[GRASS-dev] [GRASS GIS] #3278: Unble to import an AQUA image data (Level 2)in netcdf file format

GDAL · February 7, 2017, 1:44pm

#3278: Unble to import an AQUA image data (Level 2)in netcdf file format
------------------------+-------------------------
Reporter: laurent001 | Owner: grass-dev@…
Type: defect | Status: new
Priority: normal | Milestone: 7.2.1
Component: LibRaster | Version: unspecified
Keywords: | CPU: x86-64
Platform: MacOSX |
------------------------+-------------------------
GRASS versions : 7.2.0 and 7.3.0 (current).

Failure to import a netcdf file (extension : .nc)(raster data) of an AQUA
(satellite) image in the L2 level.

Seems to fail with HDF5 and GDAL according to error the log file.

Not tested L3 level satellite image (raster) data, nor L0 and L1.

GDAL, netCDF and HDF5 libraries were rebuild. Everything was OK but GRASS.

Consequence : unable to process satellite image adta with GRASS.

Encl. Log file generated by GRASS 7.2.0 as a text file.

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Ticket URL: <https://trac.osgeo.org/grass/ticket/3278>
GRASS GIS <https://grass.osgeo.org>

GDAL · February 7, 2017, 1:45pm

#3278: Unble to import an AQUA image data (Level 2)in netcdf file format
-------------------------+-------------------------
  Reporter: laurent001 | Owner: grass-dev@…
      Type: defect | Status: new
  Priority: normal | Milestone: 7.2.1
Component: LibRaster | Version: unspecified
Resolution: | Keywords:
       CPU: x86-64 | Platform: MacOSX
-------------------------+-------------------------
Changes (by laurent001):

* Attachment "grass_cmd_output-L2_AQUA_data_netcdf-2017-02-07.txt" added.

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Ticket URL: <https://trac.osgeo.org/grass/ticket/3278>
GRASS GIS <https://grass.osgeo.org>

GDAL · February 7, 2017, 1:56pm

#3278: Unble to import an AQUA image data (Level 2)in netcdf file format
-------------------------+-------------------------
  Reporter: laurent001 | Owner: grass-dev@…
      Type: defect | Status: new
  Priority: normal | Milestone: 7.2.1
Component: LibRaster | Version: unspecified
Resolution: | Keywords: r.in.gdal
       CPU: x86-64 | Platform: MacOSX
-------------------------+-------------------------
Changes (by neteler):

* keywords: => r.in.gdal

Comment:

From the log...:

{{{
r.import input=/Volumes/Data_1/_Image-Data/_NASA-
Ocean_colour/_AQUA/_AQUA-2016-11-30-Bay_of_Biscay/A2016335134000.L2_LAC_OC.nc
output=A2016335134000 -o
3 HDF5-DIAG: Error detected in HDF5 (1.8.18) thread 0:
4 #000: /Volumes/External_1/_Other-Apps-
5 GNOME/_HDF/_Source/_V5/hdf5-1.8.18/src/H5G.c line 812 in
6 H5Gclose(): not a group
7 major: Invalid arguments to routine
8 minor: Inappropriate type
9 HDF5-DIAG: Error detected in HDF5 (1.8.18) thread 0:
...
}}}

r.import is a wrapper script for r.in.gdal which used GDAL.

Does "gdalinfo" accept the file?

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Ticket URL: <https://trac.osgeo.org/grass/ticket/3278#comment:1>
GRASS GIS <https://grass.osgeo.org>

GDAL · February 7, 2017, 3:37pm

#3278: Unble to import an AQUA image data (Level 2)in netcdf file format
-------------------------+-------------------------
  Reporter: laurent001 | Owner: grass-dev@…
      Type: defect | Status: new
  Priority: normal | Milestone: 7.2.1
Component: LibRaster | Version: unspecified
Resolution: | Keywords: r.in.gdal
       CPU: x86-64 | Platform: MacOSX
-------------------------+-------------------------

Comment (by Veronica Andreo):

I just checked. It seems it is not supported (gdal 2.0.2)

{{{
gdalinfo A2017012160000.L2_LAC_OC.nc
Warning 1: Variable has 0 dimension(s) - not supported.
gdalinfo failed - unable to open 'A2017012160000.L2_LAC_OC.nc'.
}}}

Global Level 3 products are recognized and imported normally, though:

{{{
r.in.gdal -o -l
input=NETCDF:A20030012003008.L3m_8D_CHL_chl_ocx_4km.nc:chl_ocx
output=prueba_clor_new
}}}

Maybe, SeaDAS, the software provided by NASA for oceancolor, is needed to
read L2 products and export into a different format. Just guessing, no
idea.

