Merge pull request #48 from dmurdoch/rgl

Change rgl.* calls to *3d calls.

NAMESPACE

@@ -252,18 +252,16 @@ importFrom(rgl,next3d)
 importFrom(rgl,open3d)
 importFrom(rgl,par3d)
 importFrom(rgl,play3d)
-importFrom(rgl,rgl.lines)
-importFrom(rgl,rgl.open)
 importFrom(rgl,rgl.postscript)
 importFrom(rgl,rgl.snapshot)
-importFrom(rgl,rgl.viewpoint)
 importFrom(rgl,segments3d)
 importFrom(rgl,shade3d)
 importFrom(rgl,spin3d)
 importFrom(rgl,text3d)
 importFrom(rgl,tmesh3d)
 importFrom(rgl,translate3d)
 importFrom(rgl,triangles3d)
+importFrom(rgl,view3d)
 importFrom(rgl,wire3d)
 importFrom(squash,blueorange)
 importFrom(squash,cmap)

R/coloredmesh.R

@@ -25,7 +25,7 @@
 #'
 #' @export
 #' @importFrom squash cmap makecmap
-#' @importFrom rgl tmesh3d rgl.open wire3d
+#' @importFrom rgl tmesh3d open3d wire3d
 coloredmesh.from.morph.native <- function(subjects_dir, subject_id, measure, hemi, surface="white", clip=NULL, cortex_only=FALSE, makecmap_options=mkco.seq()) {
 
     if(!(hemi %in% c("lh", "rh"))) {
@@ -113,7 +113,7 @@ tmesh3d.to.fs.surface <- function(tmesh) {
 #' @note Do not call this directly, use \code{\link[fsbrain]{coloredmeshes.from.color}} instead.
 #'
 #' @keywords internal
-#' @importFrom rgl tmesh3d rgl.open wire3d
+#' @importFrom rgl tmesh3d open3d wire3d
 coloredmesh.from.color <- function(subjects_dir, subject_id, color_data, hemi, surface="white", metadata=list()) {
 
     if(!(hemi %in% c("lh", "rh"))) {
@@ -221,7 +221,7 @@ coloredmeshes.from.color <- function(subjects_dir, subject_id, color_data, hemi,
 #'
 #' @export
 #' @importFrom squash cmap makecmap
-#' @importFrom rgl tmesh3d rgl.open wire3d
+#' @importFrom rgl tmesh3d open3d wire3d
 coloredmesh.from.morph.standard <- function(subjects_dir, subject_id, measure, hemi, fwhm, surface="white", template_subject='fsaverage', template_subjects_dir=NULL, clip = NULL, cortex_only=FALSE, makecmap_options=mkco.seq()) {
 
     if(!(hemi %in% c("lh", "rh"))) {
@@ -290,7 +290,7 @@ coloredmesh.from.morph.standard <- function(subjects_dir, subject_id, measure, h
 #'
 #' @export
 #' @importFrom squash cmap makecmap
-#' @importFrom rgl tmesh3d rgl.open wire3d
+#' @importFrom rgl tmesh3d open3d wire3d
 #' @importFrom utils modifyList
 coloredmesh.from.morphdata <- function(subjects_dir, vis_subject_id, morph_data, hemi, surface="white", makecmap_options=mkco.seq()) {
 
@@ -388,7 +388,7 @@ coloredmesh.from.preloaded.data <- function(fs_surface, morph_data=NULL, col=NUL
 #'
 #' @export
 #' @importFrom squash cmap makecmap
-#' @importFrom rgl tmesh3d rgl.open wire3d
+#' @importFrom rgl tmesh3d open3d wire3d
 #' @importFrom utils modifyList
 coloredmesh.from.annot <- function(subjects_dir, subject_id, atlas, hemi, surface="white", outline=FALSE) {
 
@@ -445,7 +445,7 @@ coloredmesh.from.annot <- function(subjects_dir, subject_id, atlas, hemi, surfac
 #'
 #' @export
 #' @importFrom squash cmap makecmap rainbow2
-#' @importFrom rgl tmesh3d rgl.open wire3d
+#' @importFrom rgl tmesh3d open3d wire3d
 coloredmesh.from.label <- function(subjects_dir, subject_id, label, hemi, surface="white", makecmap_options=list('colFn'=squash::rainbow2), binary = TRUE) {
 
     if(!(hemi %in% c("lh", "rh"))) {

R/highlight.R

@@ -196,7 +196,7 @@ highlight.points.spheres <- function(coords, color = "#FF0000", radius = 1.0) {
     if(is.vector(coords)) {
         coords = matrix(coords, ncol = 3, byrow = TRUE);
     }
-    rgl::rgl.spheres(coords[,1], coords[,2], coords[,3], radius = radius, col = color);
+    rgl::spheres3d(coords[,1], coords[,2], coords[,3], radius = radius, col = color);
 }
 
