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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,56 +1,57 @@ | ||
| # Generated by roxygen2: do not edit by hand | ||
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| S3method(as.character,templatebrain) | ||
| S3method(as.im3d,templatebrain) | ||
| S3method(as.templatebrain,character) | ||
| S3method(as.templatebrain,im3d) | ||
| S3method(as.templatebrain,templatebrain) | ||
| S3method(boundingbox,templatebrain) | ||
| S3method(dim,templatebrain) | ||
| S3method(display_slice,templatebrain) | ||
| S3method(origin,templatebrain) | ||
| S3method(plot3d,templatebrain) | ||
| S3method(print,templatebrain) | ||
| S3method(voxdims,templatebrain) | ||
| export("regtemplate<-") | ||
| export(add_reg_folders) | ||
| export(add_reglist) | ||
| export(all_templatebrains) | ||
| export(allreg_dataframe) | ||
| export(as.templatebrain) | ||
| export(bridging_graph) | ||
| export(bridging_sequence) | ||
| export(display_slice) | ||
| export(download_reg_repo) | ||
| export(extra_reg_folders) | ||
| export(fit_xform) | ||
| export(fit_xform_brain) | ||
| export(guess_templatebrain) | ||
| export(is.templatebrain) | ||
| export(local_reg_dir_for_url) | ||
| export(mirror_brain) | ||
| export(regtemplate) | ||
| export(shortest_bridging_seq) | ||
| export(templatebrain) | ||
| export(update_reg_repos) | ||
| export(xform_brain) | ||
| importFrom(digest,digest) | ||
| importFrom(igraph,"E<-") | ||
| importFrom(igraph,E) | ||
| importFrom(igraph,get.shortest.paths) | ||
| importFrom(igraph,graph.edgelist) | ||
| importFrom(igraph,shortest.paths) | ||
| importFrom(igraph,vertex_attr) | ||
| importFrom(memoise,forget) | ||
| importFrom(nat,as.im3d) | ||
| importFrom(nat,boundingbox) | ||
| importFrom(nat,origin) | ||
| importFrom(nat,pointsinside) | ||
| importFrom(nat,read.im3d) | ||
| importFrom(nat,voxdims) | ||
| importFrom(nat,xform) | ||
| importFrom(nat,xyzmatrix) | ||
| importFrom(rappdirs,user_data_dir) | ||
| importFrom(rgl,as.mesh3d) | ||
| importFrom(rgl,persp3d) | ||
| importFrom(rgl,plot3d) | ||
| # Generated by roxygen2: do not edit by hand | ||
|
|
||
| S3method(as.character,templatebrain) | ||
| S3method(as.im3d,templatebrain) | ||
| S3method(as.templatebrain,character) | ||
| S3method(as.templatebrain,im3d) | ||
| S3method(as.templatebrain,templatebrain) | ||
| S3method(boundingbox,templatebrain) | ||
| S3method(dim,templatebrain) | ||
| S3method(display_slice,default) | ||
| S3method(display_slice,templatebrain) | ||
| S3method(origin,templatebrain) | ||
| S3method(plot3d,templatebrain) | ||
| S3method(print,templatebrain) | ||
| S3method(voxdims,templatebrain) | ||
| export("regtemplate<-") | ||
| export(add_reg_folders) | ||
| export(add_reglist) | ||
| export(all_templatebrains) | ||
| export(allreg_dataframe) | ||
| export(as.templatebrain) | ||
| export(bridging_graph) | ||
| export(bridging_sequence) | ||
| export(display_slice) | ||
| export(download_reg_repo) | ||
| export(extra_reg_folders) | ||
| export(fit_xform) | ||
| export(fit_xform_brain) | ||
| export(guess_templatebrain) | ||
| export(is.templatebrain) | ||
| export(local_reg_dir_for_url) | ||
| export(mirror_brain) | ||
| export(regtemplate) | ||
| export(shortest_bridging_seq) | ||
| export(templatebrain) | ||
| export(update_reg_repos) | ||
| export(xform_brain) | ||
| importFrom(digest,digest) | ||
| importFrom(igraph,"E<-") | ||
| importFrom(igraph,E) | ||
| importFrom(igraph,get.shortest.paths) | ||
| importFrom(igraph,graph.edgelist) | ||
| importFrom(igraph,shortest.paths) | ||
| importFrom(igraph,vertex_attr) | ||
| importFrom(memoise,forget) | ||
| importFrom(nat,as.im3d) | ||
| importFrom(nat,boundingbox) | ||
| importFrom(nat,origin) | ||
| importFrom(nat,pointsinside) | ||
| importFrom(nat,read.im3d) | ||
| importFrom(nat,voxdims) | ||
| importFrom(nat,xform) | ||
| importFrom(nat,xyzmatrix) | ||
| importFrom(rappdirs,user_data_dir) | ||
| importFrom(rgl,as.mesh3d) | ||
| importFrom(rgl,persp3d) | ||
| importFrom(rgl,plot3d) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,29 +1,30 @@ | ||
| #' Display an image slice in 3D | ||
| #' | ||
| #' @param brain template brain (e.g. IS2) of the slice. | ||
| #' @param slice Path to PNG image containing slice to display. | ||
| #' @param ... extra arguments to pass to \code{\link[rgl]{persp3d}}. | ||
| #' @export | ||
| display_slice <- function(brain, slice, ...) { | ||
| UseMethod("display_slice") | ||
| } | ||
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| #' @method display_slice default | ||
| display_slice.default <- function(brain, slice, ...) { | ||
| } | ||
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| #' @importFrom rgl persp3d | ||
| #' @method display_slice templatebrain | ||
| #' @export | ||
| display_slice.templatebrain <- function(brain, slice, z=NULL, ...) { | ||
| bbox <- brain$BoundingBox | ||
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| x <- c(bbox[1, 1], bbox[2, 1]) | ||
| y <- c(bbox[1, 2], bbox[2, 2]) | ||
| if(is.null(z)) { | ||
| z <- (bbox[2, 3] - bbox[1, 3]) / 2 | ||
| } | ||
| z <- matrix(rep(z, 4), nrow=2) | ||
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| persp3d(x,y,z, col='white', specular='black', texture=slice, xlab='', ylab='', zlab='', box=F, axes=F, add=T, ...) | ||
| } | ||
| #' Display an image slice in 3D | ||
| #' | ||
| #' @param brain template brain (e.g. IS2) of the slice. | ||
| #' @param slice Path to PNG image containing slice to display. | ||
| #' @param ... extra arguments to pass to \code{\link[rgl]{persp3d}}. | ||
| #' @export | ||
| display_slice <- function(brain, slice, ...) { | ||
| UseMethod("display_slice") | ||
| } | ||
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| #' @method display_slice default | ||
| #' @export | ||
| display_slice.default <- function(brain, slice, ...) { | ||
| } | ||
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| #' @importFrom rgl persp3d | ||
| #' @method display_slice templatebrain | ||
| #' @export | ||
| display_slice.templatebrain <- function(brain, slice, z=NULL, ...) { | ||
| bbox <- brain$BoundingBox | ||
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| x <- c(bbox[1, 1], bbox[2, 1]) | ||
| y <- c(bbox[1, 2], bbox[2, 2]) | ||
| if(is.null(z)) { | ||
| z <- (bbox[2, 3] - bbox[1, 3]) / 2 | ||
| } | ||
| z <- matrix(rep(z, 4), nrow=2) | ||
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| persp3d(x,y,z, col='white', specular='black', texture=slice, xlab='', ylab='', zlab='', box=F, axes=F, add=T, ...) | ||
| } |