[GRASS-dev] [GRASS GIS] #3247: i.superpixels.slic fails when region larger than 500x500 pix (on Win7)

GDAL · January 10, 2017, 8:21am

#3247: i.superpixels.slic fails when region larger than 500x500 pix (on Win7)
--------------------------------+-------------------------
Reporter: tgrippa | Owner: grass-dev@…
Type: defect | Status: new
Priority: normal | Milestone: 7.0.6
Component: Imagery | Version: unspecified
Keywords: i.superpixels.slic | CPU: Unspecified
Platform: MSWindows 7 |
--------------------------------+-------------------------
Hi,

I tested the new i.superpixels.slic add-on on the North Carolina dataset.
It is very fast and interesting.

Unfortunately, when reaching a region of more than 500x500 pixels (it is
what I've found), the add-on crashes.

Here after the command I used

OK:

g.remove -f type=group name=ortho

i.group group=ortho input=ortho_2001_t792_1m

g.region raster=ortho_2001_t792_1m n=219956 s=219456 e=637533 w=637033
rows=500 cols=500

g.region -p

i.superpixels.slic --overwrite group=ortho k=500 output=slic_segment

Failing:

g.remove -f type=group name=ortho

i.group group=ortho input=ortho_2001_t792_1m

g.region raster=ortho_2001_t792_1m n=219966 s=219456 e=637543 w=637033
rows=510 cols=510

g.region -p

i.superpixels.slic --overwrite group=ortho k=500 output=slic_segment

A pop-up window appears with an "APPCRASH" message saying that GRASS 7
stops working.

FYI: my PC runs with an Intel core i5-3570 CPU (64 bits) (3.4Ghz) and 32Go
RAM

--
Ticket URL: <https://trac.osgeo.org/grass/ticket/3247>
GRASS GIS <https://grass.osgeo.org>

GDAL · January 10, 2017, 8:22am

#3247: i.superpixels.slic fails when region larger than 500x500 pix (on Win7)
--------------------------+--------------------------------
  Reporter: tgrippa | Owner: grass-dev@…
      Type: defect | Status: new
  Priority: normal | Milestone: 7.0.6
Component: Imagery | Version: unspecified
Resolution: | Keywords: i.superpixels.slic
       CPU: Unspecified | Platform: MSWindows 7
--------------------------+--------------------------------
Changes (by tgrippa):

* Attachment "Capture_APPCRASH.JPG" added.

APPCRASH_message

--
Ticket URL: <https://trac.osgeo.org/grass/ticket/3247>
GRASS GIS <https://grass.osgeo.org>

GDAL · January 10, 2017, 10:58am

#3247: i.superpixels.slic fails when region larger than 500x500 pix (on Win7)
--------------------------+--------------------------------
  Reporter: tgrippa | Owner: grass-dev@…
      Type: defect | Status: new
  Priority: normal | Milestone: 7.0.6
Component: Imagery | Version: unspecified
Resolution: | Keywords: i.superpixels.slic
       CPU: Unspecified | Platform: MSWindows 7
--------------------------+--------------------------------

Comment (by mlennert):

I can confirm segfault on Linux, but with different number of pixels:

{{{
g.region raster=ortho_2001_t792_1m n=220477 s=219456 e=638054 w=637033
res=1 -p
projection: 99 (Lambert Conformal Conic)
zone: 0
datum: nad83
ellipsoid: a=6378137 es=0.006694380022900787
north: 220477
south: 219456
west: 637033
east: 638054
nsres: 1
ewres: 1
rows: 1021
cols: 1021
cells: 1042441

i.superpixels.slic --overwrite group=ortho k=500 output=slic_segment
}}}

works, but

{{{
g.region raster=ortho_2001_t792_1m n=220479 s=219456 e=638056 w=637033
res=1 -p
projection: 99 (Lambert Conformal Conic)
zone: 0
datum: nad83
ellipsoid: a=6378137 es=0.006694380022900787
north: 220479
south: 219456
west: 637033
east: 638056
nsres: 1
ewres: 1
rows: 1023
cols: 1023
cells: 1046529

i.superpixels.slic --overwrite group=ortho k=500 output=slic_segment
}}}

gives me a segfault. 1022x1022 sometimes does, sometimes doesn't.

