annotate src/of-dicom-1-fixes.patch @ 3908:5863c4ed08b1

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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5863c4ed08b1 of-dicom: patch to compile in octave 4.0.0 (Bug #44624)
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1 diff -ur dicom.orig/src/dicominfo.cpp dicom/src/dicominfo.cpp
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2 --- dicom.orig/src/dicominfo.cpp 2015-04-15 21:36:10.000000000 -0400
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3 +++ dicom/src/dicominfo.cpp 2015-04-15 21:41:21.000000000 -0400
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4 @@ -76,10 +76,10 @@
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5 char* byteval2string(char * d, int d_len_p, const gdcm::ByteValue *bv);
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6 char* name2Keyword(char *d, int *d_len_p, const char* s);
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7 Matrix str2DoubleVec(const char*);
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8 -Octave_map dump(const char filename[], int chatty);
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9 -void dumpDataSet(Octave_map *om, const gdcm::DataSet *ds, int chatty, int sequenceDepth);
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10 +octave_map dump(const char filename[], int chatty);
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11 +void dumpDataSet(octave_map *om, const gdcm::DataSet *ds, int chatty, int sequenceDepth);
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12 void getFileModTime(char *timeStr, const char *filename);
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13 -void dumpElement(Octave_map *om, const gdcm::DataElement * elem, int chatty, int sequenceDepth);
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14 +void dumpElement(octave_map *om, const gdcm::DataElement * elem, int chatty, int sequenceDepth);
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15 void dumpSequence(octave_value *ov, gdcm::SequenceOfItems *seq, int chatty, int sequenceDepth);
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16 int element2value(std::string & varname, octave_value *ov, const gdcm::DataElement * elem, int chatty, int sequenceDepth) ;
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17
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18 @@ -163,7 +163,7 @@
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19 }
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20 }
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21
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22 - Octave_map om=dump(filename.c_str(),chatty);
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23 + octave_map om=dump(filename.c_str(),chatty);
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24 retval(0)=om;
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25
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26 load_dicom_dict(current_dict.c_str()); // reset dictionary to initial value
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27 @@ -172,9 +172,9 @@
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28 #endif
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29
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30
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31 -Octave_map dump(const char filename[], int chatty) {
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32 +octave_map dump(const char filename[], int chatty) {
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33 // output struct
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34 - Octave_map om;
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35 + octave_map om;
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36 // Instantiate the reader:
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37 gdcm::Reader reader;
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38 reader.SetFileName( filename );
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39 @@ -202,7 +202,7 @@
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40 return om;
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41 }
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42
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43 -void dumpDataSet(Octave_map *om, const gdcm::DataSet *ds, int chatty, int sequenceDepth) {
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44 +void dumpDataSet(octave_map *om, const gdcm::DataSet *ds, int chatty, int sequenceDepth) {
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45
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46 const gdcm::DataSet::DataElementSet DES=ds->GetDES(); // gdcm::DataSet::DataElementSet is a std::set
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47 gdcm::DataSet::Iterator it;
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48 @@ -212,7 +212,7 @@
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49 }
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50 }
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51
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52 -void dumpElement(Octave_map *om, const gdcm::DataElement * elem,
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53 +void dumpElement(octave_map *om, const gdcm::DataElement * elem,
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54 int chatty, int sequenceDepth) {
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55 std::string varname;
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56 octave_value ov;
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57 @@ -453,10 +453,10 @@
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58 const octave_idx_type nDataSet=seq->GetNumberOfItems(); // objects in sequence
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59 if (chatty) octave_stdout << nDataSet << " object" << ((nDataSet==1)?"":"s") << std::endl;
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60 char item_name_buf[16];
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61 - Octave_map om;
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62 + octave_map om;
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63 for (octave_idx_type j=1; j<=nDataSet; j++ ) {
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64 const gdcm::DataSet::DataElementSet des=seq->GetItem(j).GetNestedDataSet().GetDES() ;
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65 - Octave_map subom;
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66 + octave_map subom;
