[gdal-dev] NetCDF data upside down when read by gdal
Roger André
randre at gmail.com
Fri Feb 20 11:50:07 EST 2009
Rockin`!
Thanks so much, that helps very much.
Roger
--
On Fri, Feb 20, 2009 at 8:32 AM, Gong, Shawn (Contractor) <
Shawn.Gong at drdc-rddc.gc.ca> wrote:
> hi Roger,
>
>
>
> Here are cpp and h files that I modified to flip netCDF images.
>
> They are in ..\gdal-1.6.0\frmts\netcdf\
>
>
>
> hope that they help,
> Shawn
>
>
> ------------------------------
>
> *From:* gdal-dev-bounces at lists.osgeo.org [mailto:
> gdal-dev-bounces at lists.osgeo.org] *On Behalf Of *Roger André
> *Sent:* Wednesday, February 18, 2009 3:45 PM
> *To:* gdal-dev
> *Subject:* [gdal-dev] NetCDF data upside down when read by gdal
>
>
>
> Hi All,
>
> - I am attempting to use a NetCDF file as a data source for a raster layer
> in Mapserver. According to a very useful email sent in November 2005 from
> Norman Barker,
> http://lists.osgeo.org/pipermail/mapserver-users/2005-November/012153.html,
> and from Mapserver documentation at
> http://www.mapserver.org/ogc/wcs_format.html#netcdf, it seems like this
> should be possible using Mapserver's gdal driver to read the file. However,
> I am running into some problems when trying to implement these examples
> using GDAL 1.5.2, released 2008/05/29.
>
> - The NetCDF file which I am using to test with is a "CF Convention" sample
> file which I downloaded from
> http://www.unidata.ucar.edu/software/netcdf/examples/tos_O1_2001-2002.nc.
> This file contains information about sea-surface temperatures, and when
> viewed by gdalinfo has the following characteristics:
>
> $ gdalinfo tos_O1_2001-2002.nc
> Driver: netCDF/Network Common Data Format
> Files: tos_O1_2001-2002.nc
> Size is 512, 512
> Coordinate System is `'
> Metadata:
> NC_GLOBAL#title=IPSL model output prepared for IPCC Fourth Assessment
> SRES A2 experiment
> NC_GLOBAL#institution=IPSL (Institut Pierre Simon Laplace, Paris, France)
> NC_GLOBAL#source=IPSL-CM4_v1 (2003) : atmosphere : LMDZ (IPSL-CM4_IPCC,
> 96x71x19) ; ocean ORCA2 (ipsl_cm4_v1_8, 2x2L31); sea ice LIM (ipsl_cm4_v
> NC_GLOBAL#contact=Sebastien Denvil, sebastien.denvil at ipsl.jussieu.fr
> NC_GLOBAL#project_id=IPCC Fourth Assessment
> NC_GLOBAL#table_id=Table O1 (13 November 2004)
> NC_GLOBAL#experiment_id=SRES A2 experiment
> NC_GLOBAL#realization=1
> NC_GLOBAL#cmor_version=9.600000e-01
> NC_GLOBAL#Conventions=CF-1.0
> NC_GLOBAL#history=YYYY/MM/JJ: data generated; YYYY/MM/JJ+1 data
> transformed At 16:37:23 on 01/11/2005, CMOR rewrote data to comply with CF
> standards and IPCC Fourth Assessment requirements
> NC_GLOBAL#references=Dufresne et al, Journal of Climate, 2015, vol XX, p
> 136
> NC_GLOBAL#comment=Test drive
> Subdatasets:
> SUBDATASET_1_NAME=NETCDF:"tos_O1_2001-2002.nc":lon_bnds
> SUBDATASET_1_DESC=[180x2] lon_bnds (64-bit floating-point)
> SUBDATASET_2_NAME=NETCDF:"tos_O1_2001-2002.nc":lat_bnds
> SUBDATASET_2_DESC=[170x2] lat_bnds (64-bit floating-point)
> SUBDATASET_3_NAME=NETCDF:"tos_O1_2001-2002.nc":time_bnds
> SUBDATASET_3_DESC=[24x2] time_bnds (64-bit floating-point)
> SUBDATASET_4_NAME=NETCDF:"tos_O1_2001-2002.nc":tos
> SUBDATASET_4_DESC=[24x170x180] sea_surface_temperature (32-bit
> floating-point)
> Corner Coordinates:
> Upper Left ( 0.0, 0.0)
> Lower Left ( 0.0, 512.0)
> Upper Right ( 512.0, 0.0)
> Lower Right ( 512.0, 512.0)
> Center ( 256.0, 256.0)
>
