Re: [Teem-users] ridge/creases extraction with seek and gage

[Wei L. <wei...@gm...>]

I reproduced the segfault with static linking to teem library, and now we
have more information:

--- begin trace ------

(gdb) where

#0  0x00000000004dee06 in airArrayLenSet (a=0x776010, newlen=33)

    at /home/weiliu/packages/teem-1.11.0-src/src/air/array.c:270

#1  0x00000000004deed8 in airArrayLenIncr (a=0x776010, delta=1)

    at /home/weiliu/packages/teem-1.11.0-src/src/air/array.c:313

#2  0x000000000040f4c6 in airMopAdd (arr=0x776010, ptr=0x776010,
mop=0x4246dd <nrrdNuke>, when=3)

    at /home/weiliu/packages/teem-1.11.0-src/src/air/mop.c:100

#3  0x000000000040d98b in main (argc=2, argv=0x7fffffffe388) at
/home/weiliu/projects/seismic/code/C/creases.c:21

---- end trace -----


I hope this mail list is still being monitored.  I appreciate anyone share
your insights.

On Tue, Apr 25, 2017 at 11:01 AM, Wei Liu <wei...@gm...> wrote:

> Hi Teem users,
>
>
>
> Instead of using the trv.c example, I copy-pasted Schultz’s code in [1]
> below and it compiles OK. Then I generated the Mobius image as suggested,
> and run the code as:
>
>
>
> > find_creases mobius-noisy.nrrd
>
>
>
> But then I got a segfault, and trace looks like:
>
>
>
> Program received signal SIGSEGV, Segmentation fault.
>
> 0x00007ffff78012ca in airArrayLenSet () from /home/weiliu/packages/teem-1.1
> 1.0-src/build/bin/libteem.so.1
>
> (gdb) where
>
> #0  0x00007ffff78012ca in airArrayLenSet () from
> /home/weiliu/packages/teem-1.11.0-src/build/bin/libteem.so.1
>
> #1  0x00007ffff780139c in airArrayLenIncr () from
> /home/weiliu/packages/teem-1.11.0-src/build/bin/libteem.so.1
>
> #2  0x00007ffff7807e57 in airMopAdd () from /home/weiliu/packages/teem-1.1
> 1.0-src/build/bin/libteem.so.1
>
> #3  0x000000000040159b in main (argc=2, argv=0x7fffffffe2f8) at
> /home/weiliu/projects/seismic/code/C/creases.c:21
>
>
>
> I appreciate any insights of this issue.
>
>
>
>
>
> p.s the code is exactly same as in [1], but here is relevant part:
>
>
>
> int main(int argc, char * argv[])
>
> {
>
>      airArray *mop = airMopNew();
>
>      airMopError(mop);
>
>
>
>
>
>      const char *filename = argv[1];
>
>
>
>      Nrrd *nin = nrrdNew();
>
>
>
>      if (nrrdLoad(nin, filename, NULL)) {
>
>                  char *err;
>
>                  airMopAdd(mop, err = biffGetDone(NRRD), airFree,
> airMopAlways);
>
>                  fprintf(stderr, "ERROR: Could not open input file
> \"%s\"\n"
>
>                                 "Reason: %s\n", filename, err);
>
>                  airMopError(mop); return 1;
>
> }
>
>      airMopAdd(mop, nin, (airMopper)nrrdNuke, airMopAlways);
>
>
>
>
>
>      gageContext *gctx = gageContextNew();
>
>      airMopAdd(mop, gctx, (airMopper)gageContextNix, airMopAlways);
>
>     double kparm[3]={1, 1.0, 0.0}; /* parameters of the cubic kernel */
>
>      gagePerVolume *pvl;
>
>      if (!(pvl = gagePerVolumeNew(gctx, nin, gageKindScl))
>
>                || gagePerVolumeAttach(gctx, pvl)
>
>                || gageKernelSet(gctx, gageKernel00, nrrdKernelBCCubic,
> kparm)
>
>                || gageKernelSet(gctx, gageKernel11, nrrdKernelBCCubicD,
> kparm)
>
>                || gageKernelSet(gctx, gageKernel22, nrrdKernelBCCubicDD,
> kparm)
>
>                || gageQueryItemOn(gctx, pvl, gageSclNormal)
>
>                || gageQueryItemOn(gctx, pvl, gageSclHessEval)
>
>                || gageQueryItemOn(gctx, pvl, gageSclHessEvec)
>
>                || gageQueryItemOn(gctx, pvl, gageSclHessEval2) /* ridge
> strength */
>
>                || gageUpdate(gctx)) {
>
>                  char *err;
>
>                  airMopAdd(mop, err = biffGetDone(GAGE), airFree,
> airMopAlways);
>
>                  fprintf(stderr, "ERROR while setting up Gage:\n%s\n",
> err);
>
>                  airMopError(mop); return 1;
>
>      }
>
> On Mon, Apr 24, 2017 at 11:41 AM, Wei Liu <wei...@gm...> wrote:
>
>> Hi Teem users,
>>
>>
>>
>> I’m trying to use the ridge extraction code as descripted in [1], and I’m
>> running into issue similar to a previous post [2]. Here are what I did: I
>> build trv.c and run it as
>>
>>
>>
>> trv -i ./mobius-noisy.nrrd -k scalar -s 150 -gi 'gageSclNormal'
>>
>>
>>
>> And I got errors:
>>
>>
>>
>> [gage] gageQueryItemOn: 0 not a valid gageScl value
>>
>>
>>
>> I understand that my ‘gi’ parameter is not in the correct format, but I
>> have no idea where to find the correct way to set it. I’m reading the
>> official ‘gage’ document now.
>>
>>
>>
>> Thanks for your input.
>>
>>
>>
>> [1] http://web.ci.uchicago.edu/~schultz/sphinx/creases.html
>>
>> [2] https://sourceforge.net/p/teem/mailman/message/25609154/
>>
>
>