Title: Read and Write 'ImageJ' Region of Interest (ROI) Files
Description: Provides functions to read and write 'ImageJ' (https://imagej.net) Region of Interest (ROI) files, to plot the ROIs and to convert them to 'spatstat' (https://spatstat.org/) spatial patterns.
Version: 0.1.3
URL: https://github.com/davidcsterratt/RImageJROI
BugReports: https://github.com/davidcsterratt/RImageJROI/issues
Date: 2024-08-17
Depends: R (≥ 3.0.2)
Imports: spatstat.geom
Suggests: png, testthat
License: GPL-3
RoxygenNote: 7.2.3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-08-17 10:40:05 UTC; dcs
Author: David C Sterratt [aut, cph, cre], Mikko Vihtakari [aut, cph], Le Gao [aut, cph]
Maintainer: David C Sterratt <david.c.sterratt@ed.ac.uk>
Repository: CRAN
Date/Publication: 2024-08-17 11:10:02 UTC

Read and write ImageJ Region of Interest (ROI) files

Description

Provides functions to read and write ImageJ (https://imagej.net/) Region of Interest (ROI) files, to plot the ROIs and to convert them as spatstat (https://spatstat.org/) spatial patterns.

Details

ImageJ ROI files can be read into R using the read.ijroi and read.ijzip functions, resulting in ijroi and ijzip objects.

The objects can be plotted using generic plot command and converted to spatstat.geom spatial patterns by using ij2spatstat function.

The ijroi and ijzip objects can be written to file using the write.ijroi and write.ijzip functions.

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
)

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.

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.

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.

Author(s)

Mikko Vihtakari

See Also

read.ijroi read.ijzip

Examples

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

Plot ijroi object

Description

Plots ImageJ ROI objects using the 'base' graphics package.

Usage

## S3 method for class 'ijroi'
plot(x, add = FALSE, xlab = "", ylab = "", main = "", asp = 1, ...)

Arguments

x

The ijroi object.

add

Whether to add to an existing plot.

xlab

a title for the x axis: title.

ylab

a title for the y axis: title.

main

an overall title for the plot: title.

asp

numeric defining the aspect ratio y/x: see plot.window. Defaults to 1.

...

Additional parameters.

Details

ImageJ ROI objects created with following tools are plotted using following graphics commands:

All graphics allow the additional parameters from appropriate functions. Aspect ratio (asp) is 1 by default leading to correct representation of ImageJ objects. If correct representation is not important, set asp = NA to use the R base-graphics default setting.

Author(s)

David Sterratt, Mikko Vihtakari

See Also

read.ijroi, read.ijzip, plot.ijzip

Examples

# type 0 'polygon' ROIs are plotted using lines()
file <- file.path(system.file(package = "RImageJROI"), "extdata", "ijroi", "polygon.roi")
x <- read.ijroi(file)
plot(x, col = "red")

# type 1 'rect' ROIs are plotted using rect()
file <- file.path(system.file(package = "RImageJROI"), "extdata", "ijroi", "rect.roi")
x <- read.ijroi(file)
plot(x, border = "red")

# type 2 'oval' ROIs are plotted using polygon()
file <- file.path(system.file(package = "RImageJROI"), "extdata", "ijroi", "oval.roi")
x <- read.ijroi(file)
plot(x, border = "red")

# type 3 'line' ROIs (among others listed in 'details') are plotted using lines()
file <- file.path(system.file(package = "RImageJROI"), "extdata", "ijroi", "line.roi")
x <- read.ijroi(file)
plot(x, col = "red")

# type 3 arrows are a subtype of 'line'. Plotted using arrows(). The stroke width is
# carried over. To change width, use lwd argument
file <- file.path(system.file(package = "RImageJROI"), "extdata", "ijroi", "arrow.roi")
x <- read.ijroi(file)
plot(x, col = "red")

# type 4 'freeline' ROIs are plotted using lines()
file <- file.path(system.file(package = "RImageJROI"), "extdata", "ijroi", "freehand_line.roi")
x <- read.ijroi(file)
plot(x, col = "red")

# type 5 'polyline' ROIs are plotted using lines()
file <- file.path(system.file(package = "RImageJROI"), "extdata", "ijroi", "segmented_line.roi")
x <- read.ijroi(file)
plot(x, col = "red")

# type 7 'freehand' selection ROIs are plotted using lines()
file <- file.path(system.file(package = "RImageJROI"), "extdata", "ijroi", "freehand_selection.roi")
x <- read.ijroi(file)
plot(x, col = "red")

# type 7 Objects created using 'Elliptical selections' tool are also saved as
# 'freehand', but with subtype 'ELLIPSE'. The coordinates for this type are flawed
# and plotting is done using equation for an ellipse
file <- file.path(system.file(package = "RImageJROI"), "extdata", "ijroi", "elliptical.roi")
x <- read.ijroi(file)
plot(x, border = "red")
lines(x$coords[,1], x$coords[,2]) ## plotted based on coordinates.

