Problem creating raster from NetCDF file for SST

[Nina O'Hanlon]

Hi

I am trying to extract Chlorophyll a and SST information around gull colonies to relate to diet/ egg traits etc. as part of my PhD.

I have downloaded NetCDF of seawifs Chlorophyll a and SST (from http://oceancolor.gsfc.nasa.gov/cgi/l3) and have managed to create rasters of Chlorophyll a using Make NetCDF Raster Layer in the Multidimesion Tools (in ArcMap 10.1 on Windows 7).  However, using the same tool I am not able to create rasters for SST.  

The website has recently changed the file format from SMI HDF files.  In the past when creating SST rasters from these files I used the Marine Geospatial Ecology Tools toolbox and  Convert SDS in HDF to ArcGIS raster.  However, I have tried this with the convert 2D variable in NetCDF to ArcGIS Raster and get an error saying that the file is not a NetCDF file?
 

I was wondering if anyone else has experienced this problem and may know where I am going wrong?

Thanks very much in advance

Nina

[GIS in Ecology]

Hi Nina,

 

I had a quick look at the Ocean Color website today, and it seems that the SMI HDF files are still available to download (by clicking on the lower left corner of the thumbnail for the composite you want to download), so these should still be convertible with MGET toolbox. However, this might just be for the period I had a quick look at as I haven't had the chance to explore this more fully.

 

If the only way you can download the data which you are interested in is as a netCDF, then things might be a bit more difficult. Personally, I've always found the way that ArcGIS handles netCDFs with the multi-dimensional toolbox as being difficult at best, and often barely functional (this is based on experience with ArcGIS 9.3 rather than the more recent versions and things might have improved since then). Instead, it might be worth downloading QGIS and using the netCDF browser plug in to do your conversions (https://plugins.qgis.org/plugins/netcdfbrowser/). You can find a tutorial on how to use this here: http://www.ggiuliani.ch/download/netcdf_qgis_GG.pdf.  Again speaking from a personal perspective, I've often found that QGIS is much better at handling non-standard formats that ArcGIS, and I'll often use that to convert such file formats into those which are compatible with ArcGIS.

 

I know this probably isn't the answer that you're looking for here, but I think it's a path that's at least worth exploring as it might be a quick way to solve your problem converting your data into an ArcGIS-compatible format.

 

All the best,

 

Colin

[Silvia]

Hi Colin,
I have a similar problem… I need to extrapolate chl-a value from specific GPS points of my navigation routes, but I’m struggling to create a raster file from NetCDF file dowloaded from NASA…

I dowloaded Chl-a data from the NASA ocean color website, from OceanData Home > MODIS-Aqua > L3SMI
My setting were: daily data, 4x4 km resolution.
I obtained, for example, file named: A2018091.L3m_DAY_CHL_chlor_a_4km.nc

I also tried from: oceancolor.gsfc.nasa.gov/l3/
with the following settings: daily data, 4x4 km resolution, binned
I obtained file: A2018091.L3b_DAY_CHL.x.nc
Same problem, no matter if I choose ‘download’ or ‘extract’ as retrieval method.

I loaded them in ArcGIS 10.4 with “make NetCDF raster layer” tool. I input the netCDF file, but then the fields of variable, X dimension and Y dimension are not filled. It seems that ArcGIS is not able to read the data from file. Even if I manually write the name of the variable and the two dimensions, it does not work. When I write “lon” in the X_dimension I get an error “Error 000237 One or more dimensions are invalid”

As in another post you suggested to use QGIS instead of ArcGIS, I also tried with it.
With QGIS 2.18.0, I imported them with “Add raster layer” but I get the following error “unsupported data source: the file is not a supported data source, the file is a netCDF file but without any dimensions >=2"

I tried with the netCDF browser plugin but when I select the file, it does not even shown the variables and I cannot proceed.

What am I doing wrong?

Thank you very much for any help you might provide!

silvia-