GMT crashes when grdcut a tiff file #3992

seisman · 2020-08-18T05:49:39Z

$ gmt grdcut @earth_day_05m -R0/30/0/30 -Gabc.tiff
ERROR: Caught signal number 11 (Segmentation fault) at
0   libgmt.6.dylib                      0x0000000103aa61e9 gmt_gdal_read_grd + 2057
1   ???                                 0x00007ffa8bdf1000 0x0 + 140714065203200
Stack backtrace:
0   libgmt.6.dylib                      0x0000000103a56695 sig_handler + 581
1   libsystem_platform.dylib            0x00007fff685495fd _sigtramp + 29
2   ???                                 0x00007ffa89500000 0x0 + 140714022273024
3   libgmt.6.dylib                      0x0000000103ab9149 gmtlib_read_grd + 185
4   libgmt.6.dylib                      0x0000000103a89445 gmtapi_import_grid + 4885
5   libgmt.6.dylib                      0x0000000103a837c5 gmtapi_import_data + 437
6   libgmt.6.dylib                      0x0000000103a70b2c gmtapi_get_data + 348
7   libgmt.6.dylib                      0x0000000103a68f01 GMT_Read_Data + 4849
8   libgmt.6.dylib                      0x0000000103ccf478 GMT_grdcut + 11640
9   libgmt.6.dylib                      0x0000000103a78b7c GMT_Call_Module + 2156
10  gmt                                 0x0000000103a469a8 main + 2568
11  libdyld.dylib                       0x00007fff68350cc9 start + 1
12  ???                                 0x0000000000000005 0x0 + 5

The text was updated successfully, but these errors were encountered:

PaulWessel · 2020-08-18T05:52:49Z

Cannot immediately reproduce that:

gmt grdcut @earth_day_05m -R0/30/0/30 -Gabc.tiff
gmt grdinfo abc.tiff
abc.tiff: Title: Produced by grdcut
abc.tiff: Command: grdcut @earth_day_05m_p -R0/30/0/30 -Gabc.tiff
abc.tiff: Remark: 
abc.tiff: Pixel node registration used [Geographic grid]
abc.tiff: Grid file format: nf = GMT netCDF format (32-bit float), CF-1.7
abc.tiff: x_min: 0 x_max: 30 x_inc: 0.0833333333333 (5 min) name: longitude n_columns: 360
abc.tiff: y_min: 0 y_max: 30 y_inc: 0.0833333333333 (5 min) name: latitude n_rows: 360
abc.tiff: z_min: 0 z_max: 255 name: z
abc.tiff: scale_factor: 1 add_offset: 0
abc.tiff: format: netCDF-4 chunk_size: 180,180 shuffle: on deflation_level: 3
GEOGCS["unknown",
    DATUM["unknown",
        SPHEROID["unknown",6378137,0]],
    PRIMEM["Greenwich",0,
        AUTHORITY["EPSG","8901"]],
    UNIT["degree",0.0174532925199433,
        AUTHORITY["EPSG","9122"]],
    AXIS["Longitude",EAST],
    AXIS["Latitude",NORTH]]

seisman · 2020-08-18T06:08:02Z

Tried both GDAL 2.4.4 and 3.1.2. They both crash.

PaulWessel · 2020-08-18T06:15:50Z

OK, after dinner and movie...

joa-quim · 2020-08-18T21:50:36Z

It doesn't crash for me neither.

PaulWessel · 2020-09-03T07:21:53Z

Remember that although you ask for -Gabc.tiff, what is written here is a grid (netCDF). And you loose the green and blue layers since a grid is z only. I think you were imagining a subset of an image to be written? Also, you had some other GDAL related troubles so perhaps the crash is part of that?