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67 for (gdcm::DataSet::Iterator it=des.begin(); it != des.end(); it++) {
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68 std::string key("");
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69 octave_value subov;
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70 diff -ur dicom.orig/src/dicomwrite.cpp dicom/src/dicomwrite.cpp
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71 --- dicom.orig/src/dicomwrite.cpp 2015-04-15 21:36:10.000000000 -0400
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72 +++ dicom/src/dicomwrite.cpp 2015-04-15 21:41:49.000000000 -0400
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73 @@ -43,7 +43,7 @@
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74 // TODO all fns here should throw exceptions, not use this "std::string & err" arg
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75
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76 void struct2metadata(gdcm::ImageWriter *w, gdcm::File *file, const octave_value & ov, bool trial, int sequenceDepth) ;
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77 -void structarray2sequence(gdcm::SequenceOfItems & sq, Octave_map * om, bool trial, int sequenceDepth);
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78 +void structarray2sequence(gdcm::SequenceOfItems & sq, octave_map * om, bool trial, int sequenceDepth);
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79 void value2element (gdcm::DataElement * de, const octave_value * ov, gdcm::Tag * tag, const std::string & keyword, bool trial, bool * handled, int sequenceDepth);
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80 void octaveVal2dicomImage(gdcm::ImageWriter *w, octave_value *pixval) ;
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81 void genMinimalMetaData(gdcm::ImageWriter *w, gdcm::File *file);
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82 @@ -132,9 +132,9 @@
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83 }
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84 gdcm::DataSet ds;
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85 gdcm::FileMetaInformation hds;
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86 - Octave_map om=ov.map_value();
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87 + octave_map om=ov.map_value();
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88 uint32_t skipped = 0;
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89 - for (Octave_map::iterator it = om.begin(); it != om.end(); it++) {
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90 + for (octave_map::iterator it = om.begin(); it != om.end(); it++) {
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91 std::string keyword(om.key(it));
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92 Cell cell = om.contents(it);
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93 if (!dicom_is_present(keyword)) {
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94 @@ -179,17 +179,17 @@
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95 return ;
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96 }
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97
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98 -void structarray2sequence(gdcm::SequenceOfItems & sq, Octave_map * om, bool trial, int sequenceDepth) {
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99 - for (Octave_map::iterator it = om->begin(); it != om->end(); it++) {
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100 +void structarray2sequence(gdcm::SequenceOfItems & sq, octave_map * om, bool trial, int sequenceDepth) {
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101 + for (octave_map::iterator it = om->begin(); it != om->end(); it++) {
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102 gdcm::Item item;
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103 // item.SetVLToUndefined(); //TODO: does VL need to be set for items that contain datasets?
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104 gdcm::DataSet &nds = item.GetNestedDataSet();
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105 std::string itemname(om->key(it));
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106 // TODO: test itemname is something like Item_n.
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107 Cell cell = om->contents(it);
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108 - Octave_map subom = cell(0).map_value();
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109 + octave_map subom = cell(0).map_value();
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110 // octave_stdout << itemname <<std::endl;
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111 - for (Octave_map::iterator subit = subom.begin(); subit != subom.end(); subit++) {
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112 + for (octave_map::iterator subit = subom.begin(); subit != subom.end(); subit++) {
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113 std::string subkeyword(subom.key(subit));
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114 gdcm::DataElement de;
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115 gdcm::Tag tag;
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116 @@ -289,7 +289,7 @@
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117 }
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118 octave_stdout << std::endl;
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119 //int nObj = ov->numel() ;
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120 - Octave_map subom = ov->map_value();
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121 + octave_map subom = ov->map_value();
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122 gdcm::SmartPointer<gdcm::SequenceOfItems> sq = new gdcm::SequenceOfItems();
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123 try {
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124 structarray2sequence(*sq, &subom, trial, ++sequenceDepth) ;
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125 diff -ur dicom.orig/src/Makefile dicom/src/Makefile
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126 --- dicom.orig/src/Makefile 2015-04-15 21:36:10.000000000 -0400
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127 +++ dicom/src/Makefile 2015-04-15 21:40:04.000000000 -0400
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128 @@ -15,10 +15,11 @@
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129 # Please see the file, "COPYING" for further details of GNU General
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130 # Public License version 3.
