knitr::opts_knit$set(global.par = TRUE) options(rmarkdown.html_vignette.check_title = FALSE)
mcws function computes crown maps as a raster, many users find that having crowns as polygons is more useful for analytical purposes. Therefore, a
format argument was added which, when set to
format = "polygons", makes the function convert the raster map to a set of polygons. As an added benefit, the function also carries over the attributes of the
treetops argument into the newly created polygons, i.e.: if an input treetop has a height field associated with it, its corresponding crown polygon will also have that same value. The
mcws function also computes the crowns' horizontal area, which is stored in the output's crownArea field.
However, the underlying function used to convert rasters to polygons is
rasterToPolygons, from the raster package. This function is problematic due to its slow processing speed and its tendency to leak memory when applied to multiple datasets.
An alternative option is available for users who have installed OSGeo for Windows. OSGeo4W is a suite of free open source geospatial software, such as GDAL, GRASS and QGIS. In particular, it contains the gdal_polygonize.py GDAL utility, which performs the same function as
rasterToPolygons but with a much better performance.
John Baumgartner and Francisco Rodriguez-Sanchez developed a script to run the gdal_polygonize.py utility from R. This solution has been integrated into the
First, ensure that the
APfun library (on which the
ForestTools is dependent) is up-to-date (it should be version 0.1.1 at a minimum).
The GDAL utility requires three things to be installed:
All three can be installed simultaneously by downloading the OSGeo4W installer. Once the installer is downloaded, select either Express Desktop Install or Advanced Install.
Selecting Express Desktop Install is recommended, and will install the standard suite of OSGeo software (including everything needed here). However, to select only the required components for running gdal_polygonize.py utility, follow these steps:
Once OSGeo4W has been installed, the only new argument that must be defined when using
OSGeoPath, the path to the OSGeo4W installation directory. By default, the path for the 64-bit version of OSGeo4W is 'C:\OSGeo4W64'. Simply add this parameter to
mcws, and the function will use the GDAL library for computing crown polygons.
This should significantly improve processing speeds and resolve memory leak issues from earlier version.
library(ForestTools) data("kootenayCHM") data("kootenayTrees") kootenayCrowns <- mcws(kootenayTrees, kootenayCHM, minHeight = 1.5, format = "polygons", OSGeoPath = "C:\\OSGeo4W64")
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