Package 'ImageArray'

Title: ImageArray: a framework for on-disk and in-memory image arrays
Description: ImageArray provides a framework for on-disk and in-memory image arrays, specifically for pyramidal images stored in either HDF5 files or Zarr stores.
Authors: Artür Manukyan [aut, cre, fnd] (ORCID: <https://orcid.org/0000-0002-0441-9517>)
Maintainer: Artür Manukyan <[email protected]>
License: MIT + file LICENSE
Version: 0.99.6
Built: 2026-06-01 09:55:40 UTC
Source: https://github.com/Artur-man/ImageArray

Help Index

as.raster method for ImageArray object

Description

as.raster method for ImageArray object

Usage

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

Arguments

x

an ImageArray object
level

level
max.pixel.size

maximum pixel size
min.pixel.size

minimum pixel size

Value

A raster array

Examples

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

# create ImageArray
dir.create(td <- tempfile())
output_h5ad <- file.path(td, "h5test")
imgarray <- writeImageArray(img.file,
                          output = output_h5ad,
                          name = "image",
                          format = "HDF5ImageArray",
                          replace = TRUE, verbose = FALSE)
imgarray_raster <- as.raster(imgarray)

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)

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)

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_h5ad <- file.path(td, "h5test")
imgarray <- writeImageArray(img.file,
                          output = output_h5ad,
                          name = "image",
                          format = "HDF5ImageArray",
                          replace = TRUE, verbose = FALSE)
getImageInfo(imgarray)

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

Methods for ImageArray

Description

Methods for ImageArray objects

Usage

## S4 method for signature 'ImageArray,numeric,numeric,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'
rotate(object, degrees)

## 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(object)

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

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

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

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
degrees

value between 0 and 360 for how many degrees to rotate
perm

perm
brightness

the brightness of the new image in percentage, e.g. 120
ind

index list

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

  • 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

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 <- rotate(imgarray, degrees = 90)
imgarray <- flip(imgarray)
imgarray <- flop(imgarray)

path of ImageArray image

Description

path of ImageArray image

Usage

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

Arguments

object

an ImageArray object

Value

the path to ImageArray object store

path of ImageArray image

Description

path of ImageArray image

Usage

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

Arguments

object

an ImageArray object
value

the new path

Value

does not return a value, updates the path of the ImageArray object

as.array

Description

as.array method for ImageArray object

Usage

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

Arguments

x

an ImageArray object
level

level
max.pixel.size

maximum pixel size
min.pixel.size

minimum pixel size

Value

An array object

Examples

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

# create ImageArray
dir.create(td <- tempfile())
output_h5ad <- file.path(td, "h5test")
imgarray <- writeImageArray(img.file,
                          output = output_h5ad,
                          name = "image",
                          format = "HDF5ImageArray",
                          replace = TRUE, verbose = FALSE)
imgarray <- realize(imgarray)

writeImageArray

Description

Writing image arrays on disk

Usage

writeImageArray(
  image,
  output = "my_image",
  name = "",
  format = c("InMemoryImageArray", "HDF5ImageArray", "ZarrImageArray"),
  replace = FALSE,
  n.levels = NULL,
  chunkdim = NULL,
  level = NULL,
  engine = "EBImage",
  verbose = FALSE,
  ...
)

Arguments

image

image
output

output file name
name

name of the group
format

on disk format
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_h5ad <- file.path(td, "h5test")
imgarray <- writeImageArray(img.file,
                          output = output_h5ad,
                          name = "image",
                          format = "HDF5ImageArray",
                          replace = TRUE, verbose = FALSE)
imgarray_raster <- as.raster(imgarray)
plot(imgarray_raster)

zarrcreateGroup

Description

get information of an ImgArray object

Usage

zarrcreateGroup(store, name)

open_zarr(dir, name)

Arguments

store

the location of (zarr) store
name

name of the zarr store or group
dir

directory/location of zarr store

Value

does not return anything, creates a zarr group in the store instead

does not return anything, opens a zarr store instead

Functions

  • zarrcreateGroup(): create zarr group

  • open_zarr(): open zarr stores

Examples

# zarr store path
dir.create(td <- tempfile())
zarr_name <- "test.zarr"
output_zarr <- file.path(td, zarr_name)

# open zarr store
open_zarr(dir = td, name = zarr_name)

# create group
zarrcreateGroup(store = output_zarr, name = "sample")