Flags:¶

--overwrite

Allow output files to overwrite existing files

--help

Print usage summary

--verbose

Verbose module output

--quiet

Quiet module output

--ui

Force launching GUI dialog

Parameters:¶

input=name [required]

Name of input 3D raster map

output=name [required]

Name for output 3D raster map

method=string [required]

Aggregate operation
Options: average, median, mode, minimum, maximum, range, stddev, sum, count, variance, diversity, interspersion, quart1, quart3, perc90, quantile

quantile=float

Quantile to calculate for method=quantile
Options: 0.0-1.0

window=x,y,z [required]

The size of the window in x, y and z direction, values must be odd integer numbers, eg: 3,3,3

OPTIONS¶

The user must specify the names of the 3D raster map layers to be used for input and output, the method used to analyze neighborhood values (i.e., the neighborhood function or operation to be performed), and the moving window of the neighborhood.

Neighborhood Operation Methods: The neighborhood operators determine what new value a center voxel in a neighborhood will have after examining values inside its neighboring voxels. Each voxel in a 3D raster map layer becomes the center voxel of a neighborhood as the neighborhood window moves from voxel to voxel throughout the map layer. r3.neighbors can perform the following operations:

average

The average value within the neighborhood.

median

The value found half-way through a list of the neighborhood’s values, when these are ranged in numerical order.

mode

The most frequently occurring value in the neighborhood.

minimum

The minimum value within the neighborhood.

maximum

The maximum value within the neighborhood.

range

The range value within the neighborhood.

stddev

The statistical standard deviation of values within the neighborhood.

sum

The sum of values within the neighborhood.

variance

The statistical variance of values within the neighborhood.

diversity

The number of different values within the neighborhood.

interspersion

The percentage of voxels containing values which differ from the values assigned to the center voxel in the neighborhood, plus 1.

Neighborhood Size: The neighborhood moving window specifies which voxel surrounding any given voxel fall into the neighborhood for that voxel. The window must be three comma separated odd integers. The dimension order is: x,y,z. For example: the parameter window=3,3,3 specifies a moving window (a cube) with 27 voxel.