New upstream version 3.0.3 (0dcd0210) · Commits · Debian Med / gdcm

Applications/Cxx/gdcmscanner.cxx

+63 −32

Original line number	Diff line number	Diff line
		@@ -32,6 +32,10 @@
		#include "gdcmTrace.h"
		#include "gdcmVersion.h"
		#include "gdcmSimpleSubjectWatcher.h"
		#include "gdcmGlobal.h"
		#include "gdcmDicts.h"
		#include "gdcmDict.h"
		#include "gdcmDictEntry.h"

		#include <string>
		#include <iostream>
		@@ -57,10 +61,13 @@ static void PrintHelp()
		std::cout << "Parameter (required):" << std::endl;
		std::cout << " -d --dir DICOM directory" << std::endl;
		std::cout << " -t --tag %d,%d DICOM tag(s) to look for" << std::endl;
		std::cout << " -k --keyword %s DICOM keyword(s) to look for" << std::endl;
		std::cout << " -P --private-tag %d,%d,%s DICOM private tag(s) to look for" << std::endl;
		std::cout << "Options:" << std::endl;
		std::cout << " -p --print Print output." << std::endl;
		std::cout << " -r --recursive Recusively descend directory." << std::endl;
		std::cout << " -r --recursive Recursively descend directory." << std::endl;
		std::cout << " --strict Use strict parser (faster but less tolerant with bogus DICOM files)." << std::endl;
		std::cout << " --table Use Table output." << std::endl;
		std::cout << "General Options:" << std::endl;
		std::cout << " -V --verbose more verbose (warning+error)." << std::endl;
		std::cout << " -W --warning print warning info." << std::endl;
		@@ -75,7 +82,7 @@ typedef std::vector<gdcm::PrivateTag> VectorPrivateTags;
		template < typename TScanner >
		static int DoIt(
		gdcm::Directory const & d,
		bool const & print ,
		bool const & print , int table,
		VectorTags const & tags,
		VectorPrivateTags const & privatetags)
		{
		@@ -96,7 +103,13 @@ static int DoIt(
		std::cerr << "Scanner failed" << std::endl;
		return 1;
		}
		if (print) s.Print( std::cout );
		if (print)
		{
		if(table)
		s.PrintTable( std::cout );
		else
		s.Print( std::cout );
		}

		return 0;
		}
		@@ -114,8 +127,12 @@ int main(int argc, char *argv[])
		VectorPrivateTags privatetags;
		gdcm::Tag tag;
		gdcm::PrivateTag privatetag;
		static const gdcm::Global &g = gdcm::Global::GetInstance();
		static const gdcm::Dicts &dicts = g.GetDicts();
		static const gdcm::Dict &pubdict = dicts.GetPublicDict();

		int strict = 0;
		int table = 0;
		int verbose = 0;
		int warning = 0;
		int debug = 0;
		@@ -127,25 +144,27 @@ int main(int argc, char *argv[])
		//int this_option_optind = optind ? optind : 1;
		int option_index = 0;
		static struct option long_options[] = {
		{"dir", 1, nullptr, 0},
		{"tag", 1, nullptr, 0},
		{"recursive", 1, nullptr, 0},
		{"print", 1, nullptr, 0},
		{"private-tag", 1, nullptr, 0},
		{"strict", 0, &strict, 1},
		{"dir", required_argument, nullptr, 'd'},
		{"tag", required_argument, nullptr, 't'},
		{"recursive", no_argument, nullptr, 'r'},
		{"print", no_argument, nullptr, 'p'},
		{"private-tag", required_argument, nullptr, 'P'},
		{"keyword", required_argument, nullptr, 'k'},
		{"strict", no_argument, &strict, 1},
		{"table", no_argument, &table, 1},

		// General options !
		{"verbose", 0, &verbose, 1},
		{"warning", 0, &warning, 1},
		{"debug", 0, &debug, 1},
		{"error", 0, &error, 1},
		{"help", 0, &help, 1},
		{"version", 0, &version, 1},
		{"verbose", no_argument, nullptr, 'V'},
		{"warning", no_argument, nullptr, 'W'},
		{"debug", no_argument, nullptr, 'D'},
		{"error", no_argument, nullptr, 'E'},
		{"help", no_argument, nullptr, 'H'},
		{"version", no_argument, nullptr, 'v'},

		{nullptr, 0, nullptr, 0}
		};

		c = getopt_long (argc, argv, "d:t:rpP:VWDEhv",
		c = getopt_long (argc, argv, "d:t:rpP:k:VWDEhv",
		long_options, &option_index);
		if (c == -1)
		{
		@@ -155,18 +174,10 @@ int main(int argc, char *argv[])
		switch (c)
		{
		case 0:
		if (optarg)
		{
		//const char *s = long_options[option_index].name;
		//printf ("option %s", s);
		//if (optarg)
		// {
		// if( option_index == 0 ) /* input */
		// {
		// assert( strcmp(s, "input") == 0 );
		// }
		// printf (" with arg %s", optarg);
		// }
		//printf ("\n");
		const char *s = long_options[option_index].name; (void)s;
		assert(0);
		}
		break;

