Commit 8d6ed31edcb063f964adb5955cd471b448a0e427 - gdcm

+6

-2

.travis.yml less more

24	24	- CFLAGS="-g -O2"
25	25	- CXXFLAGS="-g -O2"
26	26	- B_NAME=default
	27	- CPACK_NAME=Linux
27	28	- compiler: gcc
28	29	os: linux
29	30	addons: {apt: {packages: [default-jdk, mono-devel, swig, libcharls-dev, libvtk5-dev, libopenjpeg-dev, libexpat-dev, libz-dev, uuid-dev, python-all-dev, libpoppler-dev, xsltproc, docbook-xsl, dcmtk]}}

32	33	- CXXFLAGS="-Wall -Wextra -m64"
33	34	- CMAKE_EXTRA="-DGDCM_USE_SYSTEM_OPENSSL:BOOL=ON -DGDCM_WRAP_PYTHON:BOOL=ON -DGDCM_WRAP_CSHARP:BOOL=ON -DGDCM_WRAP_JAVA:BOOL=ON -DGDCM_WRAP_PHP:BOOL=OFF -DGDCM_USE_SYSTEM_EXPAT:BOOL=ON -DGDCM_USE_SYSTEM_JSON:BOOL=OFF -DGDCM_USE_SYSTEM_LIBXML2:BOOL=ON -DGDCM_USE_SYSTEM_OPENJPEG:BOOL=ON -DGDCM_USE_SYSTEM_POPPLER:BOOL=ON -DGDCM_USE_SYSTEM_UUID:BOOL=ON -DGDCM_USE_SYSTEM_ZLIB:BOOL=ON -DGDCM_WEAK_SWIG_CHECK:BOOL=ON -DGDCM_LEGACY_SILENT:BOOL=ON"
34	35	- B_NAME=system
	36	- CPACK_NAME=Linux
35	37	- compiler: clang
36	38	os: linux
37	39	env:
38	40	- CFLAGS="-g -O0 -Wall -Wextra -m64 -fsanitize=address,undefined,shift"
39	41	- CXXFLAGS="-g -O0 -Wall -Wextra -m64 -fsanitize=address,undefined,shift"
40	42	- B_NAME=fsanitize
	43	- CPACK_NAME=Linux
41	44	- compiler: clang
42	45	os: osx
43	46	env:
44	47	- CFLAGS="-Wall -Wextra" # -m64 -fsanitize=address,undefined
45	48	- CXXFLAGS="-Wall -Wextra" # -m64 -fsanitize=address,undefined
46	49	- B_NAME=default
	50	- CPACK_NAME=Darwin
47	51
48	52	before_install:
49	53	#- env

79	83	api_key:
80	84	secure: 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
81	85	file:
82		- GDCM-$VTAG-Linux-x86_64.tar.gz
83		- GDCM-$VTAG-Linux-x86_64.tar.bz2
	86	- GDCM-$VTAG-$CPACK_NAME-x86_64.tar.gz
	87	- GDCM-$VTAG-$CPACK_NAME-x86_64.tar.bz2
84	88	skip_cleanup: true
85	89	on:
86	90	repo: malaterre/GDCM

+37

-0

Applications/Cxx/gdcmimg.cxx less more

141	141	std::cout << " -C --sop-class-uid SOP Class UID (name or value)." << std::endl;
142	142	std::cout << " -T --study-uid Study UID." << std::endl;
143	143	std::cout << " -S --series-uid Series UID." << std::endl;
	144	std::cout << " --template DICOM template." << std::endl;
	145	std::cout << " --keep-meta Keep meta info from template file (advanced users only)." << std::endl;
144	146	std::cout << " --root-uid Root UID." << std::endl;
145	147	std::cout << "Fill Options:" << std::endl;
146	148	std::cout << " -R --region %d,%d Region." << std::endl;

413	415	gdcm::Filename filename;
414	416	gdcm::Directory::FilenamesType filenames;
415	417	gdcm::Filename outfilename;
	418	gdcm::Filename templatefilename;
416	419	unsigned int region[6] = {}; // Rows & Columns are VR=US anyway...
417	420	unsigned int color = 0;
418	421	int bregion = 0;

422	425	int pconf = 0; // planar configuration
423	426	int studyuid = 0;
424	427	int seriesuid = 0;
	428	int templated = 0;
	429	int keepmeta = 0;
425	430	unsigned int size[3] = {0,0,0};
426	431	unsigned int ndimension = 2;
427	432	int depth = 0;

472	477	{"pi", 1, &pinter, 1}, //
473	478	{"pf", 1, &pformat, 1}, //
474	479	{"offset", 1, &poffset, 1}, //
	480	{"template", 1, &templated, 1},
	481	{"keep-meta", 0, &keepmeta, 1}, // by default we do not want to keep
475	482
476	483	// General options !
477	484	{"verbose", 0, &verbose, 1},

585	592	assert( strcmp(s, "offset") == 0 );
586	593	poffset = 1;
587	594	start_pos = (size_t)atoll(optarg);
	595	}
	596	else if( option_index == 17 ) /* template */
	597	{
	598	assert( strcmp(s, "template") == 0 );
	599	templated = 1;
	600	templatefilename = optarg;
588	601	}
589	602	//printf (" with arg %s", optarg);
590	603	}

830	843	//if( !inputextension \|\| !outputextension ) return 1;
831	844	if( inputextension )
832	845	{
	846	gdcm::Reader reader;
	847	if( templated )
	848	{
	849	reader.SetFileName( templatefilename );
	850	if( !reader.Read() )
	851	{
	852	std::cerr << "Failed to read: " << templatefilename << std::endl;
	853	return 1;
	854	}
	855	}
833	856	if( gdcm::System::StrCaseCmp(inputextension,".raw") == 0 // watch out that .raw for kakadu means big-endian
834	857	\|\| gdcm::System::StrCaseCmp(inputextension,".rawl") == 0 // kakadu convention for raw little endian
835	858	\|\| gdcm::System::StrCaseCmp(inputextension,".gray") == 0 // imagemagick convention

843	866	}
844	867	gdcm::RAWCodec raw;
845	868	gdcm::PixmapWriter writer;
	869	writer.SetCheckFileMetaInformation( (keepmeta > 0 ? false : true) );
	870	writer.SetFile( reader.GetFile() );
846	871	// Because the RAW stream is not self sufficient, we need to pass in some extra
847	872	// user info:
848	873	unsigned int dims[3] = {};

908	933	}
909	934	gdcm::RLECodec rle;
910	935	gdcm::PixmapWriter writer;
	936	writer.SetCheckFileMetaInformation( (keepmeta > 0 ? false : true) );
	937	writer.SetFile( reader.GetFile() );
911	938	// Because the RLE stream is not self sufficient, we need to pass in some extra
912	939	// user info:
913	940	unsigned int dims[3] = {};

946	973	if( !GetPixelFormat( pf, depth, bpp, sign, pixelsign ) ) return 1;
947	974	pnm.SetPixelFormat( pf );
948	975	gdcm::PixmapWriter writer;
	976	writer.SetCheckFileMetaInformation( (keepmeta > 0 ? false : true) );
	977	writer.SetFile( reader.GetFile() );
949	978	if( !Populate( writer, pnm, filenames ) ) return 1;
950	979	// populate will guess pixel format and photometric inter from file, need
951	980	// to override after calling Populate:

976	1005	{
977	1006	gdcm::PGXCodec pnm;
978	1007	gdcm::PixmapWriter writer;
	1008	writer.SetCheckFileMetaInformation( (keepmeta > 0 ? false : true) );
	1009	writer.SetFile( reader.GetFile() );
979	1010	if( !Populate( writer, pnm, filenames ) ) return 1;
980	1011	if( !AddUIDs(sopclassuid, sopclass, study_uid, series_uid, writer ) ) return 1;
981	1012

992	1023	{
993	1024	gdcm::JPEGLSCodec jpeg;
994	1025	gdcm::PixmapWriter writer;
	1026	writer.SetCheckFileMetaInformation( (keepmeta > 0 ? false : true) );
	1027	writer.SetFile( reader.GetFile() );
995	1028	if( !Populate( writer, jpeg, filenames ) ) return 1;
996	1029	if( !AddUIDs(sopclassuid, sopclass, study_uid, series_uid, writer ) ) return 1;
997	1030

1017	1050	*/
1018	1051	gdcm::JPEG2000Codec jpeg;
1019	1052	gdcm::PixmapWriter writer;
	1053	writer.SetCheckFileMetaInformation( (keepmeta > 0 ? false : true) );
	1054	writer.SetFile( reader.GetFile() );
1020	1055	if( !Populate( writer, jpeg, filenames ) ) return 1;
1021	1056	if( !AddUIDs(sopclassuid, sopclass, study_uid, series_uid, writer ) ) return 1;
1022	1057

1041	1076	if( !GetPixelFormat( pf, depth, bpp, sign, pixelsign ) ) return 1;
1042	1077	jpeg.SetPixelFormat( pf );
1043	1078	gdcm::PixmapWriter writer;
	1079	writer.SetCheckFileMetaInformation( (keepmeta > 0 ? false : true) );
	1080	writer.SetFile( reader.GetFile() );
1044	1081	if( !Populate( writer, jpeg, filenames ) ) return 1;
1045	1082	if( !AddUIDs(sopclassuid, sopclass, study_uid, series_uid, writer ) ) return 1;
1046	1083

+10

-1

CMake/FindOpenJPEG.cmake less more

17	17	# (To distribute this file outside of CMake, substitute the full
18	18	# License text for the above reference.)
19	19
20		# Try first to locate a cmake config file
	20	# Try with pkg-config first
	21	find_package(PkgConfig)
	22	pkg_check_modules(OPENJPEG libopenjpeg1)
	23	if(OPENJPEG_FOUND)
	24	set(OPENJPEG_MAJOR_VERSION 1)
	25	set(OPENJPEG_INCLUDE_DIR ${OPENJPEG_INCLUDE_DIRS})
	26	set(OPENJPEG_LIBRARIES ${OPENJPEG_LDFLAGS})
	27	else()
	28	# Try to locate a cmake config file
21	29	find_package(OpenJPEG QUIET NO_MODULE)
22	30	mark_as_advanced(OpenJPEG_DIR)
23	31

51	59	OPENJPEG_INCLUDE_DIR
52	60	)
53	61	endif()
	62	endif()

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-1

CMakeLists.txt less more

31	31	#----------------------------------------------------------------------------
32	32	set(GDCM_MAJOR_VERSION 2)
33	33	set(GDCM_MINOR_VERSION 6)
34		set(GDCM_BUILD_VERSION 4)
	34	set(GDCM_BUILD_VERSION 5)
35	35	set(GDCM_VERSION
36	36	"${GDCM_MAJOR_VERSION}.${GDCM_MINOR_VERSION}.${GDCM_BUILD_VERSION}")
37	37	# let advanced user the option to define GDCM_API_VERSION:

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-0

Examples/Csharp/CMakeLists.txt less more

25	25	FileStreaming
26	26	FileChangeTS
27	27	FileChangeTSLossy
	28	DumpCSA
28	29	)
29	30
30	31	if(BUILD_TESTING)

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Examples/Csharp/DumpCSA.cs less more

	0	/*=========================================================================
	1
	2	Program: GDCM (Grassroots DICOM). A DICOM library
	3
	4	Copyright (c) 2006-2011 Mathieu Malaterre
	5	All rights reserved.
	6	See Copyright.txt or http://gdcm.sourceforge.net/Copyright.html for details.
	7
	8	This software is distributed WITHOUT ANY WARRANTY; without even
	9	the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
	10	PURPOSE. See the above copyright notice for more information.
	11
	12	=========================================================================*/
	13
	14	/*
	15	* Usage:
	16	* $ bin/DumpCSA.exe input.dcm
	17	*/
	18	using System;
	19	using gdcm;
	20
	21	public class DumpCSA
	22	{
	23	public static int Main(string[] args)
	24	{
	25	string filename = args[0];
	26
	27	gdcm.Reader reader = new gdcm.Reader();
	28	reader.SetFileName( filename );
	29	if (!reader.Read()) return 1;
	30
	31	gdcm.File f = reader.GetFile();
	32	gdcm.DataSet ds = f.GetDataSet();
	33
	34	string[] expectedSiemensTags = new string[] { "B_value" , "AcquisitionMatrixText" };
	35	using (PrivateTag gtag = CSAHeader.GetCSAImageHeaderInfoTag())
	36	{
	37	if (ds.FindDataElement(gtag))
	38	{
	39	using (DataElement de = ds.GetDataElement(gtag))
	40	{
	41	if (de != null && !de.IsEmpty())
	42	{
	43	using (CSAHeader csa = new CSAHeader())
	44	{
	45	if (csa.LoadFromDataElement(de))
	46	{
	47	foreach (string str in expectedSiemensTags)
	48	{
	49	if (csa.FindCSAElementByName(str))
	50	{
	51	using (CSAElement elem = csa.GetCSAElementByName(str))
	52	{
	53	if (elem != null)
	54	{
	55	System.Console.WriteLine( elem.toString() );
	56	}
	57	}
	58	}
	59	}
	60	}
	61	}
	62	}
	63	}
	64	}
	65	}
	66
	67
	68	return 0;
	69	}
	70	}