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131
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132 -
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133 +MKOCTFILE ?= mkoctfile
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134 +OCTAVE ?= octave
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135
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136 INCDIRFLAGS =
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137 -LIBDIRFLAGS = -L/usr/local/lib
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138 +LIBDIRFLAGS =
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139 GDCMLIBFLAGS = -lgdcmcharls -lgdcmjpeg8 -lgdcmjpeg12 \
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140 -lgdcmjpeg16 -lgdcmCommon \
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141 -lgdcmDICT -lgdcmDSED -lgdcmIOD -lgdcmMSFF
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142 @@ -29,35 +30,35 @@
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143
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144
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145 dicomlookup.oct: dicomdict.o dicomlookup.o
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146 - mkoctfile $(INCDIRFLAGS) $(LIBDIRFLAGS) $(GDCMLIBFLAGS) $(DEBUGFLAG) dicomlookup.o dicomdict.o -o dicomlookup.oct
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147 + $(MKOCTFILE) $(INCDIRFLAGS) $(LIBDIRFLAGS) $(GDCMLIBFLAGS) $(DEBUGFLAG) dicomlookup.o dicomdict.o -o dicomlookup.oct
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148
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149 dicomdict.oct: dicomdict.o
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150 - mkoctfile $(INCDIRFLAGS) $(DEBUGFLAG) dicomdict.o
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151 + $(MKOCTFILE) $(INCDIRFLAGS) $(DEBUGFLAG) dicomdict.o
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152
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153 dicominfo.oct: dicominfo.o dicomdict.o
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154 - mkoctfile $(INCDIRFLAGS) $(LIBDIRFLAGS) $(GDCMLIBFLAGS) $(DEBUGFLAG) dicominfo.o dicomdict.o -o dicominfo.oct
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155 + $(MKOCTFILE) $(INCDIRFLAGS) $(LIBDIRFLAGS) $(GDCMLIBFLAGS) $(DEBUGFLAG) dicominfo.o dicomdict.o -o dicominfo.oct
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156
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157 dicomwrite.oct: dicomwrite.o dicomdict.o
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158 - mkoctfile $(INCDIRFLAGS) $(LIBDIRFLAGS) $(GDCMLIBFLAGS) $(DEBUGFLAG) dicomwrite.o dicomdict.o -o dicomwrite.oct
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159 + $(MKOCTFILE) $(INCDIRFLAGS) $(LIBDIRFLAGS) $(GDCMLIBFLAGS) $(DEBUGFLAG) dicomwrite.o dicomdict.o -o dicomwrite.oct
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160
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161 dicomread.oct: dicomread.cpp
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162 - mkoctfile $(INCDIRFLAGS) $(LIBDIRFLAGS) $(GDCMLIBFLAGS) $(DEBUGFLAG) dicomread.cpp
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163 + $(MKOCTFILE) $(INCDIRFLAGS) $(LIBDIRFLAGS) $(GDCMLIBFLAGS) $(DEBUGFLAG) dicomread.cpp
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164
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165 _gendicomdict.oct: _gendicomdict.cpp
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166 - mkoctfile $(INCDIRFLAGS) $(LIBDIRFLAGS) $(GDCMLIBFLAGS) $(DEBUGFLAG) _gendicomdict.cpp
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167 + $(MKOCTFILE) $(INCDIRFLAGS) $(LIBDIRFLAGS) $(GDCMLIBFLAGS) $(DEBUGFLAG) _gendicomdict.cpp
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168
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169
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170 dicominfo.o: dicomdict.h dicominfo.cpp
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171 - mkoctfile -c $(INCDIRFLAGS) $(DEBUGFLAG) dicominfo.cpp
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172 + $(MKOCTFILE) -c $(INCDIRFLAGS) $(DEBUGFLAG) dicominfo.cpp
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173
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174 dicomwrite.o: dicomdict.h dicomwrite.cpp
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175 - mkoctfile -c $(INCDIRFLAGS) $(DEBUGFLAG) dicomwrite.cpp
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176 + $(MKOCTFILE) -c $(INCDIRFLAGS) $(DEBUGFLAG) dicomwrite.cpp
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177
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178 dicomdict.o: dicomdict.h dicomdict.cpp
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179 - mkoctfile -c $(INCDIRFLAGS) $(DEBUGFLAG) dicomdict.cpp
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180 + $(MKOCTFILE) -c $(INCDIRFLAGS) $(DEBUGFLAG) dicomdict.cpp
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181
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182 dicomlookup.o: dicomdict.h dicomlookup.cpp
