SPATIAL ECOLOGY & CONSERVATION (SPEC) LAB
  • Home
  • People
    • Alumni
    • Join us
  • Research/Data
    • Data download
    • Geospatial Plot data workflow (GeoPlot)
    • Global Aboveground biomass Potential (GAP)
    • Global Ecosystem Structure Index (GESI)
    • PARAGUAYAN PERMANENT PLOT NETWORK (PPMB)
    • 2ndFOR
    • Sustainable Tourism >
      • Lapa Rios
    • Monitoring
    • Biodiversity Frameworks
    • References
    • SPEC Lab Internal
  • GatorEye
    • Donate to GatorEye
    • Postprocessing analytics
    • Hyperspec: links & refs
    • LiDAR: links & refs
  • ORC-CCS
  • GatorEye XL
  • GatorEye Lite
    • Processing tips
  • GatorEye XTR
  • GatorEye Data Access
    • MOU
  • Teaching
    • UAS Practicum
  • Info for students
    • Templates
    • Writing resources
    • Schedule
    • Funding >
      • NASA FINESST Fellowship
  • Photos
    • Puppies
  • Directions
  • Links
    • INOGO
  • SFRC UFL
  • BigPlotNetwork
  • Osa-INOGO
  • Storm Cloud
  • CDK

GatorEye Post-processing Information and Links

https://cran.r-project.org/web/packages/rlas/rlas.pdf

​https://cran.r-project.org/web/packages/ForestTools/index.html

​https://www.rdocumentation.org/packages/uavRst/versions/0.5-2

http://blue.for.msu.edu/EA14/exercises/exercise-spLM/initial-exploration-spLM.pdf

​http://adam-erickson.github.io/gapfraction/

​https://github.com/adam-erickson/gapfraction/blob/master/R/sun.path.R

​http://wiki.awf.forst.uni-goettingen.de/wiki/index.php/Canopy_Height_Model_based_on_Airborne_Laserscanning_using_LAStools

https://www.lutraconsulting.co.uk/blog/2015/04/15/filter-lidar-in-grass/

https://geospatial.ncsu.edu/osgeorel/pubpdf/vpetras_grass_gis_loves_lidar.pdf

https://grass.osgeo.org/grass72/manuals/v.in.lidar.html

​https://cran.r-project.org/web/packages/rLiDAR/rLiDAR.pdf

https://cran.r-project.org/web/packages/MBA/MBA.pdf​

http://quantitativeecology.org/using-rlidar-and-fusion-to-delineate-individual-trees-through-canopy-height-model-segmentation/

https://www.spiedigitallibrary.org/journals/Journal-of-Applied-Remote-Sensing/volume-8/issue-1/083573/Performance-analysis-of-freeware-filtering-algorithms-for-determining-ground-surface/10.1117/1.JRS.8.083573.short?SSO=1

http://www.spdlib.org/doku.php?id=spdlib:general:faq:faq

http://www.spdlib.org/doku.php

http://www.mdpi.com/1999-4907/7/12/307/pdf

http://lidarwidgets.com/

https://forest.moscowfsl.wsu.edu/lidar/

http://dominoc925.blogspot.com/2010/11/auto-classifying-lidar-points-as-ground.html?m=1

http://www.mdpi.com/2072-4292/3/3/638/pdf

http://lbi-archpro.org/als-filtering/lbi-project/results/laserdata/filtering-algorithm-3

https://www.osapublishing.org/ao/abstract.cfm?uri=ao-56-34-9359

https://www.fs.fed.us/eng/rsac/lidar_training/pdf/10032-MAN1.pdf
https://gis.stackexchange.com/questions/101786/determining-bare-earth-dem-from-unclassified-las-file/108342#108342
https://gis.stackexchange.com/questions/101786/determining-bare-earth-dem-from-unclassified-las-file/108342#108342
 
​1. Grass, using V MCc Lidar add-on
https://grasswiki.osgeo.org/wiki/Processing_lidar_and_UAV_point_clouds_in_GRASS_GIS_(workshop_at_FOSS4G_Boston_2017)#Classify_ground_and_non-ground_points
v.lidar.mcc - https://grass.osgeo.org/grass72/manuals/addons/v.lidar.mcc.html
v.surf.rst  - interpolate in GRASS extension (addon?)
 
Notes: seems the best, as it does MCC which is highlighted among all packages as being the best results (and they implement), and then provides spline interpolation, versus grid like many others and which presents issues for large gaps of no ground point areas.
 
2. Fusion
One of the best integrated freeware opensource packages available. However, algorithsm for interpolation are not ideal, and MCC is shown to be slightly superior for classification.
 
3. LiDR package – analysis for forestry applications!
https://github.com/Jean-Romain/lidR
https://www.rdocumentation.org/packages/lidR/versions/1.2.1
Notes: does not classify ground points, need to use https://github.com/Jean-Romain/lidR/blob/master/R/lasground.r, from LiDRextra to do that

​https://rdrr.io/cran/lidR/man/LAD.html
 
Notes: may have been updated to include las ground which does the classification now
https://rdrr.io/cran/lidR/src/R/lasground.r
using a progressive morthological filter
 
Can interpolate https://rdrr.io/cran/lidR/src/R/grid_terrain.r using this code, but seems to not model shape!, just average values using various complex equations, so would be flat across an open space (not shaped like side of hill or dip / rise. So , sub-optimal.
 
4.  LiDRextra – R package
May be merged now into the  LiDR package above
 
LASTools
LASGround exe
Notes: licensing is cost prohibitive over long-term
 
BCLA
IDL Extensions for ENVI and IDL
Many tools available
 
RLiDAR package
https://www.rdocumentation.org/packages/rLiDAR/versions/0.1.1
Mostly for working with CHM to identify trees and get stats


Leaf Area Density calculation R packages:
https://rdrr.io/a/github/akamoske/LiDARforestR/
https://cran.r-project.org/web/packages/leafR/index.html

leafR package is (basically) the same as the LiDARforestR package which does the same thing but is much slower.

QT Modeller (viewer and pro)
 
Global Mapper LiDAR
 
ENVI LiDAR
 
MCC-lidar
Has independent exe file to call, or can implement via GRASS add-on
 
PLOS ++ ?
 
LIP something ?
 
LIS 3D Pro
 
ESRI Spatial Analyst
 
TopoDOT ‘extract bare earth model’
 
LiDAR Analyst (Textron for ESRI) – requires spatial analst
 
 
libLAS
 
SPDLib general
https://bitbucket.org/petebunting/spdlib
http://www.spdlib.org/doku.php
 
SPDLib MCC
multi-scale curvature algorithm, implemente din SPDLib
https://spectraldifferences.wordpress.com/2014/08/06/dem-spdlib/
 
SPDLib PML
progressive morphology filter [1]. This is available through the command spdpmfgrd.
 
PDAL - https://gis.stackexchange.com/questions/101786/determining-bare-earth-dem-from-unclassified-las-file/108342#108342
 
DTM interpolation from classified points
 
Matlab code from 2017 paper
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5415094/
 
 
MARS - http://www.merrick.com/servicelines/gis/mars.aspx  
 
Surfer – interpolation only,
 
 
Options for DTM above
 
Overview websites
https://www.idaholidar.org/tools/mcc-lidar/
 
 
Overview of methods and applications
 
https://www.fs.fed.us/eng/rsac/lidar_training/Intro_to_lidar_modeling_withR/story.html
 
Overall Notes
 
QGIS has no way to work with LiDAR directly, but you can install lastools there if you want


Terrestrial LiDAR
https://www.idaholidar.org/tools/liforest-lidar-software-for-forestry-applications/
http://greenvalleyintl.com/
http://www.3dforest.eu/
TreeLAS R package (developed by Thiago)

Tree crown segmentation and parameters
LIDAR360 Forestry Module - https://greenvalleyintl.com/software/lidar360/
https://cran.r-project.org/web/packages/ForestTools/vignettes/treetopAnalysis.html
https://cran.r-project.org/web/packages/itcSegment/itcSegment.pdf
https://carlosasilva.shinyapps.io/LiDARTreeTop/
rLiDAR package has some options
eCognition using CHM (or LAS conversion)
​

CONTACT

Center for Latin American Studies
School of Forest, Fisheries and Geomatics Sciences
University of Florida
aalmeyda@ufl.edu  / eben@ufl.edu
Picture

  • Home
  • People
    • Alumni
    • Join us
  • Research/Data
    • Data download
    • Geospatial Plot data workflow (GeoPlot)
    • Global Aboveground biomass Potential (GAP)
    • Global Ecosystem Structure Index (GESI)
    • PARAGUAYAN PERMANENT PLOT NETWORK (PPMB)
    • 2ndFOR
    • Sustainable Tourism >
      • Lapa Rios
    • Monitoring
    • Biodiversity Frameworks
    • References
    • SPEC Lab Internal
  • GatorEye
    • Donate to GatorEye
    • Postprocessing analytics
    • Hyperspec: links & refs
    • LiDAR: links & refs
  • ORC-CCS
  • GatorEye XL
  • GatorEye Lite
    • Processing tips
  • GatorEye XTR
  • GatorEye Data Access
    • MOU
  • Teaching
    • UAS Practicum
  • Info for students
    • Templates
    • Writing resources
    • Schedule
    • Funding >
      • NASA FINESST Fellowship
  • Photos
    • Puppies
  • Directions
  • Links
    • INOGO
  • SFRC UFL
  • BigPlotNetwork
  • Osa-INOGO
  • Storm Cloud
  • CDK