Mercurial > mxe-octave
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> |
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date | Wed, 15 Apr 2015 21:52:37 -0400 |
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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); |