[postgis-users] Extracting variable information from netcdf, imported as raster to a table

Wed Nov 15 17:42:16 PST 2023

I didn’t realize that netCDF also has a vector component.

https://gdal.org/drivers/vector/netcdf.html#vector-netcdf

To read the vector component, you’d use the ogr_fdw extension to read that rather than postgis_raster extension.

Details here -  https://github.com/pramsey/pgsql-ogr-fdw

So perhaps that is what your python is doing reading the vector component.  I don’t know if netcdf mixes those in one data set or not since I have no experience using netcdf.

I recall you said you are using the OSGeo Live 16 distribution.  I just checked the OSGeoLive 16 does include ogr_fdw 

So do 

CREATE EXTENSION ogr_fdw;

The list of supported formats you can see with this query:

SELECT name FROM unnest(ogr_fdw_drivers()) AS f(name) ORDER BY name;

Which for osgeolive 16, I see netCDF listed

From: Regina Obe <lr at pcorp.us> 
Sent: Wednesday, November 15, 2023 6:19 PM
To: 'PostGIS Users Discussion' <postgis-users at lists.osgeo.org>
Cc: 'Manaswini Ganjam' <manu.ganjam at gmail.com>
Subject: RE: [postgis-users] Extracting variable information from netcdf, imported as raster to a table

Just confirming some stuff, since I’m not completely following:

Raster_record.rast column is of type raster correct?  IF so ST_X and ST_Y won’t work since those are for geometry types.

Also ST_Value(raster_record.rast, band_number), won’t work either since that expects as input a geometry or x,y on the raster you want the value you.

I would think you would have gotten an error with that, which makes me feel I’m missing something critical.

If you want to extract all the pixels in a raster, you’d do something like https://postgis.net/docs/RT_ST_PixelAsPoints.html

SELECT pp.x, pp.y, pp.val, ST_X(pp.geom) AS lon, ST_Y(pp.geom) AS lat

FROM raster_record, 

ST_PixelAsPoints(raster_record.rast, 1) AS pp

From: postgis-users <postgis-users-bounces at lists.osgeo.org <mailto:postgis-users-bounces at lists.osgeo.org> > On Behalf Of Manaswini Ganjam via postgis-users
Sent: Wednesday, November 15, 2023 2:01 PM
To: postgis-users at lists.osgeo.org <mailto:postgis-users at lists.osgeo.org> 
Cc: Manaswini Ganjam <manu.ganjam at gmail.com <mailto:manu.ganjam at gmail.com> >
Subject: [postgis-users] Extracting variable information from netcdf, imported as raster to a table

Hi, 

I have been trying to download s3 cloud stored gridded climate data and generate tables with variables, lat, lon and timestamp (year, yearday). To achieve this I used raster2pgsql and imported multiple netcdf files into a database table. 

Question: How to achieve the extraction of variables using postgis? I tried using ST_value, ST_pixelaspoints but I was getting errors, mainly due to the format in which netcdfs are stored in the database (the error says can't load some characters like 00E30100082...), I even tried changing the datatype to float but still did not work. I mean it is probably not simple like selecting a variable from the netcdf. I have enclosed my sql query below: 

  -- Iterate through all raster files in the table
    FOR raster_record IN (SELECT * FROM gfdl_03_prcp) LOOP
        -- Determine the year from the raster file name, assuming the format is 'prcp_03_1950.nc <http://prcp_03_1950.nc> '
        SELECT
            regexp_replace(raster_record.filename, '.*_(\d{4})\.nc', '\1')::integer
        INTO
            year;

        -- Calculate the start date of the year
        year_start := (year || '-01-01')::date;

        -- Determine if the year is a leap year
        is_leap_year := EXTRACT(ISODOW FROM (year_start + interval '1 year')) = 7;

        -- Set the number of bands for the year (365 for non-leap years, 366 for leap years)
        FOR band_number IN 1..(CASE WHEN is_leap_year THEN 366 ELSE 365 END) LOOP
            -- Calculate the observation_time using the year and band number
            observation_time := year_start + (band_number - 1) * interval '1 day';

            -- Extract X (lon) and Y (lat) coordinates from the raster
            SELECT
                ST_X(raster_record.rast) AS lon,
                ST_Y(raster_record.rast) AS lat
            INTO
                lon,
                lat;

            -- Insert the lat, lon, prcp, and observation_time into the extracted_values table
            INSERT INTO extracted_values (lat, lon, prcp, observation_time)
            VALUES
                (lat, lon, ST_Value(raster_record.rast, band_number), observation_time);

            -- Increment the counter
            counter := counter + 1;

            -- Commit the transaction periodically in batches
            IF counter % batch_size = 0 THEN
                COMMIT;
            END IF;
        END LOOP;
    END LOOP;

The metadata for the two files is as follows: 

File from database:

{'NC_GLOBAL#Conventions': 'CF-1.5',
 'NC_GLOBAL#GDAL': 'GDAL 3.6.4, released 2023/04/17',
 'NC_GLOBAL#history': 'Wed Nov 15 13:32:13 2023: GDAL CreateCopy( not_clipped_prcp.nc <http://not_clipped_prcp.nc> , ... )'}
File before loading into the database:
{'lat#units': 'degrees_north',
 'lon#units': 'degrees_east',
 'NC_GLOBAL#title': 'Daily statistically downscaled CMIP5 data for the United States and southern Canada east of the Rocky Mountains, version 1.0, realization 1, 0.1x0.1 degree spatial resolution.',
 'NETCDF_DIM_EXTRA': '{time}',
 'NETCDF_DIM_time_DEF': '{366,4}',
 'NETCDF_DIM_time_VALUES': '{0,1,2,3,4,5,6,7,8,9,10,11,12,13,14....362,363,364,365}',
 'prcp#add_offset': '819.17499',
 'prcp#long_name': 'daily precipitation accumulation',
 'prcp#missing_value': '-32768',
 'prcp#scale_factor': '0.025',
 'prcp#units': 'mm',
 'prcp#_FillValue': '-32768',
 'time#units': 'days since 1952-1-1 0:0:0.0'}

In case this information is useful: Previously I used python to extract variable information and generate a csv or table using this variable information, and the code is enclosed below. In the code I extracted variable values using lon = dataset.variables['lon'][:] and iterated for loops to write them all in csv. 

Python code:

import netCDF4 as nc

# Step 1: Read the NetCDF file
filename = "/home/manaswini/prcp_03_1950.nc <http://prcp_03_1950.nc> "
dataset = nc.Dataset(filename)
dataset.set_auto_mask(False)
dataset.set_auto_scale(True)

lon = dataset.variables['lon'][:]
lat = dataset.variables['lat'][:]
time = dataset.variables['time'][:]
prcp = dataset.variables['prcp'][:]

import numpy as np
import csv

# csv_buffer
csv_buffer = open('output.csv', 'w', newline='')
csv_writer = csv.writer(csv_buffer)

# Iterate through grid points and write to CSV buffer
for i in enumerate(lon):
    for j in enumerate(lat):
        for k in enumerate(time):
         csv_writer.writerow([lat[j], lon[i], prcp[i][j][k], year[k], yearday[k]])

# Close the CSV buffer
csv_buffer.close()

Thank you, 

Manaswini Ganjam

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.osgeo.org/pipermail/postgis-users/attachments/20231115/f2eec0f3/attachment.htm>