RImageJROI (version 0.1.3)

ij2spatstat: Convert 'ijroi' and 'ijzip' objects to spatstat spatial patterns

Description

Converts ijroi and ijzip objects to a list of spatstat.geom spatial patterns.

Usage

ij2spatstat(
  X,
  window = NULL,
  pattern.type = NULL,
  unitname = NULL,
  scale = 1,
  return.type = FALSE,
  convert.only = NULL
)

Value

Returns a list of spatstat.geom patterns of approperiate type (see 'Details'). If return.type = TRUE returns a list with two levels specifying the spatstat.geom pattern and the ROI type.

Arguments

X

ijroi or ijzip object to be converted.

window

the window for returned spatial patterns. Can be an owin object defining a common window for all returned patterns, a character string 'range' leading to a common window based range of all returned patterns, or NULL (default) leading to separate windows for each pattern.

pattern.type

a character string specifying the desired pattern type to be returned (ppp, psp or owin). Works only if X is an ijroi object. Ignored otherwise. Defaults to an appropriate pattern type depending on the ROI type (see 'Details').

unitname

Name of the unit of length for the resulting window(s) (see owin).

scale

A numeric value defining the scale of photograph in pixels / unitname. Defaults to 1.

return.type

should the type of ROI object(s) be returned in addition to spatstat.geom spatial patterns? Defaults to FALSE.

convert.only

a character vector specifying the strType of ROI objects to be converted (see plot.ijroi for possible pattern types). Pattern types not mentioned will not be converted. Works only if X is an ijzip object. Ignored otherwise.

Author

Mikko Vihtakari

Details

The function converts ijroi and ijzip objects to spatstat.geom spatial patterns for further calculations with the objects. By default, areal types ("rect", "oval", "ELLIPSE", "polygon") are converted to owin objects. Line types ("line" (including "ARROW"), "freeline", "polyline", "angle", "freehand" (excluding "ELLIPSE")) are converted to psp objects and "point" types to ppp objects.

See Also

read.ijroi read.ijzip

Examples

file <- file.path(system.file(package = "RImageJROI"), "extdata", "ijroi", "ijzip.zip")
x <- read.ijzip(file)
ij2spatstat(x)