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of-dicom: patch to compile in octave 4.0.0 (Bug #44624) * src/of-dicom-1-fixes.patch: new file * dist-files.mk: add of-dicom-1-fixes.patch * src/of-dicom.mk: allow cross compile
author John Donoghue <john.donoghue@ieee.org>
date Wed, 15 Apr 2015 21:52:37 -0400
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diff -ur dicom.orig/src/dicominfo.cpp dicom/src/dicominfo.cpp
--- dicom.orig/src/dicominfo.cpp	2015-04-15 21:36:10.000000000 -0400
+++ dicom/src/dicominfo.cpp	2015-04-15 21:41:21.000000000 -0400
@@ -76,10 +76,10 @@
 char* byteval2string(char * d, int d_len_p, const gdcm::ByteValue *bv);
 char* name2Keyword(char *d, int *d_len_p, const char* s);
 Matrix str2DoubleVec(const char*);
-Octave_map dump(const char filename[], int chatty);
-void dumpDataSet(Octave_map *om, const gdcm::DataSet *ds, int chatty, int sequenceDepth);
+octave_map dump(const char filename[], int chatty);
+void dumpDataSet(octave_map *om, const gdcm::DataSet *ds, int chatty, int sequenceDepth);
 void getFileModTime(char *timeStr, const char *filename);
-void dumpElement(Octave_map *om, const gdcm::DataElement * elem, int chatty, int sequenceDepth);
+void dumpElement(octave_map *om, const gdcm::DataElement * elem, int chatty, int sequenceDepth);
 void dumpSequence(octave_value *ov, gdcm::SequenceOfItems *seq, int chatty, int sequenceDepth);
 int element2value(std::string & varname, octave_value *ov, const gdcm::DataElement * elem, int chatty, int sequenceDepth) ;
 
@@ -163,7 +163,7 @@
 		}
 	}
 	
-	Octave_map om=dump(filename.c_str(),chatty);
+	octave_map om=dump(filename.c_str(),chatty);
 	retval(0)=om;
 
 	load_dicom_dict(current_dict.c_str()); // reset dictionary to initial value
@@ -172,9 +172,9 @@
 #endif
 
 
-Octave_map dump(const char filename[], int chatty) {
+octave_map dump(const char filename[], int chatty) {
 	// output struct
-	Octave_map om;
+	octave_map om;
 	// Instantiate the reader:
 	gdcm::Reader reader;
 	reader.SetFileName( filename );
@@ -202,7 +202,7 @@
 	return om;
 }
 
-void dumpDataSet(Octave_map *om, const gdcm::DataSet *ds, int chatty, int sequenceDepth) {
+void dumpDataSet(octave_map *om, const gdcm::DataSet *ds, int chatty, int sequenceDepth) {
 	
 	const gdcm::DataSet::DataElementSet DES=ds->GetDES(); // gdcm::DataSet::DataElementSet is a std::set
 	gdcm::DataSet::Iterator it;
@@ -212,7 +212,7 @@
 	}
 }
 
-void dumpElement(Octave_map *om, const gdcm::DataElement * elem, 
+void dumpElement(octave_map *om, const gdcm::DataElement * elem, 
 				int chatty, int sequenceDepth) {
 	std::string varname;
 	octave_value ov;
@@ -453,10 +453,10 @@
 	const octave_idx_type nDataSet=seq->GetNumberOfItems(); // objects in sequence
 	if (chatty) octave_stdout << nDataSet << " object" << ((nDataSet==1)?"":"s") << std::endl;
 	char item_name_buf[16];
-	Octave_map om;
+	octave_map om;
 	for (octave_idx_type j=1; j<=nDataSet; j++ ) {
 		const gdcm::DataSet::DataElementSet des=seq->GetItem(j).GetNestedDataSet().GetDES() ;
-		Octave_map subom;
+		octave_map subom;
 		for (gdcm::DataSet::Iterator it=des.begin(); it != des.end(); it++) {
 			std::string key("");
 			octave_value subov;
diff -ur dicom.orig/src/dicomwrite.cpp dicom/src/dicomwrite.cpp
--- dicom.orig/src/dicomwrite.cpp	2015-04-15 21:36:10.000000000 -0400
+++ dicom/src/dicomwrite.cpp	2015-04-15 21:41:49.000000000 -0400
@@ -43,7 +43,7 @@
 // TODO all fns here should throw exceptions, not use this "std::string & err" arg
 