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183 - mkoctfile -c $(INCDIRFLAGS) $(DEBUGFLAG) dicomlookup.cpp
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184 + $(MKOCTFILE) -c $(INCDIRFLAGS) $(DEBUGFLAG) dicomlookup.cpp
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185
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186 clean:
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187 rm -f *.o *.oct *~
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188 @@ -65,13 +66,14 @@
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189 test: test_dicominfo test_dicomdict test_dicomread test_dicomlookup
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190
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191 test_dicominfo: dicominfo.oct
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192 - octave -q --eval "test dicominfo.cpp"
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193 + $(OCTAVE) -q --eval "test dicominfo.cpp"
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194
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195 test_dicomdict: dicomdict.oct
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196 - octave -q --eval "test dicomdict.cpp"
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197 + $(OCTAVE) -q --eval "test dicomdict.cpp"
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198
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199 test_dicomread: dicomread.oct
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200 - octave -q --eval "test dicomread.cpp"
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201 + $(OCTAVE) -q --eval "test dicomread.cpp"
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202
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203 test_dicomlookup: dicomlookup.oct
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204 - octave -q --eval "test dicomlookup.cpp"
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205 \ No newline at end of file
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206 + $(OCTAVE) -q --eval "test dicomlookup.cpp"
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207 +
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208 diff -ur dicom.orig/src/dicominfo.cpp dicom/src/dicominfo.cpp
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209 --- dicom.orig/src/dicominfo.cpp 2015-04-15 21:44:32.000000000 -0400
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210 +++ dicom/src/dicominfo.cpp 2015-04-15 21:47:48.000000000 -0400
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211 @@ -187,10 +187,10 @@
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212 gdcm::DataSet &ds = file.GetDataSet();
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213 gdcm::FileMetaInformation &hds=file.GetHeader();
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214
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215 - om.assign("Filename",filename);
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216 + om.assign("Filename",octave_value(filename));
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217 char dateStr[TIME_STR_LEN+1];
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218 getFileModTime(dateStr, filename);
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219 - om.assign("FileModDate", dateStr);
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220 + om.assign("FileModDate", octave_value(dateStr));
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221 if(chatty) octave_stdout << "# file info\nFilename:"
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222 << filename << "\nFileModDate:" << dateStr << '\n';
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223
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224 @@ -220,7 +220,7 @@
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225 om->assign(varname.c_str(), ov);
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226 } else {
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227 if (0==varname.length()) return ;
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228 - om->assign(varname.c_str(), "not assigned");
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229 + om->assign(varname.c_str(), octave_value("not assigned"));
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230 }
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231 }
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232
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233 @@ -464,7 +464,7 @@
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234 subom.assign(key.c_str(), subov);
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235 } else {
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236 if (0==key.length()) continue ;
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237 - subom.assign(key.c_str(), "not assigned");
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238 + subom.assign(key.c_str(), octave_value("not assigned"));
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239 }
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240 }
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241 snprintf(item_name_buf,15,"Item_%i",j);