 

R/spherical.R

@@ -83,13 +83,13 @@ eeg_coords <- function(label_subset=NULL) {
 #'
 #' @note The x, y and z axes are plotted in red, green, and blue, respectively.
 #'
-#' @importFrom rgl rgl.lines
+#' @importFrom rgl segments3d
 #' @keywords internal
 rgl.coord.lines <- function(len = 100) {
     len = recycle(len, 3L);
-    rgl::rgl.lines(x=c(0, len[1]), y=c(0,0), z=c(0,0), col="red");
-    rgl::rgl.lines(x=c(0, 0), y=c(0,len[2]), z=c(0,0), col="green");
-    rgl::rgl.lines(x=c(0, 0), y=c(0,0), z=c(0,len[3]), col="blue");
+    rgl::segments3d(x=c(0, len[1]), y=c(0,0), z=c(0,0), col="red");
+    rgl::segments3d(x=c(0, 0), y=c(0,len[2]), z=c(0,0), col="green");
+    rgl::segments3d(x=c(0, 0), y=c(0,0), z=c(0,len[3]), col="blue");
     return(invisible(NULL));
 }
 

R/vis_meshes.R

@@ -203,7 +203,7 @@ vis.coloredmeshes.rotating <- function(coloredmeshes, background="white", skip_a
     for(cmesh in coloredmeshes) {
         vis.renderable(cmesh, skip_all_na=TRUE, style=style);
     }
-    rgl::rgl.viewpoint(-90, 0);
+    rgl::view3d(-90, 0);
 
     if (!rgl::rgl.useNULL()) {
         if(rglactions.has.key(rglactions, 'movie')) {

R/vis_multiview.R

@@ -103,7 +103,7 @@ get.view.angle.names <- function(angle_set="all", add_sd_prefix=TRUE) {
 #' @param draw_colorbar logical, whether to draw a colorbar. WARNING: The colorbar is drawn to a subplot, and this only works if there is enough space for it. You will have to increase the plot size using the 'rlgoptions' parameter for the colorbar to show up. Defaults to FALSE.
 #'
 #' @keywords internal
-#' @importFrom rgl open3d bg3d wire3d shade3d mfrow3d next3d text3d rgl.viewpoint
+#' @importFrom rgl open3d bg3d wire3d shade3d mfrow3d next3d text3d view3d
 brainview.si <- function(coloredmeshes, background="white", skip_all_na=TRUE, style="default", draw_labels = FALSE, rgloptions = rglo(), rglactions=list(), draw_colorbar = FALSE) {
 
     if(!is.list(coloredmeshes)) {
@@ -161,7 +161,7 @@ brainview.si <- function(coloredmeshes, background="white", skip_all_na=TRUE, st
 #' @param draw_colorbar logical, whether to draw a colorbar. WARNING: The colorbar is drawn to a subplot, and this only works if there is enough space for it. You will have to increase the plot size using the 'rlgoptions' parameter for the colorbar to show up. Defaults to FALSE.
 #'
 #' @keywords internal
-#' @importFrom rgl open3d bg3d wire3d shade3d mfrow3d next3d text3d rgl.viewpoint
+#' @importFrom rgl open3d bg3d wire3d shade3d mfrow3d next3d text3d view3d
 brainview.sr <- function(coloredmeshes, background="white", skip_all_na=TRUE, style="default", draw_labels = FALSE, x=0, y=1, z=0, rpm=6, duration=10, rgloptions = rglo(), rglactions=list(), draw_colorbar = FALSE) {
 
     if(!is.list(coloredmeshes)) {
@@ -245,7 +245,7 @@ handle.rglactions.highlight.points <- function(rglactions, angle_rad, x, y, z, h
 #' @param draw_colorbar logical, whether to draw a colorbar. WARNING: The colorbar is drawn to a subplot, and this only works if there is enough space for it. You will have to increase the plot size using the 'rlgoptions' parameter for the colorbar to show up. Defaults to FALSE.
 #'
 #' @keywords internal
-#' @importFrom rgl open3d bg3d wire3d shade3d mfrow3d next3d text3d rgl.viewpoint
+#' @importFrom rgl open3d bg3d wire3d shade3d mfrow3d next3d text3d view3d
 brainview.t4 <- function(coloredmeshes, background="white", skip_all_na=TRUE, style="default", draw_labels = FALSE, rgloptions = rglo(), rglactions = list(), draw_colorbar = FALSE) {
 
