Welcome to gistool’s documentation!
gistool is an HPC-indepenent workflow enabling end-users extracting
subsets from community geospatial datasets through a simple
command-line interface (CLI). The tool works at large with geospatial files,
but is not limited to any file format, structure, or dataset.
Through crowsourcing, gistool aims to enable end-users extract subsets
from any dataset available to the community members.
Dependencies
The tool requires several basic dependencies to function properly. Below is a list of the minimum versions required for each dependency:
Dependency |
Minimum Version |
|---|---|
jq |
1.6 |
m4 |
1.4.18 |
gdal |
3.9.1 |
hdf |
4.2.16 |
r |
4.4.0 |
udunits |
2.2.28 |
geos |
3.12.0 |
proj |
9.2.0 |
(p)7zip |
16.02 |
getopt |
2.38.1 |
getopts |
4.2 |
bash |
5 |
These dependencies are essential for the tool to operate correctly. Ensure that all dependencies are installed and meet the minimum version requirements before using the tool.
User Interface
This repository contains scripts to process meteorological datasets in NetCDF
file format. The general usage of the script (i.e., ./extract-dataset.sh)
is as follows:
Usage:
extract-gis [options...]
Script options:
-d, --dataset Geospatial dataset of interest
-i, --dataset-dir=DIR The source path of the dataset file(s)
-r, --crs=INT The EPSG code of interest; optional
[defaults to 4326]
-v, --variable=var1[,var2[...]] If applicable, variables to process
-o, --output-dir=DIR Writes processed files to DIR
-s, --start-date=DATE If applicable, start date of the geospatial
data; optional
-e, --end-date=DATE If applicable, end date of the geospatial
data; optional
-l, --lat-lims=REAL,REAL Latitude's upper and lower bounds; optional
-n, --lon-lims=REAL,REAL Longitude's upper and lower bounds; optional
-f, --shape-file=PATH Path to the ESRI '.shp' file; optional
-F, --fid=STR Column name representing elements of the
Polygons to report statistics; optional
[defaults to the first column]
-j, --submit-job Submit the data extraction process as a job
to HPC's scheduler; optional
-t, --print-geotiff=BOOL Extract the subsetted GeoTIFF file; optional
[defaults to 'true']
-a, --stat=stat1[,stat2[...]] If applicable, extract the statistics of
interest, currently available options are:
'min';'max';'mean';'majority';'minority';
'median';'quantile';'variety';'variance';
'stdev';'coefficient_of_variation';'frac';
'coords'; 'count'; 'sum'; optional
-U, --include-na Include NA values in generated
statistics, optional
-q, --quantile=q1[,q2[...]] Quantiles of interest to be produced if 'quantile'
is included in the '--stat' argument. The values
must be comma delimited float numbers between
0 and 1; optional [defaults to every 5th quantile]
-p, --prefix=STR Prefix prepended to the output files
-b, --parsable Parsable SLURM message mainly used
for chained job submissions
-D, --dependency Executation dependency submission ID, optional
-c, --cache=DIR Path of the cache directory; optional
-E, --email=STR E-mail when job starts, ends, and fails; optional
-C, --cluster=JSON JSON file detailing cluster-specific details
-V, --version Show version
-h, --help Show this screen and exit
Use the navigation menu on the left to explore the gistool’s
documentation!
User Manual
Datasets
License