chmseg_GWS: seeded region growing tree crown segmentation based on 'SAGA...
In uavRst: Unmanned Aerial Vehicle Remote Sensing Tools

Description Usage Arguments Value Author(s) Examples

Tree segmentation based on a CHM, basically returns a vector data set with the tree crown geometries and a bunch of corresponding indices. After the segementation itself, the results are hole filled and optionally, it can be filtered by a majority filter.

chmseg_GWS(
  treepos = NULL,
  chm = NULL,
  minTreeAlt = 2,
  minTreeAltParam = "chm_Q20",
  minCrownArea = 3,
  maxCrownArea = 100,
  leafsize = 256,
  normalize = 0,
  neighbour = 1,
  method = 0,
  thVarFeature = 1,
  thVarSpatial = 1,
  thSimilarity = 0.002,
  segmentationBands = c("chm"),
  majorityRadius = 3,
  parallel = 1,
  giLinks = NULL
)

`treepos`	raster* object
`chm`	raster*. Canopy height model in `raster` format. Should be the same that was used to create the input for `treepos`.
`minTreeAlt`	numeric. The minimum height value for a `chm` pixel is 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 `treepos`.
`minTreeAltParam`	character. code for the percentile that is used as tree height treshold. It is build using the key letters `chmQ` and adding the percentile i.e. "10". Default is `chmQ20`
`minCrownArea`	numeric. A single value of the minimum projected tree crown area allowed. Default 3 sqm
`maxCrownArea`	numeric. A single value of the maximum projected tree crown area allowed. Default 100 sqm.
`leafsize`	integer. bin size of grey value sampling range from 1 to 256 see also: SAGA GIS Help
`normalize`	integer. logical switch if data will be normalized (1) see also: SAGA GIS Help
`neighbour`	integer. von Neumanns' neighborhood (0) or Moore's (1) see also: SAGA GIS Help
`method`	integer. growing algorithm for feature space and position (0) or feature space only (1), see also: SAGA GIS Help
`thVarFeature`	numeric. Variance in Position Space see also: SAGA GIS Help
`thVarSpatial`	numeric. Variance in Feature Space see also: SAGA GIS Help
`thSimilarity`	mumeric. Similarity Threshold see also: SAGA GIS Help
`segmentationBands`	character. a list of raster data that is used for the segmentation. The canopy height model `c("chm")` is mandantory. see also: SAGA GIS Help
`majorityRadius`	numeric. kernel size for the majority filter out spurious pixel
`parallel`	running parallel or not default = 1
`giLinks`	list. of GI tools cli paths

sp* object

Chris Reudenbach

## Not run: 
##- required packages
require(uavRst)
require(link2GI)
##- linkages
##- create and check the links to the GI software
giLinks<-uavRst::linkGI(linkItems = c("saga","gdal"))
if (giLinks$saga$exist ) {

##- project folder
projRootDir<-tempdir()

##- create subfolders please mind that the pathes are exported as global variables
paths<-link2GI::initProj(projRootDir = projRootDir,
                         projFolders = c("data/","data/ref/","output/","run/","las/"),
                         global = TRUE,
                         path_prefix = "path_")
##- overide trailing backslash issue
 path_run<-ifelse(Sys.info()["sysname"]=="Windows", sub("/$", "",path_run),path_run)
 setwd(path_run)
 unlink(paste0(path_run,"*"), force = TRUE)

##- get the data
 data(chm_seg)
 data(trp_seg)

##- tree segmentation
crowns_GWS <- chmseg_GWS( treepos = trp_seg[[1]],
                      chm = chm_seg[[1]],
                      minTreeAlt = 10,
                      neighbour = 0,
                      thVarFeature = 1.,
                      thVarSpatial = 1.,
                      thSimilarity = 0.003,
                      giLinks = giLinks )[[2]]

##- visualize it
raster::plot(crowns_GWS)
}

## End(Not run)