 void struct2metadata(gdcm::ImageWriter *w, gdcm::File *file, const octave_value  & ov, bool trial, int sequenceDepth) ;
-void structarray2sequence(gdcm::SequenceOfItems & sq, Octave_map * om, bool trial, int sequenceDepth);
+void structarray2sequence(gdcm::SequenceOfItems & sq, octave_map * om, bool trial, int sequenceDepth);
 void value2element (gdcm::DataElement * de, const octave_value * ov, gdcm::Tag * tag, const std::string & keyword, bool trial, bool * handled, int sequenceDepth);
 void octaveVal2dicomImage(gdcm::ImageWriter *w, octave_value *pixval) ;
 void genMinimalMetaData(gdcm::ImageWriter *w, gdcm::File *file);
@@ -132,9 +132,9 @@
 	}
 	gdcm::DataSet ds;
 	gdcm::FileMetaInformation hds;
-	Octave_map om=ov.map_value();
+	octave_map om=ov.map_value();
 	uint32_t skipped = 0;
-	for (Octave_map::iterator it = om.begin(); it != om.end(); it++) {
+	for (octave_map::iterator it = om.begin(); it != om.end(); it++) {
 		std::string keyword(om.key(it));
 		Cell cell = om.contents(it);
 		if (!dicom_is_present(keyword)) {
@@ -179,17 +179,17 @@
 	return ;
 }
 
-void structarray2sequence(gdcm::SequenceOfItems & sq, Octave_map * om, bool trial, int sequenceDepth) {
-	for (Octave_map::iterator it = om->begin(); it != om->end(); it++) {
+void structarray2sequence(gdcm::SequenceOfItems & sq, octave_map * om, bool trial, int sequenceDepth) {
+	for (octave_map::iterator it = om->begin(); it != om->end(); it++) {
 		gdcm::Item item;
 		// item.SetVLToUndefined(); //TODO: does VL need to be set for items that contain datasets?
 		gdcm::DataSet &nds = item.GetNestedDataSet();
 		std::string itemname(om->key(it));
 		// TODO: test itemname is something like Item_n.
 		Cell cell = om->contents(it);
-		Octave_map subom = cell(0).map_value();
+		octave_map subom = cell(0).map_value();
 		// octave_stdout << itemname <<std::endl;
-		for (Octave_map::iterator subit = subom.begin(); subit != subom.end(); subit++) {
+		for (octave_map::iterator subit = subom.begin(); subit != subom.end(); subit++) {
 			std::string subkeyword(subom.key(subit));
 			gdcm::DataElement de;
 			gdcm::Tag tag;
@@ -289,7 +289,7 @@
 		}
 		octave_stdout << std::endl;
 		//int nObj = ov->numel() ;
-		Octave_map subom = ov->map_value();
+		octave_map subom = ov->map_value();
 		gdcm::SmartPointer<gdcm::SequenceOfItems> sq = new gdcm::SequenceOfItems();
 		try {
 			structarray2sequence(*sq, &subom, trial, ++sequenceDepth) ;
diff -ur dicom.orig/src/Makefile dicom/src/Makefile
--- dicom.orig/src/Makefile	2015-04-15 21:36:10.000000000 -0400
+++ dicom/src/Makefile	2015-04-15 21:40:04.000000000 -0400
@@ -15,10 +15,11 @@
 #   Please see the file, "COPYING" for further details of GNU General 
 #   Public License version 3.
   
- 
+MKOCTFILE ?= mkoctfile 
+OCTAVE ?= octave
 
 INCDIRFLAGS =	
-LIBDIRFLAGS =	-L/usr/local/lib
+LIBDIRFLAGS =
 GDCMLIBFLAGS =	-lgdcmcharls  -lgdcmjpeg8 -lgdcmjpeg12 \
 -lgdcmjpeg16 -lgdcmCommon \
 -lgdcmDICT -lgdcmDSED -lgdcmIOD -lgdcmMSFF  
@@ -29,35 +30,35 @@
 
 
 dicomlookup.oct: dicomdict.o dicomlookup.o
-	mkoctfile $(INCDIRFLAGS) $(LIBDIRFLAGS) $(GDCMLIBFLAGS) $(DEBUGFLAG) dicomlookup.o dicomdict.o -o dicomlookup.oct
+	$(MKOCTFILE) $(INCDIRFLAGS) $(LIBDIRFLAGS) $(GDCMLIBFLAGS) $(DEBUGFLAG) dicomlookup.o dicomdict.o -o dicomlookup.oct
 
 dicomdict.oct: dicomdict.o
-	mkoctfile $(INCDIRFLAGS) $(DEBUGFLAG) dicomdict.o
+	$(MKOCTFILE) $(INCDIRFLAGS) $(DEBUGFLAG) dicomdict.o
 
 dicominfo.oct: dicominfo.o dicomdict.o
-	mkoctfile $(INCDIRFLAGS) $(LIBDIRFLAGS) $(GDCMLIBFLAGS) $(DEBUGFLAG) dicominfo.o dicomdict.o -o dicominfo.oct
+	$(MKOCTFILE) $(INCDIRFLAGS) $(LIBDIRFLAGS) $(GDCMLIBFLAGS) $(DEBUGFLAG) dicominfo.o dicomdict.o -o dicominfo.oct
 
