[Gdcm-hackers] [ gdcm-Bugs-3067845 ] segfault in gdcmFileMetaInformation.cxx while writing RTPlan

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Bugs item #3067845, was opened at 2010-09-16 12:21
Message generated for change (Comment added) made by malat
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Category: General (default)
>Group: 2.0.19
>Status: Pending
Resolution: None
>Priority: 1
Private: No
Submitted By: andy buckle (blondandy)
Assigned to: Mathieu Malaterre (malat)
Summary: segfault in gdcmFileMetaInformation.cxx while writing RTPlan

Initial Comment:
gdcm 2.0.16. My code is loading a dicom file, turning everything into GNU Octave variables, turning everything back into GDCM objects, and then saving.

Below is
(1) part of a backtrace (the problem is bv being a null pointer, but I
can't see why it is).
(2) a snippet of my code, before it does the writing. I print the
SOPClassUID to see if I made the File and Writer objects properly.
This prints OK.

Note: This is RTPlan, so no image. I did it this way because this is
supposed to be general purpose (image or not) code.

Mathieu - I hope you are recovering rapidly.

Thanks,

Andy

(1)
#0  0x00007fffee35d485 in gdcm::FileMetaInformation::FillFromDataSet
(this=0x7fffffffca60, ds=...)
   at /home/andy/gdcm/gdcm-2-0/Source/DataStructureAndEncodingDefinition/gdcmFileMetaInformation.cxx:178
       sopclass = @0x139bb10
       mssopclass = {TagField = {ElementTag = {tag = 131074, tags =
{2, 2}, bytes = "\002\000\002"}}, ValueLengthField = {ValueLength =
30},
         VRField = {VRField = UI}, ValueField = {Pointer =
0x15f5fa0}}
       bv = 0x0
       dicomdir = false
       xde = {TagField = {ElementTag = {tag = 65538, tags = {2, 1},
bytes = "\002\000\001"}}, ValueLengthField = {ValueLength = 2},
VRField = {
           VRField = OB}, ValueField = {Pointer = 0x15f94b0}}
       dummy = @0x7ffff6bfaa59
       filemetagrouplength = {Internal = {4294952800}}
       glen = 32767
#1  0x00007fffee38ff9f in gdcm::Writer::Write (this=0x7fffffffcdc0)
   at /home/andy/gdcm/gdcm-2-0/Source/DataStructureAndEncodingDefinition/gdcmWriter.cxx:73
       duplicate = {<gdcm::DataSet> = {DES = std::set with 5 elements
= {[0] = {TagField = {ElementTag = {tag = 65538, tags = {2, 1},
                   bytes = "\002\000\001"}}, ValueLengthField =
{ValueLength = 2}, VRField = {VRField = OB}, ValueField = {Pointer =
0x15f94b0}},
             [1] = {TagField = {ElementTag = {tag = 131074, tags =
{2, 2}, bytes = "\002\000\002"}}, ValueLengthField = {ValueLength =
30}, VRField = {
                 VRField = UI}, ValueField = {Pointer = 0x15f5fa0}},
[2] = {TagField = {ElementTag = {tag = 196610, tags = {2, 3},
                   bytes = "\002\000\003"}}, ValueLengthField =
{ValueLength = 46}, VRField = {VRField = UI}, ValueField = {Pointer =
0x15fb4f0}},
             [3] = {TagField = {ElementTag = {tag = 1048578, tags =
{2, 16}, bytes = "\002\000\020"}}, ValueLengthField = {ValueLength =
18},
               VRField = {VRField = UI}, ValueField = {Pointer =
0x139b310}}, [4] = {TagField = {ElementTag = {tag = 1179650, tags =
{2, 18},
                   bytes = "\002\000\022"}}, ValueLengthField =
{ValueLength = 20}, VRField = {VRField = UI}, ValueField = {Pointer =
0x15fae90}}},
           static DEEnd = {TagField = {ElementTag = {tag =
4294967295, tags = {65535, 65535}, bytes = "\377\377\377\377"}},
ValueLengthField = {
               ValueLength = 0}, VRField = {VRField = INVALID},
ValueField = {Pointer = 0x0}}}, DataSetTS = {TSField = TS_END},
         MetaInformationTS = Unknown, DataSetMS = MS_END, P =
{Internal = 0x1376640 ""},
         static GDCM_FILE_META_INFORMATION_VERSION = 0x7fffee39eadf
"",
         static GDCM_IMPLEMENTATION_CLASS_UID = 0x7fffee39eb00
"1.2.826.0.1.3680043.2.1143.107.104.103.115.2.0.16",
         static GDCM_IMPLEMENTATION_VERSION_NAME = 0x7fffee39eb32
"GDCM 2.0.16", static GDCM_SOURCE_APPLICATION_ENTITY_TITLE =
0x7fffee39eb3e "GDCM",
         static ImplementationClassUID =
"1.2.826.0.1.3680043.2.1143.107.104.103.115.2.0.16", static
ImplementationVersionName = "GDCM 2.0.16",
         static SourceApplicationEntityTitle = "GDCM"}
       os = @0x110ad80
       Header = @0x1111f60
       DS = @0x1111fa8
       ts = @0x1111f50
#2  0x00007fffed90c26f in Fdicomwrite (args=<value optimized out>,
nargout=<value optimized out>) at dicomwrite.cpp:119
....

(2)
#if 1 /* debug */
       gdcm::File fc=w.GetFile();
       gdcm::DataSet dsc=fc.GetDataSet();
       const gdcm::DataElement & sopclass = dsc.GetDataElement(
gdcm::Tag(0x0008, 0x0016) ); // SOPClassUID
       const gdcm::ByteValue *bv = sopclass.GetByteValue();
       char * bufc=(char *) malloc((bv->GetLength()+1)*sizeof(char));
       memcpy(bufc, bv->GetPointer(), bv->GetLength());
       bufc[bv->GetLength()]='\0';
       octave_stdout << bufc << '\n' ;
       free(bufc);
#endif

       if( !trial ) {
               // if not writing image, use superclass
               if (writing_image ? !w.ImageWriter::Write() : !w.Writer::Write()){
                       error(QUOTED(OCT_FN_NAME)": unable to save");
                       return retval;
               }
       }

----------------------------------------------------------------------

>Comment By: Mathieu Malaterre (malat)
Date: 2011-12-30 01:44

Message:
Andy, could you give the latest git/release a try ? Pierre recently made a
commit about something very similar.

----------------------------------------------------------------------

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