Here's the backtrace I get in gdb, but I guess the addon needs to be
recompiled with debugging enabled:

{{{
#0 0x00007ffff70f9d3e in _IO_vfprintf_internal (s=0x7fffff7ff180,
format=0x7ffff7790b7b "%4d%%\b\b\b\b\b", ap=0x7fffff801828)
     at vfprintf.c:1267
#1 0x00007ffff70fcc23 in buffered_vfprintf (s=0x7ffff744c520
<_IO_2_1_stderr_>, format=<optimized out>, args=<optimized out>)
     at vfprintf.c:2325
#2 0x00007ffff70f9f15 in _IO_vfprintf_internal (s=0x7ffff744c520
<_IO_2_1_stderr_>, format=0x7ffff7790b7b "%4d%%\b\b\b\b\b",
     ap=ap@entry=0x7fffff801828) at vfprintf.c:1293
#3 0x00007ffff7102157 in __fprintf (stream=<optimized out>,
format=format@entry=0x7ffff7790b7b "%4d%%\b\b\b\b\b")
     at fprintf.c:32
#4 0x00007ffff7780e4a in G_percent (n=0, d=10, s=<optimized out>) at
percent.c:83
#5 0x0000555555555c21 in main (argc=<optimized out>, argv=<optimized
out>) at main.c:338
}}}

Here's the output with g.gisenv set=DEBUG=3:

{{{
D1/3: G_find_raster2(): name=ortho_2001_t792_1m mapset=PERMANENT
D2/3: G_file_name(): path =
/data/GRASS/DATA7/nc_spm_08/PERMANENT/cell/ortho_2001_t792_1m
D2/3: G_file_name(): path =
/data/GRASS/DATA7/nc_spm_08/PERMANENT/fcell/ortho_2001_t792_1m
D2/3: G_file_name(): path =
/data/GRASS/DATA7/nc_spm_08/PERMANENT/g3dcell/ortho_2001_t792_1m
D1/3: G_find_raster2(): name=ortho_2001_t792_1m mapset=PERMANENT
D2/3: G_file_name(): path =
/data/GRASS/DATA7/nc_spm_08/PERMANENT/cell/ortho_2001_t792_1m
D1/3: G_find_raster2(): name=ortho_2001_t792_1m mapset=PERMANENT
D2/3: G_file_name(): path =
/data/GRASS/DATA7/nc_spm_08/PERMANENT/cell/ortho_2001_t792_1m
D2/3: G_file_name(): path =
/data/GRASS/DATA7/nc_spm_08/PERMANENT/fcell/ortho_2001_t792_1m
D2/3: G_file_name(): path =
/data/GRASS/DATA7/nc_spm_08/PERMANENT/g3dcell/ortho_2001_t792_1m
D2/3: G_file_name(): path =
/data/GRASS/DATA7/nc_spm_08/PERMANENT/cell_misc/ortho_2001_t792_1m/gdal
D2/3: G_file_name(): path =
/data/GRASS/DATA7/nc_spm_08/PERMANENT/cell/ortho_2001_t792_1m
D2/3: G_file_name(): path =
/data/GRASS/DATA7/nc_spm_08/PERMANENT/cell/ortho_2001_t792_1m
D3/3: create window mapping (1023 columns)
D2/3: G_file_name(): path =
/data/GRASS/DATA7/nc_spm_08/PERMANENT/cell_misc/ortho_2001_t792_1m/null
D2/3: G_file_name(): path =
/data/GRASS/DATA7/nc_spm_08/PERMANENT/cell_misc/ortho_2001_t792_1m/null
D1/3: G_find_raster(): name=MASK mapset=user1
D2/3: G_file_name(): path = /data/GRASS/DATA7/nc_spm_08/user1/cell/MASK
D1/3: G_find_raster2(): name=ortho_2001_t792_1m mapset=PERMANENT
D2/3: G_file_name(): path =
/data/GRASS/DATA7/nc_spm_08/PERMANENT/cell/ortho_2001_t792_1m
D2/3: G_file_name(): path =
/data/GRASS/DATA7/nc_spm_08/PERMANENT/fcell/ortho_2001_t792_1m
D2/3: G_file_name(): path =
/data/GRASS/DATA7/nc_spm_08/PERMANENT/g3dcell/ortho_2001_t792_1m
Erreur de segmentation
}}}

