Merge pull request InsightSoftwareConsortium#4275 from dzenanz/update…

…GDCM

GDCM 2023-10-30 (b578ec5d)

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

@@ -319,7 +319,7 @@ option(GDCM_USE_SYSTEM_PAPYRUS3 "Use system papyrus3" OFF)
 option(GDCM_USE_SYSTEM_SOCKETXX "Use system socket++" OFF)
 option(GDCM_USE_SYSTEM_LJPEG "Use system ljpeg (ijg lib)" OFF)
 option(GDCM_USE_SYSTEM_OPENJPEG "Use system openjpeg" OFF)
-option(GDCM_USE_SYSTEM_CHARLS "Use system CharLS" OFF)
+option(GDCM_USE_SYSTEM_CHARLS "Use system charls" OFF)
 mark_as_advanced(
   GDCM_USE_SYSTEM_ZLIB
   GDCM_USE_SYSTEM_OPENSSL
@@ -352,8 +352,9 @@ else()
 endif()
 
 if(GDCM_USE_SYSTEM_CHARLS)
-  find_package(CharLS 2.0.0 REQUIRED)
-  set(GDCM_CHARLS_LIBRARIES ${CHARLS_LIBRARIES})
+  find_package(charls 2.2.0 REQUIRED)
+  set(GDCM_CHARLS_LIBRARIES charls)
+  message(STATUS "Found charls version " ${charls_VERSION})
 else()
   set(GDCM_CHARLS_LIBRARIES gdcmcharls)
 endif()

Modules/ThirdParty/GDCM/src/gdcm/Source/DataDictionary/gdcmPrivateDefaultDicts.cxx

