Package 'ImageArray'

BFArray constructor method

Description

A function for creating objects of BFArray class

Usage

BFArray(image.file, series, resolution)

## S4 method for signature 'BFArraySeed'
dim(x)

## S4 method for signature 'BFArraySeed'
type(x)

Arguments

image.file	the path to the image read by RBioFormats
series	the series IDs of the pyramidal image, typical an integer starting from 1
resolution	the resolution IDs of the pyramidal image, typical an integer starting from 1
x	A BFArray object

Value

A BFArray object

Functions

• dim(BFArraySeed): dim function for BFArray objects

• type(BFArraySeed): type function for BFArray objects

Examples

# get image
library(RBioFormats)
img.file <- system.file("extdata",
                        "xy_12bit__plant.ome.tiff",
                        package = "ImageArray")
bfa <- BFArray(img.file, series = 1, resolution = 2)
dim(bfa)
type(bfa)

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create_zarr

Description

Create zarr store

Usage

create_zarr(store, version = "v2")

Arguments

store	the location of zarr store
version	zarr version

Value

'NULL'

Examples

store <- tempfile(fileext = ".zarr")
create_zarr(store)

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create_zarr_group

Description

Create a zarr group

Usage

create_zarr_group(store, name, version = "v2")

Arguments

store	the location of (zarr) store
name	name of the group
version	zarr version

Value

'NULL'

Examples

store <- tempfile(fileext = ".zarr")
create_zarr(store)
create_zarr_group(store, "gp")

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createImageArray

Description

creates an object of ImageArray class

Usage

createImageArray(
  image,
  n.levels = NULL,
  series = NULL,
  resolution = NULL,
  max.pixel.threshold = 700,
  engine = "EBImage",
  verbose = FALSE
)

Arguments

image	the image
n.levels	the number of levels of the pyramidal image, typical an integer starting from 1
series	the series IDs of the pyramidal image, typical an integer starting from 1.
resolution	the resolution IDs of the pyramidal image, typical an integer starting from 1.
max.pixel.threshold	the maximum width and height pixel dimension that the lowest level of the image pyramid should have, thus the image will be downscaled two folds until both width and height is below the threshold. Default is 700 pixels. If n.levels is provided, this parameter will be ignored.
engine	the package to use for each image layer: either EBImage or magick-image
verbose	verbose

Value

An ImageArray object

Examples

# get image
library(EBImage)
img.file <- system.file("images", "sample.png", package="EBImage")

# create ImageArray
imgarray <- createImageArray(img.file, n.levels = 3)
imgarray_raster <- as.raster(imgarray, max.pixel.size = 300)
plot(imgarray_raster)

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getImageInfo

Description

get information of an ImageArray object

Usage

getImageInfo(object)

Arguments

object

an ImageArray object

Value

a data frame of width and height info

Examples

# get image
library(EBImage)
img.file <- system.file("images", "sample.png", package="EBImage")

# create ImageArray
dir.create(td <- tempfile())
output_h5 <- tempfile(fileext = ".h5")
imgarray <- writeImageArray(img.file,
                          output = output_h5,
                          name = "image",
                          verbose = FALSE)
getImageInfo(imgarray)

# create ImageArray
imgarray <- createImageArray(img.file, n.levels = 3)
imgarray_raster <- as.raster(imgarray, max.pixel.size = 300)
getImageInfo(imgarray)

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Methods for ImageArray

Description

Methods for ImageArray objects

Usage

## S4 method for signature 'ImageArray,ANY,ANY,ANY'
x[i, j, ..., drop = FALSE]

## S4 method for signature 'ImageArray,numeric'
x[[i]]

## S4 replacement method for signature 'ImageArray,numeric'
x[[i, j, ...]] <- value

## S4 method for signature 'ImageArray'
dim(x)

## S4 method for signature 'ImageArray'
type(x)

## S4 method for signature 'ImageArray'
length(x)

ImageArray(meta, levels)