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-1

Examples/Java/CMakeLists.txt less more

0		find_package(Java REQUIRED) # javac, jar
	0	find_package(Java ${GDCM_DEFAULT_JAVA_VERSION} REQUIRED) # javac, jar
1	1	find_package(JNI REQUIRED)
2	2	include_directories(
3	3	#${JNI_INCLUDE_PATH}

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-19

Source/Common/gdcmTesting.cxx less more

322	322	{ 0,"D_CLUNIE_VL4_RLE.dcm" },
323	323	{ 0,"D_CLUNIE_RG1_RLE.dcm" },
324	324	{ 1,"JDDICOM_Sample2.dcm" },
325		{0,"AMIInvalidPrivateDefinedLengthSQasUN.dcm" },
	325	{ 0,"AMIInvalidPrivateDefinedLengthSQasUN.dcm" },
326	326	{ 0,"SIEMENS_MAGNETOM-12-MONO2-FileSeq3.dcm" },
327	327	{ 0,"CT-MONO2-8-abdo.dcm" },
328	328	{ 0,"D_CLUNIE_SC1_RLE.dcm" },

415	415	{ 1,"multiframegrayscalewordscis.dcm" },
416	416	{ 1,"multiframesinglebitscis.dcm" },
417	417	{ 1,"multiframetruecolorscis.dcm" },
418		{ 1, "SinglePrecisionSC.dcm" },
419		{ 0, "signedtruecoloroldsc.dcm" },
420		{ 0, "o.dcm" },
421		{ 0, "UnexpectedSequenceDelimiterInFixedLengthSequence.dcm" },
422		{ 0, "IM-0001-0066.CommandTag00.dcm" },
423		{ 0, "NM_Kakadu44_SOTmarkerincons.dcm" },
424		{ 0, "GDCMJ2K_TextGBR.dcm" },
425		{ 0, "PhilipsInteraSeqTermInvLen.dcm" },
426		{ 0, "LIBIDO-24-ACR_NEMA-Rectangle.dcm" },
427		{ 0, "TOSHIBA_J2K_SIZ1_PixRep0.dcm" },
428		{ 0, "TOSHIBA_J2K_SIZ0_PixRep1.dcm" },
429		{ 0, "TOSHIBA_J2K_OpenJPEGv2Regression.dcm" },
430		{ 0, "NM-PAL-16-PixRep1.dcm" },
431		{ 0, "MEDILABInvalidCP246_EVRLESQasUN.dcm" },
432		{ 0, "JPEGInvalidSecondFrag.dcm" },
433		{ 0, "SC16BitsAllocated_8BitsStoredJ2K.dcm" },
434		{ 0, "SC16BitsAllocated_8BitsStoredJPEG.dcm" },
435		{ 0, "SIEMENS_SYNGO-12-MONO2-LUTWrongLength512.dcm" },
	418	{ 1,"SinglePrecisionSC.dcm" },
	419	{ 0,"signedtruecoloroldsc.dcm" },
	420	{ 0,"o.dcm" },
	421	{ 0,"UnexpectedSequenceDelimiterInFixedLengthSequence.dcm" },
	422	{ 0,"IM-0001-0066.CommandTag00.dcm" },
	423	{ 0,"NM_Kakadu44_SOTmarkerincons.dcm" },
	424	{ 0,"GDCMJ2K_TextGBR.dcm" },
	425	{ 0,"PhilipsInteraSeqTermInvLen.dcm" },
	426	{ 0,"LIBIDO-24-ACR_NEMA-Rectangle.dcm" },
	427	{ 0,"TOSHIBA_J2K_SIZ1_PixRep0.dcm" },
	428	{ 0,"TOSHIBA_J2K_SIZ0_PixRep1.dcm" },
	429	{ 0,"TOSHIBA_J2K_OpenJPEGv2Regression.dcm" },
	430	{ 0,"NM-PAL-16-PixRep1.dcm" },
	431	{ 0,"MEDILABInvalidCP246_EVRLESQasUN.dcm" },
	432	{ 0,"JPEGInvalidSecondFrag.dcm" },
	433	{ 0,"SC16BitsAllocated_8BitsStoredJ2K.dcm" },
	434	{ 0,"SC16BitsAllocated_8BitsStoredJPEG.dcm" },
	435	{ 0,"SIEMENS_SYNGO-12-MONO2-LUTWrongLength512.dcm" },
	436	{ 0,"JPEGLS_CharLS_10742.dcm" },
	437	{ 1,"JPEGLosslessYBR_FULL_422.dcm" },
	438	{ 1,"JPEGNote_empty.dcm" },
	439	{ 1,"JPEGNote_missing.dcm" },
	440	{ 1,"JPEGNote_bogus.dcm" },
	441	{ 0,"RLEDebianBug816607Orig.dcm" },
	442	{ 0,"IllegalGroup2ImplicitTS.dcm" },
436	443	{ 0, NULL }
437	444	};
438	445

+27

-0

Source/DataStructureAndEncodingDefinition/gdcmFileMetaInformation.cxx less more

777	777	}
778	778	}
779	779	// Now is a good time to find out the dataset transfer syntax
	780	try {
780	781	ComputeDataSetTransferSyntax();
	782	} catch( gdcm::Exception & ex ) {
	783	// We were able to read some of the Meta Header, but failed to compute the DataSetTS
	784	// technically GDCM is able to cope with any value here. But be kind and try to have a good guess:
	785
	786	gdcmWarningMacro( "Meta Header is bogus. Guessing DataSet TS." );
	787	Tag t;
	788	if( !t.Read<SwapperNoOp>(is) )
	789	{
	790	throw Exception( "Cannot read very first tag" );
	791	}
	792
	793	char vr_str[3];
	794	is.read(vr_str, 2);
	795	vr_str[2] = '\0';
	796	VR::VRType vr = VR::GetVRType(vr_str);
	797	if( vr != VR::VR_END )
	798	{
	799	DataSetTS = TransferSyntax::ExplicitVRLittleEndian;
	800	}
	801	else
	802	{
	803	DataSetTS = TransferSyntax::ImplicitVRLittleEndian;
	804	}
	805	is.seekg(-6, std::ios::cur); // Seek back
	806
	807	}
781	808	}
782	809	}
783	810	// else

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Source/DataStructureAndEncodingDefinition/gdcmWriter.h less more

83	83	protected:
84	84	std::ostream *Stream;
85	85	std::ofstream *Ofstream;
	86	bool GetCheckFileMetaInformation() const { return CheckFileMetaInformation; }
86	87
87	88	private:
88	89	SmartPointer<File> F;

+16

-0

Source/MediaStorageAndFileFormat/gdcmBitmap.cxx less more

95	95	{
96	96	assert( NumberOfDimensions );
97	97	//assert( Dimensions.empty() );
	98	#if 0
98	99	Dimensions = std::vector<unsigned int>(dims,
99	100	dims+NumberOfDimensions);
	101	#else
	102	assert( Dimensions.size() == 3 );
	103	Dimensions[0] = dims[0];
	104	Dimensions[1] = dims[1];
	105	if( NumberOfDimensions == 2 )
	106	Dimensions[2] = 1;
	107	else
	108	Dimensions[2] = dims[2];
	109	#endif
100	110	}
101	111
102	112	void Bitmap::SetDimension(unsigned int idx, unsigned int dim)

395	405	i->SetPixelFormat( codec.GetPixelFormat() );
396	406	}
397	407	#endif
	408	if( GetDimensions()[0] != codec.GetDimensions()[0]
	409	\|\| GetDimensions()[1] != codec.GetDimensions()[1] )
	410	{
	411	gdcmWarningMacro( "dimension mismatch for JPEG" );
	412	((Bitmap*)this)->SetDimensions( codec.GetDimensions() ); //JPEGNote_bogus.dcm
	413	}
398	414
399	415	return true;
400	416	}

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Source/MediaStorageAndFileFormat/gdcmImageRegionReader.h less more

23	23	class ImageRegionReaderInternals;
24	24	/**
25	25	* \brief ImageRegionReader
	26	* This class is able to read a region from a DICOM file containing an image. This implementation
	27	* requires that the information stored in the DICOM header are consistent with what is in the
	28	* encapsulated Pixel Data. This is technically not required by DICOM standard, which makes
	29	* this implementation illegal with regards to the famous JPEG note:
	30	* http://dicom.nema.org/medical/dicom/current/output/chtml/part05/sect_8.2.html\#para_4bcb841e-c6bf-4e26-82a5-3fad3c942da0
26	31	* \see ImageReader
27	32	*/
28	33	class GDCM_EXPORT ImageRegionReader : public ImageReader