     label_shift_y = -20;
@@ -293,7 +293,7 @@ brainview.t4 <- function(coloredmeshes, background="white", skip_all_na=TRUE, st
     rgl::next3d(reuse=TRUE);
     vis.rotated.coloredmeshes(lh_meshes, pi/2, 1, 0, 0, style=style);
     handle.rglactions.highlight.points(rglactions, pi/2, 1, 0, 0, hemi = "lh");
-    rgl::rgl.viewpoint(-90, 0, fov=0, interactive=FALSE);
+    rgl::view3d(-90, 0, fov=0, interactive=FALSE);
     if(draw_labels) {
         rgl::text3d(0,label_shift_y,0,"lateral lh");
     }
@@ -306,7 +306,7 @@ brainview.t4 <- function(coloredmeshes, background="white", skip_all_na=TRUE, st
     rgl::next3d(reuse=FALSE);
     vis.rotated.coloredmeshes(rh_meshes, pi/2, 1, 0, 0, style=style);
     handle.rglactions.highlight.points(rglactions, pi/2, 1, 0, 0, hemi = "rh");
-    rgl::rgl.viewpoint(90, 0, fov=0, interactive=FALSE);
+    rgl::view3d(90, 0, fov=0, interactive=FALSE);
     if(draw_labels) {
         rgl::text3d(0,label_shift_y,0,"lateral rh");
     }
@@ -319,7 +319,7 @@ brainview.t4 <- function(coloredmeshes, background="white", skip_all_na=TRUE, st
     rgl::next3d(reuse=FALSE);
     vis.rotated.coloredmeshes(lh_meshes, pi/2, 1, 0, 0, style=style);
     handle.rglactions.highlight.points(rglactions, pi/2, 1, 0, 0, hemi = "lh");
-    rgl::rgl.viewpoint(90, 0, fov=0, interactive=FALSE);
+    rgl::view3d(90, 0, fov=0, interactive=FALSE);
     if(draw_labels) {
         rgl::text3d(0,label_shift_y,0,"medial lh");
     }
@@ -332,7 +332,7 @@ brainview.t4 <- function(coloredmeshes, background="white", skip_all_na=TRUE, st
     rgl::next3d(reuse=FALSE);
     vis.rotated.coloredmeshes(rh_meshes, pi/2, 1, 0, 0, style=style);
     handle.rglactions.highlight.points(rglactions, pi/2, 1, 0, 0, hemi = "rh");
-    rgl::rgl.viewpoint(-90, 0, fov=0, interactive=FALSE);
+    rgl::view3d(-90, 0, fov=0, interactive=FALSE);
     if(draw_labels) {
         rgl::text3d(0,label_shift_y,0,"medial rh");
     }
@@ -375,7 +375,7 @@ brainview.t4 <- function(coloredmeshes, background="white", skip_all_na=TRUE, st
 #' @param draw_colorbar logical, whether to draw a colorbar. WARNING: The colorbar is drawn to a subplot, and this only works if there is enough space for it. You will have to increase the plot size using the 'rlgoptions' parameter for the colorbar to show up. Defaults to FALSE.
 #'
 #' @keywords internal
-#' @importFrom rgl open3d bg3d wire3d shade3d mfrow3d next3d text3d rgl.viewpoint
+#' @importFrom rgl open3d bg3d wire3d shade3d mfrow3d next3d text3d view3d
 brainview.t9 <- function(coloredmeshes, background="white", skip_all_na=TRUE, style="default", draw_labels = FALSE, rgloptions = rglo(), rglactions = list(), draw_colorbar = FALSE) {
 