--
Ticket URL: <https://trac.osgeo.org/grass/ticket/3247#comment:1>
GRASS GIS <https://grass.osgeo.org>

GDAL · January 10, 2017, 11:23am

#3247: i.superpixels.slic fails when region larger than 500x500 pix (on Win7)
--------------------------+--------------------------------
  Reporter: tgrippa | Owner: grass-dev@…
      Type: defect | Status: new
  Priority: normal | Milestone: 7.0.6
Component: Imagery | Version: unspecified
Resolution: | Keywords: i.superpixels.slic
       CPU: Unspecified | Platform: MSWindows 7
--------------------------+--------------------------------

Comment (by mlennert):

No more segfault when I decomment the allocation of the distvect array in
line 317-18:

{{{
@@ -314,10 +314,10 @@
memset (sigmay, 0, sizeof (double) * numk);

- //double *distvec;
- // distvec = G_malloc (sizeof (double) * sz);
+ double *distvec;
+ distvec = G_malloc (sizeof (double) * sz);

- double distvec[sz];
+ /*double distvec[sz];*/
int p;
for( p = 0; p < sz; p++ ) distvec[p] = 1E+9;
}}}

Don't know why this was commented, though, so I'll wait for Rashad to
react.

--
Ticket URL: <https://trac.osgeo.org/grass/ticket/3247#comment:2>
GRASS GIS <https://grass.osgeo.org>

GDAL · January 11, 2017, 9:37am

#3247: i.superpixels.slic fails when region larger than 500x500 pix (on Win7)
--------------------------+--------------------------------
  Reporter: tgrippa | Owner: grass-dev@…
      Type: defect | Status: new
  Priority: normal | Milestone: 7.0.6
Component: Imagery | Version: unspecified
Resolution: | Keywords: i.superpixels.slic
       CPU: Unspecified | Platform: MSWindows 7
--------------------------+--------------------------------

Comment (by mlennert):

I attach a more complete patch. It also includes assigning a random color
table and writing to the output file history.

Rashad, I don't want to commit because I don't know if you have been
working locally on the module. Please let me know if you will do it, or if
you want me to commit.

--
Ticket URL: <https://trac.osgeo.org/grass/ticket/3247#comment:3>
GRASS GIS <https://grass.osgeo.org>

GDAL · January 11, 2017, 9:38am

#3247: i.superpixels.slic fails when region larger than 500x500 pix (on Win7)
--------------------------+--------------------------------
  Reporter: tgrippa | Owner: grass-dev@…
      Type: defect | Status: new
  Priority: normal | Milestone: 7.0.6
Component: Imagery | Version: unspecified
Resolution: | Keywords: i.superpixels.slic
       CPU: Unspecified | Platform: MSWindows 7
--------------------------+--------------------------------
Changes (by mlennert):

* Attachment "distc_segfault_patch.diff" added.