+268

-47

Source/MediaStorageAndFileFormat/gdcmJPEG2000Codec.cxx less more

35	35
36	36	namespace gdcm
37	37	{
	38
	39	/* Part 1 Table A.2 List of markers and marker segments */
	40	typedef enum {
	41	FF30 = 0xFF30,
	42	FF31 = 0xFF31,
	43	FF32 = 0xFF32,
	44	FF33 = 0xFF33,
	45	FF34 = 0xFF34,
	46	FF35 = 0xFF35,
	47	FF36 = 0xFF36,
	48	FF37 = 0xFF37,
	49	FF38 = 0xFF38,
	50	FF39 = 0xFF39,
	51	FF3A = 0xFF3A,
	52	FF3B = 0xFF3B,
	53	FF3C = 0xFF3C,
	54	FF3D = 0xFF3D,
	55	FF3E = 0xFF3E,
	56	FF3F = 0xFF3F,
	57	SOC = 0xFF4F,
	58	CAP = 0xFF50,
	59	SIZ = 0xFF51,
	60	COD = 0xFF52,
	61	COC = 0xFF53,
	62	TLM = 0xFF55,
	63	PLM = 0XFF57,
	64	PLT = 0XFF58,
	65	QCD = 0xFF5C,
	66	QCC = 0xFF5D,
	67	RGN = 0xFF5E,
	68	POC = 0xFF5F,
	69	PPM = 0XFF60,
	70	PPT = 0XFF61,
	71	CRG = 0xFF63,
	72	COM = 0xFF64,
	73	SOT = 0xFF90,
	74	SOP = 0xFF91,
	75	EPH = 0XFF92,
	76	SOD = 0xFF93,
	77	EOC = 0XFFD9 /* EOI in old jpeg */
	78	} MarkerType;
	79
	80	typedef enum {
	81	JP = 0x6a502020,
	82	FTYP = 0x66747970,
	83	JP2H = 0x6a703268,
	84	JP2C = 0x6a703263,
	85	JP2 = 0x6a703220,
	86	IHDR = 0x69686472,
	87	COLR = 0x636f6c72,
	88	XML = 0x786d6c20,
	89	CDEF = 0x63646566,
	90	CMAP = 0x636D6170,
	91	PCLR = 0x70636c72,
	92	RES = 0x72657320,
	93	} OtherType;
	94
	95	static inline bool hasnolength( uint_fast16_t marker )
	96	{
	97	switch( marker )
	98	{
	99	case FF30:
	100	case FF31:
	101	case FF32:
	102	case FF33:
	103	case FF34:
	104	case FF35:
	105	case FF36:
	106	case FF37:
	107	case FF38:
	108	case FF39:
	109	case FF3A:
	110	case FF3B:
	111	case FF3C:
	112	case FF3D:
	113	case FF3E:
	114	case FF3F:
	115	case SOC:
	116	case SOD:
	117	case EOC:
	118	case EPH:
	119	return true;
	120	}
	121	return false;
	122	}
	123
	124
	125	static inline bool read16(const char ** input, size_t * len, uint16_t * ret)
	126	{
	127	if( *len >= 2 )
	128	{
	129	union { uint16_t v; char bytes[2]; } u;
	130	memcpy(u.bytes, *input, 2);
	131	*ret = SwapperDoOp::Swap(u.v);
	132	input += 2; len -= 2;
	133	return true;
	134	}
	135	return false;
	136	}
	137
	138
	139	static inline bool read32(const char ** input, size_t * len, uint32_t * ret)
	140	{
	141	if( *len >= 4 )
	142	{
	143	union { uint32_t v; char bytes[4]; } u;
	144	memcpy(u.bytes, *input, 4);
	145	*ret = SwapperDoOp::Swap(u.v);
	146	input += 4; len -= 4;
	147	return true;
	148	}
	149	return false;
	150	}
	151
	152	static inline bool read64(const char ** input, size_t * len, uint64_t * ret)
	153	{
	154	if( *len >= 8 )
	155	{
	156	union { uint64_t v; char bytes[8]; } u;
	157	memcpy(u.bytes, *input, 8);
	158	*ret = SwapperDoOp::Swap(u.v);
	159	input += 8; len -= 8;
	160	return true;
	161	}
	162	return false;
	163	}
	164
	165
	166	static bool parsej2k_imp( const char * const stream, const size_t file_size, bool * lossless )
	167	{
	168	uint16_t marker;
	169	uintmax_t sotlen = 0;
	170	size_t lenmarker;
	171	const char * cur = stream;
	172	size_t cur_size = file_size;
	173	*lossless = false; // default init
	174	while( read16(&cur, &cur_size, &marker) )
	175	{
	176	if ( !hasnolength( marker ) )
	177	{
	178	uint16_t l;
	179	bool r = read16( &cur, &cur_size, &l );
	180	if( !r \|\| l < 2 )
	181	break;
	182	lenmarker = (size_t)l - 2;
	183
	184	if( marker == COD )
	185	{
	186	const uint8_t Transformation = *(cur+9);
	187	if( Transformation == 0x0 ) { *lossless = false; return true; }
	188	else if( Transformation == 0x1 ) *lossless = true;
	189	else return false;
	190	}
	191	cur += lenmarker; cur_size -= lenmarker;
	192	}
	193	else if( marker == SOD )
	194	return true;
	195	}
	196	return false;
	197	}
	198
	199	static bool parsejp2_imp( const char * const stream, const size_t file_size, bool * lossless )
	200	{
	201	uint32_t marker;
	202	uint64_t len64; /* ref */
	203	uint32_t len32; /* local 32bits op */
	204	const char * cur = stream;
	205	size_t cur_size = file_size;
	206
	207	while( read32(&cur, &cur_size, &len32) )
	208	{
	209	bool b = read32(&cur, &cur_size, &marker);
	210	if( !b ) break;
	211	len64 = len32;
	212	if( len32 == 1 ) /* 64bits ? */
	213	{
	214	bool b = read64(&cur, &cur_size, &len64);
	215	assert( b );
	216	len64 -= 8;
	217	}
	218	if( marker == JP2C )
	219	{
	220	const size_t start = cur - stream;
	221	if( !len64 )
	222	{
	223	len64 = (size_t)(file_size - start + 8);
	224	}
	225	assert( len64 >= 8 );
	226	return parsej2k_imp( cur, len64 - 8, lossless );
	227	}
	228	const size_t lenmarker = len64 - 8;
	229	cur += lenmarker;
	230	}
	231
	232	return false;
	233	}
	234
38	235
39	236	/**
40	237	sample error callback expecting a FILE* client object

93	290
94	291	void gdcm_error_callback(const char* msg, void* f)
95	292	{
	293	#if 0
96	294	if( strcmp( msg, "Cannot read data with no size known, giving up\n" ) == 0 )
97	295	{
98	296	OPJ_UINT32 s = (OPJ_UINT32)f;
99	297	s[1] = s[0];
100	298	gdcmWarningMacro( "Recovering from odd J2K file" );
101		}
102		// else
103		// {
104		// fprintf( stderr, msg );
105		// }
106		}
107
108
109		OPJ_UINT32 opj_read_from_memory(void * p_buffer, OPJ_UINT32 p_nb_bytes, myfile* p_file)
	299	assert(0);
	300	}
	301	else
	302	#endif
	303	{
	304	fprintf( stderr, msg );
	305	}
	306	}
	307
	308
	309	OPJ_SIZE_T opj_read_from_memory(void * p_buffer, OPJ_SIZE_T p_nb_bytes, myfile* p_file)
110	310	{
111	311	//OPJ_UINT32 l_nb_read = fread(p_buffer,1,p_nb_bytes,p_file);
112		OPJ_UINT32 l_nb_read;
113		if( p_file->cur + p_nb_bytes < p_file->mem + p_file->len )
	312	OPJ_SIZE_T l_nb_read;
	313	if( p_file->cur + p_nb_bytes <= p_file->mem + p_file->len )
114	314	{
115	315	l_nb_read = 1*p_nb_bytes;
116	316	}
117	317	else
118	318	{
119		l_nb_read = (OPJ_UINT32)(p_file->mem + p_file->len - p_file->cur);
	319	l_nb_read = (OPJ_SIZE_T)(p_file->mem + p_file->len - p_file->cur);
120	320	assert( l_nb_read < p_nb_bytes );
121	321	}
122	322	memcpy(p_buffer,p_file->cur,l_nb_read);
123	323	p_file->cur += l_nb_read;
124	324	assert( p_file->cur <= p_file->mem + p_file->len );
125	325	//std::cout << "l_nb_read: " << l_nb_read << std::endl;
126		return l_nb_read ? l_nb_read : ((OPJ_UINT32)-1);
127		}
128
129		OPJ_UINT32 opj_write_from_memory (void * p_buffer, OPJ_UINT32 p_nb_bytes, myfile* p_file)
	326	return l_nb_read ? l_nb_read : ((OPJ_SIZE_T)-1);
	327	}
	328
	329	OPJ_SIZE_T opj_write_from_memory (void * p_buffer, OPJ_SIZE_T p_nb_bytes, myfile* p_file)
130	330	{
131	331	//return fwrite(p_buffer,1,p_nb_bytes,p_file);
132		OPJ_UINT32 l_nb_write;
	332	OPJ_SIZE_T l_nb_write;
133	333	//if( p_file->cur + p_nb_bytes < p_file->mem + p_file->len )
134	334	// {
135	335	l_nb_write = 1*p_nb_bytes;

147	347	//return p_nb_bytes;
148	348	}
149	349
150		OPJ_SIZE_T opj_skip_from_memory (OPJ_SIZE_T p_nb_bytes, myfile * p_file)
	350	OPJ_OFF_T opj_skip_from_memory (OPJ_OFF_T p_nb_bytes, myfile * p_file)
151	351	{
152	352	//if (fseek(p_user_data,p_nb_bytes,SEEK_CUR))
153	353	// {
154	354	// return -1;
155	355	// }
156		if( p_file->cur + p_nb_bytes < p_file->mem + p_file->len )
	356	if( p_file->cur + p_nb_bytes <= p_file->mem + p_file->len )
157	357	{
158	358	p_file->cur += p_nb_bytes;
159	359	return p_nb_bytes;
160	360	}
161	361
162	362	p_file->cur = p_file->mem + p_file->len;
163		return (OPJ_SIZE_T)-1;
164		}
165
166		bool opj_seek_from_memory (OPJ_SIZE_T p_nb_bytes, myfile * p_file)
	363	return -1;
	364	}
	365
	366	OPJ_BOOL opj_seek_from_memory (OPJ_OFF_T p_nb_bytes, myfile * p_file)
167	367	{
168	368	//if (fseek(p_user_data,p_nb_bytes,SEEK_SET))
169	369	// {
170	370	// return false;
171	371	// }
172	372	//return true;
173		if( p_file->cur + p_nb_bytes < p_file->mem + p_file->len )
174		{
175		p_file->cur += p_nb_bytes;
176		return true;
177		}
	373	if( p_nb_bytes <= p_file->len )
	374	{
	375	p_file->cur = p_file->mem + p_nb_bytes;
	376	return OPJ_TRUE;
	377	}
	378
178	379	p_file->cur = p_file->mem + p_file->len;
179		return false;
180		}
181
182		opj_stream_t* OPJ_CALLCONV opj_stream_create_memory_stream (myfile* p_mem,OPJ_UINT32 p_size,bool p_is_read_stream)
	380	return OPJ_FALSE;
	381	}
	382
	383	opj_stream_t* OPJ_CALLCONV opj_stream_create_memory_stream (myfile* p_mem,OPJ_SIZE_T p_size,bool p_is_read_stream)
183	384	{
184	385	opj_stream_t* l_stream = 00;
185	386	if

198	399	opj_stream_set_write_function(l_stream, (opj_stream_write_fn) opj_write_from_memory);
199	400	opj_stream_set_skip_function(l_stream, (opj_stream_skip_fn) opj_skip_from_memory);
200	401	opj_stream_set_seek_function(l_stream, (opj_stream_seek_fn) opj_seek_from_memory);
	402	opj_stream_set_user_data_length(l_stream, p_mem->len /* p_size/); / important to avoid an assert() */
201	403	return l_stream;
202	404	}
203	405

537	739	s[1] = 0;
538	740	opj_set_error_handler(dinfo, gdcm_error_callback, s);
539	741
540		#ifdef OPJ_J2K_STREAM_CHUNK_SIZE
541	742	cio = opj_stream_create_memory_stream(fsrc,OPJ_J2K_STREAM_CHUNK_SIZE, true);
542		#else
543		cio = opj_stream_create_memory_stream(fsrc,J2K_STREAM_CHUNK_SIZE, true);
544		#endif
545	743
546	744	/* setup the decoder decoding parameters using user parameters */
547		opj_setup_decoder(dinfo, &parameters);
548	745	bool bResult;
	746	bResult = opj_setup_decoder(dinfo, &parameters);
	747	assert( bResult );
549	748	OPJ_INT32 l_tile_x0,l_tile_y0;
550	749	OPJ_UINT32 l_tile_width,l_tile_height,l_nb_tiles_x,l_nb_tiles_y;
551	750	#if 0

567	766	#endif
568	767	assert( bResult );
569	768
570		#if OPENJPEG_MAJOR_VERSION == 1
571		#else
572	769	#if 0
573		// needs to be before call to opj_decode...
574		reversible = opj_get_reversible(dinfo, &parameters );
575		assert( reversible == 0 \|\| reversible == 1 );
576		#else
577		reversible = 0;
578		#endif
	770	/* Optional if you want decode the entire image */
	771	opj_set_decode_area(dinfo, image, (OPJ_INT32)parameters.DA_x0,
	772	(OPJ_INT32)parameters.DA_y0, (OPJ_INT32)parameters.DA_x1, (OPJ_INT32)parameters.DA_y1);
579	773	#endif
580	774
581	775	bResult = opj_decode(dinfo, cio,image);

631	825	gdcmErrorMacro( "Impossible happen" );
632	826	return std::make_pair<char*,size_t>(0,0);
633	827	}
	828	#else
	829	bool b = false;
	830	bool lossless;
	831	if( parameters.decod_format == JP2_CFMT )
	832	b = parsejp2_imp( dummy_buffer, buf_size, &lossless);
	833	else if( parameters.decod_format == J2K_CFMT )
	834	b = parsej2k_imp( dummy_buffer, buf_size, &lossless);
	835
	836	reversible = 0;
	837	if( b )
	838	reversible = lossless;
634	839	#endif // OPENJPEG_MAJOR_VERSION == 1
635	840	LossyFlag = !reversible;
636	841