PaulWessel · 2020-09-03T07:34:27Z

If we actually wanted grdcut to work on images like you probably expected, the shortcut to implementation would be

Detect that the input file is an image (simply by examining extensions, possibly by reading header)
If image, set up a series of grdmix calls to split into three grids, cut each of them, then reassmble:

gmt grdmix @earth_day_05m -D -Glayer%c.grd
gmt grdcut layerR.grd -R0/30/0/30 -GR.grd
gmt grdcut layerG.grd -R0/30/0/30 -GG.grd
gmt grdcut layerB.grd -R0/30/0/30 -GB.grd
gmt grdmix R.grd G.grd B.grd -C -Gcut.tif -N

Coded up as a short functions that sets the virtual files stuff it is all done in memory.

joa-quim · 2020-09-03T13:29:40Z

We talked this before. The solution should go into grdgdal.

seisman · 2020-09-03T19:25:35Z

Remember that although you ask for -Gabc.tiff, what is written here is a grid (netCDF). And you loose the green and blue layers since a grid is z only. I think you were imagining a subset of an image to be written?

I didn't realize that. I expect to have a subset of an image, written in tiff format.

Also, you had some other GDAL related troubles so perhaps the crash is part of that?

gmt grdinfo @earth_day_05m works well for me. gmt grdcut @earth_day_05m -R0/30/0/30 -Gabc.tiff -Vd shows the following messages before crashing:

grdcut [DEBUG]: gmt_get_filename: In: /Users/seisman/.gmt/server/earth/earth_day/earth_day_05m_p.hdr Out: /Users/seisman/.gmt/server/earth/earth_day/earth_day_05m_p.hdr
grdcut [DEBUG]: Found readable file /Users/seisman/.gmt/server/earth/earth_day/earth_day_05m_p.tif
grdcut [INFORMATION]: File /Users/seisman/.gmt/server/earth/earth_day/earth_day_05m_p.tif reads with GDAL driver GTiff
grdcut [DEBUG]: Found readable file /Users/seisman/.gmt/server/earth/earth_day/earth_day_05m_p.tif
grdcut [DEBUG]: Geographic input grid, longitudes span less than 360
grdcut [DEBUG]: Call gmtgrdio_doctor_geo_increments on a geographic grid
grdcut [DEBUG]: Map distance calculation will be using great circle approximation with authalic auxiliary latitudes and authalic (R_2) radius = 6371007.1809 m, in meter.
grdcut [DEBUG]: Geographic input grid, longitudes span exactly 360
grdcut [DEBUG]: GMT_End_IO: Input resource access is now disabled
grdcut [DEBUG]: gmtapi_begin_io: Input resource access is now enabled [container]
grdcut [DEBUG]: gmtapi_import_grid: Passed ID = 0 and mode = 2
grdcut [INFORMATION]: Reading grid from file /Users/seisman/.gmt/server/earth/earth_day/earth_day_05m_p.tif
grdcut [INFORMATION]: Read band(s):	1
grdcut [DEBUG]: Found readable file /Users/seisman/.gmt/server/earth/earth_day/earth_day_05m_p.tif
grdcut [DEBUG]: Found readable file /Users/seisman/.gmt/server/earth/earth_day/earth_day_05m_p.tif
ERROR: Caught signal number 11 (Segmentation fault: 11) at
0   libgmt.6.dylib                      0x0000000104c06439 gmt_gdal_read_grd + 2057
1   ???                                 0x00007ff9778e2000 0x0 + 140709429387264
Stack backtrace:
0   libgmt.6.dylib                      0x0000000104bb5ef2 sig_handler + 578
1   libsystem_platform.dylib            0x00007fff6fe815fd _sigtramp + 29
2   ???                                 0x0000000000000006 0x0 + 6
3   libgmt.6.dylib                      0x0000000104c195a9 gmtlib_read_grd + 185
4   libgmt.6.dylib                      0x0000000104be9635 gmtapi_import_grid + 4885
5   libgmt.6.dylib                      0x0000000104be39b5 gmtapi_import_data + 437
6   libgmt.6.dylib                      0x0000000104bd090c gmtapi_get_data + 348
7   libgmt.6.dylib                      0x0000000104bc8d11 GMT_Read_Data + 4849
8   libgmt.6.dylib                      0x0000000104e35218 GMT_grdcut + 11640
9   libgmt.6.dylib                      0x0000000104bd895c GMT_Call_Module + 2156
10  gmt                                 0x0000000104ba59a8 main + 2568
11  libdyld.dylib                       0x00007fff6fc88cc9 start + 1
12  ???                                 0x0000000000000006 0x0 + 6

Debugging in xcode shows the crash point:

head->size is 132694, and j is 131072.

stale · 2020-12-04T22:02:32Z

This issue has been automatically marked as stale because it has not had activity in the last 90 days. It will be closed if no further activity occurs within 7 days. Thank you for your contributions.

joa-quim · 2021-03-15T00:17:31Z

Hmm, but this tiff file is indexed so it should have ~worked (though loose the cpt).

