NrrdProject: Make projections along a nrrd axis, typically also rescaling

In jefferis/runu: R wrapper for the unu image processing tool

Description

Make projections along a nrrd axis, typically also rescaling

Usage

NrrdProject(infile, outfile, axis, measure = c("max", "min", "mean",
  "median", "mode", "variance", "skew", "intc", "slope", "error", "sd",
  "product", "sum", "L1", "L2", "Linf"), scale = "x0.3333 x0.333",
  kernel = "cheap", gamma = NA, cropmin = NULL, cropmax = NULL,
  suffix = NULL, CreateDirs = TRUE, Verbose = TRUE, Force = FALSE,
  UseLock = FALSE)

Arguments

infile	Input/output files
outfile	Optional path to output file (constructed automatically when missing)
axis	Number indicating 0-indexed axis or character "x", "y" or "z"
measure	Character vector indicating summary function to apply to values in each column. Choose from c("max", "min", "mean", "median", "mode", "variance", "skew", "intc", "slope", "error", "sd", "product", "sum", "L1", "L2", "Linf")
scale	How to scale each axis (see details)
kernel	Type of smoothing kernel to use (see details)
gamma	Exponent for the mapping of input to output values (see details)
cropmin, cropmax	triples defining the lower and higher corners of bounding box
suffix	A suffix added to the input file to construct an output filename
CreateDirs	Whether to create implied output directories
Verbose	Print status messages
Force	Whether to overwrite an existing file
UseLock	Whether to use file-based locking to enable simple parallelisation

Details

gamma: Just as in xv, the gamma value here is actually the reciprocal of the exponent actually used to transform the values. Note also that for cropmin,cropmax the special value M can be used to indicate the maximum index for that axis (i.e. n-1 when there are n samples).

scale: For each axis, information about how many samples in output:

• "=": leave this axis completely untouched: no resampling whatsoever

• "x<float>": multiply the number of input samples by <float>, and round to the nearest integer, to get the number of output samples. Use "x1" to resample the axis but leave the number of samples unchanged

• "/<float>": divide number of samples by <float>

• "+=<uint>", "-=<uint>": add <uint> to or subtract <uint> from number input samples to get number output samples

• "<uint>": exact number of output samples

• "a": resample this axis to whatever number of samples preserves the aspect ratio of other resampled axes. Currently needs to be used on all but one of the resampled axes, if at all. (1 or more sampling specifications)

Kernel: The kernel to use for resampling. Kernels logically live in the input index space for upsampling, and in the output index space for downsampling. Possibilities include:

• "box": nearest neighbor interpolation on upsampling, and uniform averaging on downsampling

• "cheap": nearest neighbor interpolation for upsampling, and non-blurring sub-sampling (pick subset of input samples) on downsampling

• "tent": linear interpolation

• "cubic:B,C": Mitchell/Netravali BC-family of cubics: "cubic:1,0": B-spline; maximal blurring "cubic:0,0.5": Catmull-Rom; good interpolating kernel

• "c4h": 6-sample-support, C^4 continuous, accurate

• "c4hai": discrete pre-filter to make c4h interpolate

• "bspl3", "bspl5", "bspl7": cubic (same as cubic:1,0), quintic, and 7th order B-spline

• "bspl3ai", "bspl5ai", "bspl7ai": discrete pre-filters to make bspl3, bspl5, bspl7 interpolate

• "hann:R": Hann (cosine bell) windowed sinc, radius R

• "black:R": Blackman windowed sinc, radius R

• "gauss:S,C": Gaussian blurring, with standard deviation S and cut-off at C standard deviations

• "dgauss:S,C": Lindeberg's discrete Gaussian. default: "cubic:0,0.5"

Crop max, min:

• <int> gives 0-based index

• M, M+<int>, M-<int> give index relative to the last sample on the axis (M == #samples-1).

• m+<int> give index relative to minimum axis (only relevant for max)

Value

Logical indicating success

See Also

NrrdSave, NrrdMerge

Examples

## Not run: 
# NB cropping from 50th slice to 50 before final slice
NrrdProject(infile,axis='z',cropmin='0 0 50',cropmax='0 0 M-50')

## End(Not run)

jefferis/runu documentation built on May 14, 2019, 2:43 p.m.