[ncl-talk] ncl core dump when accessing hdf5 group

Tue Jul 14 14:43:42 MDT 2015

Zhifeng,

“=>” is used to access groups (if the file has, which usually this file is HDF5, NetCDF4, or HE5).

G = f=>group_name

Is to read the first group_name.

G = f=>/group_name

Is to read group_name from the root.

Or say “=>” is a relative path, and “=>/” is absolute path.

Similar to “->”, and “->/”.

If use:
V = f->var_name

Means read first var_name (which most cases, a file only have one variable named var_name).

V = f->/grp/var_name

Is to read “var_name” from “grp”, where “f” may have many groups, and there may be one than one
Group has variable named “var_name”.

Hope this help,

Wei Huang

From: Zhifeng Yang [mailto:yangzf01 at gmail.com]
Sent: Tuesday, July 14, 2015 3:35 PM
To: Pan, Jianfu (GSFC-423.0)[COLUMBUS TECHNOLOGIES AND SERVICES INC]
Cc: Wei Huang; ncl-talk at ucar.edu
Subject: Re: [ncl-talk] ncl core dump when accessing hdf5 group

Hi Wei & Jianfu,
I am curious about the meaning of "=>/". Could you please exploit it a little bit? And what are the differences of "=>/", "=>", "->/", and "->"? Actually, I only use "->" while I read variables from NCL supported files (like .nc, .hdf files). Thank you.
Best,
Zhifeng

On Tue, Jul 14, 2015 at 3:33 PM, Pan, Jianfu (GSFC-423.0)[COLUMBUS TECHNOLOGIES AND SERVICES INC] <jianfu.pan at nasa.gov<mailto:jianfu.pan at nasa.gov>> wrote:
Hi Wei,

Adding "/" to the group name, g = f=>/Global_Projection, didn't seem to help.  I'll try the new version of NCL.  Thanks!

Jianfu
________________________________
From: Wei Huang [whuang at univ-wea.com<mailto:whuang at univ-wea.com>]
Sent: Tuesday, July 14, 2015 2:29 PM

To: Pan, Jianfu (GSFC-423.0)[COLUMBUS TECHNOLOGIES AND SERVICES INC]; ncl-talk at ucar.edu<mailto:ncl-talk at ucar.edu>
Subject: RE: ncl core dump when accessing hdf5 group

Jianfu,

You may try switch from:
g = f=>Global_Projection

to

g = f=>/Global_Projection

to see if it makes a difference.

Also, NCL has released 6.3.0, you may want to update your NCL,
As there are quite few bug fixed regarding read HDF5 files.

Regards,

Wei Huang

From: Pan, Jianfu (GSFC-423.0)[COLUMBUS TECHNOLOGIES AND SERVICES INC] [mailto:jianfu.pan at nasa.gov<mailto:jianfu.pan at nasa.gov>]
Sent: Tuesday, July 14, 2015 2:22 PM
To: Wei Huang; ncl-talk at ucar.edu<mailto:ncl-talk at ucar.edu>
Subject: RE: ncl core dump when accessing hdf5 group

Thanks Wei for your quick response.  I was able to dump or print(f).  It has too much text to put it here, including metadata in ISO XML format.  The following is part of the printout.  Thanks.  -Jianfu

ncl_filedump outputs:
Copyright (C) 1995-2014 - All Rights Reserved
 University Corporation for Atmospheric Research
 NCAR Command Language Version 6.2.1
 The use of this software is governed by a License Agreement.
 See http://www.ncl.ucar.edu/ for more details.

Variable: f
Type: file
filename:       SMAP_L1C_TB_00869_D_20150331T235250_R11340_001
path:   /SMAP/SPL1CTB/SMAP_L1C_TB_00869_D_20150331T235250_R11340_001.h5
   file global attributes:
   dimensions:
      DIM_000 = 8286
      DIM_001 = 8162
      DIM_002 = 16521
   variables:
      group </Global_Projection>

