Iss49 (#50)

* Updating examples to avoid using MERIT-Basins links * Updating copyright dates
CH-Earth · Jun 25, 2024 · 6d028fa · 6d028fa
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diff --git a/example/depth-to-bedrock.sh b/example/depth-to-bedrock.sh
@@ -2,7 +2,7 @@
 
 # Geospatial Dataset Processing Workflow
 # Copyright (C) 2022-2023, University of Saskatchewan
-# Copyright (C) 2023, University of Calgary
+# Copyright (C) 2023-2024, University of Calgary
 #
 # This file is part of the Geospatial Dataset Processing Workflow
 #
@@ -19,27 +19,30 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-# This is a simple example to extract common statistics for the 
-# pfaf 71 - Saskatchewan-Nelson System Shapefiles of MERIT-Basins -
-# from the Depth-to-Bedrock rasters.
+# This is a simple example to extract common statistics for the extents 
+# of pfaf 71 - Saskatchewan-Nelson System Shapefiles of MERIT-Basin
+#
+# If you have a Shapefile containing polygons, you may able to use
+# the `--shapefile` argument to provide the Shapefile instead of spatial
+# limits. 
+#
+# If you would like to extract zonal statistics out of polygons, you can
+# use the following options as an example:
+#    --stat="mean,min,max,median,quantile" \
+#    --quantile="0.1,0.5,0.9" \
 
 # Always call the script in the root directory of this repository
 cd ..
 echo "The current directory is: $(pwd)"
 
-# first download a sample shapefile - could be any shapefile
-wget -m -nd -nv -q -A "cat_pfaf_71_MERIT_Hydro_v07_Basins_v01_bugfix1.*" \
-     "http://hydrology.princeton.edu/data/mpan/MERIT_Basins/MERIT_Hydro_v07_Basins_v01_bugfix1/pfaf_level_02/"; 
-
 # implement subsetting and zonal statistics
 ./extract-gis.sh --dataset="depth-to-bedrock" \
   --dataset-dir="/project/rpp-kshook/Model_Output/DTB/" \
   --variable="BDRICM_M_10km_ll,BDRLOG_M_10km_ll" \
-  --shape-file="$(pwd)/cat_pfaf_71_MERIT_Hydro_v07_Basins_v01_bugfix1.shp" \
+  --lat-lims="44,60" \
+  --lon-lims="-118,-78" \
   --print-geotiff=true \
   --output-dir="$HOME/scratch/depth-to-bedrock-test/" \
   --prefix="dtb_" \
-  --stat="mean,min,max" \
-  --email="[email protected]" \ 
   -j;
 
diff --git a/example/gsde.sh b/example/gsde.sh
@@ -2,7 +2,7 @@
 
 # Geospatial Dataset Processing Workflow
 # Copyright (C) 2022-2023, University of Saskatchewan
-# Copyright (C) 2023, University of Calgary
+# Copyright (C) 2023-2024, University of Calgary
 #
 # This file is part of the Geospatial Dataset Processing Workflow
 #
@@ -19,27 +19,31 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-# This is a simple example to extract common statistics for the 
-# pfaf 71 - Saskatchewan-Nelson System Shapefiles of MERIT-Basins -
-# from the GSDE rasters.
+# This is a simple example to extract common statistics for the extents 
+# of pfaf 71 - Saskatchewan-Nelson System Shapefiles of MERIT-Basin
+#
+# If you have a Shapefile containing polygons, you may able to use
+# the `--shapefile` argument to provide the Shapefile instead of spatial
+# limits. 
+#
+# If you would like to extract zonal statistics out of polygons, you can
+# use the following options as an example:
+#    --stat="mean,min,max,median,quantile" \
+#    --quantile="0.1,0.5,0.9" \
 
