GDCM 2020-06-30 (c0824c0a)

Code extracted from:

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

at commit c0824c0ae66e9f9e3c8bddba8b65238c1c28481d (release).

Change-Id: I5508c45eb7b3e2dbdc53203dbcb08b08ccd421d1

Author: GDCM Upstream

CMakeLists.txt

@@ -17,7 +17,7 @@ endif()
 #----------------------------------------------------------------------------
 
 project(GDCM
-  VERSION 3.0.5
+  VERSION 3.0.7
   LANGUAGES CXX C
 )
 ## NOTE: the "DESCRIPTION" feature of project() was introduced in cmake 3.10.0

Source/Common/gdcmDirectory.cxx

@@ -43,39 +43,52 @@ unsigned int Directory::Load(FilenameType const &name, bool recursive)
   return 0;
 }
 
+#ifdef _MSC_VER
+static inline std::string ToUtf8(std::wstring const &str) {
+  std::string ret;
+  int len = WideCharToMultiByte(CP_UTF8, 0, str.c_str(), (int)str.length(),
+                                nullptr, 0, NULL, NULL);
+  if (len > 0) {
+    ret.resize(len);
+    WideCharToMultiByte(CP_UTF8, 0, str.c_str(), (int)str.length(), &ret[0],
+                        len, NULL, NULL);
+  }
+  return ret;
+}
+#endif
+
 unsigned int Directory::Explore(FilenameType const &name, bool recursive)
 {
   unsigned int nFiles = 0;
-  std::string fileName;
-  std::string dirName = name;
-  //assert( System::FileIsDirectory( dirName ) );
-  Directories.push_back( dirName );
 #ifdef _MSC_VER
-  WIN32_FIND_DATA fileData;
-  if ('/' != dirName[dirName.size()-1]) dirName.push_back('/');
-  assert( '/' == dirName[dirName.size()-1] );
-  const FilenameType firstfile = dirName+"*";
-  HANDLE hFile = FindFirstFile(firstfile.c_str(), &fileData);
+  std::wstring fileName;
+  std::wstring dirName = System::ConvertToUNC(name.c_str());
+  Directories.push_back(ToUtf8(dirName));
+  WIN32_FIND_DATAW fileData;
+  if ('\\' != dirName[dirName.size()-1]) dirName.push_back('\\');
+  assert( '\\' == dirName[dirName.size()-1] );
+  const std::wstring firstfile = dirName+L"*";
+  HANDLE hFile = FindFirstFileW(firstfile.c_str(), &fileData);
 
   for(BOOL b = (hFile != INVALID_HANDLE_VALUE); b;
-    b = FindNextFile(hFile, &fileData))
+    b = FindNextFileW(hFile, &fileData))
     {
     fileName = fileData.cFileName;
     if ( fileData.dwFileAttributes & FILE_ATTRIBUTE_DIRECTORY )
       {
       // Need to check for . and .. to avoid infinite loop
-      if ( fileName != "." && fileName != ".."
+      if ( fileName != L"." && fileName != L".."
         && fileName[0] != '.' // discard any hidden dir
         && recursive )
         {
-        nFiles += Explore(dirName+fileName,recursive);
+        nFiles += Explore(ToUtf8(dirName + fileName), recursive);
         }
       }
     else
       {
       if (fileName[0] != '.') // discard "unix like" hidden files such as .git in submodules
         {
-        Filenames.push_back(dirName+fileName);
+        Filenames.push_back(ToUtf8(dirName+fileName));
         nFiles++;
         }
       }
@@ -89,6 +102,10 @@ unsigned int Directory::Explore(FilenameType const &name, bool recursive)
     }
 
 #else
+  std::string fileName;
+  std::string dirName = name;
+  // assert( System::FileIsDirectory( dirName ) );
+  Directories.push_back(dirName);
   // Real POSIX implementation: scandir is a BSD extension only, and doesn't
   // work on debian for example
 

