tractor.base (version 1.6.0)

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", windowLimits = NULL, clearance = NULL, nColumns = NULL)
createProjectionGraphic(image, axis, device = c("internal", "png"), colourScale = 1, add = FALSE, file = NULL, zoomFactor = 1, filter = "Mitchell", windowLimits = NULL)
createSliceGraphic(image, x = NA, y = NA, z = NA, device = c("internal", "png"), colourScale = 1, add = FALSE, file = NULL, zoomFactor = 1, filter = "Mitchell", windowLimits = NULL)
createContactSheetGraphic(image, axis, device = c("internal", "png"), colourScale = 1, add = FALSE, file = NULL, zoomFactor = 1, filter = "Mitchell", windowLimits = NULL, clearance = NULL, nColumns = NULL)

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.

windowLimits

Numeric vector of length 2 giving the limits of the colour scale, or NULL for limits matching the range of the image data. Passed as the zlim argument to image.

clearance

Number of voxels' clearance to leave around each slice image in the contact sheet. Passed to newMriImageByTrimming.

nColumns

Number of slices per row in the contact sheet grid. If NULL, the function will aim for a square grid.

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), 2 (red to yellow heat scale, red background), 3 (blue to red rainbow scale, blue background) and 4 (blue to white to red diverging scale, white 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

image, colours, rgb