> - The SUBDATASET of interest is the "tos" one, and when queried by gdalinfo
> it shows that it contains 24 bands, each of which varies by
> NETCDF_DIMENSION_time that increments by 15. When specifically queried by
> gdalinfo, this SUBDATASET looks like this:
>
> $ gdalinfo NETCDF:"tos_O1_2001-2002.nc":tos
> Driver: netCDF/Network Common Data Format
> Files: none associated
> Size is 180, 170
> Coordinate System is `'
> Origin = (0.000000000000000,90.000000000000000)
> Pixel Size = (2.000000000000000,-1.000000000000000)
> Metadata:
> NC_GLOBAL#title=IPSL model output prepared for IPCC Fourth Assessment
> SRES A2 experiment
> NC_GLOBAL#institution=IPSL (Institut Pierre Simon Laplace, Paris, France)
> NC_GLOBAL#source=IPSL-CM4_v1 (2003) : atmosphere : LMDZ (IPSL-CM4_IPCC,
> 96x71x19) ; ocean ORCA2 (ipsl_cm4_v1_8, 2x2L31); sea ice LIM (ipsl_cm4_v
> NC_GLOBAL#contact=Sebastien Denvil, sebastien.denvil at ipsl.jussieu.fr
> NC_GLOBAL#project_id=IPCC Fourth Assessment
> NC_GLOBAL#table_id=Table O1 (13 November 2004)
> NC_GLOBAL#experiment_id=SRES A2 experiment
> NC_GLOBAL#realization=1
> NC_GLOBAL#cmor_version=9.600000e-01
> NC_GLOBAL#Conventions=CF-1.0
> NC_GLOBAL#history=YYYY/MM/JJ: data generated; YYYY/MM/JJ+1 data
> transformed At 16:37:23 on 01/11/2005, CMOR rewrote data to comply with CF
> standards and IPCC Fourth Assessment requirements
> NC_GLOBAL#references=Dufresne et al, Journal of Climate, 2015, vol XX, p
> 136
> NC_GLOBAL#comment=Test drive
> tos#standard_name=sea_surface_temperature
> tos#long_name=Sea Surface Temperature
> tos#units=K
> tos#cell_methods=time: mean (interval: 30 minutes)
> tos#_FillValue=1.000000e+20
> tos#missing_value=1.000000e+20
> tos#original_name=sosstsst
> tos#original_units=degC
> tos#history= At 16:37:23 on 01/11/2005: CMOR altered the data in the
> following ways: added 2.73150E+02 to yield output units; Cyclical dimension
> was output starting at a different lon;
> lon#standard_name=longitude
> lon#long_name=longitude
> lon#units=degrees_east
> lon#axis=X
> lon#bounds=lon_bnds
> lon#original_units=degrees_east
> lat#standard_name=latitude
> lat#long_name=latitude
> lat#units=degrees_north
> lat#axis=Y
> lat#bounds=lat_bnds
> lat#original_units=degrees_north
> time#standard_name=time
> time#long_name=time
> time#units=days since 2001-1-1
> time#axis=T
> time#calendar=360_day
> time#bounds=time_bnds
> time#original_units=seconds since 2001-1-1
> Corner Coordinates:
> Upper Left ( 0.0000000, 90.0000000)
> Lower Left ( 0.0000000, -80.0000000)
> Upper Right ( 360.000, 90.000)
> Lower Right ( 360.000, -80.000)
> Center ( 180.0000000, 5.0000000)
> Band 1 Block=180x1 Type=Float32, ColorInterp=Undefined
> NoData Value=1.00000002004087734e+20
> Metadata:
> NETCDF_VARNAME=tos
> NETCDF_DIMENSION_time=15
> NETCDF_time_units=days since 2001-1-1
> Band 2 Block=180x1 Type=Float32, ColorInterp=Undefined
> NoData Value=1.00000002004087734e+20
> Metadata:
> NETCDF_VARNAME=tos
> NETCDF_DIMENSION_time=45
> NETCDF_time_units=days since 2001-1-1
> Band 3 Block=180x1 Type=Float32, ColorInterp=Undefined
> NoData Value=1.00000002004087734e+20
> Metadata:
> NETCDF_VARNAME=tos
> NETCDF_DIMENSION_time=75
> NETCDF_time_units=days since 2001-1-1
> Band 4 Block=180x1 Type=Float32, ColorInterp=Undefined
> NoData Value=1.00000002004087734e+20
> Metadata:
> NETCDF_VARNAME=tos
> NETCDF_DIMENSION_time=105
> NETCDF_time_units=days since 2001-1-1
> Band 5 Block=180x1 Type=Float32, ColorInterp=Undefined