@@ -469,7 +469,7 @@ static const DICT_ENTRY DICOMV3DataDict [] = {
   {0x0019,0x00f0,"CANON_MEC_MR3^10",VR::SL,VM::VM1,"?",false },
   {0x0019,0x00f1,"CANON_MEC_MR3^10",VR::FL,VM::VM1,"?",false },
   {0x0019,0x00f1,"CANON_MEC_MR3^12",VR::LO,VM::VM1,"?",false },
-  {0x0019,0x00f1,"CANON_MEC_MR3^11",VR::SL,VM::VM3,"?",false },
+  {0x0019,0x00f1,"CANON_MEC_MR3^11",VR::SL,VM::VM3,"Diffusion b-value x Toshiba Orientation",false },
   {0x0019,0x00f2,"CANON_MEC_MR3^10",VR::FL,VM::VM1,"?",false },
   {0x0019,0x00f2,"CANON_MEC_MR3^11",VR::FL,VM::VM3,"?",false },
   {0x0019,0x00f3,"CANON_MEC_MR3^10",VR::SL,VM::VM1,"?",false },
@@ -521,7 +521,7 @@ static const DICT_ENTRY DICOMV3DataDict [] = {
   {0x0021,0x001f,"CANON_MEC_MR3^10",VR::US,VM::VM1,"?",false },
   {0x0021,0x0022,"CANON_MEC_MR3^10",VR::US,VM::VM1,"?",false },
   {0x0021,0x0023,"CANON_MEC_MR3^10",VR::SS,VM::VM1,"?",false },
-  {0x0029,0x0001,"CANON_MEC_MR3^10",VR::SL,VM::VM1,"?",false },
+  {0x0029,0x0001,"CANON_MEC_MR3^10",VR::SL,VM::VM3,"Diffusion Gradient Orientation / Toshiba Orientation",false },
   {0x0029,0x0005,"CANON_MEC_MR3^10",VR::SQ,VM::VM1,"?",false },
   {0x0029,0x0006,"CANON_MEC_MR3^10",VR::FL,VM::VM1,"?",false },
   {0x0029,0x0007,"CANON_MEC_MR3^10",VR::FL,VM::VM1,"?",false },
@@ -532,7 +532,7 @@ static const DICT_ENTRY DICOMV3DataDict [] = {
   {0x0029,0x0051,"CANON_MEC_MR3^10",VR::LO,VM::VM1,"?",false },
   {0x0029,0x0052,"CANON_MEC_MR3^10",VR::LO,VM::VM1,"?",false },
   {0x0029,0x0054,"CANON_MEC_MR3^10",VR::LO,VM::VM1,"?",false },
-  {0x0029,0x0067,"CANON_MEC_MR3^10",VR::FD,VM::VM4,"?",false },
+  {0x0029,0x0067,"CANON_MEC_MR3^10",VR::FD,VM::VM4,"Series Diffusion Info (b-value,x,y,z)",false },
   {0x0029,0x0068,"CANON_MEC_MR3^10",VR::SS,VM::VM1,"?",false },
   {0x0029,0x006e,"CANON_MEC_MR3^10",VR::OB,VM::VM1,"?",false },
   {0x0029,0x0001,"CANON_MEC_MR3",VR::SQ,VM::VM1,"Other Private Data",false },
@@ -1025,7 +1025,7 @@ static const DICT_ENTRY DICOMV3DataDict [] = {
   {0x0019,0x00f0,"TOSHIBA_MEC_MR3^11",VR::SL,VM::VM4,"?",false },
   {0x0019,0x00f1,"TOSHIBA_MEC_MR3^10",VR::FL,VM::VM1,"?",false },
   {0x0019,0x00f1,"TOSHIBA_MEC_MR3^12",VR::LO,VM::VM1,"?",false },
-  {0x0019,0x00f1,"TOSHIBA_MEC_MR3^11",VR::SL,VM::VM3,"?",false },
+  {0x0019,0x00f1,"TOSHIBA_MEC_MR3^11",VR::SL,VM::VM3,"Diffusion b-value x Toshiba Orientation",false },
   {0x0019,0x00f2,"TOSHIBA_MEC_MR3^10",VR::FL,VM::VM1,"?",false },
   {0x0019,0x00f2,"TOSHIBA_MEC_MR3^11",VR::FL,VM::VM3,"?",false },
   {0x0019,0x00f3,"TOSHIBA_MEC_MR3^10",VR::SL,VM::VM1,"?",false },
@@ -1077,7 +1077,7 @@ static const DICT_ENTRY DICOMV3DataDict [] = {
   {0x0021,0x001f,"TOSHIBA_MEC_MR3^10",VR::US,VM::VM1,"?",false },
   {0x0021,0x0022,"TOSHIBA_MEC_MR3^10",VR::US,VM::VM1,"?",false },
   {0x0021,0x0023,"TOSHIBA_MEC_MR3^10",VR::SS,VM::VM1,"?",false },
-  {0x0029,0x0001,"TOSHIBA_MEC_MR3^10",VR::SL,VM::VM1,"?",false },
+  {0x0029,0x0001,"TOSHIBA_MEC_MR3^10",VR::SL,VM::VM3,"Diffusion Gradient Orientation / Toshiba Orientation",false },
   {0x0029,0x0005,"TOSHIBA_MEC_MR3^10",VR::SQ,VM::VM1,"?",false },
   {0x0029,0x0006,"TOSHIBA_MEC_MR3^10",VR::FL,VM::VM1,"?",false },
   {0x0029,0x0007,"TOSHIBA_MEC_MR3^10",VR::FL,VM::VM1,"?",false },
@@ -1088,7 +1088,7 @@ static const DICT_ENTRY DICOMV3DataDict [] = {
   {0x0029,0x0051,"TOSHIBA_MEC_MR3^10",VR::LO,VM::VM1,"?",false },
   {0x0029,0x0052,"TOSHIBA_MEC_MR3^10",VR::LO,VM::VM1,"?",false },
   {0x0029,0x0054,"TOSHIBA_MEC_MR3^10",VR::LO,VM::VM1,"?",false },
-  {0x0029,0x0067,"TOSHIBA_MEC_MR3^10",VR::FD,VM::VM4,"?",false },
+  {0x0029,0x0067,"TOSHIBA_MEC_MR3^10",VR::FD,VM::VM4,"Series Diffusion Info (b-value,x,y,z)",false },
   {0x0029,0x0068,"TOSHIBA_MEC_MR3^10",VR::SS,VM::VM1,"?",false },
   {0x0029,0x006e,"TOSHIBA_MEC_MR3^10",VR::OB,VM::VM1,"?",false },
   {0x0029,0x0089,"TOSHIBA_MEC_MR3",VR::LO,VM::VM1,"?",false },
@@ -1770,7 +1770,7 @@ static const DICT_ENTRY DICOMV3DataDict [] = {
   {0x0021,0x001a,"PMTF INFORMATION DATA^10",VR::US,VM::VM1,"?num2?",false },
   {0x0021,0x001d,"PMTF INFORMATION DATA^10",VR::IS,VM::VM1,"?num3?",false },
   {0x0021,0x001f,"PMTF INFORMATION DATA^10",VR::US,VM::VM1,"?num?",false },
-  {0x0029,0x0001,"PMTF INFORMATION DATA^10",VR::SL,VM::VM3,"Diffusion Gradient Orientation / Toshiba Orientation ",false },
+  {0x0029,0x0001,"PMTF INFORMATION DATA^10",VR::SL,VM::VM3,"Diffusion Gradient Orientation / Toshiba Orientation",false },
   {0x0029,0x0005,"PMTF INFORMATION DATA^10",VR::SQ,VM::VM1,"?seq?",false },
   {0x0029,0x0006,"PMTF INFORMATION DATA^10",VR::FL,VM::VM1,"?num?",false },
   {0x0029,0x0007,"PMTF INFORMATION DATA^10",VR::FL,VM::VM1,"?num?",false },
@@ -4045,7 +4045,7 @@ static const DICT_ENTRY DICOMV3DataDict [] = {
   {0x0011,0x0040,"GEMS_GDXE_FALCON_04",VR::SL,VM::VM1,"Pasting Overlap",false },
   {0x0011,0x0041,"GEMS_GDXE_FALCON_04",VR::IS,VM::VM24,"Sub-image Collimator Vertices",false },
   {0x0011,0x0042,"GEMS_GDXE_FALCON_04",VR::LO,VM::VM1,"View IP",false },
-  {0x0011,0x0043,"GEMS_GDXE_FALCON_04",VR::IS,VM::VM24,"Key-stone Co-ordinates",false },
+  {0x0011,0x0043,"GEMS_GDXE_FALCON_04",VR::IS,VM::VM24,"Key-stone Coordinates",false },
   {0x0011,0x0044,"GEMS_GDXE_FALCON_04",VR::CS,VM::VM1,"Receptor Type",false },
   {0x0011,0x0046,"GEMS_GDXE_FALCON_04",VR::LO,VM::VM1_n,"?",false },
   {0x0011,0x0047,"GEMS_GDXE_FALCON_04",VR::DS,VM::VM1,"?",false },

