From c558bc3677c3ede517711db29b6d4739035fc71f Mon Sep 17 00:00:00 2001
From: bw4sz <benweinstein2010@gmail.com>
Date: Fri, 13 Sep 2024 10:46:30 -0700
Subject: [PATCH] add provisional tree ID

---
 .DS_Store            | Bin 12292 -> 12292 bytes
 R/crop_lidar_plots.R |   5 ++++-
 R/segment_trees.R    |   2 +-
 analysis/.DS_Store   | Bin 14340 -> 14340 bytes
 4 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/.DS_Store b/.DS_Store
index b626c58b9b3d5bbce095ad90801a0e01566edcd5..748e2d7eb8a8bf9761f43909a588aeb801c2ef37 100644
GIT binary patch
delta 16
XcmZokXi3=MtT;JAQFL>J;u<~xHme2f

delta 18
ZcmZokXi3=MtjNeXIZ;t$bA;j=J^(y?1?~U<

diff --git a/R/crop_lidar_plots.R b/R/crop_lidar_plots.R
index fe2486e..08cb752 100644
--- a/R/crop_lidar_plots.R
+++ b/R/crop_lidar_plots.R
@@ -77,7 +77,10 @@ crop_lidar_plots<-function(site_name="TEAK",year="2018"){
     #if null, return NA
     if(nrow(clipped_las@data)==0){
       next
-      }
+    }
+
+    # add predicted treeid from segment_trees
+    clipped_las<-lidR::segment_trees(las, lidR::li2012(dt1 = 1,dt2=2,hmin=2,speed_up = 10))
 
     lidR::writeLAS(clipped_las,cname)
     print(cname)
diff --git a/R/segment_trees.R b/R/segment_trees.R
index ec57620..de00669 100644
--- a/R/segment_trees.R
+++ b/R/segment_trees.R
@@ -59,7 +59,7 @@ segment_trees<-function(las,algorithm="watershed",chm=chm,plots=F, max_cr_factor
     tree = lidR::filter_poi(crowns, !is.na(treeID))
 
     if(plots){
-      plot(tree, color = "treeID", colorPalette = pastel.colors(100), size = 1)
+      plot(tree, color = "treeID", pal = pastel.colors(100), size = 1)
     }
 
   }
diff --git a/analysis/.DS_Store b/analysis/.DS_Store
index d08d585a640c8e55de0ea5116f4c0e34cc56c2de..1fcdd89c17c007833a0e6d8478eaebeec63ba21b 100644
GIT binary patch
delta 92
zcmZoEXepTB&*;1{pqy><5+z$k9tH*mMj!?P4(`nxrNmh_tMfb&R?z|qa5KaMVF5!W
nLo!1m5N9x?f<#h^lXH^t^K%$C^C;Zl-^_0CiDmOO6>eq#0mK(Q

delta 57
zcmZoEXepTB&*-!<pqy><D<ua;PDTbW;Naf8QA(U;vpUZcVMfi(`U*GrCpIW=W;gi6
KvROuzn;8J;0}w?3