> NoData Value=1.00000002004087734e+20
> Metadata:
> NETCDF_VARNAME=tos
> NETCDF_DIMENSION_time=135
> NETCDF_time_units=days since 2001-1-1
> Band 6 Block=180x1 Type=Float32, ColorInterp=Undefined
> NoData Value=1.00000002004087734e+20
> Metadata:
> NETCDF_VARNAME=tos
> NETCDF_DIMENSION_time=165
> NETCDF_time_units=days since 2001-1-1
> Band 7 Block=180x1 Type=Float32, ColorInterp=Undefined
> NoData Value=1.00000002004087734e+20
> Metadata:
> NETCDF_VARNAME=tos
> NETCDF_DIMENSION_time=195
> NETCDF_time_units=days since 2001-1-1
> Band 8 Block=180x1 Type=Float32, ColorInterp=Undefined
> NoData Value=1.00000002004087734e+20
> Metadata:
> NETCDF_VARNAME=tos
> NETCDF_DIMENSION_time=225
> NETCDF_time_units=days since 2001-1-1
> Band 9 Block=180x1 Type=Float32, ColorInterp=Undefined
> NoData Value=1.00000002004087734e+20
> Metadata:
> NETCDF_VARNAME=tos
> NETCDF_DIMENSION_time=255
> NETCDF_time_units=days since 2001-1-1
> Band 10 Block=180x1 Type=Float32, ColorInterp=Undefined
> NoData Value=1.00000002004087734e+20
> Metadata:
> NETCDF_VARNAME=tos
> NETCDF_DIMENSION_time=285
> NETCDF_time_units=days since 2001-1-1
> Band 11 Block=180x1 Type=Float32, ColorInterp=Undefined
> NoData Value=1.00000002004087734e+20
> Metadata:
> NETCDF_VARNAME=tos
> NETCDF_DIMENSION_time=315
> NETCDF_time_units=days since 2001-1-1
> Band 12 Block=180x1 Type=Float32, ColorInterp=Undefined
> NoData Value=1.00000002004087734e+20
> Metadata:
> NETCDF_VARNAME=tos
> NETCDF_DIMENSION_time=345
> NETCDF_time_units=days since 2001-1-1
> Band 13 Block=180x1 Type=Float32, ColorInterp=Undefined
> NoData Value=1.00000002004087734e+20
> Metadata:
> NETCDF_VARNAME=tos
> NETCDF_DIMENSION_time=375
> NETCDF_time_units=days since 2001-1-1
> Band 14 Block=180x1 Type=Float32, ColorInterp=Undefined
> NoData Value=1.00000002004087734e+20
> Metadata:
> NETCDF_VARNAME=tos
> NETCDF_DIMENSION_time=405
> NETCDF_time_units=days since 2001-1-1
> Band 15 Block=180x1 Type=Float32, ColorInterp=Undefined
> NoData Value=1.00000002004087734e+20
> Metadata:
> NETCDF_VARNAME=tos
> NETCDF_DIMENSION_time=435
> NETCDF_time_units=days since 2001-1-1
> Band 16 Block=180x1 Type=Float32, ColorInterp=Undefined
> NoData Value=1.00000002004087734e+20
> Metadata:
> NETCDF_VARNAME=tos
> NETCDF_DIMENSION_time=465
> NETCDF_time_units=days since 2001-1-1
> Band 17 Block=180x1 Type=Float32, ColorInterp=Undefined
> NoData Value=1.00000002004087734e+20
> Metadata:
> NETCDF_VARNAME=tos
> NETCDF_DIMENSION_time=495
> NETCDF_time_units=days since 2001-1-1
> Band 18 Block=180x1 Type=Float32, ColorInterp=Undefined
> NoData Value=1.00000002004087734e+20
> Metadata:
> NETCDF_VARNAME=tos
> NETCDF_DIMENSION_time=525
> NETCDF_time_units=days since 2001-1-1
> Band 19 Block=180x1 Type=Float32, ColorInterp=Undefined
> NoData Value=1.00000002004087734e+20
> Metadata:
> NETCDF_VARNAME=tos
> NETCDF_DIMENSION_time=555
> NETCDF_time_units=days since 2001-1-1
> Band 20 Block=180x1 Type=Float32, ColorInterp=Undefined
> NoData Value=1.00000002004087734e+20
> Metadata:
> NETCDF_VARNAME=tos
> NETCDF_DIMENSION_time=585
> NETCDF_time_units=days since 2001-1-1
> Band 21 Block=180x1 Type=Float32, ColorInterp=Undefined
> NoData Value=1.00000002004087734e+20
> Metadata:
> NETCDF_VARNAME=tos
> NETCDF_DIMENSION_time=615
> NETCDF_time_units=days since 2001-1-1
> Band 22 Block=180x1 Type=Float32, ColorInterp=Undefined
