Merge branch 'release'

.codespellrc

@@ -0,0 +1,3 @@
+[codespell]
+skip = ./Utilities/gdcmcharls,./Utilities/gdcmopenjpeg,./Utilities/gdcmrle,./Utilities/gdcmexpat,./Utilities/gdcmjpeg,./Utilities/gdcmzlib,./Utilities/pvrg,./Utilities/socketxx
+ignore-words-list = convertor,possibile,iif,comando,oly,ofthe,didi,promis,alue,tutoriels,som,tabl,psot,cna,varian,pres,comparaison,serie,ore,ect,mor,setts,unknow,inout,te,nd,te,pinter,fo,ot,siz,ist,shs,invers,studi,wallthickness,vas,fith

Applications/Cxx/puff.c

@@ -623,7 +623,7 @@ local int fixed(struct state *s)
  *   are themselves compressed using Huffman codes and run-length encoding.  In
  *   the list of code lengths, a 0 symbol means no code, a 1..15 symbol means
  *   that length, and the symbols 16, 17, and 18 are run-length instructions.
- *   Each of 16, 17, and 18 are follwed by extra bits to define the length of
+ *   Each of 16, 17, and 18 are followed by extra bits to define the length of
  *   the run.  16 copies the last length 3 to 6 times.  17 represents 3 to 10
  *   zero lengths, and 18 represents 11 to 138 zero lengths.  Unused symbols
  *   are common, hence the special coding for zero lengths.

Examples/Csharp/BasicImageAnonymizer.cs

@@ -23,7 +23,7 @@ public static int Main(string[] args)
     {
     string filename = args[0];
 
-    // instanciate the reader:
+    // instantiate the reader:
     gdcm.ImageReader reader = new gdcm.ImageReader();
     reader.SetFileName( filename );
 

Examples/Csharp/DecompressImageMultiframe.cs

@@ -74,7 +74,7 @@ public static int Main(string[] args)
     // Create a new SequenceOfFragments C++ object, store it as a SmartPointer :
     SmartPtrFrag sq = SequenceOfFragments.New();
 
-    // Yeah, the file are not garantee to be in order, please adapt...
+    // Yeah, the files are not guaranteed to be in order, please adapt...
     for(uint i = 0; i < nfiles; ++i)
       {
       System.Console.WriteLine( filenames[(int)i] );

Examples/Csharp/ReformatFile.cs

@@ -46,7 +46,7 @@ public static int Main(string[] args)
 
     UIDGenerator uid = new UIDGenerator(); // helper for uid generation
     FileDerivation fd = new FileDerivation();
-    // For the pupose of this execise we will pretend that this image is referencing
+    // For the purpose of this exercise we will pretend that this image is referencing
     // two source image (we need to generate fake UID for that).
     string ReferencedSOPClassUID = "1.2.840.10008.5.1.4.1.1.7"; // Secondary Capture
     fd.AddReference( ReferencedSOPClassUID, uid.Generate() );

Examples/Csharp/StandardizeFiles.cs

@@ -35,7 +35,7 @@ public static bool ProcessOneFile( string filename, string outfilename )
       }
 
     ImageChangeTransferSyntax change = new ImageChangeTransferSyntax();
-    change.SetForce( false ); // do we really want to recompress when input is alread compressed in same alg ?
+    change.SetForce( false ); // do we really want to recompress when input is already compressed in same alg ?
     change.SetCompressIconImage( false ); // Keep it simple
     change.SetTransferSyntax( new TransferSyntax( TransferSyntax.TSType.JPEG2000Lossless ) );
     change.SetInput( reader.GetPixmap() );

Examples/Cxx/DumpExamCard.cxx

@@ -242,7 +242,7 @@ struct param
   void read( std::istream & is )
     {
     is.read( name, 32 + 1);
-    // This is always the same issue the string can contains garbarge from previous run,
+    // This is always the same issue the string can contains garbage from previous run,
     // we need to print only until the first \0 character:
     assert( strlen( name ) <= 32 );
     is.read( (char*)&boolean,1);
@@ -528,7 +528,7 @@ Wotsit ?
       //fn += ".xml";
       std::ofstream csv( fn.c_str() );
 
