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Convert an ijtiff_img to an EBImage::Image.

Source: R/class_constructors.R
as_EBImage.Rd

This is for interoperability with the the EBImage package.

Usage

as_EBImage(img, colormode = NULL, scale = TRUE, force = TRUE)

Arguments

img

An ijtiff_img object (or something coercible to one).

colormode

A numeric or a character string containing the color mode which can be either "Grayscale" or "Color". If not specified, a guess is made. See 'Details'.

scale

Scale values in an integer image to the range [0, 1]? Has no effect on floating-point images.

force

This function is designed to take ijtiff_imgs as input. To force any old array through this function, use force = TRUE, but take care to check that the result is what you'd like it to be.

Value

An EBImage::Image.

Details

The guess for the colormode is made as follows: * If img has an attribute color_space with value "RGB", then colormode is set to "Color". * Else if img has 3 or 4 channels, then colormode is set to "Color". * Else colormode is set to "Grayscale".

Examples

if (rlang::is_installed("EBImage")) {
  img <- read_tif(system.file("img", "Rlogo.tif", package = "ijtiff"))
  str(img)
  str(as_EBImage(img))
}
#> Reading image from /usr/local/lib/R/site-library/ijtiff/img/Rlogo.tif
#> Reading an 8-bit, float image with dimensions 76x100x4x1 (y,x,channel,frame) . . .
#>  'ijtiff_img' num [1:76, 1:100, 1:4, 1] 0 0 0 0 0 0 0 0 0 0 ...
#>  - attr(*, "ImageWidth")= int 100
#>  - attr(*, "ImageLength")= int 76
#>  - attr(*, "ImageDepth")= int 1
#>  - attr(*, "BitsPerSample")= int 8
#>  - attr(*, "SamplesPerPixel")= int 4
#>  - attr(*, "SampleFormat")= chr "unsigned integer data"
#>  - attr(*, "PlanarConfiguration")= chr "contiguous"
#>  - attr(*, "RowsPerStrip")= int 76
#>  - attr(*, "Compression")= chr "LZW"
#>  - attr(*, "Threshholding")= int 1
#>  - attr(*, "XResolution")= num 300
#>  - attr(*, "YResolution")= num 300
#>  - attr(*, "ResolutionUnit")= chr "inch"
#>  - attr(*, "Orientation")= chr "top_left"
#>  - attr(*, "PhotometricInterpretation")= chr "RGB"
#>  - attr(*, "tags_by_frame")=List of 1
#>   ..$ frame1:List of 26
#>   .. ..$ ImageWidth               : int 100
#>   .. ..$ ImageLength              : int 76
#>   .. ..$ ImageDepth               : int 1
#>   .. ..$ BitsPerSample            : int 8
#>   .. ..$ SamplesPerPixel          : int 4
#>   .. ..$ SampleFormat             : chr "unsigned integer data"
#>   .. ..$ PlanarConfiguration      : chr "contiguous"
#>   .. ..$ RowsPerStrip             : int 76
#>   .. ..$ TileWidth                : NULL
#>   .. ..$ TileLength               : NULL
#>   .. ..$ Compression              : chr "LZW"
#>   .. ..$ Threshholding            : int 1
#>   .. ..$ XResolution              : num 300
#>   .. ..$ YResolution              : num 300
#>   .. ..$ XPosition                : NULL
#>   .. ..$ YPosition                : NULL
#>   .. ..$ ResolutionUnit           : chr "inch"
#>   .. ..$ Orientation              : chr "top_left"
#>   .. ..$ Copyright                : NULL
#>   .. ..$ Artist                   : NULL
#>   .. ..$ DocumentName             : NULL
#>   .. ..$ DateTime                 : NULL
#>   .. ..$ ImageDescription         : NULL
#>   .. ..$ Software                 : NULL
#>   .. ..$ PhotometricInterpretation: chr "RGB"
#>   .. ..$ ColorMap                 : NULL
#> Formal class 'Image' [package "EBImage"] with 2 slots
#>   ..@ .Data    : num [1:100, 1:76, 1:4, 1] 0 0 0 0 0 0 0 0 0 0 ...
#>   ..@ colormode: int 2
#>   ..$ dim: int [1:4] 100 76 4 1