make_hillslope_geometry

Dockerfile

@@ -1,38 +1,38 @@
 # Pull any base image that includes R
-FROM r-base:4.2.0
+FROM rocker/geospatial
 
 # the parameter parsing function always needs the rjson and yaml packages
 RUN R -e "install.packages(c('jsonlite', 'yaml'))"
 
-# install json2aRgs v0.3.0 to parse parameters from /in/parameters.json
-RUN wget -q https://cran.r-project.org/src/contrib/json2aRgs_0.3.0.tar.gz
-RUN R CMD INSTALL json2aRgs_0.3.0.tar.gz
-
-# remove json2aRgs tarball
-RUN rm json2aRgs_0.3.0.tar.gz
+# install json2aRgs latest version from github
+RUN R -e 'install.packages("remotes")'
+RUN R -e 'remotes::install_github("VForWaTer/json2aRgs")'
 
 # install Catflow-R-Package dependencies
 RUN R -e "install.packages(c('deSolve', 'RColorBrewer', 'zoo', 'xts'))"
 
-# install gdal
-RUN apt-get update && apt-get install -y libgdal-dev
-
-# install representative hillslope dependencies
-RUN R -e "install.packages(c('rgdal', 'raster'))"
-
 # create the tool input structure
 RUN mkdir /in
 COPY ./in /in
 RUN mkdir /out
 RUN mkdir /src
 COPY ./src /src
 
+RUN R -e "install.packages(c('raster'))"
+
 # download latest version of Catflow-R-Package from github, untar and rename
 RUN wget -qO- https://github.com/CATFLOW/Catflow-R-Package/archive/refs/heads/main.tar.gz | tar xz -C src/ && mv /src/Catflow-R-Package-main /src/Catflow-R-Package
 
 # install Catflow-R-Package from source
 RUN R -e "install.packages('/src/Catflow-R-Package/Catflow', repos = NULL, type = 'source')"
 
+# install representative hillslope dependencies
+# Download rgdal package archive, untar, and rename
+RUN wget -qO- https://cran.r-project.org/src/contrib/Archive/rgdal/rgdal_1.6-7.tar.gz | tar xz -C src/ 
+
+# Install rgdal package from source
+RUN R -e "install.packages('/src/rgdal', repos = NULL, type = 'source')"
+
 # delete Catflow-R-Pacakge source code
 RUN rm -rf /src/Catflow-R-Package
 

in/input.json

@@ -0,0 +1,21 @@
+{
+    "make_representative_hillslope": {
+        "parameters":{ 
+            "hillslope_id" : -1,
+            "no_flow_area" : 0.30,
+            "min_cells" : 10,
+            "hill_type" : "constant",
+            "depth" : 2.1
+        },
+        "data":{ 
+            "flow_accumulation" : "/in/flow_accumulation.tif",
+            "hillslopes" : "/in/hillslope.tif",
+            "elev2river" : "/in/elevation.tif",
+            "dist2river" : "/in/distance.tif",
+            "filled_dem" : "/in/fill_DEM.tif",
+            "aspect" : "/in/aspect.tif",
+            "river_id" : "/in/streams.tif"
+        } 
+
+    }
+}