		@@ -180,6 +191,20 @@ int main(int argc, char *argv[])
		//std::cerr << optarg << std::endl;
		break;

		case 'k':
		{
		const char * keyword = optarg;
		/const gdcm::DictEntry &dictentry =/ pubdict.GetDictEntryByKeyword(keyword, tag);
		if( tag != gdcm::Tag(0xffff,0xffff) )
		tags.push_back( tag );
		else
		{
		std::cerr << "Invalid keyword: " << keyword << std::endl;
		return 1;
		}
		}
		break;

		case 'P':
		privatetag.ReadFromCommaSeparatedString(optarg);
		privatetags.push_back( privatetag );
		@@ -290,10 +315,16 @@ int main(int argc, char *argv[])

		gdcm::Directory d;
		unsigned int nfiles = d.Load( dirname.c_str(), recursive );
		if( !nfiles )
		{
		std::cerr << "No files found in: " << dirname << std::endl;
		return 1;
		}
		if( verbose ) d.Print( std::cout );
		if( !table )
		std::cout << "done retrieving file list " << nfiles << " files found." << std::endl;

		if( strict )
		return DoIt<gdcm::StrictScanner>(d,print,tags,privatetags);
		return DoIt<gdcm::Scanner>(d,print,tags,privatetags);
		return DoIt<gdcm::StrictScanner>(d,print,table,tags,privatetags);
		return DoIt<gdcm::Scanner>(d,print,table,tags,privatetags);
		}

CMakeLists.txt

+22 −18

Original line number	Diff line number	Diff line
		@@ -17,7 +17,7 @@ endif()
		#----------------------------------------------------------------------------

		project(GDCM
		VERSION 3.0.2
		VERSION 3.0.3
		LANGUAGES CXX C
		)
		## NOTE: the "DESCRIPTION" feature of project() was introduced in cmake 3.10.0
		@@ -590,22 +590,6 @@ if(GDCM_STANDALONE)
		else()
		set(BUILD_APPLICATIONS OFF)
		endif()
		add_subdirectory(Utilities)
		add_subdirectory(Source)

		if(GDCM_STANDALONE)
		add_subdirectory(Wrapping)
		if(GDCM_WRAP_CSHARP)
		add_subdirectory(Wrapping/Csharp)
		endif()
		endif()

		if(GDCM_STANDALONE)
		# After Wrapping please
		if(BUILD_EXAMPLES)
		add_subdirectory(Examples)
		endif()
		endif()

		#-----------------------------------------------------------------------------
		# Need pthread for the following class:
		@@ -618,7 +602,7 @@ if(GDCM_STANDALONE)
		endif()

		if(GDCM_STANDALONE)
		if(BUILD_TESTING)
		if(GDCM_BUILD_TESTING)
		configure_file(${GDCM_SOURCE_DIR}/CMake/CTestCustom.ctest.in
		${GDCM_BINARY_DIR}/CMake/CTestCustom.ctest @ONLY)
		file(WRITE ${GDCM_BINARY_DIR}/CTestCustom.cmake
		@@ -635,6 +619,21 @@ if(GDCM_STANDALONE)
		endif()
		endif()

		# After enable_testing()
		add_subdirectory(Utilities)
		add_subdirectory(Source)

		if(GDCM_STANDALONE)
		add_subdirectory(Wrapping)
		endif()

		if(GDCM_STANDALONE)
		# After Wrapping please
		if(BUILD_EXAMPLES)
		add_subdirectory(Examples)
		endif()
		endif()

		#-----------------------------------------------------------------------------
		if(GDCM_STANDALONE)
		option(GDCM_DOCUMENTATION "Build source documentation using doxygen." OFF)
		@@ -680,6 +679,11 @@ include(CMake/InstallRequiredVTKLibraries.cmake)
		endif()
		endif()

		# Make sure to run doxygen after everything else (in particular vtkgdcm):
		if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Utilities/doxygen)
		add_subdirectory(Utilities/doxygen)
		endif()

		#-----------------------------------------------------------------------------
		# CPack stuff
		if(GDCM_STANDALONE) # disabled for ITK distribution of gdcm

Examples/Cxx/CMakeLists.txt

+1 −0

Original line number	Diff line number	Diff line
		@@ -35,6 +35,7 @@ set(EXAMPLES_SRCS
		PrintLUT
		EmptyMask
		DumpSiemensBase64
		DumpVisusChange
		TemplateEmptyImage
		MakeTemplate
		DeriveSeries

Examples/Cxx/DumpVisusChange.cxx

0 → 100644

+143 −0

Original line number	Diff line number	Diff line
		/*=========================================================================

		Program: GDCM (Grassroots DICOM). A DICOM library

		Copyright (c) 2006-2011 Mathieu Malaterre
		All rights reserved.
		See Copyright.txt or http://gdcm.sourceforge.net/Copyright.html for details.

