ForestTools (version 0.1.5)

SegmentCrowns: SegmentCrowns

Description

Implements the watershed function to segment (i.e.: outline) crowns from a canopy height model. Segmentation is guided by the point locations of treetops, typically detected using the TreeTopFinder function. See Meyer & Beucher (1990) for details on watershed segmentation.

Usage

SegmentCrowns(treetops, CHM, minHeight = 0, format = "raster",
  OSGeoPath = NULL, verbose = FALSE)

Arguments

treetops

SpatialPointsDataFrame. The point locations of treetops. The function will generally produce a number of crown segments equal to the number of treetops.

CHM

Canopy height model in raster format. Should be the same that was used to create the input for treetops.

minHeight

numeric. The minimum height value for a CHM pixel to be considered as part of a crown segment. All CHM pixels beneath this value will be masked out. Note that this value should be lower than the minimum height of treetops.

format

string. Format of the function's output. Can be set to either 'raster' or 'polygons'.

OSGeoPath

character. Optional path to the OSGeo4W installation directory. If both OSGeo4W and Python are installed, this will enable the function to use a faster algorithm for producing polygonal crown outlines (see Details below).

verbose

logical. Print processing progress to console.

Value

Depending on the argument set with format, this function will return a map of outlined crowns as either a RasterLayer (see raster), in which distinct crowns are given a unique cell value, or a SpatialPolygonsDataFrame, in which each crown is represented by a polygon.

Details

This function can return a crown map as either a raster or a SpatialPolygonsDataFrame, as defined using the format argument. For most analytical purposes, it is preferable to have crown outlines as polygons. However, polygonal crown maps take up significantly more disk space, and take longer to process. It is advisable to run this function using a raster output first, in order to check its results and adjust parameters.

Using the 'polygons' output format provides the added benefit of transferring treetop attributes (such as height) to the newly created polygons. The area of each crown will also automatically be calculated and added to the polygons' data under the crownArea field. Furthermore, "orphaned" segments (i.e.: outlines without an associated treetop) will be removed when format is set to 'polygons'.

By default, polygonal crown outlines are produced internally using the the rasterToPolygons function from the raster package. This function is problematic due to it being 1) very slow and 2) leaking memory when applied to multiple datasets. An alternative is provided for users who've installed OSGeo4W and Python. By setting the OSGeoPath path to the OSGeo4W installation directory (usually 'C:\OSGeo4W64'), the function will use the gdal_polygonize.py GDAL utility to generate polygonal crown outlines instead.

References

Meyer, F., & Beucher, S. (1990). Morphological segmentation. Journal of visual communication and image representation, 1(1), 21-46.

See Also

TreeTopFinder SpatialStatistics watershed OSGeo4W download page: https://trac.osgeo.org/osgeo4w/

Examples

# NOT RUN {
# Use TreeTopFinder to detect treetops in demo canopy height model
ttops <- TreeTopFinder(CHMdemo, winFun = function(x){x * 0.06 + 0.5}, minHeight = 2)

# Set minimum tree crown height (should be LOWER than minimum treetop height)
minCrwnHgt <- 1

# Use SegmentCrowns to outline tree crowns
segs <- SegmentCrowns(ttops, CHMdemo, minCrwnHgt)

# }