 dicomwrite.oct: dicomwrite.o dicomdict.o
-	mkoctfile $(INCDIRFLAGS) $(LIBDIRFLAGS) $(GDCMLIBFLAGS) $(DEBUGFLAG) dicomwrite.o dicomdict.o -o dicomwrite.oct
+	$(MKOCTFILE) $(INCDIRFLAGS) $(LIBDIRFLAGS) $(GDCMLIBFLAGS) $(DEBUGFLAG) dicomwrite.o dicomdict.o -o dicomwrite.oct
 
 dicomread.oct: dicomread.cpp
-	mkoctfile $(INCDIRFLAGS) $(LIBDIRFLAGS) $(GDCMLIBFLAGS) $(DEBUGFLAG) dicomread.cpp
+	$(MKOCTFILE) $(INCDIRFLAGS) $(LIBDIRFLAGS) $(GDCMLIBFLAGS) $(DEBUGFLAG) dicomread.cpp
 
 _gendicomdict.oct: _gendicomdict.cpp
-	mkoctfile $(INCDIRFLAGS) $(LIBDIRFLAGS) $(GDCMLIBFLAGS) $(DEBUGFLAG) _gendicomdict.cpp
+	$(MKOCTFILE) $(INCDIRFLAGS) $(LIBDIRFLAGS) $(GDCMLIBFLAGS) $(DEBUGFLAG) _gendicomdict.cpp
 
 
 dicominfo.o: dicomdict.h dicominfo.cpp
-	mkoctfile -c $(INCDIRFLAGS) $(DEBUGFLAG) dicominfo.cpp
+	$(MKOCTFILE) -c $(INCDIRFLAGS) $(DEBUGFLAG) dicominfo.cpp
 
 dicomwrite.o: dicomdict.h dicomwrite.cpp
-	mkoctfile -c $(INCDIRFLAGS) $(DEBUGFLAG) dicomwrite.cpp
+	$(MKOCTFILE) -c $(INCDIRFLAGS) $(DEBUGFLAG) dicomwrite.cpp
 
 dicomdict.o: dicomdict.h dicomdict.cpp
-	mkoctfile -c $(INCDIRFLAGS) $(DEBUGFLAG) dicomdict.cpp
+	$(MKOCTFILE) -c $(INCDIRFLAGS) $(DEBUGFLAG) dicomdict.cpp
 
 dicomlookup.o: dicomdict.h dicomlookup.cpp
-	mkoctfile -c $(INCDIRFLAGS) $(DEBUGFLAG) dicomlookup.cpp
+	$(MKOCTFILE) -c $(INCDIRFLAGS) $(DEBUGFLAG) dicomlookup.cpp
 
 clean:
 	rm -f *.o *.oct *~
@@ -65,13 +66,14 @@
 test: test_dicominfo test_dicomdict test_dicomread test_dicomlookup
 	
 test_dicominfo: dicominfo.oct
-	octave -q --eval "test dicominfo.cpp"
+	$(OCTAVE) -q --eval "test dicominfo.cpp"
 
 test_dicomdict: dicomdict.oct
-	octave -q --eval "test dicomdict.cpp"
+	$(OCTAVE) -q --eval "test dicomdict.cpp"
 
 test_dicomread: dicomread.oct
-	octave -q --eval "test dicomread.cpp"
+	$(OCTAVE) -q --eval "test dicomread.cpp"
 
 test_dicomlookup: dicomlookup.oct
-	octave -q --eval "test dicomlookup.cpp"
\ No newline at end of file
+	$(OCTAVE) -q --eval "test dicomlookup.cpp"
+
diff -ur dicom.orig/src/dicominfo.cpp dicom/src/dicominfo.cpp
--- dicom.orig/src/dicominfo.cpp	2015-04-15 21:44:32.000000000 -0400
+++ dicom/src/dicominfo.cpp	2015-04-15 21:47:48.000000000 -0400
@@ -187,10 +187,10 @@
 	gdcm::DataSet &ds = file.GetDataSet();
 	gdcm::FileMetaInformation &hds=file.GetHeader();
 	
-	om.assign("Filename",filename);
+	om.assign("Filename",octave_value(filename));
 	char dateStr[TIME_STR_LEN+1];
 	getFileModTime(dateStr, filename);
-	om.assign("FileModDate", dateStr);
+	om.assign("FileModDate", octave_value(dateStr));
 	if(chatty) octave_stdout << "# file info\nFilename:" 
 		<< filename << "\nFileModDate:" << dateStr << '\n';
 	
@@ -220,7 +220,7 @@
 		om->assign(varname.c_str(), ov);
 	} else {
 		if (0==varname.length()) return ;
-		om->assign(varname.c_str(), "not assigned");
+		om->assign(varname.c_str(), octave_value("not assigned"));
 	}
 }
 
@@ -464,7 +464,7 @@
 				subom.assign(key.c_str(), subov);
 			} else {
 				if (0==key.length()) continue ;
-				subom.assign(key.c_str(), "not assigned");
+				subom.assign(key.c_str(), octave_value("not assigned"));
 			}
 		}
 		snprintf(item_name_buf,15,"Item_%i",j);