 # Always call the script in the root directory of this repository
 cd ..
 echo "The current directory is: $(pwd)"
 
-# first download a sample shapefile - could be any shapefile
-wget -m -nd -nv -q -A "cat_pfaf_71_MERIT_Hydro_v07_Basins_v01_bugfix1.*" \
-     "http://hydrology.princeton.edu/data/mpan/MERIT_Basins/MERIT_Hydro_v07_Basins_v01_bugfix1/pfaf_level_02/"; 
-
 # implement subsetting and zonal statistics
 ./extract-gis.sh --dataset="GSDE" \
   --dataset-dir="/project/rpp-kshook/Model_Output/GSDE/download/gsde-30sec/" \
   --variable="BD" \
-  --shape-file="$(pwd)/cat_pfaf_71_MERIT_Hydro_v07_Basins_v01_bugfix1.shp" \
+  --lat-lims="44,60" \
+  --lon-lims="-118,-78" \
   --print-geotiff=true \
   --output-dir="$HOME/scratch/depth-to-bedrock-test/" \
   --prefix="dtb_" \
-  --stat="mean,min,max" \
   --email="[email protected]" \ 
   -j;
 
diff --git a/example/landsat.sh b/example/landsat.sh
@@ -2,7 +2,7 @@
 
 # Geospatial Dataset Processing Workflow
 # Copyright (C) 2022-2023, University of Saskatchewan
-# Copyright (C) 2023, University of Calgary
+# Copyright (C) 2023-2024, University of Calgary
 #
 # This file is part of the Geospatial Dataset Processing Workflow
 #
@@ -19,30 +19,33 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-# This is a simple example to extract common statistics for the 
-# pfaf 71 - Saskatchewan-Nelson System Shapefiles of Landsat landcover
-# from the MERIT-Hydro rasters.
+# This is a simple example to extract common statistics for the extents 
+# of pfaf 71 - Saskatchewan-Nelson System Shapefiles of MERIT-Basin
+#
+# If you have a Shapefile containing polygons, you may able to use
+# the `--shapefile` argument to provide the Shapefile instead of spatial
+# limits. 
+#
+# If you would like to extract zonal statistics out of polygons, you can
+# use the following options as an example:
+#    --stat="mean,min,max,median,quantile" \
+#    --quantile="0.1,0.5,0.9" \
 
 # Always call the script in the root directory of this repository
 cd ..
 echo "The current directory is: $(pwd)"
 
-# first download a sample shapefile - could be any shapefile
-wget -m -nd -nv -q -A "cat_pfaf_71_MERIT_Hydro_v07_Basins_v01_bugfix1.*" \
-     "http://hydrology.princeton.edu/data/mpan/MERIT_Basins/MERIT_Hydro_v07_Basins_v01_bugfix1/pfaf_level_02/"; 
-
-
 # Example 1: implement subsetting and zonal statistics on 2010 and 2015 landcover datasets
 ./extract-gis.sh --dataset="landsat" \
   --dataset-dir="/project/rpp-kshook/Model_Output/Landsat/" \
   --variable="land-cover" \
-  --shape-file="$(pwd)/cat_pfaf_71_MERIT_Hydro_v07_Basins_v01_bugfix1.shp" \
+  --lat-lims="44,60" \
+  --lon-lims="-118,-78" \
   --print-geotiff=true \
   --output-dir="$HOME/scratch/landsat-test/" \
   --prefix="landsat_test_" \
   --start-date=2010 \
   --end-date=2015 \
-  --stat="majority,minority,frac" \
   [email protected] \
   -j;
 
@@ -51,10 +54,10 @@ wget -m -nd -nv -q -A "cat_pfaf_71_MERIT_Hydro_v07_Basins_v01_bugfix1.*" \
 ./extract-gis.sh --dataset="landsat" \
   --dataset-dir="/project/rpp-kshook/Model_Output/Landsat/" \
   --variable="land-cover-change" \
-  --shape-file="$(pwd)/cat_pfaf_71_MERIT_Hydro_v07_Basins_v01_bugfix1.shp" \
   --print-geotiff=false \
+  --lat-lims="44,60" \
+  --lon-lims="-118,-78" \
   --output-dir="$HOME/scratch/landsat-test/" \
   --prefix="landsat_test_" \
-  --stat="majority,minority,frac" \
   [email protected] \
   -j;
diff --git a/example/merit-hydro.sh b/example/merit-hydro.sh
@@ -2,7 +2,7 @@
 