980	1185	}
981	1186
982	1187	if(parameters.cp_comment == NULL) {
983		const char comment[] = "Created by GDCM/OpenJPEG version 2.0";
	1188	#if OPENJPEG_MAJOR_VERSION == 1
	1189	const char comment[] = "Created by GDCM/OpenJPEG version 1.4.0";
984	1190	parameters.cp_comment = (char*)malloc(strlen(comment) + 1);
985	1191	strcpy(parameters.cp_comment, comment);
	1192	#else
	1193	const char comment[] = "Created by GDCM/OpenJPEG version %s";
	1194	const char * vers = opj_version();
	1195	parameters.cp_comment = (char*)malloc(strlen(comment) + 10);
	1196	snprintf( parameters.cp_comment, strlen(comment) + 10, comment, vers );
	1197	#endif
986	1198	/* no need to delete parameters.cp_comment on exit */
987	1199	//delete_comment = false;
988	1200	}

1064	1276	myfile *fsrc = &mysrc;
1065	1277	char *buffer_j2k = new char[inputlength]; // overallocated
1066	1278	fsrc->mem = fsrc->cur = buffer_j2k;
1067		fsrc->len = 0;
	1279	fsrc->len = 0; //inputlength;
1068	1280
1069	1281	/* open a byte stream for writing */
1070	1282	/* allocate memory for all tiles */

1362	1574	// FIXME
1363	1575	assert( mct == 0 \|\| mct == 1 );
1364	1576	#else
	1577	bool b = false;
	1578	bool lossless;
	1579	if( parameters.decod_format == JP2_CFMT )
	1580	b = parsejp2_imp( dummy_buffer, buf_size, &lossless);
	1581	else if( parameters.decod_format == J2K_CFMT )
	1582	b = parsej2k_imp( dummy_buffer, buf_size, &lossless);
	1583
1365	1584	reversible = 0;
	1585	if( b )
	1586	reversible = lossless;
1366	1587	#endif
1367	1588	#endif // OPENJPEG_MAJOR_VERSION == 1
1368	1589	LossyFlag = !reversible;

+9

-3

Source/MediaStorageAndFileFormat/gdcmJPEGBITSCodec.cxx less more

550	550	\|\| cinfo.Y_density != 1
551	551	)
552	552	{
553		gdcmErrorMacro( "Pixel Density from JFIF Marker is not supported (for now)" );
	553	gdcmWarningMacro( "Pixel Density from JFIF Marker is not supported (for now)" );
554	554	//return false;
555	555	}
556	556

792	792	if( cinfo.image_width != dims[0]
793	793	\|\| cinfo.image_height != dims[1] )
794	794	{
795		gdcmErrorMacro( "Unhandled: dimension mismatch. JPEG is " <<
	795	gdcmWarningMacro( "dimension mismatch. JPEG is " <<
796	796	cinfo.image_width << "," << cinfo.image_height << " while DICOM " << dims[0] <<
797		"," << dims[1] ); // FIXME is this ok by standard ?
	797	"," << dims[1] );
	798	//this->Dimensions[0] = cinfo.image_width;
	799	//this->Dimensions[1] = cinfo.image_height;
	800	/*
	801	* Long story short, the real issue is that class such as ImageRegionReader expect to read the
	802	* image information without ever touching the JPEG codestream...
	803	*/
798	804	return false;
799	805	}
800	806	assert( cinfo.image_width == dims[0] );

+1

-1

Source/MediaStorageAndFileFormat/gdcmOverlay.cxx less more

261	261	//assert( Internal->BitPosition >= 12 );
262	262	if( ds.FindDataElement( Tag(0x7fe0,0x0010) ) )
263	263	{
264		gdcmErrorMacro("Could not find Pixel Data. Cannot extract Overlay." );
	264	gdcmWarningMacro("Could not find Pixel Data. Cannot extract Overlay." );
265	265	return false;
266	266	}
267	267	const DataElement &pixeldata = ds.GetDataElement( Tag(0x7fe0,0x0010) );

+36

-16

Source/MediaStorageAndFileFormat/gdcmPixmapWriter.cxx less more

572	572	}
573	573	else
574	574	{
575		assert( ds.FindDataElement( at1.GetTag() ) );
576		//assert( ds.FindDataElement( at3.GetTag() ) );
577		at1.Set( ds );
578		assert( atoi(at1.GetValue().c_str()) == 1 );
	575	if( ds.FindDataElement( at1.GetTag() ) ) {
	576	//assert( ds.FindDataElement( at3.GetTag() ) );
	577	at1.Set( ds );
	578	if( atoi(at1.GetValue().c_str()) != 1 ) {
	579	gdcmWarningMacro( "Invalid value for LossyImageCompression" );
	580	}
	581	} else {
	582	gdcmWarningMacro( "Missing attribute for LossyImageCompression" );
	583	}
579	584	}
580	585	}
581	586

756	761	}
757	762
758	763	FileMetaInformation &fmi = file.GetHeader();
759		fmi.Clear();
760		//assert( ts == TransferSyntax::ImplicitVRLittleEndian );
761		{
762		const char *tsuid = TransferSyntax::GetTSString( ts );
763		DataElement de( Tag(0x0002,0x0010) );
764		VL::Type strlenTSUID = (VL::Type)strlen(tsuid);
765		de.SetByteValue( tsuid, strlenTSUID );
766		de.SetVR( Attribute<0x0002, 0x0010>::GetVR() );
767		fmi.Replace( de );
768		fmi.SetDataSetTransferSyntax(ts);
769		}
770		fmi.FillFromDataSet( ds );
	764	if( GetCheckFileMetaInformation() )
	765	{
	766	fmi.Clear();
	767	//assert( ts == TransferSyntax::ImplicitVRLittleEndian );
	768	{
	769	const char *tsuid = TransferSyntax::GetTSString( ts );
	770	DataElement de( Tag(0x0002,0x0010) );
	771	VL::Type strlenTSUID = (VL::Type)strlen(tsuid);
	772	de.SetByteValue( tsuid, strlenTSUID );
	773	de.SetVR( Attribute<0x0002, 0x0010>::GetVR() );
	774	fmi.Replace( de );
	775	fmi.SetDataSetTransferSyntax(ts);
	776	}
	777	fmi.FillFromDataSet( ds );
	778	}
	779	else
	780	{
	781	Attribute<0x0002,0x0010> at;
	782	at.SetFromDataSet( fmi );
	783	const char *tsuid = TransferSyntax::GetTSString( ts );
	784	UIComp tsui = at.GetValue();
	785	if( tsui != tsuid )
	786	{
	787	gdcmErrorMacro( "Incompatible TransferSyntax." );
	788	return false;
	789	}
	790	}
771	791
772	792
773	793	return true;

+9

-0

Testing/Source/Common/Cxx/TestMD5.cxx less more

228	228	{ "027faefc8031768dad1afc100f7aee27" , "SC16BitsAllocated_8BitsStoredJ2K.dcm" },
229	229	{ "f7c4fbb93b0347101e21e36f223b4d46" , "SC16BitsAllocated_8BitsStoredJPEG.dcm" },
230	230	{ "af580e6202a240005a5a05adc5c691f2" , "SIEMENS_SYNGO-12-MONO2-LUTWrongLength512.dcm" },
	231	{ "236713383dd9d315415f3a5957707ad1" , "JPEGNote_empty.dcm" },
	232	{ "5b6f7f59dbefd679aa29e9082f100ff5" , "JPEGLS_CharLS_10742.dcm" },
	233	{ "66fe7d517941802364e7ad8dee7149e7" , "JPEGLosslessYBR_FULL_422.dcm" },
	234	{ "dcb4b29b7e0f0da441ab3e5cdcb506b4" , "JPEGNote_missing.dcm" },
	235	{ "2c30e74ee3db1895027932bb0566f54e" , "JPEGNote_bogus.dcm" },
	236	{ "c71a2cf95325395264c4dc6e15a898bd" , "RLEDebianBug816607Orig.dcm" },
	237	{ "e49c403278663d9739014ad1d57c276f" , "IllegalGroup2ImplicitTS.dcm" },
	238	{ "299df0175ea4d3ab1f02651f88ffe9f3" , "JPEG_LS_InvalidEscapeSequence_COM_padding.dcm" },
	239	{ "9add5fd3c83cc0946633e792f448f732" , "LengthOfItemLarger.dcm" },
231	240
232	241	{ NULL, NULL}
233	242	};

+6

-0

Testing/Source/Common/Cxx/TestSHA1.cxx less more

227	227	{ "d17a34f8ae066048442ab5b110d43c412472ea7e" , "SC16BitsAllocated_8BitsStoredJ2K.dcm" },
228	228	{ "71517fce6c32625f1051b72085cfceeee58bd164" , "SC16BitsAllocated_8BitsStoredJPEG.dcm" },
229	229	{ "0d19e4a98265afc3c782db02bc64bd32124ed2f6" , "SIEMENS_SYNGO-12-MONO2-LUTWrongLength512.dcm" },
	230	{ "5cb6c554e80b552ea68cad05409dce4fe92b6dd7" , "IllegalGroup2ImplicitTS.dcm" },
	231	{ "031f8cb2cbbe7b5e524b1f79aef6674a66e7f390" , "JPEGLosslessYBR_FULL_422.dcm" },
	232	{ "4710e6cfd86c0d349c61b60ae69a684b246db3ff" , "JPEGNote_bogus.dcm" },
	233	{ "197e47b5afeeeb75eccafe04e5a1bb0af1a7957a" , "JPEGNote_empty.dcm" },
	234	{ "08828e913a7a1ebbc0129c42974b64ce702814b6" , "JPEGNote_missing.dcm" },
	235	{ "99c169688190a66100b61319eaeefb3db1936125" , "RLEDebianBug816607Orig.dcm" },
230	236
231	237	{ NULL, NULL}
232	238	};

+6

-0

Testing/Source/Data/CMakeLists.txt less more

63	63	MR-MONO2-12-angio-an1.acr
64	64	# Openjpeg / Part 2:
65	65	lena512_rot90.j2k.dcm
	66	# Remove this one for now:
	67	LengthOfItemLarger.dcm
	68	# Need CharLS 1.1
	69	JPEG_LS_InvalidEscapeSequence_COM_padding.dcm
	70	# something wrong with OPJ 1.4
	71	JPEGLS_CharLS_10742.dcm
66	72	)
67	73	if(NOT GDCM_USE_PVRG)
68	74	set(BLACK_LIST_READER

+10

-0

Testing/Source/Data/gdcmMD5DataImages.cxx less more

688	688
689	689	{ "4a5d8549791432b29948dd8ff63e2534" , "SIEMENS_SYNGO-12-MONO2-LUTWrongLength512.dcm" },
690	690
	691	{ "2c8630ae1bff925b258d98e742dfc632" , "JPEGLS_CharLS_10742.dcm" },
	692	{ "f666a95dde9ddfdec0cf9574a7985ae3" , "IllegalGroup2ImplicitTS.dcm" },
	693
	694	{ "b85686dd3169b99725149abb00181254" , "RLEDebianBug816607Orig.dcm" },
	695	{ "464960d948dff0ded72b0380080f18a3" , "JPEGNote_empty.dcm" },
	696	{ "cdfb5dd0c999d88badeb00a16f96554f" , "JPEGLosslessYBR_FULL_422.dcm" },
	697	{ "464960d948dff0ded72b0380080f18a3" , "JPEGNote_missing.dcm" },
	698	{ "161e9fd986ea87adf2596e8e16641f11" , "JPEGNote_bogus.dcm" },
	699
	700
691	701
692	702	/* Stopping condition */
693	703	{ 0 ,0 }

+9

-0

Testing/Source/Data/gdcmMediaStorageDataFiles.cxx less more

238	238	{ "SC16BitsAllocated_8BitsStoredJPEG.dcm" , "1.2.840.10008.5.1.4.1.1.7" },
239	239	{ "SC16BitsAllocated_8BitsStoredJ2K.dcm" , "1.2.840.10008.5.1.4.1.1.7" },
240	240	{ "SIEMENS_SYNGO-12-MONO2-LUTWrongLength512.dcm" , "1.2.840.10008.5.1.4.1.1.4" },
	241	{ "JPEGNote_empty.dcm" , "1.2.840.10008.5.1.4.1.1.7" },
	242	{ "JPEGLS_CharLS_10742.dcm" , "1.2.840.10008.5.1.4.1.1.7" },
	243	{ "JPEGLosslessYBR_FULL_422.dcm" , "1.2.840.10008.5.1.4.1.1.7" },
	244	{ "JPEGNote_missing.dcm" , "1.2.840.10008.5.1.4.1.1.7" },
	245	{ "JPEGNote_bogus.dcm" , "1.2.840.10008.5.1.4.1.1.7" },
	246	{ "RLEDebianBug816607Orig.dcm" , "1.2.840.10008.5.1.4.1.1.7" },
	247	{ "IllegalGroup2ImplicitTS.dcm" , "1.2.840.10008.5.1.4.1.1.1" },
	248	{ "JPEG_LS_InvalidEscapeSequence_COM_padding.dcm" , "1.2.840.10008.5.1.4.1.1.7" },
	249	{ "LengthOfItemLarger.dcm" , "1.2.840.10008.5.1.4.1.1.4" },
241	250
242	251	/* Stopping condition */
243	252	{ 0 ,0 }