Source/Common/gdcmSystem.cxx

@@ -135,6 +135,16 @@ const char * System::GetCWD()
 */
 }
 
+static inline int Mkdir2(const char *utf8)
+{
+#ifdef _MSC_VER
+  const std::wstring unc = System::ConvertToUNC(utf8);
+  return _wmkdir(unc.c_str());
+#else
+  return Mkdir(utf8);
+#endif
+}
+
 bool System::MakeDirectory(const char *path)
 {
   if( !path || !*path )
@@ -156,7 +166,7 @@ bool System::MakeDirectory(const char *path)
   while(ok && (pos = dir.find('/', pos)) != std::string::npos)
     {
     topdir = dir.substr(0, pos+1);
-    ok = ok && (System::FileIsDirectory(topdir.c_str()) || 0 == Mkdir(topdir.c_str()));
+    ok = ok && (System::FileIsDirectory(topdir.c_str()) || 0 == Mkdir2(topdir.c_str()));
     pos++;
     }
   if( !ok ) return false;
@@ -168,7 +178,7 @@ bool System::MakeDirectory(const char *path)
     {
     topdir = dir;
     }
-  if(Mkdir(topdir.c_str()) != 0)
+  if(Mkdir2(topdir.c_str()) != 0)
     {
     // There is a bug in the Borland Run time library which makes MKDIR
     // return EACCES when it should return EEXISTS
@@ -189,13 +199,15 @@ bool System::MakeDirectory(const char *path)
 // return true if the file exists
 bool System::FileExists(const char* filename)
 {
-#ifdef _MSC_VER
-# define access _access
-#endif
 #ifndef R_OK
 # define R_OK 04
 #endif
+#ifdef _MSC_VER
+    const std::wstring unc = System::ConvertToUNC(filename);
+    if (_waccess(unc.c_str(), R_OK) != 0)
+#else
   if ( access(filename, R_OK) != 0 )
+#endif
     {
     return false;
     }
@@ -208,8 +220,14 @@ bool System::FileExists(const char* filename)
 
 bool System::FileIsDirectory(const char* name)
 {
+#ifdef _MSC_VER
+    struct _stat64i32 fs;
+    const std::wstring wname = System::ConvertToUNC(name);
+    if (_wstat(wname.c_str(), &fs) == 0)
+#else
   struct stat fs;
   if(stat(name, &fs) == 0)
+#endif
     {
 #if _WIN32
     return ((fs.st_mode & _S_IFDIR) != 0);
@@ -366,6 +384,83 @@ bool System::DeleteDirectory(const char *source)
 #define PATH_MAX 4096
 #endif
 
+#ifdef _MSC_VER
+  namespace {
+  static inline std::wstring ToUtf16(std::string const &str) {
+    std::wstring ret;
+    int len = MultiByteToWideChar(CP_UTF8, 0, str.c_str(), (int)str.length(),
+                                  nullptr, 0);
+    if (len > 0) {
+      ret.resize(len);
+      MultiByteToWideChar(CP_UTF8, 0, str.c_str(), (int)str.length(), &ret[0],
+                          len);
+    }
+    return ret;
+  }
+  // http://arsenmk.blogspot.com/2015/12/handling-long-paths-on-windows.html
+  static inline bool ComputeFullPath(std::wstring const &in,
+                                     std::wstring &out) {
+    // consider an input fileName of type PCWSTR (const wchar_t*)
+    const wchar_t *fileName = in.c_str();
+    DWORD requiredBufferLength =
+        GetFullPathNameW(fileName, 0, nullptr, nullptr);
+
+    if (0 == requiredBufferLength)  // means failure
+    {
+      return false;
+    }
+
+    out.resize(requiredBufferLength);
+    wchar_t *buffer = &out[0];
+
+    DWORD result =
+        GetFullPathNameW(fileName, requiredBufferLength, buffer, nullptr);
+
+    if (0 == result) {
+      return false;
+    }
+
+    // buffer now contains the full path name of fileName, use it.
+    return true;
+  }
+
+  static inline std::wstring HandleMaxPath(std::wstring const &in) {
+    if (in.size() >= MAX_PATH) {
+      std::wstring out;
+      bool ret = ComputeFullPath(in, out);
+      if (!ret) return in;
+      if (out.size() < 4) return in;
+      if (out[0] == '\\' && out[1] == '\\' && out[2] == '?') {
+        // nothing to do
+      } else if (out[0] == '\\' && out[1] == '\\' && out[2] != '?') {
+        // server path
+        const std::wstring prefix = LR"(\\?\UNC\)";
+        out = prefix + (out.c_str() + 2);
+      } else {
+        // regular C:\ style path:
+        assert(out[1] == ':');
+        const std::wstring prefix = LR"(\\?\)";
+        out = prefix + out.c_str();
+      }
+      return out;
+    }
+    return in;
+  }
+  }  // namespace
+#endif
+
+std::wstring System::ConvertToUNC(const char *utf8path)
+{
+#ifdef _MSC_VER
+    const std::wstring uft16path = ToUtf16(utf8path);
+    const std::wstring uncpath = HandleMaxPath(uft16path);
+    return uncpath;
+#else
+    (void)utf8path;
+    return std::wstring();
+#endif
+}
+
 // return size of file; also returns zero if no file exists
 size_t System::FileSize(const char* filename)
 {