Modules/ThirdParty/GDCM/src/gdcm/Source/DataDictionary/privatedicts.xml

@@ -3516,7 +3516,7 @@
   <entry owner="GEMS_GDXE_FALCON_04" group="0011" element="xx40" vr="SL" vm="1" name="Pasting Overlap"/>
   <entry owner="GEMS_GDXE_FALCON_04" group="0011" element="xx41" vr="IS" vm="24" name="Sub-image Collimator Vertices"/>
   <entry owner="GEMS_GDXE_FALCON_04" group="0011" element="xx42" vr="LO" vm="1" name="View IP"/>
-  <entry owner="GEMS_GDXE_FALCON_04" group="0011" element="xx43" vr="IS" vm="24" name="Key-stone Co-ordinates"/>
+  <entry owner="GEMS_GDXE_FALCON_04" group="0011" element="xx43" vr="IS" vm="24" name="Key-stone Coordinates"/>
   <entry owner="GEMS_GDXE_FALCON_04" group="0011" element="xx44" vr="CS" vm="1" name="Receptor Type"/>
   <entry owner="GEMS_GDXE_FALCON_04" group="0011" element="xx46" vr="LO" vm="1-n" name="?"/>
   <entry owner="GEMS_GDXE_FALCON_04" group="0011" element="xx47" vr="DS" vm="1" name="?"/>