-      // let's do some bookeeping:
+      // let's do some bookkeeping:
       uint32_t nfloats = 0;
       uint32_t nints = 0;
       uint32_t nstrings = 0;

Examples/Cxx/FixBrokenJ2K.cxx

@@ -22,7 +22,7 @@
 // -> BuggyJ2Kvvvua-fixed2-j2k.dcm
 
 /*
- * This program attemps to fix a broken J2K/DICOM:
+ * This program attempts to fix a broken J2K/DICOM:
  * It contains 2 bugs:
  * 1. The first 8 bytes seems to be random bytes: remove them
  * 2. YCC is set to 1, while image is grayscale need to set it back to 0

Examples/Cxx/FixJAIBugJPEGLS.cxx

@@ -100,7 +100,7 @@ int main(int argc, char *argv[])
     char errorMsg[256+1]={'\0'};
     if (JpegLsReadHeader(buffer, totalLen, &metadata, errorMsg) != charls::ApiResult::OK)
       {
-      std::cerr << "Cant parse jpegls: " << errorMsg << std::endl;
+      std::cerr << "Can't parse jpegls: " << errorMsg << std::endl;
       return 1;
       }
 
@@ -170,7 +170,7 @@ int main(int argc, char *argv[])
       }
     if( !marker_lse )
       {
-      std::cerr << "Cant handle: " << metadata.bitsPerSample << std::endl;
+      std::cerr << "Can't handle: " << metadata.bitsPerSample << std::endl;
       return 1;
       }
 
@@ -184,7 +184,7 @@ int main(int argc, char *argv[])
 #endif
 
     const char *pbyteCompressed = vbuffer.data();
-    size_t cbyteCompressed = vbuffer.size(); // updated legnth
+    size_t cbyteCompressed = vbuffer.size(); // updated length
 
     JlsParameters params;
     JpegLsReadHeader(pbyteCompressed, cbyteCompressed, &params, nullptr);

Examples/Cxx/GenFakeImage.cxx

@@ -85,7 +85,7 @@ int main(int, char *[])
 
   // Step 2: DERIVED object
   gdcm::FileDerivation fd;
-  // For the pupose of this execise we will pretend that this image is referencing
+  // For the purpose of this exercise we will pretend that this image is referencing
   // two source image (we need to generate fake UID for that).
   const char ReferencedSOPClassUID[] = "1.2.840.10008.5.1.4.1.1.7"; // Secondary Capture
   fd.AddReference( ReferencedSOPClassUID, uid.Generate() );

Examples/Cxx/HelloVizWorld.cxx

@@ -33,7 +33,7 @@ int main(int argc, char *argv[])
   const char *filename = argv[1];
   const char *outfilename = argv[2];
 
-  // Instanciate the image reader:
+  // Instantiate the image reader:
   gdcm::ImageReader reader;
   reader.SetFileName( filename );
   if( !reader.Read() )

Examples/Cxx/HelloWorld.cxx

@@ -31,7 +31,7 @@ int main(int argc, char *argv[])
   const char *filename = argv[1];
   const char *outfilename = argv[2];
 
-  // Instanciate the reader:
+  // Instantiate the reader:
   gdcm::Reader reader;
   reader.SetFileName( filename );
   if( !reader.Read() )
@@ -50,7 +50,7 @@ int main(int argc, char *argv[])
   // the dataset is the the set of element we are interested in:
   gdcm::DataSet &ds = file.GetDataSet();
 
-  // Contruct a static(*) type for Image Comments :
+  // Construct a static(*) type for Image Comments :
   gdcm::Attribute<0x0020,0x4000> imagecomments;
   imagecomments.SetValue( "Hello, World !" );
 

Examples/Cxx/LargeVRDSExplicit.cxx

@@ -23,7 +23,7 @@
  *  gdcmConformanceTests/RTStruct_VRDSAsVRUN.dcm
  *
  * This is an advanced example. Its goal is to explain one dark corner of DICOM PS 3.10
- * file format. The idea is that when writting an Attribute in an Explicit Transfer
+ * file format. The idea is that when writing an Attribute in an Explicit Transfer
  * Syntax one, cannot always use V:DS for writing a VR:DS attribute since dong so
  * would imply using a VL:16bits.
  * This example shows that converting from Implicit to Explicit should preserver VR:UN

Examples/Cxx/MrProtocol.cxx

@@ -493,7 +493,7 @@ One can find it also in the protocol:
 ...
 
