// for Secondary Capture Image Storage.
+  static void SetSecondaryCaptureImagePlaneModule(bool);
+  static bool GetSecondaryCaptureImagePlaneModule();
+
   /// This function checks tags (0x0028, 0x0010) and (0x0028, 0x0011) for the
   /// rows and columns of the image in pixels (as opposed to actual distances).
   /// The output is {col , row}
@@ -156,6 +162,7 @@ class GDCM_EXPORT ImageHelper
   static bool ForceRescaleInterceptSlope;
   static bool PMSRescaleInterceptSlope;
   static bool ForcePixelSpacing;
+  static bool SecondaryCaptureImagePlaneModule;
 };
 
 } // end namespace gdcm