--
Ticket URL: <https://trac.osgeo.org/grass/ticket/3247>
GRASS GIS <https://grass.osgeo.org>

GDAL · January 11, 2017, 3:51pm

#3247: i.superpixels.slic fails when region larger than 500x500 pix (on Win7)
--------------------------+--------------------------------
  Reporter: tgrippa | Owner: grass-dev@…
      Type: defect | Status: new
  Priority: normal | Milestone: 7.0.6
Component: Imagery | Version: unspecified
Resolution: | Keywords: i.superpixels.slic
       CPU: Unspecified | Platform: MSWindows 7
--------------------------+--------------------------------

Comment (by mmetz):

Replying to [comment:3 mlennert]:
> I attach a more complete patch. It also includes assigning a random
color table and writing to the output file history.

There is more to fix around L157, see also my comments in the dev ml [0]

[0] https://lists.osgeo.org/pipermail/grass-dev/2017-January/083745.html

--
Ticket URL: <https://trac.osgeo.org/grass/ticket/3247#comment:4>
GRASS GIS <https://grass.osgeo.org>

GDAL · January 12, 2017, 7:51am

#3247: i.superpixels.slic fails when region larger than 500x500 pix (on Win7)
--------------------------+--------------------------------
  Reporter: tgrippa | Owner: grass-dev@…
      Type: defect | Status: new
  Priority: normal | Milestone: 7.0.6
Component: Imagery | Version: unspecified
Resolution: | Keywords: i.superpixels.slic
       CPU: Unspecified | Platform: MSWindows 7
--------------------------+--------------------------------

Comment (by mlennert):

Replying to [comment:4 mmetz]:
> Replying to [comment:3 mlennert]:
> > I attach a more complete patch. It also includes assigning a random
color table and writing to the output file history.
>
> There is more to fix around L157, see also my comments in the dev ml [0]
>
> [0] https://lists.osgeo.org/pipermail/grass-dev/2017-January/083745.html

Yes, sorry, I had overlooked that you had already solved this issue and
others in that mail. I don't know how much of this might become redundant
when the SEG library is used.

If Rashad doesn't tell me otherwise, I'll commit your fixes + my additions
later today.

--
Ticket URL: <https://trac.osgeo.org/grass/ticket/3247#comment:5>
GRASS GIS <https://grass.osgeo.org>

GDAL · January 26, 2017, 12:11pm

#3247: i.superpixels.slic fails when region larger than 500x500 pix (on Win7)
--------------------------+--------------------------------
  Reporter: tgrippa | Owner: grass-dev@…
      Type: defect | Status: closed
  Priority: normal | Milestone: 7.0.6
Component: Imagery | Version: unspecified
Resolution: fixed | Keywords: i.superpixels.slic
       CPU: Unspecified | Platform: MSWindows 7
--------------------------+--------------------------------
Changes (by mlennert):

* status: new => closed
* resolution: => fixed

Comment:

In [changeset:"70434" 70434]:
{{{
#!CommitTicketReference repository="" revision="70434"
i.superpixels.slic: allocate on the heap, not the stack (fixes #3247)
}}}

--
Ticket URL: <https://trac.osgeo.org/grass/ticket/3247#comment:6>
GRASS GIS <https://grass.osgeo.org>

GDAL · January 26, 2017, 12:13pm

#3247: i.superpixels.slic fails when region larger than 500x500 pix (on Win7)
--------------------------+--------------------------------
  Reporter: tgrippa | Owner: grass-dev@…
      Type: defect | Status: closed
  Priority: normal | Milestone: 7.0.6
Component: Imagery | Version: unspecified
Resolution: fixed | Keywords: i.superpixels.slic
       CPU: Unspecified | Platform: MSWindows 7
--------------------------+--------------------------------

Comment (by mlennert):

For now I've committed (r70434) just the fix for the segmentation fault,
not the rest of the patch, so that others can work with the module.

Please test (AFAIK for Windows users you will have to wait until tomorrow
to get the binary compiled) and tell us if we can close this ticket.

--
Ticket URL: <https://trac.osgeo.org/grass/ticket/3247#comment:7>
GRASS GIS <https://grass.osgeo.org>