r.in.xyz(1)

NAME
r.in.xyz - Create a raster map from an assemblage of many coordinates using univariate statistics.

KEYWORDS
raster

SYNOPSIS
r.in.xyz
r.in.xyz help
r.in.xyz [-sg] input=name output=name [method=string] [type=string] [fs=character] [x=integer] [y=integer] [z=integer] [zrange=min,max] [percent=integer] [--overwrite]

  Flags:

-s  Scan data file for extent then exit

-g  In scan mode, print using shell script style

--overwrite

  Parameters:

input=name
    ASCII file containing input data

output=name
    Name for output raster map

method=string
    Statistic to use for raster values Options: n,min,max,range,sum,mean,stddev,variance,coeff_var Default: mean

type=string
    Storage type for resultant raster map Options: CELL,FCELL,DCELL Default: FCELL

fs=character
    Field separator Default: |

x=integer
    Column number of x coordinates in input file (first column is 1) Default: 1

y=integer
    Column number of y coordinates in input file Default: 2

z=integer
    Column number of data values in input file Default: 3

zrange=min,max
    Filter range for z data (min,max)

percent=integer
    Percent of map to keep in memory Options: 1-100 Default: 100

DESCRIPTION
The r.in.xyz module will load and bin ungridded x,y,z ASCII data into a new raster map. The user may choose from a variety of statistical methods in creating the new raster.

r.in.xyz is designed for processing massive point cloud datasets, for example raw LIDAR or sidescan sonar swath data.

Available statistics for populating the raster are:
    n number of points in cell min minimum value of points in cell max maximum value of points in cell range range of points in cell sum sum of points in cell mean average value of points in cell stddev standard deviation of points in cell variance variance of points in cell coeff_var coefficient of variance of points in cell

        Variance and derivatives use the biased estimator (n). [subject to change]

        Coefficient of variance is given in percentage and defined as (stddev/mean)*100.

NOTES
Memory use While the input file can be arbitrarily large, r.in.xyz will use a large amount of system memory for large raster regions (10000x10000). If the module refuses to start complaining that there isn't enough memory, use the percent parameter to run the module in several passes. In addition using a less precise map format (CELL [integer] or FCELL [floating point]) will use less memory than a DCELL [double precision floating point] output map. Methods such as n, min, max, sum will also use less memory, while stddev, variance, and coeff_var will use more. The default map type=FCELL is intended as compromise between preserving data precision and limiting system resource consumption. Setting region bounds and resolution You can use the -s scan flag to find the extent of the input data (and thus point density) before performing the full import. Use g.region to adjust the region bounds to match. The -g shell style flag prints the extent suitable as parameters for g.region. A suitable resolution can be found by dividing the number of input points by the area covered. e.g.
  wc -l inputfile.txt
  g.region -p
  # points_per_cell = n_points / (rows * cols)
  g.region -e
  # UTM location:
  # points_per_sq_m = n_points / (ns_extent * ew_extent)
  # Lat/Lon location:
  # points_per_sq_m = n_points / (ns_extent * ew_extent*cos(lat) * (1852*60)^2)

If you only intend to interpolate the data with r.to.vect and v.surf.rst, then there is little point to setting the region resolution so fine that you only catch one data point per cell -- you might as well use "v.in.ascii -zbt" directly. Filtering Points falling outside the current region will be skipped. This includes points falling exactly on the southern region bound. (to capture those adjust the region with "g.region s=s-0.000001"; see g.region)

Blank lines and comment lines starting with the hash symbol (#) will be skipped.

The zrange parameter may be used for filtering the input data by vertical extent. Example uses might include preparing multiple raster sections to be combined into a 3D raster array with r.to.rast3, or for filtering outliers on relatively flat terrain.

In varied terrain the user may find that min maps make for a good noise filter as most LIDAR noise is from premature hits. The min map may also be useful to find the underlying topography in a forested or urban environment if the cells are over sampled.

