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tractor.base (version 1.1.0)

visualisation: Visualise MriImage objects

Description

Visualise MriImage objects.

Usage

createCombinedGraphics(images, modes, colourScales, axes = 1:3, sliceLoc = NULL, device = c("internal", "png"), alphaImages = NULL, prefix = "image", zoomFactor = 1, filter = "Mitchell")
createProjectionGraphic(image, axis, device = c("internal", "png"), colourScale = 1, add = FALSE, file = NULL, zoomFactor = 1, filter = "Mitchell")
createSliceGraphic(image, x = NA, y = NA, z = NA, device = c("internal", "png"), colourScale = 1, add = FALSE, file = NULL, zoomFactor = 1, filter = "Mitchell")

Arguments

images
A list of MriImage objects.
image
A single MriImage object.
modes
A character vector of the same length as images, each element being "slice" or "projection" (or abbreviations), indicating which type of visualisation should be applied to each image.
colourScale, colourScales
A single colour scale definition, or a list in the plural case. See Details.
axis, axes
A vector of axes along which slice/projection images should be created. 1 is left-right, 2 is anterior-posterior, 3 is superior-inferior.
x, y, z
Integer vectors, each of length 1. Exactly one of these must be specified to indicate the plane of interest.
sliceLoc
Like x, y and z, except that a point in 3 dimensions is specified. Must not be NA for each axis requested.
device
Either "internal" for display on the default graphics device, or "png" for creating PNG format image file(s). Abbreviations are fine.
alphaImages
A list of MriImage objects to be used as transparency masks. Must be the same length as images if not NULL. NULL values in the list indicate no mask.
prefix, file
A file name or prefix (to which "axial", "coronal" or "sagittal" will be added) to be used when device is "png".
zoomFactor
Factor by which to enlarge the image. Applies only when device is "png".
filter
Interpolation filter to be used by ImageMagick.
add
Overlay the graphic on a previous one. Used only when device is "internal".

Value

  • These functions are called for their side effects.

Details

These functions create 2D visualisations of 3D images by slicing or maximum intensity projection. Colour scales can be specified in any of three ways. Firstly, by a single number, representing a predefined colour scale. Currently valid values are 1 (greyscale, black background) and 2 (red to yellow heat scale, red background). Secondly, a single colour name can be given (see colours); in this case the background will be black. This is useful for binary images. Thirdly and most flexibly, a list with two named elements can be given: colours, a vector of colours representing the colour scale, perhaps created using rgb; and background, a single colour representing the background.

NB: When the device option is set to "png", ImageMagick is required by these functions.

See Also

colours, rgb