 # Geospatial Dataset Processing Workflow
 # Copyright (C) 2022-2023, University of Saskatchewan
-# Copyright (C) 2023, University of Calgary
+# Copyright (C) 2023-2024, University of Calgary
 #
 # This file is part of the Geospatial Dataset Processing Workflow
 #
@@ -19,26 +19,30 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-# This is a simple example to extract common statistics for the 
-# pfaf 71 - Saskatchewan-Nelson System Shapefiles of MERIT-Basins -
-# from the MERIT-Hydro rasters.
+# This is a simple example to extract common statistics for the extents 
+# of pfaf 71 - Saskatchewan-Nelson System Shapefiles of MERIT-Basin
+#
+# If you have a Shapefile containing polygons, you may able to use
+# the `--shapefile` argument to provide the Shapefile instead of spatial
+# limits. 
+#
+# If you would like to extract zonal statistics out of polygons, you can
+# use the following options as an example:
+#    --stat="mean,min,max,median,quantile" \
+#    --quantile="0.1,0.5,0.9" \
 
 # Always call the script in the root directory of this repository
 cd ..
 echo "The current directory is: $(pwd)"
 
-# first download a sample shapefile - could be any shapefile
-wget -m -nd -nv -q -A "cat_pfaf_71_MERIT_Hydro_v07_Basins_v01_bugfix1.*" \
-     "http://hydrology.princeton.edu/data/mpan/MERIT_Basins/MERIT_Hydro_v07_Basins_v01_bugfix1/pfaf_level_02/"; 
-
 # implement subsetting and zonal statistics
-./extract-gis.sh  --dataset="merit-hydro" \
+./extract-gis.sh \
+  --dataset="merit-hydro" \
   --dataset-dir="/project/rpp-kshook/CompHydCore/merit_hydro/raw_data/" \
   --output-dir="$HOME/scratch/merit-hydro-test" \
-  --shape-file="$(pwd)/cat_pfaf_71_MERIT_Hydro_v07_Basins_v01_bugfix1.shp" \
+  --lat-lims="44,60" \
+  --lon-lims="-118,-78" \
   --print-geotiff=true \
-  --stat="min,max,mean,median,quantile" \
-  --quantile="0.1,0.5,0.9" \
   --variable="elv,hnd" \
   --prefix="merit_test_" \
   -j;

diff --git a/example/modis.sh b/example/modis.sh
@@ -2,7 +2,7 @@
 
 # Geospatial Dataset Processing Workflow
 # Copyright (C) 2022-2023, University of Saskatchewan
-# Copyright (C) 2023, University of Calgary
+# Copyright (C) 2023-2024, University of Calgary
 #
 # This file is part of the Geospatial Dataset Processing Workflow
 #
@@ -19,28 +19,32 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-# This is a simple example to extract common statistics for the 
-# pfaf 71 - Saskatchewan-Nelson System Shapefiles of MERIT-Basins -
-# from the MERIT-Hydro rasters.
+# This is a simple example to extract common statistics for the extents 
+# of pfaf 71 - Saskatchewan-Nelson System Shapefiles of MERIT-Basin
+#
+# If you have a Shapefile containing polygons, you may able to use
+# the `--shapefile` argument to provide the Shapefile instead of spatial
+# limits. 
+#
+# If you would like to extract zonal statistics out of polygons, you can
+# use the following options as an example:
+#    --stat="mean,min,max,median,quantile" \
+#    --quantile="0.1,0.5,0.9" \
 
