Mercurial > mxe-octave
view src/of-dicom-1-fixes.patch @ 4140:d38d0e08ef4c
tiff: update to 4.0.6
* src/tiff.mk: update version and checksum
author | John Donoghue |
---|---|
date | Wed, 04 May 2016 08:42:44 -0400 |
parents | 5863c4ed08b1 |
children |
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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);