SimpleGrid is a package for efficient aggregation of ocean profile data onto a regular x-y grid. This tool was designed to work with profiles in the netcdf format used by the [EN4 database][EN4-ref] or output from the package SynthPro.
SimpleGrid was developed using Python 2.7 and requires the installation of the following python libraries and their associated dependencies: numpy, netCDF4, ConfigParser, argparse, sys, shutil, os, time, and scipy.
To retrieve a copy of the SimpleGrid source code and create a working directory, run the following on the command line:
> git clone git@github.com:cdr30/SimpleGrid.git
or
> git clone https://github.com/cdr30/SimpleGrid.git
SimpleGrid is invoked from the command line using the run_simplegrid.py script. Executing this script without any arguments will return an error message that demonstrates the correct usage:
> python2.7 run_simplegrid.py
usage: run_simplegrid.py [-h] namelist
run_simplegrid.py: error: too few arguments
The namelist argument is a path to an [INI][INI-ref] configuration file containing data paths and other options. An example namelist is available in the ./config subdirectory and an annotated version is described the section below.
This section provides an annotated examples of a SimpleGrid namelist congiguration file.
dir = /profile/dir/ ### Directory containing profile data
fpattern = ${YYYY}${MM}profiles.nc ### File pattern for profile netcdf files.
datavar = POTM_CORRECTED ### Variable name of data to be gridded.
zvar = DEPH_CORRECTED ### Variable name for z-coord.
yvar = LATITUDE ### Variable name for y-coord.
xvar = LONGITUDE ### Variable name for x-coord.
minyr = 2000 ### Start year for analysis.
maxyr = 2015 ### End year of analysis.
qcvar = POTM_CORRECTED_QC ### Variable name for profile quality control flag.
posqcvar = POSITION_QC ### Variable name for position quality control flag.
qcreject = 4 ### Reject value for profile quality control flag.
posqcreject = 4 ### Reject value for position quality control flag.
minyr=2000 ### First year to use for calculation of climatology.
maxyr=2015 ### Last year to use for calculation of climatology.
##### `[grid]`
dir = /output/dir/ ### Output directory
xmin=-180 ### Minimum boundary for x-coord. Used to generate grid.
xmax=180 ### Maximum boundary for x-coord. Used to generate grid.
ymin=-90 ### Minimum boundary for y-coord. Used to generate grid.
ymax=90 ### Maximum boundary for y-coord. Used to generate grid.
dx=2 ### Grid spacing in x direction.
dy=2 ### Grid spacing in y direction.
zbounds=0.0,10.0,20.1,30.2,40.4,50.6,60.9,71.3,81.9,92.7,104.0,115.8,128.4,142.0,157.3,174.8,195.5,220.6,251.9,291.6,342.4,407.6,490.9,595.9,725.2,880.5,1061.8,1267.5,1494.7,1739.9,1999.4,2270.0,2548.9,2833.9,3123.3,3415.9,3710.7,4007.0,4304.5,4602.7,4901.5,5200.6,5500 ### Comma-separated list of boundaries for z-coordinate.
calc_anomalies = True ### If True, calculate anomalies relative to the specified climatology.
An example script for the interpolation of missing data using an inverse-distance weighting approach is provided in the scripts directory. Help is available from the command line:
>python2.7 infill_gridded_data.py -h
usage: infill_gridded_data.py [-h] [--bathyf BATHYF] [--bathyvar BATHYVAR]
[-c CUTOFF] [-p POWER] [-s SMOOTH]
namelist gridf infillf
Infill missing data in gridded data using an inverse-distance weighting
approach.
positional arguments:
namelist Path to namelist.ini file used to create gridded data.
gridf Path to netcdf file containing gridded data.
infillf Output file containing infilled data.
optional arguments:
-h, --help show this help message and exit
--bathyf BATHYF Path to netcdf file containing bathymetry data for
estimation of land-sea mask
--bathyvar BATHYVAR Variable name for bathymetry data.
-c CUTOFF, --cutoff CUTOFF
Maximum distance (km) used for interpolation.
-p POWER, --power POWER
Power used for inverse-distance weighting.
-s SMOOTH, --smooth SMOOTH
If True, apply inverse-distance weighting everywhere
to smooth field.