		This software is distributed WITHOUT ANY WARRANTY; without even
		the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
		PURPOSE. See the above copyright notice for more information.

		=========================================================================*/
		#include "gdcmReader.h"
		#include "gdcmDirectory.h"
		#include "gdcmStringFilter.h"

		#include <vector>
		#include <algorithm>

		/*
		*/
		static bool process( std::vector<gdcm::DataElement> & ms, const char * filename)
		{
		using namespace gdcm;
		Tag pd(0x7fe0,0x0000);
		std::set<gdcm::Tag> skiptags;
		skiptags.insert( pd );

		gdcm::Reader reader;
		reader.SetFileName( filename );
		if( !reader.ReadUpToTag( pd, skiptags ) )
		{
		std::cerr << "Failure to read: " << filename << std::endl;
		return false;
		}

		gdcm::File &file = reader.GetFile();
		gdcm::DataSet &ds1 = file.GetDataSet();

		const gdcm::PrivateTag tseq1(0x5533,0x33,"Visus Change");
		if( !ds1.FindDataElement( tseq1 ) ) return true;
		const gdcm::DataElement& seq1 = ds1.GetDataElement( tseq1 );

		SmartPointer<SequenceOfItems> sqi1 = seq1.GetValueAsSQ();

		const size_t nitems = sqi1->GetNumberOfItems();
		for( size_t item = 1; item < nitems; ++item )
		{
		Item &item1 = sqi1->GetItem(item);
		DataSet &ds2 = item1.GetNestedDataSet();
		for(DataSet::ConstIterator it = ds2.Begin(); it != ds2.End(); ++it )
		{
		DataElement const & de = *it;
		// cannot simply use std::set here, see there is a discrepancy in between
		// operator== and operator<.
		// So only use operator== here:
		std::vector<DataElement>::iterator vit = std::find(ms.begin(), ms.end(), de);
		if( vit == ms.end() )
		ms.push_back(de);
		}
		}
		return true;
		}

		int main(int argc, char *argv[])
		{
		bool usefastpath = true;

		if( argc < 2 ) return 1;
		using namespace gdcm;
		const char *filename = argv[1];
		gdcm::Directory::FilenamesType filenames;
		if( !gdcm::System::FileExists(filename) )
		{
		std::cerr << "Could not find file: " << filename << std::endl;
		return 1;
		}

		gdcm::Directory dir;
		if( gdcm::System::FileIsDirectory(filename) )
		{
		unsigned int nfiles = dir.Load(filename, false);
		if( nfiles == 0 )
		{
		std::cerr << "Could not find files: " << filename << std::endl;
		return 1;
		}
		filenames = dir.GetFilenames();
		}
		else
		{
		filenames.push_back( filename );
		}
		gdcm::StringFilter sf;

		Tag pd(0x7fe0,0x0000);
		std::set<gdcm::Tag> skiptags;
		skiptags.insert( pd );

		gdcm::Reader reader;
		reader.SetFileName( filenames[0].c_str() );
		if( !reader.ReadUpToTag( pd, skiptags ) )
		{
		std::cerr << "Could not read file: " << filename << std::endl;
		return 1;
		}
		gdcm::File &file = reader.GetFile();
		sf.SetFile(file);

		if( usefastpath ) {
		// Heuristic, assume if private tag cannot be found in first file, skip the directory
		gdcm::DataSet &ds1 = file.GetDataSet();

		const gdcm::PrivateTag tseq1(0x5533,0x33,"Visus Change");
		if( !ds1.FindDataElement( tseq1 ) ){
		std::cerr << "Could not find private tag in first file skipping whole directory: " << filename << std::endl;
		return 0;
		}
		}

		std::vector<DataElement> ms;
		for(gdcm::Directory::FilenamesType::const_iterator cit = filenames.begin(); cit != filenames.end(); ++cit )
		{
		if( !process(ms, cit->c_str()) ) {
		return 1;
		}
		}

		if( !ms.empty() ) {
		std::sort(ms.begin(), ms.end());
		std::cout << filename << ",\"";
		for(std::vector<DataElement>::const_iterator it = ms.begin(); it != ms.end(); ++it )
		{
		DataElement const & de = *it;
		std::string const & s = sf.ToString( de );
		std::cout << de.GetTag() << " " << s << std::endl;
		}
		std::cout << "\"" << std::endl;
		}

		return 0;
		}

Source/Common/gdcmDirectory.cxx

+1 −1

Original line number	Diff line number	Diff line
		@@ -40,7 +40,7 @@ unsigned int Directory::Load(FilenameType const &name, bool recursive)
		Toplevel = name;
		return Explore( Toplevel, recursive );
		}
		return false;
		return 0;
		}

		unsigned int Directory::Explore(FilenameType const &name, bool recursive)