The user can use a combination of r.in.xyz output maps to create custom filters. e.g. use r.mapcalc to create a mean-(2*stddev) map. [In this example the user may want to include a lower bound filter in r.mapcalc to remove highly variable points (small n) or run r.neighbors to smooth the stddev map before further use.] Reprojection If the raster map is to be reprojected, it may be more appropriate to reproject the input points with m.proj or cs2cs before running r.in.xyz. Interpolation into a DEM The vector engine's topographic abilities introduce a finite memory overhead per vector point which will typically limit a vector map to approximately 3 million points (~ 1750^2 cells). If you want more, use the r.to.vect -b flag to skip building topology. Without topology, however, all you'll be able to do with the vector map is display with d.vect and interpolate with v.surf.rst. Run r.univar on your raster map to check the number of non-NULL cells and adjust bounds and/or resolution as needed before proceeding.

Typical commands to create a DEM using a regularized spline fit:
  r.univar lidar_min
  r.to.vect -z feature=point in=lidar_min out=lidar_min_pt
  v.surf.rst layer=0 in=lidar_min_pt elev=lidar_min.rst

EXAMPLE
Import the Jockey's Ridge, NC, LIDAR dataset, and process into a clean DEM:
    # scan and set region bounds
  r.in.xyz -s fs=, in=lidaratm2.txt out=test
  g.region n=35.969493 s=35.949693 e=-75.620999 w=-75.639999
  g.region res=0:00:00.075 -a
    # create "n" map containing count of points per cell for checking density
  r.in.xyz in=lidaratm2.txt out=lidar_n fs=, method=n zrange=-2,50
    # check point density [rho = n_sum / (rows*cols)]
  r.univar lidar_n | grep sum
    # create "min" map (elevation filtered for premature hits)
  r.in.xyz in=lidaratm2.txt out=lidar_min fs=, method=min zrange=-2,50
    # zoom to area of interest
  g.region n=35:57:56.25N s=35:57:13.575N w=75:38:23.7W e=75:37:15.675W
    # check number of non-null cells (try and keep under a few million)
  r.univar lidar_min | grep '^n:'
    # convert to points
  r.to.vect -z feature=point in=lidar_min out=lidar_min_pt
    # interpolate using a regularized spline fit
  v.surf.rst layer=0 in=lidar_min_pt elev=lidar_min.rst
    # set color scale to something interesting
  r.colors lidar_min.rst rule=bcyr
    # prepare a 1:1:1 scaled version for NVIZ visualization (for lat/lon input)
  r.mapcalc "lidar_min.rst_scaled = lidar_min.rst / (1852*60)"
  r.colors lidar_min.rst_scaled rule=bcyr

TODO

         Support for advanced statistics (in parallel with r.univar). Especially useful for dealing with outliers would be median and 5-10% trimmed means.
        The equivalent module from GRASS 5 ( s.cellstats ) contains code for additional statistical options, claiming to use only 16 bytes per cell: skewness, kurtosis, mean of squares, mean of absolute values, first quartile, median, third quartile.

         Support for multiple map output from a single run.
        method=string[,string,...] output=name[,name,...]

BUGS

         n map sum can be ever-so-slightly more than `wc -l` with e.g. percent=10 or less.
        Cause unknown.

         n map percent=100 and percent=xx maps differ slightly (point will fall above/below the segmentation line)
        Investigate with "r.mapcalc diff=bin_n.100 - bin_n.33" etc.
        Cause unknown.

         "nan" can leak into coeff_var maps.
        Cause unknown. Possible work-around: "r.null setnull=nan"
If you encounter any problems (or solutions!) please contact the GRASS Development Team.

SEE ALSO
g.region, m.proj, r.fillnulls, r.in.ascii, r.mapcalc, r.neighbors, r.to.rast3, r.to.vect, r.univar, r.univar2, v.in.ascii, v.surf.rst

AUTHOR
Hamish Bowman
Department of Marine Science
University of Otago
New Zealand

Last changed: $Date: 2006/06/17 06:23:49 $

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