> NoData Value=1.00000002004087734e+20
> Metadata:
> NETCDF_VARNAME=tos
> NETCDF_DIMENSION_time=645
> NETCDF_time_units=days since 2001-1-1
> Band 23 Block=180x1 Type=Float32, ColorInterp=Undefined
> NoData Value=1.00000002004087734e+20
> Metadata:
> NETCDF_VARNAME=tos
> NETCDF_DIMENSION_time=675
> NETCDF_time_units=days since 2001-1-1
> Band 24 Block=180x1 Type=Float32, ColorInterp=Undefined
> NoData Value=1.00000002004087734e+20
> Metadata:
> NETCDF_VARNAME=tos
> NETCDF_DIMENSION_time=705
> NETCDF_time_units=days since 2001-1-1
>
> - I am able to test that I can extract one of these bands with GDAL, and
> convert it to GeoTIFF with the following command:
> gdal_translate -b 1 NETCDF:"tos_O1_2001-2002.nc":tos sea_temp_band_1.tif.
> Here however is where the first problem appears. As you can see from the
> screenshot of the sea_temp_band_1.tif that I've posted at
> http://2.bp.blogspot.com/_-yICqdt0mtY/SZxtI4yUHdI/AAAAAAAAA-I/z7W_O6qBXho/s1600-h/upside_down_netcdf.jpg,
> the data in the file appears to be represented upside down. Since this file
> is a sample from the Unidata web site, I'm reasonably confident that the
> file follows the CF convention. Every NetCDF file I have tried to read with
> GDAL has had this problem, including ones that I have created with
> gdal_translate. As you can see from the gdalinfo output above, the
> georeferencing and pixel dimensions seem to be reasonable. In the past I
> have used flip_raster.py to "fix" this, and created an intermediary
> GeoTIFF. Now that I would like to use the NetCDF itself as the data source
> to feed a WCS service, this is no longer an acceptable solution. Of
> interest though, is that the georeferencing info between the flipped and
> unflipped files are exactly the same. See below:
>
> - Flipped file:
> ---------------
> $ gdalinfo flipped_sea_temp_band_1.tif
> Driver: GTiff/GeoTIFF
> Files: flipped_sea_temp_band_1.tif
> Size is 180, 170
> Coordinate System is `'
> Origin = (0.000000000000000,90.000000000000000)
> Pixel Size = (2.000000000000000,-1.000000000000000)
> Image Structure Metadata:
> INTERLEAVE=BAND
> Corner Coordinates:
> Upper Left ( 0.0000000, 90.0000000)
> Lower Left ( 0.0000000, -80.0000000)
> Upper Right ( 360.000, 90.000)
> Lower Right ( 360.000, -80.000)
> Center ( 180.0000000, 5.0000000)
> Band 1 Block=180x11 Type=Float32, ColorInterp=Gray
>
> - Unflipped file:
> -----------------
> $ gdalinfo sea_temp_band_1.tif
> Driver: GTiff/GeoTIFF
> Files: sea_temp_band_1.tif
> Size is 180, 170
> Coordinate System is `'
> Origin = (0.000000000000000,90.000000000000000)
> Pixel Size = (2.000000000000000,-1.000000000000000)
> <snip> (Metadata removed for clarity)
> Image Structure Metadata:
> INTERLEAVE=BAND
> Corner Coordinates:
> Upper Left ( 0.0000000, 90.0000000)
> Lower Left ( 0.0000000, -80.0000000)
> Upper Right ( 360.000, 90.000)
> Lower Right ( 360.000, -80.000)
> Center ( 180.0000000, 5.0000000)
> Band 1 Block=180x11 Type=Float32, ColorInterp=Gray
> NoData Value=1.00000002004087734e+20
> Metadata:
> NETCDF_VARNAME=tos
> NETCDF_DIMENSION_time=15
> NETCDF_time_units=days since 2001-1-1
>
> - I'm unsure if this is a bug in GDAL, or an incorrectly formatted NetCDF
> file. So, would it be possible for someone who has a NetCDF file that is
> read "right-side-up" to post it as a sample for me to test with?
>
> Thanks in advance,
>
> Roger
>
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