PaulWessel · 2021-03-15T17:39:41Z

Does this still crash for @seisman ? Works fine for me.

seisman · 2021-03-15T17:48:33Z

It still crashes for me.

joa-quim · 2021-03-15T17:50:47Z

And for me too, but Kristof showed as the example of the land cover file where he was able to do a grdcut on a single band tif file.

stale · 2021-06-16T23:05:19Z

This issue has been automatically marked as stale because it has not had activity in the last 90 days. It will be closed if no further activity occurs within 7 days. Thank you for your contributions.

maxrjones · 2021-09-27T21:50:38Z

@seisman, would you be able to check whether #5798 fixes this crash? For me, it works fine but it seems that the problem was not easily reproducible to start with.

seisman · 2021-09-27T23:27:52Z

Yes, it works with PR #5798.

maxrjones · 2021-09-27T23:29:56Z

Yes, it works with PR #5798.

Great, thanks!

maxrjones · 2021-09-28T18:44:52Z

Fixed by #5798

weiji14 mentioned this issue Sep 3, 2020

Wrapper for grdmix GenericMappingTools/pygmt#578

Open

stale bot added the stale This will not be worked on label Dec 4, 2020

seisman removed the stale This will not be worked on label Dec 4, 2020

stale bot added the stale This will not be worked on label Jun 16, 2021

seisman removed the stale This will not be worked on label Jun 17, 2021

maxrjones added the bug Something isn't working label Sep 22, 2021

maxrjones added this to the 6.3.0 milestone Sep 22, 2021

maxrjones closed this as completed Sep 28, 2021

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GMT crashes when grdcut a tiff file #3992

GMT crashes when grdcut a tiff file #3992

seisman commented Aug 18, 2020

PaulWessel commented Aug 18, 2020

seisman commented Aug 18, 2020

PaulWessel commented Aug 18, 2020

joa-quim commented Aug 18, 2020

PaulWessel commented Sep 3, 2020

PaulWessel commented Sep 3, 2020

joa-quim commented Sep 3, 2020

seisman commented Sep 3, 2020

stale bot commented Dec 4, 2020

joa-quim commented Mar 15, 2021

PaulWessel commented Mar 15, 2021

seisman commented Mar 15, 2021

joa-quim commented Mar 15, 2021 •

edited

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stale bot commented Jun 16, 2021

maxrjones commented Sep 27, 2021

seisman commented Sep 27, 2021

maxrjones commented Sep 27, 2021

maxrjones commented Sep 28, 2021

GMT crashes when grdcut a tiff file #3992

GMT crashes when grdcut a tiff file #3992

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seisman commented Aug 18, 2020

PaulWessel commented Aug 18, 2020

seisman commented Aug 18, 2020

PaulWessel commented Aug 18, 2020

joa-quim commented Aug 18, 2020

PaulWessel commented Sep 3, 2020

PaulWessel commented Sep 3, 2020

joa-quim commented Sep 3, 2020

seisman commented Sep 3, 2020

stale bot commented Dec 4, 2020

joa-quim commented Mar 15, 2021

PaulWessel commented Mar 15, 2021

seisman commented Mar 15, 2021

joa-quim commented Mar 15, 2021 • edited Loading

stale bot commented Jun 16, 2021

maxrjones commented Sep 27, 2021

seisman commented Sep 27, 2021

maxrjones commented Sep 27, 2021

maxrjones commented Sep 28, 2021

joa-quim commented Mar 15, 2021 •

edited

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