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Tree extraction

tree_extraction.Rd

creates a data.frame with segment id, height and coordinates of maxima, surface and volume, computed from three images: initial, local maxima and segmented, obtained with tree_segmentation. The 2D polygon associated to each crown can be added as a WKT field

Usage

tree_extraction(
  r_dem_nl,
  r_maxi = NULL,
  r_dem_w = NULL,
  r_mask = NULL,
  crown = FALSE
)

Arguments

r_dem_nl

SpatRaster object. Output raster of tree_segmentation. Otherwise a raster of canopy height model, preferably filtered to avoid effect of holes on volume and surface computation can be provided. In this case arguments `r_maxi`, `r_dem_w` have to be provided

r_maxi

SpatRaster object. raster with positive values at local maxima (in case `r_dem_nl` does not contain it)

r_dem_w

SpatRaster object. segmented raster (in case `r_dem_nl` does not contain it)

r_mask

SpatRaster object. only segments which maxima are inside the mask are extracted. Values should be NA outside the mask, 1 inside.

crown

boolean. Should the 2D crown geometry be added in wkt format to the output data.frame ?

Value

A sf collection of POINTs with 7 fields: tree id, local maximum stats (height, dominance radius), segment stats (surface and volume), coordinates (x and y). In case argument `crown` is `TRUE`, a `crown` field containing the WKT geometry of the 2D crown is also present. Coordinates are written with one decimal to the right of the order of magnitude of the SpatRaster resolution (e.g. if resolution is 1/3 then 2 decimals are written).

See also

tree_segmentation, tree_detection

Examples

data(chm_chablais3)
chm_chablais3 <- terra::rast(chm_chablais3)

# tree segmentation
segments <- tree_segmentation(chm_chablais3)

# tree extraction
trees <- tree_extraction(segments, crown = TRUE)
# create crown polygons from WKT field
trees_crowns <- sf::st_as_sf(sf::st_drop_geometry(trees), wkt = "crown")

# summary of trees without wkt field
summary(trees[, -which(names(trees) == "crown")])
#>        id               x                y                 h        
#>  Min.   :  1.00   Min.   :974331   Min.   :6581624   Min.   : 6.25  
#>  1st Qu.: 37.75   1st Qu.:974346   1st Qu.:6581645   1st Qu.:15.57  
#>  Median : 74.50   Median :974362   Median :6581662   Median :19.77  
#>  Mean   : 74.85   Mean   :974364   Mean   :6581662   Mean   :19.23  
#>  3rd Qu.:112.25   3rd Qu.:974379   3rd Qu.:6581682   3rd Qu.:23.32  
#>  Max.   :150.00   Max.   :974403   Max.   :6581697   Max.   :29.89  
#>    dom_radius          s               v                     geometry  
#>  Min.   :1.000   Min.   : 1.50   Min.   :   9.158   POINT        :136  
#>  1st Qu.:2.000   1st Qu.:18.75   1st Qu.: 225.905   epsg:2154    :  0  
#>  Median :3.000   Median :30.25   Median : 381.076   +proj=lcc ...:  0  
#>  Mean   :3.496   Mean   :31.43   Mean   : 474.763                      
#>  3rd Qu.:5.500   3rd Qu.:42.25   3rd Qu.: 660.259                      
#>  Max.   :6.000   Max.   :95.25   Max.   :1869.152                      

# plot initial image
terra::plot(chm_chablais3, main = "CHM and extracted trees")

# add treetop positions
plot(trees["h"], add = TRUE, cex = trees$h/20, col = "black")
# add crowns
plot(sf::st_geometry(trees_crowns), add = TRUE, border = "black", col = NA)


# plot segments
terra::plot(segments$segments_id, main = "Segments")
# add crowns
plot(sf::st_geometry(trees_crowns), add = TRUE, border = "black", col = NA)