Source/Common/gdcmSystem.h

@@ -39,6 +39,11 @@ class GDCM_EXPORT System
   /// remove a directory named source
   static bool DeleteDirectory(const char *source);
 
+  /// When needed convert a PATH into a UNC equivalent. This allow
+  /// transparent support for path longer that MAX_PATH.
+  /// Only on _MSC_VER compiler, return empty string otherwise.
+  static std::wstring ConvertToUNC(const char *utf8path);
+
   /// Return the last error
   static const char *GetLastSystemError();
 

Source/Common/gdcmTesting.cxx

@@ -448,6 +448,9 @@ static const LossyFile gdcmLossyFilenames[] = {
 { 0,"JPEGLosslessSeNonZero.dcm" },
 { 1,"US-YBR_FULL_422-EVRLE.dcm" },
 { 0,"Osirix10vs8BitsStored.dcm" },
+{ 0,"Bug_Siemens_PrivateIconNoItem.dcm" },
+{ 0,"HardcopyColor_YBR_RCT_J2K_PC1.dcm" },
+{ 0,"PET-GE-dicomwrite-PixelDataSQUNv2.dcm" },
 { 0, nullptr }
 };
 

Source/DataDictionary/gdcmPrivateDefaultDicts.cxx

@@ -8236,6 +8236,7 @@ static const DICT_ENTRY DICOMV3DataDict [] = {
   {0x0051,0x0011,"SIEMENS MR HEADER",VR::LO,VM::VM1,"PAT Mode (Ima PAT Mode)",false },
   {0x0051,0x0012,"SIEMENS MR HEADER",VR::SH,VM::VM1,"?Table Position?",false },
   {0x0051,0x0013,"SIEMENS MR HEADER",VR::SH,VM::VM1,"Positive PCS Directions",false },
+  {0x0051,0x0014,"SIEMENS MR HEADER",VR::SH,VM::VM1,"?v150_through?",false },
   {0x0051,0x0015,"SIEMENS MR HEADER",VR::SH,VM::VM1,"?Data Filter?",false },
   {0x0051,0x0016,"SIEMENS MR HEADER",VR::LO,VM::VM1,"?Image Type?",false },
   {0x0051,0x0017,"SIEMENS MR HEADER",VR::SH,VM::VM1,"?Slice Thickness?",false },

Source/DataStructureAndEncodingDefinition/gdcmBasicOffsetTable.h

@@ -70,7 +70,7 @@ class GDCM_EXPORT BasicOffsetTable : public Fragment
     bv->SetLength(ValueLengthField);
     if( !bv->Read<TSwap>(is) )
       {
-      assert(0 && "Should not happen");
+      gdcmAssertAlwaysMacro(0 && "Should not happen");
       return is;
       }
     ValueField = bv;

Source/DataStructureAndEncodingDefinition/gdcmExplicitDataElement.txx

@@ -339,6 +339,7 @@ std::istream &ExplicitDataElement::ReadValue(std::istream &is, bool readvalues)
 #ifdef GDCM_SUPPORT_BROKEN_IMPLEMENTATION
   if( SequenceOfItems *sqi = dynamic_cast<SequenceOfItems*>(&GetValue()) )
     {
+    assert( ValueField->GetLength() == ValueLengthField );
     // Recompute the total length:
     if( !ValueLengthField.IsUndefined() )
       {