 # Always call the script in the root directory of this repository
 cd ..
 echo "The current directory is: $(pwd)"
 
-# first download a sample shapefile - could be any shapefile
-wget -m -nd -nv -q -A "cat_pfaf_71_MERIT_Hydro_v07_Basins_v01_bugfix1.*" \
-     "http://hydrology.princeton.edu/data/mpan/MERIT_Basins/MERIT_Hydro_v07_Basins_v01_bugfix1/pfaf_level_02/"; 
-
 # implement subsetting and zonal statistics
 ./extract-gis.sh --dataset="modis" \
   --dataset-dir="/project/rpp-kshook/Model_Output/MODIS/" \
   --variable="MCD12Q1.006" \
   --start-date="2001-01-01" \
+  --lat-lims="44,60" \
+  --lon-lims="-118,-78" \
   --end-date="2002-01-01" \
-  --shape-file="$(pwd)/cat_pfaf_71_MERIT_Hydro_v07_Basins_v01_bugfix1.shp" \
   --print-geotiff=true \
   --output-dir="$HOME/scratch/modis-test/" \
   --prefix="test_" \
-  --stat="majority,minority,frac" \
   -j;
 
diff --git a/example/soil-grids.sh b/example/soil-grids.sh
@@ -2,7 +2,7 @@
 
 # Geospatial Dataset Processing Workflow
 # Copyright (C) 2022-2023, University of Saskatchewan
-# Copyright (C) 2023, University of Calgary
+# Copyright (C) 2023-2024, University of Calgary
 #
 # This file is part of the Geospatial Dataset Processing Workflow
 #
@@ -19,27 +19,30 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-# This is a simple example to extract common statistics for the 
-# pfaf 71 - Saskatchewan-Nelson System Shapefiles of MERIT-Basins -
-# from the MERIT-Hydro rasters.
+# This is a simple example to extract common statistics for the extents 
+# of pfaf 71 - Saskatchewan-Nelson System Shapefiles of MERIT-Basin
+#
+# If you have a Shapefile containing polygons, you may able to use
+# the `--shapefile` argument to provide the Shapefile instead of spatial
+# limits. 
+#
+# If you would like to extract zonal statistics out of polygons, you can
+# use the following options as an example:
+#    --stat="mean,min,max,median,quantile" \
+#    --quantile="0.1,0.5,0.9" \
 
 # Always call the script in the root directory of this repository
 cd ..
 echo "The current directory is: $(pwd)"
 
-# first download a sample shapefile - could be any shapefile
-wget -m -nd -nv -q -A "cat_pfaf_71_MERIT_Hydro_v07_Basins_v01_bugfix1.*" \
-     "http://hydrology.princeton.edu/data/mpan/MERIT_Basins/MERIT_Hydro_v07_Basins_v01_bugfix1/pfaf_level_02/"; 
-
 # implement subsetting and zonal statistics
 ./extract-gis.sh --dataset="soil-grids-v1" \
   --dataset-dir="/project/rpp-kshook/Model_Output/SoilGridsV1/soilgrids/former/2017-03-10/data" \
   --variable="BDRICM_M_250m_ll,BLDFIE_M_sl4_250m_ll" \
-  --shape-file="$(pwd)/cat_pfaf_71_MERIT_Hydro_v07_Basins_v01_bugfix1.shp" \
+  --lat-lims="44,60" \
+  --lon-lims="-118,-78" \
   --print-geotiff=true \
   --output-dir="$HOME/scratch/soil-grids-test/" \
   --prefix="test_" \
-  --stat="mean,min,max,median,quantile" \
-  --quantile="0.1,0.5,0.9" \
   -j;
 
diff --git a/soil_grids/soil_grids_v1.sh b/soil_grids/soil_grids_v1.sh
@@ -2,7 +2,7 @@
 # Geospatial Data Processing Workflow
 # Copyright (C) 2021, Wouter Knoben
 # Copyright (C) 2022-2023, University of Saskatchewan
-# Copyright (C) 2023, University of Calgary
+# Copyright (C) 2023-2024, University of Calgary
 #
 # This file is part of Geospatial Data Processing Workflow
 #