      float cell_antenna_scan_angle_aft ( DIM_002 )
         _FillValue :   -9999
         coordinates :  /Global_Projection/cell_lat /Global_Projection/cell_lon
         long_name :    Representative scan angle of the SMAP antenna on the spacecraft for all aft looking footprints within the cell.
         units :        degreesntative scan angle of the SMAP antenna on the spacecraft for all aft looking footprints within the cell.
         valid_max :    359.999
         valid_min :     0
......
      ushort cell_tb_qual_flag_3_aft ( DIM_002 )
         _FillValue :   65534
         coordinates :  /Global_Projection/cell_lat /Global_Projection/cell_lonrature for all forward looking footprints that fall within the grid cell.thin the grid cell.l.the grid cell.vector for forward looking footprints within the cell.
         flag_masks :   1s, 2s, 4s, 8s, 16s, 32s, 64s, 128s, 256s, 512s, 1024s, 4096s, 8192s, 16384sd looking footprints that fall within the grid cell.thin the grid cell.l.the grid cell.vector for forward looking footprints within the cell.
         flag_meanings :        Aft_looking_3rd_Stokes_quality_flag Aft_looking_3rd_Stokes_range_flag Aft_looking_3rd_Stokes_RFI_clean_flag Aft_looking_3rd_Stokes_RFI_repair_flag Aft_looking_3rd_Stokes_NEDT_flag Aft_looking_3rd_Stokes_direct_sun_correction Aft_looking_3rd_Stokes_reflected_sun_correction Aft_looking_3rd_Stokes_reflected_moon_correction Aft_looking_3rd_Stokes_direct_galaxy_correction Aft_looking_3rd_Stokes_reflected_galaxy_correction Aft_looking_3rd_Stokes_correction_for_atmospheric_conditions Aft_looking_3rd_Stokes_null_value_bit Aft_looking_3rd_Stokes_parameter_half_orbit_location Aft_looking_3rd_Stokes_RFI_check
         long_name :    Bit flags that represent the quality of the aft looking third stokes parameters within each grid cell._flag Aft_looking_3rd_Stokes_RFI_repair_flag Aft_looking_3rd_Stokes_NEDT_flag Aft_looking_3rd_Stokes_direct_sun_correction Aft_looking_3rd_Stokes_reflected_sun_correction Aft_looking_3rd_Stokes_reflected_moon_correction Aft_looking_3rd_Stokes_direct_galaxy_correction Aft_looking_3rd_Stokes_reflected_galaxy_correction Aft_looking_3rd_Stokes_correction_for_atmospheric_conditions Aft_looking_3rd_Stokes_null_value_bit Aft_looking_3rd_Stokes_parameter_half_orbit_location Aft_looking_3rd_Stokes_RFI_check
...
________________________________
From: Wei Huang [whuang at univ-wea.com<mailto:whuang at univ-wea.com>]
Sent: Tuesday, July 14, 2015 2:06 PM
To: Pan, Jianfu (GSFC-423.0)[COLUMBUS TECHNOLOGIES AND SERVICES INC]; ncl-talk at ucar.edu<mailto:ncl-talk at ucar.edu>
Subject: RE: ncl core dump when accessing hdf5 group
Jianfu,

Do a “ncl_filedump your-filename”,
Or a “print(f)” after opened the file,
Will help you and the people who is willing to help.

Wei Huang

From: ncl-talk-bounces at ucar.edu<mailto:ncl-talk-bounces at ucar.edu> [mailto:ncl-talk-bounces at ucar.edu] On Behalf Of Pan, Jianfu (GSFC-423.0)[COLUMBUS TECHNOLOGIES AND SERVICES INC]
Sent: Tuesday, July 14, 2015 2:02 PM
To: ncl-talk at ucar.edu<mailto:ncl-talk at ucar.edu>
Subject: [ncl-talk] ncl core dump when accessing hdf5 group

When I tried to access an h5 group in ncl, I got a core dump.  Does anyone know if there is a limit on the amount of data or number of variables an h5 group can have?  Here is the snippet:

f = addfile("smap_L1C_file.h5", "r")
g = f=>Global_Projection            ; Core dump happens here

I'm using ncl version 6.2.1.  Thank you.

Jianfu

_______________________________________________
ncl-talk mailing list
ncl-talk at ucar.edu<mailto:ncl-talk at ucar.edu>
List instructions, subscriber options, unsubscribe:
http://mailman.ucar.edu/mailman/listinfo/ncl-talk

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mailman.ucar.edu/pipermail/ncl-talk/attachments/20150714/2850fd3b/attachment.html 