+9

-0

Testing/Source/Data/gdcmSelectedPrivateGroupOffsetDataFiles.cxx less more

220	220	{ "PHILIPS_Gyroscan-12-Jpeg_Extended_Process_2_4.dcm",1314},
221	221	{ "SIEMENS_SYNGO-12-MONO2-LUTWrongLength512.dcm", 1596 },
222	222	{ "00191113.dcm",536 },
	223	{ "JPEGNote_empty.dcm", 482 },
	224	{ "JPEGLS_CharLS_10742.dcm", 532 },
	225	{ "JPEGLosslessYBR_FULL_422.dcm", 534 },
	226	{ "JPEGNote_missing.dcm", 406 },
	227	{ "JPEGNote_bogus.dcm", 482 },
	228	{ "RLEDebianBug816607Orig.dcm", 534 },
	229	{ "IllegalGroup2ImplicitTS.dcm", 1088 },
	230	{ "JPEG_LS_InvalidEscapeSequence_COM_padding.dcm", 534 },
	231	{ "LengthOfItemLarger.dcm", 1044 },
223	232	{ "dicomdir_With_embedded_icons",7125212 },
224	233	{ "dicomdir_Pms_WithVisit_WithPrivate_WithStudyComponents",37218 },
225	234	{ "dicomdir_Acusson_WithPrivate_WithSR",3826 },

+9

-0

Testing/Source/Data/gdcmSelectedTagsOffsetDataFiles.cxx less more

222	222	{ "ELSCINT1_PMSCT_RLE1_priv.dcm",298002 },
223	223	{ "00191113.dcm",922 },
224	224	{ "SIEMENS_SYNGO-12-MONO2-LUTWrongLength512.dcm", 48714 },
	225	{ "JPEGNote_empty.dcm", 704 },
	226	{ "JPEGLS_CharLS_10742.dcm", 748 },
	227	{ "JPEGLosslessYBR_FULL_422.dcm", 802 },
	228	{ "JPEGNote_missing.dcm", 596 },
	229	{ "JPEGNote_bogus.dcm", 722 },
	230	{ "RLEDebianBug816607Orig.dcm", 768 },
	231	{ "IllegalGroup2ImplicitTS.dcm", 2264 },
	232	{ "JPEG_LS_InvalidEscapeSequence_COM_padding.dcm", 752 },
	233	{ "LengthOfItemLarger.dcm", 12748 },
225	234	{ "dicomdir_Acusson_WithPrivate_WithSR",3826 },
226	235	{ "dicomdir_Pms_WithVisit_WithPrivate_WithStudyComponents",37218 },
227	236	{ "dicomdir_Pms_With_heavy_embedded_sequence",3003414 },

+9

-1

Testing/Source/Data/gdcmStreamOffsetDataFiles.cxx less more

227	227	{ "SC16BitsAllocated_8BitsStoredJ2K.dcm", 764 },
228	228	{ "SC16BitsAllocated_8BitsStoredJPEG.dcm", 958 },
229	229	{ "SIEMENS_SYNGO-12-MONO2-LUTWrongLength512.dcm", 48726 },
230
	230	{ "JPEGNote_empty.dcm", 716 },
	231	{ "JPEGLS_CharLS_10742.dcm", 760 },
	232	{ "JPEGLosslessYBR_FULL_422.dcm", 814 },
	233	{ "JPEGNote_missing.dcm", 608 },
	234	{ "JPEGNote_bogus.dcm", 734 },
	235	{ "RLEDebianBug816607Orig.dcm", 780 },
	236	{ "IllegalGroup2ImplicitTS.dcm", 2272 },
	237	{ "JPEG_LS_InvalidEscapeSequence_COM_padding.dcm", 764 },
	238	{ "LengthOfItemLarger.dcm", 12748 },
231	239
232	240	/* Stopping condition */
233	241	{ 0 ,0 },

+10

-10

Testing/Source/DataStructureAndEncodingDefinition/Cxx/TestReaderCanRead.cxx less more

40	40	ret = 0;
41	41	}
42	42	// This is not an error if you are in the black list:
43		if( strcmp(name, "BuggedDicomWorksImage_Hopeless.dcm" ) != 0
44		\|\| strcmp(name, "Philips_Wrong_Terminator_XX_0277" ) != 0
45		\|\| strcmp(name, "DICOMDIR_noPATIENT_noSTUDY" ) != 0
46		\|\| strcmp(name, "JpegLosslessMultiframePapyrus.pap" ) != 0
47		\|\| strcmp(name, "Fish-1.img" ) != 0
48		\|\| strcmp(name, "NM_FromJulius_Caesar.dcm" ) != 0
49		\|\| strcmp(name, "Siemens-leonardo-bugged.dcm" ) != 0
50		\|\| strcmp(name, "illegal_UN_stands_for_OB.dcm" ) != 0
51		\|\| strcmp(name, "MR_PHILIPS_LargePreamble.dcm" ) != 0
52		\|\| strcmp(name, "illegal_UN_stands_for_OB.dcm.secu" ) != 0 )
	43	if( strcmp(name, "BuggedDicomWorksImage_Hopeless.dcm" ) == 0
	44	\|\| strcmp(name, "Philips_Wrong_Terminator_XX_0277" ) == 0
	45	\|\| strcmp(name, "DICOMDIR_noPATIENT_noSTUDY" ) == 0
	46	\|\| strcmp(name, "JpegLosslessMultiframePapyrus.pap" ) == 0
	47	\|\| strcmp(name, "Fish-1.img" ) == 0
	48	\|\| strcmp(name, "NM_FromJulius_Caesar.dcm" ) == 0
	49	\|\| strcmp(name, "Siemens-leonardo-bugged.dcm" ) == 0
	50	\|\| strcmp(name, "illegal_UN_stands_for_OB.dcm" ) == 0
	51	\|\| strcmp(name, "MR_PHILIPS_LargePreamble.dcm" ) == 0
	52	\|\| strcmp(name, "illegal_UN_stands_for_OB.dcm.secu" ) == 0 )
53	53	{
54	54	ret = 0;
55	55	}

+1

-1

Testing/Source/DataStructureAndEncodingDefinition/Java/CMakeLists.txt less more

3	3	)
4	4
5	5	# Do not change anything after here:
6		find_package(Java REQUIRED) # javac, jar
	6	find_package(Java ${GDCM_DEFAULT_JAVA_VERSION} REQUIRED) # javac, jar
7	7	find_package(JNI REQUIRED)
8	8	include_directories(
9	9	${JNI_INCLUDE_PATH}

+10

-1

Testing/Source/MediaStorageAndFileFormat/Cxx/TestFileStreamer4.cxx less more

44	44	{
45	45	checktemplate = true;
46	46	}
	47	if( strcmp(name, "JPEGNote_empty.dcm" ) == 0
	48	\|\| strcmp(name, "JPEGNote_missing.dcm" ) == 0 )
	49	{
	50	// cannot read dims from DICOM header...
	51	return 0;
	52	}
47	53
48	54	gdcm::ImageRegionReader irr;
49	55	irr.SetFileName( filename );

83	89
84	90	const gdcm::Tag pixeldata(0x7fe0,0x0010);
85	91
86		bool b;
	92	bool b = true;
	93	if( strcmp(name, "libido1.0-vol.acr" ) != 0 ) // use Planes instead of Number of Frames
	94	{
87	95	b = fs.CheckDataElement( pixeldata ); // will be checking file size
	96	}
88	97	if( !b )
89	98	{
90	99	std::cerr << "Failed to CheckDataElement: " << outfilename << std::endl;

+7

-1

Testing/Source/MediaStorageAndFileFormat/Cxx/TestImageRegionReader1.cxx less more

29	29	// attribute is (b500,b700) which make ReadUpToTag(7fe0,0010) fails...
30	30	if( strcmp(fn.GetName(), "DMCPACS_ExplicitImplicit_BogusIOP.dcm" ) == 0
31	31	\|\| strcmp(fn.GetName(), "SC16BitsAllocated_8BitsStoredJ2K.dcm" ) == 0 // mismatch pixel format in JPEG 200 vs DICOM
32		\|\| strcmp(fn.GetName(), "PHILIPS_Gyroscan-12-Jpeg_Extended_Process_2_4.dcm" ) == 0 ) // bogus JPEG cannot be streamed
	32	\|\| strcmp(fn.GetName(), "PHILIPS_Gyroscan-12-Jpeg_Extended_Process_2_4.dcm" ) == 0 // bogus JPEG cannot be streamed
	33
	34	// FIXME: we should be able to handle those at some point:
	35	\|\| strcmp(fn.GetName(), "JPEGNote_empty.dcm" ) == 0
	36	\|\| strcmp(fn.GetName(), "JPEGNote_missing.dcm" ) == 0
	37	\|\| strcmp(fn.GetName(), "JPEGNote_bogus.dcm" ) == 0
	38	)
33	39	{
34	40	std::cerr << "Skipping impossible file: " << filename << std::endl;
35	41	return 0;

+7

-1

Testing/Source/MediaStorageAndFileFormat/Cxx/TestImageRegionReader2.cxx less more

29	29	// attribute is (b500,b700) which make ReadUpToTag(7fe0,0010) fails...
30	30	if( strcmp(fn.GetName(), "DMCPACS_ExplicitImplicit_BogusIOP.dcm" ) == 0
31	31	\|\| strcmp(fn.GetName(), "SC16BitsAllocated_8BitsStoredJ2K.dcm" ) == 0 // mismatch pixel format in JPEG 200 vs DICOM
32		\|\| strcmp(fn.GetName(), "PHILIPS_Gyroscan-12-Jpeg_Extended_Process_2_4.dcm" ) == 0 ) // bogus JPEG cannot be streamed
	32	\|\| strcmp(fn.GetName(), "PHILIPS_Gyroscan-12-Jpeg_Extended_Process_2_4.dcm" ) == 0 // bogus JPEG cannot be streamed
	33
	34	// FIXME: we should be able to handle those at some point:
	35	\|\| strcmp(fn.GetName(), "JPEGNote_empty.dcm" ) == 0
	36	\|\| strcmp(fn.GetName(), "JPEGNote_missing.dcm" ) == 0
	37	\|\| strcmp(fn.GetName(), "JPEGNote_bogus.dcm" ) == 0
	38	)
33	39	{
34	40	std::cerr << "Skipping impossible file: " << filename << std::endl;
35	41	return 0;

+7

-1

Testing/Source/MediaStorageAndFileFormat/Cxx/TestImageRegionReader3.cxx less more

31	31	// attribute is (b500,b700) which make ReadUpToTag(7fe0,0010) fails...
32	32	if( strcmp(fn.GetName(), "DMCPACS_ExplicitImplicit_BogusIOP.dcm" ) == 0
33	33	\|\| strcmp(fn.GetName(), "SC16BitsAllocated_8BitsStoredJ2K.dcm" ) == 0 // mismatch pixel format in JPEG 200 vs DICOM
34		\|\| strcmp(fn.GetName(), "PHILIPS_Gyroscan-12-Jpeg_Extended_Process_2_4.dcm" ) == 0 ) // bogus JPEG cannot be streamed
	34	\|\| strcmp(fn.GetName(), "PHILIPS_Gyroscan-12-Jpeg_Extended_Process_2_4.dcm" ) == 0 // bogus JPEG cannot be streamed
	35
	36	// FIXME: we should be able to handle those at some point:
	37	\|\| strcmp(fn.GetName(), "JPEGNote_empty.dcm" ) == 0
	38	\|\| strcmp(fn.GetName(), "JPEGNote_missing.dcm" ) == 0
	39	\|\| strcmp(fn.GetName(), "JPEGNote_bogus.dcm" ) == 0
	40	)
35	41	{
36	42	std::cerr << "Skipping impossible file: " << filename << std::endl;
37	43	return 0;

