TreeSeg: FUSION R command line interface - Individual tree...

In bmcgaughey1/fusionwrapr: R Interface to FUSION-LTK Command Line Programs

FUSION R command line interface – Individual tree segmentation using CHM and point cloud.

Description

TreeSeg creates command lines for the FUSION TreeSeg program and optionally executes them.

Usage

TreeSeg(
  CHM = NULL,
  ht_threshold = NULL,
  outputfile = NULL,
  quiet = FALSE,
  verbose = FALSE,
  version = FALSE,
  newlog = FALSE,
  log = NULL,
  locale = FALSE,
  nolaszipdll = FALSE,
  skipfilecheck = FALSE,
  height = FALSE,
  ptheight = FALSE,
  maxht = NULL,
  grid = NULL,
  gridxy = NULL,
  align = NULL,
  buffer = NULL,
  ground = NULL,
  points = NULL,
  class = NULL,
  segmentpts = FALSE,
  clipfolder = NULL,
  shape = FALSE,
  cleantile = FALSE,
  htmultiplier = NULL,
  projection = NULL,
  use64bit = TRUE,
  runCmd = TRUE,
  saveCmd = TRUE,
  cmdFile = NULL,
  cmdClear = FALSE,
  echoCmd = FALSE,
  comment = NULL
)

Arguments

CHM	character (required): Name for canopy height model (PLANS DTM with .dtm extension). May be wildcard or text list file (extension .txt only). This can be a canopy surface model if the /ground option is used to specify a ground surface for normalization.
ht_threshold	numeric (required): Minimum height for object segmentation. Portions of the CHM below this height are not considered in the segmentation.
outputfile	character (required): Base name for output file. Metrics are stored in CSV format with .csv extension. Other outputs are stored in files named using the base name and additional descriptive information. If the folder for the output file does not exist, it will be created when the function is called even when saving commands to a batch file.
quiet	boolean: Suppress all output during the run.
verbose	boolean: Display all status information during the run.
version	boolean: Report version information and exit with no processing.
newlog	boolean: Erase the existing log file and start a new log
log	character: Use the name specified for the log file.
locale	boolean: Adjust program logic to input and output locale-specific numeric formats (e.g. use a comma for the decimal separator).
nolaszipdll	boolean: Suppress the use of the LASzip dll (c) Martin Isenburg... removes support for compressed LAS (LAZ) files. This option is only useful for programs that read or write point files.
skipfilecheck	boolean: Skip logic that checks for valid point files and removes those that are invalid prior to the start of point processing. This option is designed to overcome some limitations with windows and wildcard processing. This option is only useful for programs that read point data.
height	boolean: Normalize canopy surface model(s) using ground model(s).
ptheight	numeric: Normalize point heights using ground model(s).
maxht	numeric: Force the maximum height for the segmentation. This will override the actual maximum value in the CHM. Use this option to force equal vertical resolution across areas with varying maximum canopy heights.
grid	character: "X1,X2,Y1,Y2": Force the origin of the analysis grid to be (X,Y) instead of computing an origin from the data extents and force the grid to be W units wide and H units high...W and H will be rounded up to a multiple of cellsize.
gridxy	character: "X1,X2,Y1,Y2": Force the origin of the analysis grid to be (X1,Y1) instead of computing an origin from the data extents and force the grid to use (X2,Y2) as the upper right corner of the coverage area. The actual upper right corner will be adjusted to be a multiple of cellsize.
align	character: Force the origin and extent of the analysis grid to match the lower left corner and extent of the specified PLANS format DTM file.
buffer	numeric: Add a buffer to the data extent specified by /grid, /gridxy or /align when segmenting but only output data for the segments located within the extent.
ground	character: Use the specified bare-earth surface model to normalize the LIDAR data file may be wildcard or text list file (extension .txt only).
points	character: LIDAR point data file(s) in LDA or LAS format. May be wildcard or text list file (extension .txt only). Points are assigned to individual basins or crown polygons and a separate file (in LDA format) is output for each basin or polygon.
class	character: "c,c,c,...": LAS files only: Specifies that only points with classification values listed are to be included in the subsample. Classification values should be separated by a comma. e.g. (2,3,4,5) and can range from 0 to 31. If the first character in string is ~, the list is interpretted as the classes you DO NOT want included in the subsample. e.g. /class:~2,3 would include all class values EXCEPT 2 and 3.
segmentpts	boolean: Output points for the raster segments. Default is to output points for crown polygons when the /shape option is used and for raster segments when /shape is not used. Used only with the /points option.
clipfolder	character: folder name where point files for individual clips are stored. Used only with the /points option. If not specified, point files are stored in the same folder with other outputs. If the folder does not exist, it will be created when the function is called even when saving commands to a batch file.
shape	boolean: Create a shapefile containing the high points and basin metrics.
cleantile	boolean: Output an ASCII raster map that only includes basins within the reporting extent defined by the /grid, /gridxy, and /align options.
htmultiplier	numeric: Multiply the high point and surface heights by this value for output products. Also multiply individual point heights by # before writing point files (see /points option).
projection	character: Associate the specified projection file with shapefile and raster data products.
use64bit	boolean: indicates 64-bit version of the program should be used.
runCmd	boolean: indicates command line should be executed.
saveCmd	boolean: indicates command line should be written to a file.
cmdFile	character: contains the name of the file to which commands should be written.
cmdClear	boolean: indicates file for commands should be deleted (cleared) before the command line is written.
echoCmd	boolean: indicates command line should be displayed.
comment	character string containing comment to be written to command file before writing the actual command. Only used when runCmd = FALSE and saveCmd = TRUE. When written, there is always a blank line before the comment line in the command file.

Value

Return value depends on runCmd. if runCmd = TRUE, return value is the (invisible) integer value return from the operating system after running the command. if runCmd = FALSE, return value is the (invisible) command line.

Multiple Commands

LTKFunctions generate a separate command for each item when the required parameters are lists. This is useful when you want to use the same command and options but different input data and output files. However, this works only when the switches and options are the same for all commands (not lists). If you try to use a list of switches and/or options and a list of input files, you will produce commands using all sets of switches and/or options for every input file.

See Also

Other LTKFunctions: CSV2Grid(), CanopyMaxima(), CanopyModel(), Catalog(), ClipDTM(), ClipData(), CloudMetrics(), Cover(), DTMDescribe(), DensityMetrics(), FilterData(), FirstLastReturn(), GridMetrics(), GridSample(), GridSurfaceCreate(), GridSurfaceStats(), GroundFilter(), IntensityImage(), JoinDB(), MergeDTM(), MergeData(), MergeRaster(), RepairGridDTM(), ReturnDensity(), SplitDTM(), SurfaceSample(), SurfaceStats(), TINSurfaceCreate(), ThinData(), TopoMetrics(), fusionwrapr-package

Examples

## Not run: 
TreeSeg("CHM.dtm", 2.0, "trees.csv")

## End(Not run)

bmcgaughey1/fusionwrapr documentation built on Dec. 1, 2024, 7:13 a.m.