AnnotatedImage-class: AnnotatedImage: Optical images with annotations
In Cardinal: A mass spectrometry imaging toolbox for statistical analysis

Description Usage Arguments Details Slots Methods Author(s) See Also

AnnotatedImage extends the Image class from the EBImage package with metadata columns and plotting in arbitrary coordinate systems. This facilitates annotations such as region-of-interest labeling, and plotting with axes reflective of real-world coordinates.

1	AnnotatedImage(data = array(0, dim=c(1,1)), dim, colormode, ...)

`data`	A vector or array with pixel intensities of an image.
`dim`	The final dimensions of the image.
`colormode`	Either 'Grayscale' or 'Color'.
`...`	Additional arguments passed to the constructor. May be used to set the `offset` or `resolution` slots.

AnnotatedImage is extends Image, so all methods defined on that class also work here.

Metadata columns with annotations can be set via mcols(). The object's length is defined as the product of the first two dimensions. It is assumed any additional frames represent different measurement channels on the same spatial locations.

AnnotatedImage also facilitates integration with other imaging data such as a SparseImagingExperiment or MSImagingExperiment by allowing plotting of the image on arbitrary coordinate systems. This is controlled via an offset slot designating the absolute position of the top-left corner of the image in the current plotting coordinates. The height and width of the image (as plotted) are then controlled by its resolution. This is most easily changed by setting the height() and width() of the object.

.Data:: An array with the image data.
offset:: The absolute offset of the x/y position of the top-left corner of the image when plotted.
resolution:: The absolute offset of the x/y position of the top-left corner of the image when plotted.
colormode:: The color mode of the image. Either 'Grayscale' or 'Color'.
elementMetadata:: An optional DataFrame containing pixel-level annotations.
metadata:: A list containing general metadata (such as filename, etc.).

All methods for Image also work on AnnotatedImage objects. Additional methods are documented below:

mcols(x), mcols(x) <- value:: Get or set the metadata columns.
coord(object), coord(object) <- value:: Get or set the absolute offset of the top-left corner of the image.
resolution(object), resolution(object) <- value:: Get or set the pixel resolution of the image. This corresponds to the number of pixels per unit step on the x/y axes when plotted.
height(x), height(x) <- value:: Get or set the height of the image (as plotted).
width(x), width(x) <- value:: Get or set the width of the image (as plotted).