## S4 method for signature 'ImageArray'
realize(x, level = NULL, max.pixel.size = NULL, min.pixel.size = NULL)

## S3 method for class 'ImageArray'
as.raster(x, level = NULL, max.pixel.size = NULL, min.pixel.size = NULL, ...)

## S4 method for signature 'ImageArray'
rotate(x, angle)

## S4 method for signature 'ImageArray'
aperm(a, perm)

## S4 method for signature 'ImageArray'
negate(object)

## S4 method for signature 'ImageArray'
modulate(object, brightness)

## S4 method for signature 'ImageArray'
flip(x)

## S4 method for signature 'ImageArray'
flop(x)

## S4 method for signature 'ImageArray'
crop(object, index)

## S4 method for signature 'ImageArray'
axes(object)

## S4 method for signature 'ImageArray'
meta(object)

## S4 method for signature 'ImageArray'
path(object)

## S4 replacement method for signature 'ImageArray'
path(object) <- value

Arguments

x, a, object	An ImageArray object
i, j, value	Depends on the usage [[, [[<- Here i is the level of the image pyramid. You can use the length function to get the number of the layers in the pyramid. When used with crop, arguments i and j are associated with indices of image dimensions (e.g. width, height)
...	Arguments passed to other methods
drop	ignored
meta	the metadata of the ImageArray object.
levels	levels of the pyramid image, typically a vector of integers starting with 1
level	level
max.pixel.size	maximum pixel size
min.pixel.size	minimum pixel size
angle	value between 0 and 360 for degrees to rotate
perm	perm
brightness	the brightness of the new image in percentage, e.g. 120
index	a named or unnamed list of indices for cropping/subsetting the

Value

dim of the first level of the ImageArray object

type of ImageArray object

length of ImageArray object

An ImageArray object

Functions

• x[i: subset and crop for ImageArray objects

• x[[i: Layer access for ImageArray objects

• `[[`(x = ImageArray, i = numeric) <- value: Layer access for ImageArray objects

• dim(ImageArray): dimensions of an ImageArray

• type(ImageArray): dimensions of an ImageArray

• length(ImageArray): length of an ImageArray

• ImageArray(): ImageArray constructor method

  A function for creating objects of ImageArray class

• realize(ImageArray): realize the array

• as.raster(ImageArray): create a raster object

• rotate(ImageArray): rotate image array to 90, 180, 270 degrees

• aperm(ImageArray): permute image

• negate(ImageArray): negate image

• modulate(ImageArray): modulate image

• flip(ImageArray): vertical flipping image

• flop(ImageArray): horizontal flipping image

• crop(ImageArray): cropping image

• axes(ImageArray): get axes metadata of the ImageArray object

• meta(ImageArray): get metadata of the ImageArray object

• path(ImageArray): path of an ImageArray object

• path(ImageArray) <- value: replace method for path(ImageArray)

Examples

# get image
library(EBImage)
img.file <- system.file("images", "sample.png", package="EBImage")

# create ImageArray
imgarray <- createImageArray(img.file, n.levels = 3)

# access layers
imgarray[[1]]
imgarray[[2]]

# dimensions and length
dim(imgarray)
length(imgarray)

# manipulate images
imgarray <- crop(imgarray, ind = list(100:200, 100:200))
imgarray <- crop(imgarray, ind = list(x = 10:20, y = 10:20))
imgarray <- rotate(imgarray, angle = 90)
imgarray <- flip(imgarray)
imgarray <- flop(imgarray)

# create ImageArray on disk as HDF5 format
dir.create(td <- tempfile())
output_h5 <- tempfile(fileext = ".h5")
imgarray <- writeImageArray(img.file,
                          output = output_h5,
                          name = "image",
                          verbose = FALSE)

# as.raster
imgarray_raster <- as.raster(imgarray)

# realize
imgarray <- realize(imgarray)

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writeImageArray

Description

Writing image arrays on disk

Usage

writeImageArray(
  image,
  output = "my_image",
  name = "",
  format = NULL,
  replace = FALSE,
  n.levels = NULL,
  chunkdim = NULL,
  level = NULL,
  engine = "EBImage",
  verbose = FALSE,
  ...
)

Arguments

image	an Image object (EBImage), a magick object or the path to an image file,
output	output file name
name	name of the group
format	on disk format, either "h5" for HDF5 format, "zarr" for zarr format, or "in-memory" for in-memory ImageArray object. If not provided, the format will be inferred from the file extension of the output path.
replace	Should the existing file be removed or not
n.levels	the number of levels if the image supposed to be pyramidal.
chunkdim	The dimensions of the chunks to use for writing the data to disk.
level	The compression level to use for writing the data to disk.
engine	the package to use for each image layer: either EBImage or magick-image
verbose	verbose
...	additional parameters passed to createImageArray.

Value

An ImageArray object

Examples

# get image
library(EBImage)
img.file <- system.file("images", "sample.png", package="EBImage")

# create ImageArray
dir.create(td <- tempfile())
output_h5 <- tempfile(fileext = ".h5")
imgarray <- writeImageArray(img.file,
                          output = output_h5,
                          name = "image",
                          verbose = FALSE)
imgarray_raster <- as.raster(imgarray)
plot(imgarray_raster)

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