+28

-20

Testing/Source/MediaStorageAndFileFormat/Cxx/TestPrinter1.cxx less more

23	23	// GetValueAsSQ to solve that issue.
24	24	static const char * const printmd5[][2] = {
25	25	{ "a19bffac370df32acbf6b4991d1cbafe" , "00191113.dcm" } ,
26		{ "2e7d47d86dc6b541fccfa928c2ee05e8" , "012345.002.050.dcm" } ,
	26	{ "a5b2cb7d27bf0565296ae0391c07dd54" , "012345.002.050.dcm" } ,
27	27	{ "94f8c6ab090bdc11e61625bfc2dd39b7" , "05115014-mr-siemens-avanto-syngo-with-palette-icone.dcm" } ,
28	28	{ "20c11831c616eb121a405cd73de5cba2" , "05148044-mr-siemens-avanto-syngo.dcm" } ,
29	29	{ "ec10dcbf1b13ace8a6c0cc5b24c6c870" , "3E768EB7.dcm" } ,
30	30	{ "fde1da68a1707dcc687ddffd57e6b3c3" , "ACUSON-24-YBR_FULL-RLE-b.dcm" } ,
31	31	{ "a27c6628d6379783a3be223481d5cba4" , "ACUSON-24-YBR_FULL-RLE.dcm" } ,
32	32	{ "9f3aa114b955a812942f815b6b456eaf" , "ALOKA_SSD-8-MONO2-RLE-SQ.dcm" } ,
33		{ "8b9bca2a22732c6165eba2fd3114d323" , "AMIInvalidPrivateDefinedLengthSQasUN.dcm" } ,
34		{ "0df5a880b1973062f1e3850c27ee9568" , "BugGDCM2_UndefItemWrongVL.dcm" } ,
	33	{ "6c18a8fdd766660fbb475c05d0611634" , "AMIInvalidPrivateDefinedLengthSQasUN.dcm" } ,
	34	{ "9ddd03e5fd29f92bd02c3d3812b4e93e" , "BugGDCM2_UndefItemWrongVL.dcm" } ,
35	35	{ "6d2af85d2af299c223b684538d42d9e5" , "CR-MONO1-10-chest.dcm" } ,
36	36	{ "820d45cefd528e011921ea129bec9084" , "CT_16b_signed-UsedBits13.dcm" } ,
37	37	{ "fcf2ca019aa3138188edb18552983733" , "CT-MONO2-12-lomb-an2.acr" } ,

54	54	{ "b770b1ca257d7c1c885f69a5a1b58808" , "D_CLUNIE_MR2_JPLL.dcm" } ,
55	55	{ "da74aefef4e8ac49dbe1a4dd3b1dcb26" , "D_CLUNIE_MR2_JPLY.dcm" } ,
56	56	{ "023eb2a9ecbfd3c04bb148ec339865f0" , "D_CLUNIE_MR2_RLE.dcm" } ,
57		{ "dca2414a88e95ef5ed59c088d20021b8" , "D_CLUNIE_MR3_JPLL.dcm" } ,
58		{ "73c16bde7114f03b976009cba63c5f65" , "D_CLUNIE_MR3_JPLY.dcm" } ,
59		{ "d1c358c3f79a5fc5592abe2b4b4a3571" , "D_CLUNIE_MR3_RLE.dcm" } ,
	57	{ "4ac28edcc53e3c5a2b14cee29ac4b350" , "D_CLUNIE_MR3_JPLL.dcm" } ,
	58	{ "1279c4aaacd1a058fc4b101cbfebec54" , "D_CLUNIE_MR3_JPLY.dcm" } ,
	59	{ "d6ca154c96d206995023f7349f6ca861" , "D_CLUNIE_MR3_RLE.dcm" } ,
60	60	{ "1646ec013060ef3f261849db705f80f3" , "D_CLUNIE_MR4_JPLL.dcm" } ,
61	61	{ "fbbfe4caab2179641bd0de5d8ccf79ae" , "D_CLUNIE_MR4_JPLY.dcm" } ,
62	62	{ "fafdb8499580e59c2f6d9047894272ea" , "D_CLUNIE_MR4_RLE.dcm" } ,

99	99	{ "3493bf0e698798529fde6ef488289879" , "ELSCINT1_JP2vsJ2K.dcm" } ,
100	100	{ "8f5581be656bd6f1ab6c9ec94f302284" , "ELSCINT1_LOSSLESS_RICE.dcm" } ,
101	101	{ "54f138a1aa6819ec1560a7ed344cde1a" , "ELSCINT1_PMSCT_RLE1.dcm" } ,
102		{ "ff2965f3ca39bc0795df9850aa25467e" , "ExplicitVRforPublicElementsImplicitVRforShadowElements.dcm" } ,
	102	{ "d576bf8e8b2ca71fd543d29698807e85" , "ExplicitVRforPublicElementsImplicitVRforShadowElements.dcm" } ,
103	103	{ "3199cd21166043d619209d7a2073fb56" , "fffc0000UN.dcm" } ,
104	104	{ "9b426b02521cbc2f3ee25ab383ca835e" , "FUJI-10-MONO1-ACR_NEMA_2.dcm" } ,
105	105	{ "2aba3dacd00a0bc14a06e2d7142b916a" , "gdcm-ACR-LibIDO.acr" } ,

115	115	{ "9e126a24f81534e1cd653f16739a6192" , "GE_DLX-8-MONO2-Multiframe.dcm" } ,
116	116	{ "6b66f8c38fe96db805e7dedd9a997811" , "GE_DLX-8-MONO2-Multiframe-Jpeg_Lossless.dcm" } ,
117	117	{ "61ca6c5115e6f74565f6f2ca06647444" , "GE_DLX-8-MONO2-PrivateSyntax.dcm" } ,
118		{ "459247061fb21a9cbf0bbb359a0af160" , "GE_GENESIS-16-MONO2-Uncompressed-UnusualVR.dcm" } ,
	118	{ "7920bf7f1269ba54dd8d0e0d375dc4b9" , "GE_GENESIS-16-MONO2-Uncompressed-UnusualVR.dcm" } ,
119	119	{ "8d398fce426d3a248d8c3f7582e3751d" , "GE_GENESIS-16-MONO2-WrongLengthItem.dcm" } ,
120	120	{ "bb5d500a0391a399b035968496b6fd5d" , "GE_LOGIQBook-8-RGB-HugePreview.dcm" } ,
121		{ "7aad71b9c70060c0a39a73b2f489d68f" , "GE_MR_0025xx1bProtocolDataBlock.dcm" } ,
	121	{ "1ad963ca1e91932bb1ac58f3dddd981f" , "GE_MR_0025xx1bProtocolDataBlock.dcm" } ,
122	122	{ "d5efa34d8091e1ad04683eefb41f33c7" , "GE_RHAPSODE-16-MONO2-JPEG-Fragments.dcm" } ,
123	123	{ "d41d8cd98f00b204e9800998ecf8427e" , "IM-0001-0066.dcm" } ,
124	124	{ "cd085d783924d8a7fa2270ff40c6dc3e" , "ITK_GDCM124_MultiframeSecondaryCaptureInvalid.dcm" } ,

149	149	{ "497d6ea45b8f3f7f6a3bf8125dcc43b1" , "MR16BitsAllocated_8BitsStored.dcm" } ,
150	150	{ "5b23ccf10ad6358b253a7ec185deb2a9" , "MR-Brucker-CineTagging-NonSquarePixels.dcm" } ,
151	151	{ "31246836410a24124acf6bea5a36a942" , "MR_ELSCINT1_00e1_1042_SQ_feff_00e0_Item.dcm" } ,
152		{ "285433f0db3a7aae20a4734644fc959d" , "MR_GE_with_Private_Compressed_Icon_0009_1110.dcm" } ,
	152	{ "7a61574251f8788a11cfe06ddc109bd9" , "MR_GE_with_Private_Compressed_Icon_0009_1110.dcm" } ,
153	153	{ "8419613dfb8d4b190ef8a988f8927bce" , "MR-MONO2-12-an2.acr" } ,
154	154	{ "b4058b67ec1eb3d3d3acde27d51eb24a" , "MR-MONO2-12-angio-an1.acr" } ,
155	155	{ "f782f6ea25928310bd69c3ca5c6a97d2" , "MR-MONO2-12-shoulder.dcm" } ,
156	156	{ "7f6bccb00b34a7d277eacaffd2bb0362" , "MR-MONO2-16-head.dcm" } ,
157	157	{ "9bd4d79cc59c66b19c21577e12cd6226" , "MR-MONO2-8-16x-heart.dcm" } ,
158	158	{ "cd623ac04602182dc66adb505c516341" , "MR_Philips-Intera_BreaksNOSHADOW.dcm" } ,
159		{ "f295d87a398e0bcd96c5dfa20d96a419" , "MR_Philips_Intera_No_PrivateSequenceImplicitVR.dcm" } ,
160		{ "af3c49db53cfb30aa438e7369dba117b" , "MR_Philips_Intera_PrivateSequenceExplicitVR_in_SQ_2001_e05f_item_wrong_lgt_use_NOSHADOWSEQ.dcm" } ,
161		{ "d7019c1822870140965fa3345b53886c" , "MR_Philips_Intera_PrivateSequenceImplicitVR.dcm" } ,
162		{ "69ccce1a3bb1c481d90a1df109acf3b7" , "MR_Philips_Intera_SwitchIndianess_noLgtSQItem_in_trueLgtSeq.dcm" } ,
	159	{ "ced145431248f1e00e9bdc23b0c61674" , "MR_Philips_Intera_No_PrivateSequenceImplicitVR.dcm" } ,
	160	{ "8eab7fcf9c53d06968dde33f6b3a8918" , "MR_Philips_Intera_PrivateSequenceExplicitVR_in_SQ_2001_e05f_item_wrong_lgt_use_NOSHADOWSEQ.dcm" } ,
	161	{ "3d24233b19788d349f64b7b267723186" , "MR_Philips_Intera_PrivateSequenceImplicitVR.dcm" } ,
	162	{ "1693399bc1edb7cdc494095a27201eab" , "MR_Philips_Intera_SwitchIndianess_noLgtSQItem_in_trueLgtSeq.dcm" } ,
163	163	{ "5797c9dfe94e4a4bccfbf81ab0aaa957" , "MR-SIEMENS-DICOM-WithOverlays.dcm" } ,
164	164	{ "df28467760104edc923d0625a0e2a778" , "MR-SIEMENS-DICOM-WithOverlays-extracted-overlays.dcm" } ,
165	165	{ "bf324a1c91d3a09d9136f54f5910e570" , "MR_SIEMENS_forceLoad29-1010_29-1020.dcm" } ,

170	170	{ "7f4cddc9a88f8c5147b89f769eb1cae7" , "OT-PAL-8-face.dcm" } ,
171	171	{ "5fce2728bd9457d4fc1224a374829e2f" , "PET-cardio-Multiframe-Papyrus.dcm" } ,
172	172	{ "071b840050588d14fde61646e058e1c6" , "PHILIPS_Brilliance_ExtraBytesInOverlay.dcm" } ,
173		{ "244e8beb3151f9a26dd8c0650a4adede" , "PHILIPS_GDCM12xBug2.dcm" } ,
174		{ "3d7cc6eaf1c2f065290c50473bc8001a" , "PHILIPS_GDCM12xBug.dcm" } ,
	173	{ "a7eb66c4f66784ad456d060b7123ea15" , "PHILIPS_GDCM12xBug2.dcm" } ,
	174	{ "48203ef1f45cb1f7f919de53062db5d0" , "PHILIPS_GDCM12xBug.dcm" } ,
175	175	{ "c38ad661c6a14f8bd88b304755e7ba7b" , "PHILIPS_Gyroscan-12-Jpeg_Extended_Process_2_4.dcm" } ,
176	176	{ "e0a690636c608f312ca550908d4b551f" , "PHILIPS_Gyroscan-12-MONO2-Jpeg_Lossless.dcm" } ,
177	177	{ "03d88060c3bd820b96840599c0099470" , "PHILIPS_Gyroscan-8-MONO2-Odd_Sequence.dcm" } ,
178		{ "1caa6b627fa7dc0995efc2a36765055e" , "PHILIPS_Intera-16-MONO2-Uncompress.dcm" } ,
	178	{ "1f198bdb09f5e52dc3f9ad1dfced8a4d" , "PHILIPS_Intera-16-MONO2-Uncompress.dcm" } ,
179	179	{ "4f34474ed72e6a5960fc4691e588f8e0" , "PICKER-16-MONO2-Nested_icon.dcm" } ,
180	180	{ "629da04611e097e2cc532d6fe5e6454d" , "PICKER-16-MONO2-No_DicomV3_Preamble.dcm" } ,
181	181	{ "3aaca1826b4a4deb9e41ebf2af4fa6b2" , "PrivateGEImplicitVRBigEndianTransferSyntax16Bits.dcm" } ,