Source/DataStructureAndEncodingDefinition/gdcmImplicitDataElement.txx

@@ -538,6 +538,9 @@ const std::ostream &ImplicitDataElement::Write(std::ostream &os) const
     return os;
     }
   // Write Value Length
+  // The following code should always work since we are in the case of IVRLE - CP246
+  // however broken file such as PET-GE-dicomwrite-PixelDataSQUNv2.dcm breaks this assumption right here:
+  // see bug #502
   const SequenceOfItems *sqi = dynamic_cast<const SequenceOfItems*>( ValueField.GetPointer() ); //GetSequenceOfItems();
   if( sqi && !ValueLengthField.IsUndefined() )
     {

Source/DataStructureAndEncodingDefinition/gdcmReader.cxx

@@ -827,78 +827,16 @@ bool Reader::CanRead() const
   return false;
 }
 
-#ifdef _MSC_VER
-namespace {
-static inline std::wstring ToUtf16(std::string const & str) {
-  std::wstring ret;
-  int len = MultiByteToWideChar(CP_UTF8, 0, str.c_str(), (int)str.length(), nullptr, 0);
-  if (len > 0) {
-    ret.resize(len);
-    MultiByteToWideChar(CP_UTF8, 0, str.c_str(), (int)str.length(), &ret[0], len);
-  }
-  return ret;
-}
-// http://arsenmk.blogspot.com/2015/12/handling-long-paths-on-windows.html
-static inline bool ComputeFullPath(std::wstring const &in, std::wstring &out) {
-  // consider an input fileName of type PCWSTR (const wchar_t*)
-  const wchar_t *fileName = in.c_str();
-  DWORD requiredBufferLength = GetFullPathNameW(fileName, 0, nullptr, nullptr);
-
-  if (0 == requiredBufferLength)  // means failure
-  {
-    return false;
-  }
-
-  out.resize(requiredBufferLength);
-  wchar_t *buffer = &out[0];
-
-  DWORD result =
-      GetFullPathNameW(fileName, requiredBufferLength, buffer, nullptr);
-
-  if (0 == result) {
-    return false;
-  }
-
-  // buffer now contains the full path name of fileName, use it.
-  return true;
-}
-
-static inline std::wstring HandleMaxPath(std::wstring const &in) {
-  if (in.size() >= MAX_PATH) {
-    std::wstring out;
-    bool ret = ComputeFullPath(in, out);
-    if (!ret) return in;
-    if (out.size() < 4) return in;
-    if (out[0] == '\\' && out[1] == '\\' && out[2] == '?') {
-      // nothing to do
-    } else if (out[0] == '\\' && out[1] == '\\' && out[2] != '?') {
-      // server path
-      const std::wstring prefix = LR"(\\?\UNC\)";
-      out = prefix + (out.c_str() + 2);
-    } else {
-      // regular C:\ style path:
-      assert(out[1] == ':');
-      const std::wstring prefix = LR"(\\?\)";
-      out = prefix + out.c_str();
-    }
-    return out;
-  }
-  return in;
-}
-} // namespace
-#endif
-
-void Reader::SetFileName(const char *uft8path)
+void Reader::SetFileName(const char *utf8path)
 {
   if(Ifstream) delete Ifstream;
   Ifstream = new std::ifstream();
-  if (uft8path && *uft8path) {
+  if (utf8path && *utf8path) {
 #ifdef _MSC_VER
-    const std::wstring uft16path = ToUtf16(uft8path);
-    const std::wstring uncpath = HandleMaxPath(uft16path);
+    const std::wstring uncpath = System::ConvertToUNC(utf8path);
     Ifstream->open(uncpath.c_str(), std::ios::binary);
 #else
-    Ifstream->open( uft8path, std::ios::binary);
+    Ifstream->open( utf8path, std::ios::binary);
 #endif
   }
   if( Ifstream->is_open() )