error with lastrees

[ErvanCH]

Dear Jean-Romain, First of all thanks for this impressive package. Super efficient and clean! Love it. I am using some of its functions to delineate tree crowns in Switzerland, mainly on deciduous species (Quercus). As crown are wider than Douglas fire, finding treetops is more challenging. I got my way through this, but once I want to delineate the crown perimeter I got the following error message:

lastrees(las, "watershed", chm, th = 4,extra=T) # segmentation

Error: 'EBImage' package is needed for this function to work. Please read documentation.

install.packages('EBImage' )

Installing package into ‘C:/Users/Ervan/Documents/Work/R/R.library’ (as ‘lib’ is unspecified) Warning in install.packages : package ‘EBImage’ is not available (for R version 3.4.1)

Do I need to downgrade R, or am I doing anything wrong?? Merci pour votre retour et tout le temps passé! Amitiés, Ervan

[Jean-Romain]

Hi Ervan,

This question is not related to the lidR package but to the EBImage package. About the watershed method the lidR documentation says:

This method is a simple watershed segmentation method. It is based on the bioconductor package EBIimage. You need to install this package to run this method (see its github page).

And the EBImage page explains how to install this package:

source("https://bioconductor.org/biocLite.R")
biocLite("EBImage")

Indeed this not a regular CRAN package but a bioconductor package. Thus install.package tell you that EBImage does not exist.

[ErvanCH]

Hi Romain, Thanks for pointing towards the package repository. Now that everything is installed, I got the following error message: trees <- lastrees(las, "watershed", chm, th = 5,extra=F) # segmentation Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘extent’ for signature ‘"lasmetrics"’

Any hint? Thanks E

[Jean-Romain]

I guess I missed something in the code. Try:

trees <- lastrees(las, "watershed", as.raster(chm), th = 5,extra=F)

Edit: actually I didn't missed anything. This is documented :wink: .

[ErvanCH]

Sorry, I missed that line. My fault.

[ErvanCH]

Ah! I noticed a typo here: crown = lastrees(lasnorm, "watershed", chm, th = 4, extra = TRUE) library(raster) contour = rasterToPolygons(crowns, dissolve = TRUE) ## should be "crown" not "crowns" ;)

[Jean-Romain]

where ?

[ErvanCH]

https://github.com/Jean-Romain/lidR/wiki/Tree-segmentation-from-A-to-Z The "Optionally" section

[Jean-Romain]

Ok thank for reporting. There are probably many errors in the wiki pages. I cannot keep everything up-to-date alone (package + doc + wiki) :disappointed: . Do not hesitate to modify the wiki yourself without my permission if you find an error, typo or anything else :wink: