LiDAR LAS file import into R via RSAGA

wrote:

Hi Clay,

RSAGA provides a comfortable platform independent system wrapper for SAGA
but as stated  no two-way bindings.

If you want to make use of SAGA algorithms () it is IMHO the most
straightforward way to import and export the raster files using the e.g.
gdalUtils. If you use raster() directly please note that it may produce
problems writing SAGA files directly. To avoid format complications  I use
most of the time GTiff. You can easily integrate the power of rLidar in
this workaround concept.
A typical work flow may look like:


 # gdalwarp is used to convert the data format to SAGA
 # you may assign the projection information to the data (like example or
change it with t_srs=)
  gdalwarp(file.in, file.out, overwrite=TRUE,
s_srs=paste0('EPSG:',epsg.code), of='SAGA')

 # do something in SAGA using the files on the disk storage as "interface"
 # note SAGA works much more stable under differnet platforms when you
provide the env settings

  # e.g. calculate wood's terrain indices   wood=
1=planar,2=pit,3=channel,4=pass,5=ridge,6=peak
    rsaga.geoprocessor('ta_morphometry',"Morphometric Features",env=myenv,
                       list(DEM='mp_dem.sgrd',
                            FEATURES='mp_wood.sgrd',
                            SLOPE='mp_slope.sgrd',
                            LONGC='mp_longcurv.sgrd',
                            CROSC='mp_crosscurv.sgrd',
                            MINIC='mp_mincurv.sgrd',
                            MAXIC='mp_maxcurv.sgrd',
                            TOL_SLOPE=14.000000
                            TOL_CURVE=0.00001
                            EXPONENT=0.000000
                            ZSCALE=1.000000))

    # read whatever you wand directly using raster()
    peak.area<-raster('mp_wood.sdat')

For using SAGA and/or GRASS in a "mixed" environment with R you may find
some help at our course pages:

http://moc.environmentalinformatics-marburg.de/doku.php?id=courses:msc:advanced-gis:lecture-notes:ag-ln-06

cheers Chris



Am 12.02.2016 um 07:51 schrieb Clay S:

Thanks Michael Sumner

rLidar works well.  But how do I pass the lidar data to another SAGA
module
within R without saving the output of each step as a file in a whole
series
of SAGA module calls from R?

I would like something like the dplyr %>% pipe command.

Thanks
Clay

On Fri, Feb 12, 2016 at 7:44 PM, Michael Sumner <mdsumner at gmail.com>
wrote:

Try rLidar::readLAS as a straightforward alternative, it's not bullet

proof but works fine for a lot of examples. Happy to help extend it if
your
format is not supported.

Cheers, Mike

On Fri, 12 Feb 2016 7:41 am Clay S <clayms at gmail.com> wrote:

Hi

Is it possible to import a Lidar LAS file into R with the
rsaga.geoprocessor function of the RSAGA package.  The following code
runs
without an error, but all I get in R is the SAGA console output.

The R code below does save a SAGA point cloud file called "test" in my
working directory.  If I delete the `POINTS = "test"` parameter, then
nothing happens as expected.  However, I want to work with the data in
R,
and pass the point cloud to other SAGA modules. This can be done in SAGA
without having to save the point cloud.  Can the same be done from R?

How can I get the point cloud imported into the R environment?  Do I
need
to coerce it into a matrix, data frame, or Spatial Points object?


R code:

###############

library(RSAGA)


# Set RSAGA environment.

env <- rsaga.env()


# SET WORKING DIRECTORY FIRST!!

dir <- getwd()


# Get module parameters

lasfilelist <- list.files(dir, pattern =".las$", full.names=TRUE,
recursive=FALSE)


# send command to RSAGA

test <- rsaga.geoprocessor(lib = "io_shapes_las", module = "Import LAS
Files",
                    param = list(FILES = lasfilelist[1], POINTS =
"test",
                                 T=TRUE, i=TRUE, a=FALSE, r=TRUE,
c=FALSE,
u=FALSE,
                                 n=TRUE, R=FALSE, G=FALSE, B=FALSE,
e=FALSE,
d=FALSE,
                                 p=FALSE, C=FALSE, VALID=FALSE,
RGB_RANGE=FALSE),
                    env = env)

###################


Here is the console output (the test variable stores the same thing):

###########

library path: C:\OSGEO4~1\apps\saga\modules\io_shapes_las.dll
library name: Import/Export - LAS
tool name   : Import LAS Files
author      : O. Conrad, V. Wichmann (c) 2009

Parameters

Input Files: "C:/Users/whcms0/'.CPT/Tarewa/Lidar/AX300711.las"
Point Clouds: No objects
gps-time: yes
intensity: yes
scan angle: no
number of the return: yes
classification: no
user data: no
number of returns of given pulse: yes
red channel color: no
green channel color: no
blue channel color: no
edge of flight line flag: no
direction of scan flag: no
point source ID: no
rgb color: no
Check Point Validity: no
R,G,B value range: 16 bit

Parsing AX300711.las ...
Save point cloud: test...

################


Here is my env:

################

env

$workspace

[1] "."


$cmd

[1] "saga_cmd.exe"


$path

[1] "C:\\OSGeo4W64\\apps\\saga"


$modules

[1] "C:\\OSGeo4W64\\apps\\saga/modules"


$version

[1] "2.1.2"


$cores

[1] NA


$parallel

[1] FALSE


$lib.prefix

[1] ""

#################

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Dr. Michael Sumner
Software and Database Engineer
Australian Antarctic Division
203 Channel Highway
Kingston Tasmania 7050 Australia


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