 */
-  // Below is an attemp to play with the CSAHeader dict:
+  // Below is an attempt to play with the CSAHeader dict:
 #if 0
   const char gspec[] = "sGRADSPEC.flSensitivityX";
   it = mymap.find( gspec );

Examples/Cxx/PatchFile.cxx

@@ -110,7 +110,7 @@ int main(int argc, char *argv[])
     }
   std::cout << bv->GetLength() << " " << len << std::endl;
 
-  std::cout << "Sucess to rewrite image !" << std::endl;
+  std::cout << "Success to rewrite image !" << std::endl;
   image.Print( std::cout );
   return 0;
 }

Examples/Cxx/PrintLUT.cxx

@@ -30,7 +30,7 @@ int main(int argc, char *argv[])
     }
   const char *filename = argv[1];
 
-  // Instanciate the image reader:
+  // Instantiate the image reader:
   gdcm::ImageReader reader;
   reader.SetFileName( filename );
   if( !reader.Read() )

Examples/Cxx/PublicDict.cxx

@@ -29,7 +29,7 @@ int main(int , char *[])
 
   //std::cout << pub << std::endl;
 
-  // 3 differents way to access the same information
+  // 3 different ways to access the same information
 
   // 1. From the public dict only:
   gdcm::Tag patient_name(0x10,0x10);

Examples/Cxx/ReadAndDumpDICOMDIR2.cxx

@@ -224,7 +224,7 @@ const std::vector<std::shared_ptr<DICOMDIRReader::Patient>>& DICOMDIRReader::loa
     // VR field
     first_item_offset += it->GetVR().GetLength();
     // VL field
-    // For Explicit VR: adventitiously VL field lenght = VR field lenght,
+    // For Explicit VR: adventitiously VL field length = VR field length,
     // for SQ 4 bytes:
     // http://dicom.nema.org/medical/dicom/current/output/html/part05.html#table_7.1-1
     first_item_offset += it->GetVR().GetLength();

Examples/Cxx/ReadAndPrintAttributes.cxx

@@ -34,7 +34,7 @@ int main(int argc, char *argv[])
     }
   const char *filename = argv[1];
 
-  // Instanciate the reader:
+  // Instantiate the reader:
   gdcm::Reader reader;
   reader.SetFileName( filename );
   if( !reader.Read() )

Examples/Cxx/pmsct_rgb1.cxx

@@ -74,7 +74,7 @@ void delta_decode(const unsigned char *data_in, size_t data_size,
   size_t ps = plane_size;
 
   // The following is highly unoptimized as we have nested if statement in a while loop
-  // we need to switch from one algorithm to ther other (RGB <-> GRAY)
+  // we need to switch from one algorithm to the other (RGB <-> GRAY)
   while (ps)
     {
     // next byte:
@@ -130,7 +130,7 @@ void delta_decode(const unsigned char *data_in, size_t data_size,
         }
       break;
     case COLORMODE:
-      // We are swithing from one mode to the other. The stream contains an intermixed
+      // We are switching from one mode to the other. The stream contains an intermixed
       // compression of RGB codec and GRAY codec. Each one not knowing of the other
       // reset old value to 0.
       if (graymode)

Examples/Python/DumbAnonymizer.py

@@ -56,7 +56,7 @@
   (0x0018,0x1250):("Sequence Field","Receive Coil"),
   (0x0018,0x0088):("Sequence Field","Spacing Between Slice"),
   (0x0018,0x0095):("Sequence Field","Pixel Bandwidth"),
-  (0x0018,0x0082):("Sequence Field","Invertion Time"),
+  (0x0018,0x0082):("Sequence Field","Inversion Time"),
 }
 
 class MyAnon:

Examples/Python/FixCommaBug.py

@@ -73,5 +73,5 @@
   print "there is still a comma"
   sys.exit(1)
 
-print "Sucess!"
+print "Success!"
 sys.exit(0) # success

Examples/Python/HelloWorld.py

@@ -29,7 +29,7 @@
   # Get the filename from the command line
   filename = sys.argv[1]
 
-  # Instanciate a gdcm.Reader
+  # Instantiate a gdcm.Reader
   # This is the main class to handle any type of DICOM object
   # You should check for gdcm.ImageReader for reading specifically DICOM Image file
   r = gdcm.Reader()

Examples/Python/PrivateDict.py

@@ -22,7 +22,7 @@
   #gdcm.Trace.DebugOn()
   globInst = gdcm.Global.GetInstance()
   # Try to load Part3.xml file
-  # This fils is too big for being accessible directly at runtime.
+  # This file is too big for being accessible directly at runtime.
   globInst.LoadResourcesFiles()
 
 

Examples/Python/ReWriteSCAsMR.py

@@ -57,7 +57,7 @@ def CheckSecondaryCaptureObjectIsMRImageStorage(r):
 
   if( CheckSecondaryCaptureObjectIsMRImageStorage(r) ):
     # Special handling of the spacing:
-    # GDCM 1.2.0 would not rewrite correcly DICOM Object and would always set them as 'Secondary Capture Image Storage'
+    # GDCM 1.2.0 would not rewrite correctly DICOM Object and would always set them as 'Secondary Capture Image Storage'
     # while we would rather have 'MR Image Storage'
     gdcm.ImageHelper.SetForcePixelSpacing( True )
     mrspacing = gdcm.ImageHelper.GetSpacingValue( r.GetFile() )

Examples/Python/RemovePrivateTags.py

@@ -27,7 +27,7 @@
   file1 = sys.argv[1]
   file2 = sys.argv[2]
 
-  # Instanciate the reader.
+  # Instantiate the reader.
   r = gdcm.Reader()
   r.SetFileName( file1 )
   if not r.Read():

Examples/Python/ScanDirectory.py

@@ -40,7 +40,7 @@ def EndFilter(self):
   #  Get rid of any Warning while parsing the DICOM files
   gdcm.Trace.WarningOff()
 
-  # instanciate Scanner:
+  # instantiate Scanner:
   sp = gdcm.Scanner.New();
   s = sp.__ref__()
   w = ProgressWatcher(s, 'Watcher')

INSTALL.txt

@@ -31,6 +31,6 @@ Major options explained:
 * GDCM_WRAP_PHP: turn it on if you want to be able to access the GDCM API via php (experimental)
 * GDCM_USE_VTK: turn if on if you want to be able to load DICOM file in VTK context (requires VTK)
 * GDCM_BUILD_APPLICATIONS: turn it on if you want the build gdcm applications (gdcmdump, gdcmconv, gdcminfo ...)
-* GDCM_BUILD_TESTING: Turn it on if you want to be able to exectute GDCM testing suite
+* GDCM_BUILD_TESTING: Turn it on if you want to be able to execute GDCM testing suite
 * GDCM_DOCUMENTATION: turn it on if you want to generate the developer documentation (require doxygen)
 * GDCM_BUILD_EXAMPLES: turn it on if you want to build simple examples that demonstrates GDCM usage.

Source/DataDictionary/gdcmPrivateDefaultDicts.cxx

@@ -4047,7 +4047,7 @@ 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 },

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="?"/>

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;
     }

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;
 

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

Testing/Source/Common/Cxx/TestSmartPointer.cxx

@@ -26,9 +26,9 @@ class Foo : public Object {
    }
 };
 
-class Containter {
+class Container {
 public:
-  Containter():Instance(nullptr) {}
+  Container():Instance(nullptr) {}
   SmartPointer<Object> Instance;
 };
 
@@ -100,8 +100,8 @@ int TestSmartPointer(int, char *[])
   Foo &foo = *p7;
   foo.foo();
 
-  Containter c1;
-  Containter c2;
+  Container c1;
+  Container c2;
   c2 = c1;
 
   // TODO: