vislayout.from.coloredmeshes: Visualize coloredmeshes from several angles and combine the...

In dfsp-spirit/fsbrain: Managing and Visualizing Brain Surface Data

Visualize coloredmeshes from several angles and combine the images into a new figure.

Description

Create a tight layout view of coloredmeshes from several angles. Creates separate 'sd_<angle>' images, then crops and finally merges them into a single output image with image magick. The 'coloredmeshes' to pass to this function are usually obtained by running any 'vis*' function (like vis.subject.morph.native, vis.subject.morph.standard, vis.subject.label, vis.subject.annot, and others). That means you can use this function to visualize all kinds of data, e.g., morphometry data in native and standard space, labels, and brain atlases.

Usage

vislayout.from.coloredmeshes(
  coloredmeshes,
  view_angles = get.view.angle.names(angle_set = "t4"),
  rgloptions = rglo(),
  rglactions = list(),
  style = "default",
  output_img = "fsbrain_arranged.png",
  silent = FALSE,
  grid_like = TRUE,
  background_color = "white",
  transparency_color = NULL
)

Arguments

coloredmeshes	list of coloredmesh. A coloredmesh is a named list as returned by the 'coloredmesh.from*' functions (like coloredmesh.from.morph.native). It has the entries 'mesh' of type tmesh3d, a 'col', which is a color specification for such a mesh. The 'vis*' functions (like vis.subject.morph.native) all return a list of coloredmeshes.
view_angles	list of strings. See get.view.angle.names for all valid strings.
rgloptions	option list passed to par3d. Example: rgloptions = list("windowRect"=c(50,50,1000,1000)).
rglactions	named list. A list in which the names are from a set of pre-defined actions. The values can be used to specify parameters for the action.
style	character string, a rendering style, e.g., 'default', 'shiny' or 'semitransparent'. Alternatively, a named list of style parameters (see material3d), e.g., list("shininess"=50, specular="black", alpha=0.5). Use the magic word 'from_mesh' to use the 'style' field of each coloredmesh instead of a single, global style. In that case, you will have to make sure your meshes have such a field, if not, the style 'default' is used as a fallback for those which don't.
output_img	string, path to the output file. Defaults to "fsbrain_arranged.png"
silent	logical, whether to suppress all messages
grid_like	logical, whether to arrange the images in a grid-like fashion. If FALSE, they will all be merged horizontally. Passed to arrange.brainview.images.
background_color	hex color string (like '#FFFFFF'), the color to use for the background. Ignored if 'transparency_color' is not NULL. To get a transparent background, use 'transparency_color' instead of this parameter. WARNING: Do not use color names (like 'gray'), as their interpretation differs between rgl and image magick!
transparency_color	hex color string (like '#FFFFFF'), the temporary background color that will get mapped to transparency, or NULL if you do not want a transparent background. If used, it can be any color that does not occur in the foreground. Try '#FFFFFF' (white) or '#000000' (black) if in doubt. WARNING: Do not use color names (like 'gray'), as their interpretation differs between rgl and image magick!

Value

named list, see arrange.brainview.images for details

See Also

Other visualization functions: highlight.vertices.on.subject(), highlight.vertices.on.subject.spheres(), vis.color.on.subject(), vis.data.on.fsaverage(), vis.data.on.subject(), vis.labeldata.on.subject(), vis.mask.on.subject(), vis.region.values.on.subject(), vis.subject.annot(), vis.subject.label(), vis.subject.morph.native(), vis.subject.morph.standard(), vis.subject.pre(), vis.symmetric.data.on.subject()

Examples

## Not run: 
   fsbrain::download_optional_data();
   subjects_dir = fsbrain::get_optional_data_filepath("subjects_dir");
   # Use any vis function to get coloredmeshes. You can visualize morphometry,
   #  labels, an atlas, whatever. You can suppress the view unless you need it.
   coloredmeshes = vis.subject.morph.native(subjects_dir, "subject1", "thickness",
    cortex_only=TRUE, rglactions=list("clip_data"=c(0.05, 0.95)),
    views=NULL);
   # The meshes contain the surface, data, and color information and can be
   #  visualized. You could adapt the rendering style while doing so:
   vislayout.from.coloredmeshes(coloredmeshes, style='shiny');
   # You could change the rendering style on a per-mesh basis.
   coloredmeshes[[1]]$style = list("shininess"=50, alpha=0.5);
   vislayout.from.coloredmeshes(coloredmeshes, style='from_mesh');

## End(Not run)

dfsp-spirit/fsbrain documentation built on Nov. 28, 2024, 10:29 a.m.