205	205	{ "cbd59e416dd82dc14df251ea6fccb55b" , "test.acr" } ,
206	206	{ "0c2c475f6d21ae0aeadbf16565dcdbc4" , "TG18-CH-2k-01.dcm" } ,
207	207	{ "e8cc7ed19eedf9bed9ab60683f3dbfa1" , "THERALYS-12-MONO2-Uncompressed-Even_Length_Tag.dcm" } ,
208		{ "463888b21317e5816584541c7243e124" , "TheralysGDCM120Bug.dcm" } ,
	208	{ "aa708d3b15e451c8367e7909257d9346" , "TheralysGDCM120Bug.dcm" } ,
209	209	{ "e8819809884c214fe78ee2b227417e5c" , "TOSHIBA_MRT150-16-MONO2-ACR_NEMA_2.dcm" } ,
210		{ "9fcf7924fef1b48977b8c4b9a84caa87" , "undefined_length_un_vr.dcm" } ,
	210	{ "fafc22cde1c9092cb188982ecee8da9b" , "undefined_length_un_vr.dcm" } ,
211	211	{ "787ca80c8dd1aa619d5f85610862380b" , "US-GE-4AICL142.dcm" } ,
212	212	{ "f1e9c893391e1d458cffa2a1e0904160" , "US-IRAD-NoPreambleStartWith0003.dcm" } ,
213	213	{ "d1d9be67c9d066fabc8e1c4ae124f9a0" , "US-IRAD-NoPreambleStartWith0005.dcm" } ,

220	220	{ "d2cb6962750eb8f92c480e6cc2f4d104" , "GDCMJ2K_TextGBR.dcm" },
221	221	{ "2e039bbc7520f809963e051ff5144ccf" , "UnexpectedSequenceDelimiterInFixedLengthSequence.dcm" },
222	222	{ "0a90894370ba84dbe31acd1290ff9999" , "NM_Kakadu44_SOTmarkerincons.dcm" },
223		{ "bcadb7b0f72d2ea3d4e910b885f07087" , "PhilipsInteraSeqTermInvLen.dcm" },
	223	{ "fdd8a53915712a924ac74c26ec4d1051" , "PhilipsInteraSeqTermInvLen.dcm" },
224	224	{ "2940bd46f097f79012d24f47504c3c8c" , "TOSHIBA_J2K_OpenJPEGv2Regression.dcm" },
225	225	{ "696917fea41e83b9980bad82b609162c" , "TOSHIBA_J2K_SIZ0_PixRep1.dcm" },
226	226	{ "7ef3da46c43e51cfe2eb82e4d23dd623" , "TOSHIBA_J2K_SIZ1_PixRep0.dcm" },

230	230	{ "4be7f56f11ce6090b7139879c4fdc71f" , "SC16BitsAllocated_8BitsStoredJPEG.dcm" },
231	231	{ "1060ff4eb8731d4b2152db83fed2eedd" , "SC16BitsAllocated_8BitsStoredJ2K.dcm" },
232	232	{ "7dc0a8ffffc8fb441dbd4129111eaf8b" , "SIEMENS_SYNGO-12-MONO2-LUTWrongLength512.dcm" },
	233	{ "41d1baead629d878d09d6c1037faf47a" , "JPEGNote_empty.dcm" },
	234	{ "3cb9917c468226c265ef637aac5f4b61" , "JPEGLS_CharLS_10742.dcm" },
	235	{ "8381875d83ce321955a064e40d047dde" , "JPEGLosslessYBR_FULL_422.dcm" },
	236	{ "67f7b36ad6e54889b4a2581baa41afdf" , "JPEGNote_missing.dcm" },
	237	{ "807bf2aef3bc1885217c8a12d2d2bc19" , "JPEGNote_bogus.dcm" },
	238	{ "669cc0e807673ebe57124739a1874f35" , "RLEDebianBug816607Orig.dcm" },
	239	{ "1daa9bb53a8ce090041472f528248686" , "IllegalGroup2ImplicitTS.dcm" },
	240
233	241
234	242	{ 0 ,0 }
235	243	};

+11

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Utilities/Release/README.md less more

	0	GDCM binaries have moved !
	1	--------------------------
	2
	3	They are now automatically uploaded to github:
	4
	5	[github release](https://github.com/malaterre/GDCM/releases)
	6
	7	They are build using travis and appveyor automatically
	8
	9	As a side note the old zip (source) file is not available anymore on sf.net,
	10	please see instead on github.

+3

-0

Utilities/Release/release.sh less more

125	125	# https://sourceforge.net/project/admin/explorer.php?group_id=137895
126	126	# https://sourceforge.net/projects/gdcm/files/gdcm%202.x/#folder-create
127	127
	128	# Update default version:
	129	#https://sourceforge.net/p/forge/documentation/Using%20the%20Release%20API/
	130	exit 1
128	131	rsync -e ssh GDCM-$version-Linux-x86_64.tar.gz "malat,gdcm@frs.sourceforge.net:/home/frs/project/g/gd/gdcm/gdcm\ 2.x/GDCM\ $version"
129	132	check_exit_value $? "rsync did not return properly" \|\| exit 1
130	133	rsync -e ssh GDCM-$version-Linux-x86_64.tar.bz2 "malat,gdcm@frs.sourceforge.net:/home/frs/project/g/gd/gdcm/gdcm\ 2.x/GDCM\ $version"

+3

-2

Utilities/VTK/CMakeLists.txt less more

635	635
636	636	if(GDCM_WRAP_JAVA)
637	637	if(VTK_WRAP_JAVA)
638		find_package(Java 1.5 REQUIRED) # javac, jar
	638	find_package(Java ${GDCM_DEFAULT_JAVA_VERSION} REQUIRED) # javac, jar
639	639	find_package(JNI REQUIRED)
640	640	include_directories(${JNI_INCLUDE_DIRS})
641	641	set(VTK_WRAP_JAVA3_INIT_DIR "${CMAKE_CURRENT_SOURCE_DIR}")

651	651	# http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=533193
652	652	set(GDCM_VTK_JAVA_JAR ${VTK_JAVA_JAR})
653	653	else()
	654	# http://bugs.debian.org/834493
654	655	find_file(VTK_JAVA_JAR NAMES vtk.jar vtk6.jar vtk5.jar
655		PATHS ${vtkWrappingJava_RUNTIME_LIBRARY_DIRS})
	656	PATHS ${vtkWrappingJava_RUNTIME_LIBRARY_DIRS} /usr/share/java)
656	657	set(GDCM_VTK_JAVA_JAR ${VTK_JAVA_JAR})
657	658	endif()
658	659	if(EXISTS /usr/lib/jni/libvtkCommonJava.so)

+6

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Utilities/VTK/vtkGDCMTesting.cxx less more

221	221	{ "SC16BitsAllocated_8BitsStoredJPEG.dcm","c9f9d07783496fa9a9e5b28a90603a70", "c164a73ba18ab4e88977921ffc7c3a65" },
222	222	{ "SC16BitsAllocated_8BitsStoredJ2K.dcm","96639bac776d875b02f6aa9b35ee2db7", "dbf83984984741c98205d77a947b442c" },
223	223	{ "SIEMENS_SYNGO-12-MONO2-LUTWrongLength512.dcm","81f79e2fcb3caec752e55be8077441dc", "4a5d8549791432b29948dd8ff63e2534" },
	224	{ "IllegalGroup2ImplicitTS.dcm","7c922536b5cf4143ce931ff5f552f588", "f666a95dde9ddfdec0cf9574a7985ae3" },
	225	{ "JPEGLosslessYBR_FULL_422.dcm","90a95c01f320809e3f6b6c720e78d457", "cdfb5dd0c999d88badeb00a16f96554f" },
	226	{ "JPEGNote_bogus.dcm","eeb1028e53ef4dcfc6b4100f8525be41", "161e9fd986ea87adf2596e8e16641f11" },
	227	{ "JPEGNote_empty.dcm","e6add795da6e0ccd4ed02f5689a61260", "464960d948dff0ded72b0380080f18a3" },
	228	{ "JPEGNote_missing.dcm","dce9f8853a528d423efc95a9bafee938", "464960d948dff0ded72b0380080f18a3" },
	229	{ "RLEDebianBug816607Orig.dcm","bb7bb73068f494c3cf947d2375af3501", "b85686dd3169b99725149abb00181254" },
224	230
225	231
226	232	/* Stopping condition */

+1

-1

Utilities/doxygen/CMakeLists.txt less more

269	269	string(REGEX MATCH "^.systemIdStartString=\"http://docbook.sourceforge.net/release/xsl-ns/\"." out1 ${line})
270	270	string(REGEX REPLACE "^.systemIdStartString=\"http://docbook.sourceforge.net/release/xsl-ns/\".\"([A-Za-z ])\"." "\\1" output_variable ${line})
271	271	if(out1)
272		message("Your docbook install was found here :${output_variable}")
	272	message(STATUS "Your docbook install was found here :${output_variable}")
273	273	set(DOCBOOK_REWRITE_PREFIX_FOUND TRUE)
274	274	endif()
275	275	endforeach()

+1

-1

Utilities/doxygen/man/gdcmconv.xml less more

168	168	<para>convert GDCM 1.2.0 broken UN-2-bytes fields, </para>
169	169	</listitem>
170	170	<listitem>
171		<para>&... </para>
	171	<para>... </para>
172	172	</listitem>
173	173	<listitem>
174	174	<para>All other broken files listed in the supported refsection.</para>

+21

-21

Utilities/doxygen/man/gdcmdump.xml less more

100	100	</literallayout></para>
101	101
102	102	<para><literallayout># Dicom-File-Format
103		\&...
	103	...
104	104	(0008,0000) ?? (UL) 434 # 4,1 Generic Group Length
105	105	(0008,0005) ?? (CS) [ISO_IR 100] # 10,1-n Specific Character Set
106	106	(0008,0008) ?? (CS) [ORIGINAL\\PRIMARY\\SINGLE PLANE ] # 30,2-n Image Type

114	114	(0008,0031) ?? (TM) [101229.000] # 10,1 Series Time
115	115	(0008,0032) ?? (TM) [102653.000] # 10,1 Acquisition Time
116	116	(0008,0033) ?? (TM) [102653.000] # 10,1 Content Time
117		\&...
	117	...
118	118	</literallayout></para>
119	119	</refsection>
120	120	<refsection xml:id="gdcmdump_1private_attribute">

125	125	<para><literallayout>$ gdcmdump 012345.002.050.dcm
126	126	</literallayout></para>
127	127
128		<para><literallayout>\&...
	128	<para><literallayout>...
129	129	(0009,0010) LO [GEMS_IDEN_01] # 12,1 Private Creator
130	130	(0009,1001) LO [GE_GENESIS_FF ] # 14,1 Full fidelity
131	131	(0009,1002) SH [MRCV] # 4,1 Suite id