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

@@ -63,7 +63,6 @@ class GDCM_EXPORT Preamble
     }
   Preamble& operator=(Preamble const &)
     {
-    Internal = nullptr;
     Create();
     return *this;
     }

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

@@ -178,9 +178,9 @@ class GDCM_EXPORT VR
       // For some reason this seems slower on my linux box...
       is.seekg(2, std::ios::cur );
 #else
-      char dum[2];
-      is.read(dum, 2);
-      if( !(dum[0] == 0 && dum[1] == 0 ))
+      char dumb[2];
+      is.read(dumb, 2);
+      if( !(dumb[0] == 0 && dumb[1] == 0 ))
         {
         // JDDICOM_Sample4.dcm
         gdcmDebugMacro( "32bits VR contains non zero bytes. Skipped" );
@@ -205,8 +205,8 @@ class GDCM_EXPORT VR
     // See PS 3.5, Data Element Structure With Explicit VR
     if( vrfield & VL32 )
       {
-      const char dum[2] = {0, 0};
-      os.write(dum,2);
+      const char dumb[2] = {0, 0};
+      os.write(dumb,2);
       }
     return os;
     }

Modules/ThirdParty/GDCM/src/gdcm/Source/InformationObjectDefinition/gdcmIODEntry.h

@@ -51,7 +51,7 @@ Types specified in the Modules in Annex C shall be supported.
 class GDCM_EXPORT IODEntry
 {
 public:
-  IODEntry(const char *name = "", const char *ref = "", const char *usag = ""):Name(name),Ref(ref),usage(usag) {
+  IODEntry(const char *name = "", const char *ref = "", const char *inUsage = ""):Name(name),Ref(ref),usage(inUsage) {
   }
   friend std::ostream& operator<<(std::ostream& _os, const IODEntry &_val);
 
@@ -64,7 +64,7 @@ class GDCM_EXPORT IODEntry
   void SetRef(const char *ref) { Ref = ref; }
   const char *GetRef() const { return Ref.c_str(); }
 
-  void SetUsage(const char *usag) { usage = usag; }
+  void SetUsage(const char *inUsage) { usage = inUsage; }
   const char *GetUsage() const { return usage.c_str(); }
   Usage::UsageType GetUsageType() const;
 

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

@@ -150,7 +150,7 @@ int StreamImageWriter::WriteRawHeader(RAWCodec* inCodec, std::ostream* inStream)
     //Addition by Manoj
     memcpy(&(tmpBuffer1[4*sizeof(uint16_t)]), &fifthTag, sizeof(uint32_t));// Data Element Length 4 bytes
 
-    // Basic OffSet Tabl with No Item Value
+    // Basic OffSet Table with No Item Value
     memcpy(&(tmpBuffer1[4*sizeof(uint16_t)+sizeof(uint32_t)]), &sixthTag, sizeof(uint16_t)); //fffe
     memcpy(&(tmpBuffer1[5*sizeof(uint16_t)+sizeof(uint32_t)]), &seventhTag, sizeof(uint16_t));//e000
     memcpy(&(tmpBuffer1[6*sizeof(uint16_t)+sizeof(uint32_t)]), &eightthTag, sizeof(uint32_t));//00000000H

Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcm_charls.h

@@ -17,8 +17,8 @@
 /* Use the charls library configured for gdcm.  */
 #include "gdcmTypes.h"
 #ifdef GDCM_USE_SYSTEM_CHARLS
-// It is expected that version 2.0.0 is used
-# include <CharLS/charls.h>
+// It is expected that version >= 2.2.0 is used
+# include <charls/charls.h>
 #else
 #include "gdcmcharls/charls.h"
 #endif

Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmext/csa.c

@@ -228,7 +228,7 @@ static bool read_info(struct app *self, struct csa_info *i) {
   // syngodt (signed)
   s = fread_mirror(&i->syngodt, sizeof i->syngodt, 1, self);
   ERROR_RETURN(s, 1);
-  // numer of items
+  // number of items
   s = fread_mirror(&i->nitems, sizeof i->nitems, 1, self);
   if (self->csa_type == SV10) assert(i->nitems % 6 == 0);
   ERROR_RETURN(s, 1);

Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmext/mec_mr3_dict.c

@@ -208,7 +208,7 @@ static const struct mec_mr3_dict dict[] = {
     {0x02, 0x0000a81c, 0xff003200, ""},                                       //
     {0x02, 0x0000a81d, 0xff002a00, ""},                                       //
     {0x02, 0x0000a822, 0x00000500, ""},                                       //
-    {0x02, 0x0000a823, 0xff002c00, "MR Acquition Type"},                      //
+    {0x02, 0x0000a823, 0xff002c00, "MR Acquisition Type"},                      //
     {0x02, 0x0000a824, 0xff002400, ""},                                       //
     {0x02, 0x0000a825, 0xff002400, ""},                                       //
     {0x02, 0x0000a826, 0xff003200, ""},                                       //

Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmext/mec_mr3_io.c

@@ -23,7 +23,13 @@
 #include <stdlib.h>
 #include <string.h>
 
-#ifndef _MSC_VER
+#if defined(_MSC_VER) || defined(__OpenBSD__)
+#define GDCM_HAS_ICONV 0
+#else
+#define GDCM_HAS_ICONV 1
+#endif
+
+#if GDCM_HAS_ICONV
 #include <iconv.h>
 #endif
 #if defined(_MSC_VER) && (_MSC_VER < 1900)
@@ -54,15 +60,15 @@ static size_t stream_read(void *ptr, size_t size, size_t nmemb,
 
 struct app {
   struct stream *in;
-#ifndef _MSC_VER
+#if GDCM_HAS_ICONV
   iconv_t conv;
 #endif
   void *shift_jis_buffer;
 };
 
 static struct app *create_app(struct app *self, struct stream *in) {
   self->in = in;
-#ifndef _MSC_VER
+#if GDCM_HAS_ICONV
   self->conv = iconv_open("utf-8", "shift-jis");
   assert(self->conv != (iconv_t)-1);
 #endif
@@ -358,7 +364,7 @@ static char *shift_jis_to_utf8(char *str, size_t len, struct app *self) {
   const size_t guesstimate = len < 128 ? 128 : len * 2;
   self->shift_jis_buffer = realloc(self->shift_jis_buffer, guesstimate);
   char *dest_str = self->shift_jis_buffer;
-#ifndef _MSC_VER
+#if GDCM_HAS_ICONV
   char *in_str = str;
   char *out_str = dest_str;
   size_t inbytes = len;
@@ -842,7 +848,7 @@ bool mec_mr3_print(const void *input, size_t len) {
 #else
   free(data.buffer);
 #endif
-#ifndef _MSC_VER
+#if GDCM_HAS_ICONV
   iconv_close(self->conv);
 #endif
   free(self->shift_jis_buffer);

Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmjpeg/README.GDCM.txt

@@ -80,4 +80,4 @@ patch -p0 < previous-gdcm.patch                         (5)
 
 
 NOTE for later:
-(shoud we disable getenv just as dcmtk ? there is a ijg flag for that NO_ENV or something similar
+(should we disable getenv just as dcmtk ? there is a ijg flag for that NO_ENV or something similar