# type 10 'point' ROIs are plotted using points()
file <- file.path(system.file(package = "RImageJROI"), "extdata", "ijroi", "multi_point.roi")
x <- read.ijroi(file)
plot(x, col = "red")

# If following is shown as a (round) circle, asp = 1
file <- file.path(system.file(package = "RImageJROI"), "extdata", "ijroi", "circle.roi")
x <- read.ijroi(file)
plot(x, border = "red")

# text is stored as type 'rect' with subtype 'TEXT'. Currently
# only the outlining rectangle is returned
file <- file.path(system.file(package = "RImageJROI"), "extdata", "ijroi", "text.roi")
x <- read.ijroi(file)
plot(x, border = "red")

Plot ijzip object

Description

Plots .zip files containing ImageJ ROI objects using the 'base' graphics package.

Usage

## S3 method for class 'ijzip'
plot(x, add = FALSE, xlab = "", ylab = "", main = "", asp = 1, ...)

Arguments

x

The ijzip object.

add

Whether to add to an existing plot.

xlab

a title for the x axis: see title.

ylab

a title for the y axis: see title.

main

an overall title for the plot: see title.

asp

numeric defining the aspect ratio y/x: see plot.window. Defaults to 1.

...

Arguments to be passed to methods, such as graphical parameters (see par).

Details

The function loops plot.ijroi plotting function over all elements in x. See plot.ijroi for further details.

Author(s)

Mikko Vihtakari, David Sterratt

See Also

read.ijzip, plot.ijroi

Examples

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

Print ijroi objects

Description

Print ijroi objects

Usage

## S3 method for class 'ijroi'
print(x, all = FALSE, ...)

Arguments

x

ijroi object to be printed.

all

logical indicating whether to print all information from ijroi object as opposed to a subset of relevant information. Defaults to FALSE.

...

further arguments passed to print.

Author(s)

Mikko Vihtakari, David Sterratt

See Also

read.ijroi

Read an ImageJ ROI file

Description

Read an ImageJ ROI file. This returns a structure containing the ImageJ data.

Usage

read.ijroi(file, verbose = FALSE)

Arguments

file

Name of ImageJ ROI file to read

verbose

Whether to report information

Value

A structure of class ijroi containing the ROI information

Author(s)

David Sterratt

See Also

plot.ijroi for plotting single ROI objects.

read.ijzip for reading several ROI objects from .zip files.

Examples

library(png)
path <- file.path(system.file(package = "RImageJROI"), "extdata", "ijroi")
im <- as.raster(readPNG(file.path(path, "imagej-logo.png")))
plot(NA, NA, xlim=c(0, ncol(im)), ylim=c(nrow(im), 0), asp=1)
rasterImage(im, 0,  nrow(im), ncol(im), 0, interpolate=FALSE)
r <- read.ijroi(file.path(path, "rect.roi"))
plot(r, TRUE)
r <- read.ijroi(file.path(path, "polygon.roi"))
plot(r, TRUE)
r <- read.ijroi(file.path(path, "oval.roi"))
plot(r, TRUE)

Read ImageJ zip file containing several ROI files

Description

A wrapper function, which reads a zip file containing ImageJ ROI files using read.ijroi function.

Usage

read.ijzip(file, names = TRUE, list.files = FALSE, verbose = FALSE)

Arguments

file

zip file containing a collection of ImageJ ROI files

names

Logical, indicating whether the ROI file names should be used as names for the elements in the list (see Return). If FALSE a sequence of names specifying the type of ROI is automatically generated.

list.files

logical, indicating whether a data.frame of ROI files in file should be returned instead of a list of results. Defaults to FALSE. If TRUE equals to unzip(file, list = TRUE).

verbose

Whether to report information (see read.ijroi).

Value

An object of class ijzip containing a list of the coordinates and types of ImageJ ROIs. Each element is named after option specified in names.

Author(s)

Mikko Vihtakari

See Also

read.ijroi, plot.ijzip.

Examples

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

Write an ImageJ ROI file.

Description

Write an ImageJ ROI file.

Usage

write.ijroi(file, roi, verbose = TRUE)

Arguments

file

Name of ImageJ ROI file to write

roi

A structure of class ijroi containing the ROI information

verbose

Whether to report information

See Also

read.ijroi for reading an ROI file

Write ImageJ zip file containing several ROI files

Description

Write or add to a zip archive containing ImageJ ROI files using the write.ijroi function.

Usage

write.ijzip(file, roi, verbose = TRUE)

Arguments

file

zip archive to write that will contain a collection of ImageJ ROI files

roi

A list of ROIs

verbose

Whether to report information

See Also

write.ijroi