GDCM 2020-02-12 (f1797c61)

Code extracted from:

    http://git.code.sf.net/p/gdcm/gdcm.git

at commit f1797c61e24b4257b5059d56df38ee4d6a27302d (release).

Change-Id: I77b78b75f5f9d2beab0fa8980e95d00e6b3b7d5b

.gitattributes

@@ -0,0 +1 @@
+* -whitespace

CMakeLists.txt

@@ -518,6 +518,10 @@ if(GDCM_STANDALONE)
   mark_as_advanced(GDCM_USE_ACTIVIZ)
   option(GDCM_USE_JPEGLS "Build GDCM with JPEG-LS support" ON)
   mark_as_advanced(GDCM_USE_JPEGLS)
+  if(NOT DEFINED GDCM_DEFAULT_PYTHON_VERSION)
+    # override with cmake -DGDCM_DEFAULT_PYTHON_VERSION:STRING=2.7 if you dare
+    set(GDCM_DEFAULT_PYTHON_VERSION 3.2)
+  endif()
   if(NOT DEFINED GDCM_DEFAULT_JAVA_VERSION)
     # override with cmake -DGDCM_DEFAULT_JAVA_VERSION:STRING=1.5 if you dare
     set(GDCM_DEFAULT_JAVA_VERSION 1.7)

Source/Common/gdcmOpenSSLCryptographicMessageSyntax.cxx

@@ -288,6 +288,7 @@ bool OpenSSLCryptographicMessageSyntax::ParseCertificateFile( const char *keyfil
     }
   ::BIO_free(in); in = NULL;
   ::sk_X509_push(recips, x509);
+  //::X509_free(x509);
   return true;
 }
 

Source/Common/gdcmWin32.h

@@ -27,7 +27,7 @@
     #define GDCM_EXPORT __declspec( dllimport )
   #endif
 #else
-  #if __GNUC__ >= 4
+  #if __GNUC__ >= 4 && defined(GDCM_BUILD_SHARED_LIBS)
     #define GDCM_EXPORT __attribute__ ((visibility ("default")))
     #define GDCM_LOCAL  __attribute__ ((visibility ("hidden")))
   #else

Source/DataStructureAndEncodingDefinition/gdcmAttribute.h

@@ -205,7 +205,7 @@ class Attribute
 
   void SetFromDataElement(DataElement const &de) {
     // This is kind of hackish but since I do not generate other element than the first one: 0x6000 I should be ok:
-    assert( GetTag() == de.GetTag() || GetTag().GetGroup() == 0x6000 || GetTag().GetGroup() == 0x5000 );
+    assert( Tag(Group,Element) == de.GetTag() || Group == 0x6000 || Group == 0x5000 );
     assert( GetVR() != VR::INVALID );
     assert( GetVR().Compatible( de.GetVR() ) || de.GetVR() == VR::INVALID ); // In case of VR::INVALID cannot use the & operator
     if( de.IsEmpty() ) return;
@@ -224,13 +224,13 @@ class Attribute
       }
   }
   void Set(DataSet const &ds) {
-    SetFromDataElement( ds.GetDataElement( GetTag() ) );
+    SetFromDataElement( ds.GetDataElement( Tag(Group,Element) ) );
   }
   void SetFromDataSet(DataSet const &ds) {
-    if( ds.FindDataElement( GetTag() ) &&
-      !ds.GetDataElement( GetTag() ).IsEmpty() )
+    if( ds.FindDataElement( Tag(Group,Element) ) &&
+      !ds.GetDataElement( Tag(Group,Element) ).IsEmpty() )
       {
-      SetFromDataElement( ds.GetDataElement( GetTag() ) );
+      SetFromDataElement( ds.GetDataElement( Tag(Group,Element) ) );
       }
   }
 protected:
@@ -416,7 +416,7 @@ class Attribute<Group,Element,TVR,VM::VM1>
 
   // API to talk to the run-time layer: gdcm::DataElement
   DataElement GetAsDataElement() const {
-    DataElement ret( GetTag() );
+    DataElement ret( Tag(Group,Element) );
     std::ostringstream os;
     // os.imbue(std::locale::classic()); // This is not required AFAIK
     EncodingImplementation<VRToEncoding<TVR>::Mode>::Write(&Internal,
@@ -440,7 +440,7 @@ class Attribute<Group,Element,TVR,VM::VM1>
 
   void SetFromDataElement(DataElement const &de) {
     // This is kind of hackish but since I do not generate other element than the first one: 0x6000 I should be ok:
-    assert( GetTag() == de.GetTag() || GetTag().GetGroup() == 0x6000 || GetTag().GetGroup() == 0x5000 );
+    assert( Tag(Group,Element) == de.GetTag() || Group == 0x6000 || Group == 0x5000 );
     assert( GetVR() != VR::INVALID );
     assert( GetVR().Compatible( de.GetVR() ) || de.GetVR() == VR::INVALID ); // In case of VR::INVALID cannot use the & operator
     if( de.IsEmpty() ) return;
@@ -459,13 +459,13 @@ class Attribute<Group,Element,TVR,VM::VM1>
       }
   }
   void Set(DataSet const &ds) {
-    SetFromDataElement( ds.GetDataElement( GetTag() ) );
+    SetFromDataElement( ds.GetDataElement( Tag(Group,Element) ) );
   }
   void SetFromDataSet(DataSet const &ds) {
-    if( ds.FindDataElement( GetTag() ) &&
-      !ds.GetDataElement( GetTag() ).IsEmpty() )
+    if( ds.FindDataElement( Tag(Group,Element) ) &&
+      !ds.GetDataElement( Tag(Group,Element) ).IsEmpty() )
       {
-      SetFromDataElement( ds.GetDataElement( GetTag() ) );
+      SetFromDataElement( ds.GetDataElement( Tag(Group,Element) ) );
       }
   }
 protected:

Source/MediaStorageAndFileFormat/gdcmPixelFormat.cxx

@@ -130,6 +130,7 @@ void PixelFormat::SetScalarType(ScalarType st)
 PixelFormat::ScalarType PixelFormat::GetScalarType() const
 {
   ScalarType type = PixelFormat::UNKNOWN;
+  gdcmAssertAlwaysMacro( BitsStored <= BitsAllocated );
   switch( BitsAllocated )
     {
   case 0:
@@ -191,7 +192,7 @@ PixelFormat::ScalarType PixelFormat::GetScalarType() const
       }
     else
       {
-      assert(0);
+      gdcmAssertAlwaysMacro(0);
       }
     }
   return type;

Source/MediaStorageAndFileFormat/gdcmRescaler.cxx

@@ -146,6 +146,11 @@ static inline PixelFormat::ScalarType ComputeBestFit(const PixelFormat &pf, doub
       {
       st = PixelFormat::UINT32;
       }
+    else if( max <= std::numeric_limits<uint64_t>::max() )
+      {
+      // very large value in Rescale Slope ?
+      return PixelFormat::FLOAT64;
+      }
     else
       {
       gdcmErrorMacro( "Unhandled Pixel Format" );
@@ -169,6 +174,12 @@ static inline PixelFormat::ScalarType ComputeBestFit(const PixelFormat &pf, doub
       {
       st = PixelFormat::INT32;
       }
+    else if( max <= std::numeric_limits<int64_t>::max()
+      && min >= std::numeric_limits<int64_t>::min() )
+      {
+      // very large value in Rescale Slope ?
+      return PixelFormat::FLOAT64;
+      }
     else
       {
       gdcmErrorMacro( "Unhandled Pixel Format" );