137	137	(0009,10e6) SH [08] # 2,1 Genesis Version - now
138	138	(0009,10e7) UL 2757786872 # 4,1 Exam Record checksum
139	139	(0009,10e9) SL 985968523 # 4,1 Actual series data time stamp
140		\&...
	140	...
141	141	(0019,0000) UL 1208 # 4,1 Generic Group Length
142	142	(0019,0010) LO [GEMS_ACQU_01] # 12,1 Private Creator
143	143	(0019,100f) DS [424.399994] # 10,1 Horiz. Frame of ref.
144	144	(0019,1011) SS 0 # 2,1 Series contrast
145		\&...
	145	...
146	146	(0019,10e0) DS [0.000000] # 8,1 User data 24 {# DTI Diffusion Dir., release 10.0 & above}
147	147	(0019,10e2) DS [0.000000] # 8,1 Velocity Encode Scale
148	148	(0019,10f2) SS 0 # 2,1 Fast phases
149	149	(0019,10f9) DS [98] # 2,1 Transmit gain
150		\&...
	150	...
151	151	(0021,0000) UL 372 # 4,1 Generic Group Length
152	152	(0021,0010) LO [GEMS_RELA_01] # 12,1 Private Creator
153	153	(0021,1003) SS 0 # 2,1 Series from which Prescribed
154		\&...
	154	...
155	155	</literallayout></para>
156	156	</refsection>
157	157	<refsection xml:id="gdcmdump_1siemens_csa">

176	176	6 - 'B_value' VM 1, VR IS, SyngoDT 6, NoOfItems 6, Data '0 '
177	177	7 - 'Filter1' VM 1, VR IS, SyngoDT 6, NoOfItems 0, Data
178	178	8 - 'Filter2' VM 1, VR IS, SyngoDT 6, NoOfItems 0, Data
179		\&...
	179	...
180	180	</literallayout></para>
181	181	</refsection>
182	182	<refsection xml:id="gdcmdump_1gems_pdb">

205	205	TRICKSIMG "1"
206	206	TAG_SPACE "7"
207	207	TAG_TYPE "None"
208		\&...
	208	...
209	209	</literallayout></para>
210	210	</refsection>
211	211	<refsection xml:id="gdcmdump_1elscint_pi">

240	240	ACS-learn-allowed [no]
241	241	ACS-water-radius [-1.000000]
242	242	ACS-water-radius-scan [-1]
243		\&...
	243	...
244	244	</literallayout></para>
245	245	</refsection>
246	246	<refsection xml:id="gdcmdump_1vepro_pi">

301	301	<para><literallayout>$ gdcmdump --sds PMS_SeriesDataStorage.dcm
302	302	</literallayout></para>
303	303
304		<para><literallayout>\&...
	304	<para><literallayout>...
305	305	PMS/Item name: [PDF_CONTROL_GEN_PARS/IEEE_PDF/Y ]
306		\&...
	306	...
307	307	PMS/Item name: [PDF_CONTROL_PREP_PARS /IEEE_PDF/Y ]
308		\&...
	308	...
309	309	PMS/Item name: [PDF_CONTROL_RECON_PARS/IEEE_PDF/Y ]
310		\&...
	310	...
311	311	PMS/Item name: [PDF_CONTROL_SCAN_PARS /IEEE_PDF/Y ]
312		\&...
	312	...
313	313	PMS/Item name: [PDF_EXAM_PARS /IEEE_PDF/Y ]
314		\&...
	314	...
315	315	PMS/Item name: [PDF_HARDWARE_PARS /IEEE_PDF/Y ]
316		\&...
	316	...
317	317	PMS/Item name: [PDF_PREP_PARS /IEEE_PDF/Y ]
318		\&...
	318	...
319	319	PMS/Item name: [PDF_SPT_PARS/IEEE_PDF/Y ]
320	320	SP_scan_resol [256\256] # 2
321	321	SP_pda_profiles [0\0] # 2

339	339	SP_rg_result [0] # 1
340	340	SP_dc_result [0] # 1
341	341	SP_ph_result [0] # 1
342		\&...
	342	...
343	343	</literallayout></para>
344	344	</refsection>
345	345	<refsection xml:id="gdcmdump_1asn1">

350	350	<para><literallayout>$ gdcmdump encrypted.dcm
351	351	</literallayout></para>
352	352
353		<para><literallayout>\&...
	353	<para><literallayout>...
354	354	(0400,0500) SQ # u/l,1 Encrypted Attributes Sequence
355	355	(fffe,e000) na (Item with undefined length)
356	356	(0400,0510) UI [1.2.840.10008.1.2] # 18,1 Encrypted Content Transfer Syntax UID
357	357	(0400,0520) OB 30\\82\\03\\ba\\06\\09\\2a\\86\\48\\55\\04\\08\\13 # 958,1 Encrypted Content
358	358	(fffe,e00d)
359	359	(fffe,e0dd)
360		\&...
	360	...
361	361	</literallayout></para>
362	362
363	363	<para><literallayout>$ gdcmdump --asn1 encrypted.dcm

+11

-0

Utilities/doxygen/man/gdcmimg.xml less more

63	63	-C --sop-class-uid SOP Class UID (name or value).
64	64	-T --study-uid Study UID.
65	65	-S --series-uid Series UID.
	66	--template Template DICOM file.
66	67	--root-uid Root UID.
67	68	</literallayout></para>
68	69	</refsection>

220	221	<para><literallayout>$ gdcmimg --sop-class-uid 1.2.840.10008.5.1.4.1.1.77.1.4 input.jpg output.dcm
221	222	</literallayout></para>
222	223	</refsection>
	224	<refsection xml:id="gdcmimg_1template">
	225	<title>Specifying a template DICOM file</title>
	226
	227	<para>Instead of the default Secondary Capture Image Storage, generated with default values, one may want to specify a DICOM file that will serve as template to fill in the DICOM attributes.</para>
	228
	229	<para><literallayout>$ gdcmimg --sign 1 --template template.dcm input.jpg output.dcm
	230	</literallayout></para>
	231	<para>Pay attention that any values from template.dcm that are not consistent with what is found inside the reference image will be overriden (eg. image size). On particular case should be of concern: the Pixel Representation for the JPEG family.</para>
	232
	233	</refsection>
223	234	</refsection>
224	235	<refsection xml:id="gdcmimg_1multiple_files">
225	236	<title>Multiple Files</title>

+2

-2

Utilities/doxygen/man/gdcmraw.xml less more

103	103	<para><literallayout>$ gdcmdump D_CLUNIE_CT1_J2KR.dcm
104	104	</literallayout></para>
105	105
106		<para><literallayout>\&...
	106	<para><literallayout>...
107	107	(7fe0,0010) OB # u/l,1 Pixel Data
108	108	(fffe,e000) ?? [] # 0,1 Item
109	109	(fffe,e000) ?? ff\\4f\\ff\\51\\00\\29\\00\\00\\00\\00\\02\\00\\00\\00\\02\\00\\00\\00\\00\\00\\00\\00\\00\\00\\00\\00\\02\\00\\00\\00\\02\\00 # 65536,1 Item

168	168	<para><literallayout>$ gdcmdump 00191113.dcm
169	169	</literallayout></para>
170	170
171		<para><literallayout>\&...
	171	<para><literallayout>...
172	172	(7fe0,0010) OB # u/l,1 Pixel Data
173	173	(fffe,e000) ?? 00\\00\\00\\00\\6b\\38\\01\\00\\10\\77\\02\\00\\37\\b6\\03\\00\\a7\\f4\\04\\00 # 20,1 Item
174	174	(fffe,e000) ?? ff\\d8\\ff\\c3\\00\\0b\\08\\02\\00\\02\\00\\01\\00\\11\\00\\ff\\c4\\00\\1b\\00\\01\\01\\01\\01\\01\\01\\01\\01\\00\\00\\00\\00 # 79970,1 Item

+2

-2

Utilities/doxygen/man/gdcmtar.xml less more

86	86	TransferSyntax is 1.2.840.10008.1.2.1 [Explicit VR Little Endian]
87	87	NumberOfDimensions: 2
88	88	Dimensions: (384,384,1)
89		\&...
	89	...
90	90	</literallayout></para>
91	91
92	92	<para><literallayout>$ gdcmtar --mosaic -i MR-sonata-3D-as-Tile.dcm -o mosaic --pattern %03d.dcm

134	134	TransferSyntax is 1.2.840.10008.1.2.1 [Explicit VR Little Endian]
135	135	NumberOfDimensions: 2
136	136	Dimensions: (64,64,1)
137		\&...
	137	...
138	138	</literallayout></para>
139	139	</refsection>
140	140	</refsection>

+44

-36

Wrapping/Python/docstrings.i less more

5352	5352	// File: classgdcm_1_1ImageRegionReader.xml
5353	5353	%feature("docstring") gdcm::ImageRegionReader "
5354	5354
5355		ImageRegionReader.
	5355	ImageRegionReader This class is able to read a region from a DICOM
	5356	file containing an image. This implementation requires that the
	5357	information stored in the DICOM header are consistent with what is in
	5358	the encapsulated Pixel Data. This is technically not required by DICOM
	5359	standard, which makes this implementation illegal with regards to the
	5360	famous JPEG
	5361	note:http://dicom.nema.org/medical/dicom/current/output/chtml/part05/sect_8.2.html
	5362	#para_4bcb841e-c6bf-4e26-82a5-3fad3c942da0.
5356	5363
5357	5364	See: ImageReader
5358	5365

5696	5703	http://gdcm.sourceforge.net/wiki/index.php/Imager_Pixel_Spacing
5697	5704
5698	5705	Bug There are currently a couple of bugs in this implementation:
	5706
5699	5707	Gantry Tilt is not considered (always an error)
5700	5708
5701	5709	Application programmer should only sort valid DataSet (eg.

8712	8720	gdcm::PythonFilter::ToPyObject(const Tag &t) const ";
8713	8721
8714	8722	%feature("docstring") gdcm::PythonFilter::UseDictAlways "void
8715		gdcm::PythonFilter::UseDictAlways(bool use) ";
	8723	gdcm::PythonFilter::UseDictAlways(bool) ";
8716	8724
8717	8725
8718	8726	// File: classgdcm_1_1QueryBase.xml

15044	15052	// File: bug.xml
15045	15053
15046	15054
15047		// File: dir_48be02fb937e08881437e02515417ab2.xml
15048
15049
15050		// File: dir_dbdfee04788ce02e68d05e06d5e6d98f.xml
15051
15052
15053		// File: dir_422e8974cbd0b7203ed9c70ede735192.xml
15054
15055
15056		// File: dir_fc2dbd93ff698b14d78f486017ee822b.xml
15057
15058
15059		// File: dir_63e84970519399936bea68aa0151439e.xml
15060
15061
15062		// File: dir_a3a231e2bd7f702d85036607d7d87964.xml
15063
15064
15065		// File: dir_bfc3201f3b82d7ccf14c524caa3c389b.xml
15066
15067
15068		// File: dir_9a6580727919559370fc2250dcaca6b8.xml
15069
15070
15071		// File: dir_087222ad62d2f517f4e0198672951648.xml
15072
15073
15074		// File: dir_2a74275ceded0a5f3b0fb2e9bd792825.xml
15075
15076
15077		// File: dir_acafdc7d686494cf0735517ddc7a7669.xml
15078
15079
15080		// File: dir_d2ab22b73e3ee89be3a207288d7a9056.xml
	15055	// File: dir_041d54874d9fecec94d9cb4ae010b51e.xml
	15056
	15057
	15058	// File: dir_8021392154ea27d3da33100afd5b42a1.xml
	15059
	15060
	15061	// File: dir_83a82e6a2bc4a0f6429532cb237ca746.xml
	15062
	15063
	15064	// File: dir_9760e222fce508c3b7270d68e6523d76.xml
	15065
	15066
	15067	// File: dir_90174c188c639015dd869d1a853f914f.xml
	15068
	15069
	15070	// File: dir_aceed280bd27dc60f64c2cb4efae4f90.xml
	15071
	15072
	15073	// File: dir_5aab2906425e8d9a7aa9fea4f8d0a2fa.xml
	15074
	15075
	15076	// File: dir_5daaa9a41ac240f7de3019ff61b11839.xml
	15077
	15078
	15079	// File: dir_b138abe427a068e1da5116454e79caa4.xml
	15080
	15081
	15082	// File: dir_6b1a62c3f439db8dff4e3363f340e91f.xml
	15083
	15084
	15085	// File: dir_776c231028699256e0cc13f46def7474.xml
	15086
	15087
	15088	// File: dir_6285418b2babf39982c6f35dbd05cbb5.xml
15081	15089
15082	15090
15083	15091	// File: AWTMedical3_8java-example.xml