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Ticket URL: <https://trac.osgeo.org/grass/ticket/3278#comment:2>
GRASS GIS <https://grass.osgeo.org>

GDAL · April 7, 2017, 3:37pm

#3278: Unble to import an AQUA image data (Level 2)in netcdf file format
-------------------------+-------------------------
  Reporter: laurent001 | Owner: grass-dev@…
      Type: defect | Status: new
  Priority: normal | Milestone: 7.2.1
Component: LibRaster | Version: unspecified
Resolution: | Keywords: r.in.gdal
       CPU: x86-64 | Platform: MacOSX
-------------------------+-------------------------
Changes (by laurent001):

* Attachment "TEST-gdal_info-A2017048130000.L2_LAC_OC.nc.log" added.

Yes gdalinfo accepts and reads an AQUA image data. Encl. 1 log file (text
format)

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Ticket URL: <https://trac.osgeo.org/grass/ticket/3278>
GRASS GIS <https://grass.osgeo.org>

GDAL · April 7, 2017, 3:38pm

#3278: Unble to import an AQUA image data (Level 2)in netcdf file format
-------------------------+-------------------------
  Reporter: laurent001 | Owner: grass-dev@…
      Type: defect | Status: new
  Priority: normal | Milestone: 7.2.1
Component: LibRaster | Version: unspecified
Resolution: | Keywords: r.in.gdal
       CPU: x86-64 | Platform: MacOSX
-------------------------+-------------------------

Comment (by laurent001):

Yes gdalinfo accepts and reads an AQUA image data. Encl. 1 log file (text
format)

Encl. 1 log file

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Ticket URL: <https://trac.osgeo.org/grass/ticket/3278#comment:3>
GRASS GIS <https://grass.osgeo.org>

GDAL · April 10, 2017, 9:22am

#3278: Unble to import an AQUA image data (Level 2)in netcdf file format
-------------------------+-------------------------
  Reporter: laurent001 | Owner: grass-dev@…
      Type: defect | Status: new
  Priority: normal | Milestone: 7.2.1
Component: LibRaster | Version: unspecified
Resolution: | Keywords: r.in.gdal
       CPU: x86-64 | Platform: MacOSX
-------------------------+-------------------------

Comment (by mmetz):

Replying to [comment:3 laurent001]:
> Yes gdalinfo accepts and reads an AQUA image data. Encl. 1 log file
(text format)

You need to select a subdataset with HDF5:file_name:subdataset, e.g. with

{{{
r.in.gdal in=HDF5:"/Volumes/Data_1/_Image-Data/_NASA-
Ocean_colour/_AQUA/_2017-02-17-AQUA-
Bay_of_Biscay/A2017048130000.L2_LAC_OC.nc"://geophysical_data/Kd_490
}}}

See also GDAL HDF5 and NETCDF documentation.

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Ticket URL: <https://trac.osgeo.org/grass/ticket/3278#comment:4>
GRASS GIS <https://grass.osgeo.org>

GDAL · April 28, 2019, 9:19pm

#3278: Unble to import an AQUA image data (Level 2)in netcdf file format
-------------------------+-------------------------
  Reporter: laurent001 | Owner: grass-dev@…
      Type: defect | Status: closed
  Priority: normal | Milestone: 7.2.4
Component: LibRaster | Version: unspecified
Resolution: worksforme | Keywords: r.in.gdal
       CPU: x86-64 | Platform: MacOSX
-------------------------+-------------------------
Changes (by neteler):

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

Comment:

Closing as it will work when specifying the subdataset.

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Ticket URL: <https://trac.osgeo.org/grass/ticket/3278#comment:9>
GRASS GIS <https://grass.osgeo.org>