 
@@ -429,7 +429,7 @@ brainview.t9 <- function(coloredmeshes, background="white", skip_all_na=TRUE, st
     # Create the upper left view: draw only the left hemi, from the left
     rgl::next3d(reuse=TRUE);
     vis.rotated.coloredmeshes(lh_meshes, pi/2, 1, 0, 0, style=style);
-    rgl::rgl.viewpoint(-90, 0, fov=0, interactive=FALSE);
+    rgl::view3d(-90, 0, fov=0, interactive=FALSE);
     if(draw_labels) {
         rgl::text3d(0,label_shift_y,0,"lateral lh");
     }
@@ -440,7 +440,7 @@ brainview.t9 <- function(coloredmeshes, background="white", skip_all_na=TRUE, st
     # Create the upper central view: draw both hemis from above (top view)
     rgl::next3d(reuse=FALSE);
     vis.rotated.coloredmeshes(coloredmeshes_potentially_shifted, 0, 1, 0, 0, style=style);
-    rgl::rgl.viewpoint(0, 0, fov=0, interactive=FALSE);
+    rgl::view3d(0, 0, fov=0, interactive=FALSE);
     if(draw_labels) {
         rgl::text3d(0,label_shift_y_dorsal,0,"dorsal");
     }
@@ -451,7 +451,7 @@ brainview.t9 <- function(coloredmeshes, background="white", skip_all_na=TRUE, st
     # Create the upper right view
     rgl::next3d(reuse=FALSE);
     vis.rotated.coloredmeshes(rh_meshes, pi/2, 1, 0, 0, style=style);
-    rgl::rgl.viewpoint(90, 0, fov=0, interactive=FALSE);
+    rgl::view3d(90, 0, fov=0, interactive=FALSE);
     if(draw_labels) {
         rgl::text3d(0,label_shift_y,0,"lateral rh");
     }
@@ -466,7 +466,7 @@ brainview.t9 <- function(coloredmeshes, background="white", skip_all_na=TRUE, st
     # Create the 2nd row left view
     rgl::next3d(reuse=FALSE);
     vis.rotated.coloredmeshes(lh_meshes, pi/2, 1, 0, 0, style=style);
-    rgl::rgl.viewpoint(90, 0, fov=0, interactive=FALSE);
+    rgl::view3d(90, 0, fov=0, interactive=FALSE);
     if(draw_labels) {
         rgl::text3d(0,label_shift_y,0,"medial lh");
     }
@@ -477,7 +477,7 @@ brainview.t9 <- function(coloredmeshes, background="white", skip_all_na=TRUE, st
     # Create the 2nd row central view: draw both hemis from below (bottom view)
     rgl::next3d(reuse=FALSE);
     vis.rotated.coloredmeshes(coloredmeshes_potentially_shifted, pi, 1, 0, 0, style=style);
-    rgl::rgl.viewpoint(0, 0, fov=0, interactive=FALSE);
+    rgl::view3d(0, 0, fov=0, interactive=FALSE);
     if(draw_labels) {
         rgl::text3d(0,label_shift_y_ventral,0,"ventral");
     }
@@ -489,7 +489,7 @@ brainview.t9 <- function(coloredmeshes, background="white", skip_all_na=TRUE, st
     # Create the 2nd row right view
     rgl::next3d(reuse=FALSE);
     vis.rotated.coloredmeshes(rh_meshes, pi/2, 1, 0, 0, style=style);
-    rgl::rgl.viewpoint(-90, 0, fov=0, interactive=FALSE);
+    rgl::view3d(-90, 0, fov=0, interactive=FALSE);
     if(draw_labels) {
         rgl::text3d(0,label_shift_y,0,"medial rh");
     }
@@ -504,7 +504,7 @@ brainview.t9 <- function(coloredmeshes, background="white", skip_all_na=TRUE, st
     # Create the bottom left view: draw only the left hemi, from the left
     rgl::next3d(reuse=FALSE);
     vis.rotated.coloredmeshes(coloredmeshes_potentially_shifted, pi/2, 1, 0, 0, style=style);
-    rgl.viewpoint(0, 0, fov=0, interactive=FALSE);
+    view3d(0, 0, fov=0, interactive=FALSE);
     if(draw_labels) {
         rgl::text3d(0,label_shift_y,0,"rostral");
     }
@@ -521,7 +521,7 @@ brainview.t9 <- function(coloredmeshes, background="white", skip_all_na=TRUE, st
     # Create the bottom right view
     rgl::next3d(reuse=FALSE);
     vis.rotated.coloredmeshes(coloredmeshes_potentially_shifted, pi/2, 1, 0, 0, style=style);
-    rgl::rgl.viewpoint(180, 0, fov=0, interactive=FALSE);
+    rgl::view3d(180, 0, fov=0, interactive=FALSE);
     if(draw_labels) {
         rgl::text3d(0,label_shift_y,0,"caudal");
     }
@@ -563,7 +563,7 @@ brainview.t9 <- function(coloredmeshes, background="white", skip_all_na=TRUE, st
 #' @param draw_colorbar logical, whether to draw a colorbar. WARNING: The colorbar is drawn to a subplot, and this only works if there is enough space for it. You will have to increase the plot size using the 'rlgoptions' parameter for the colorbar to show up. Defaults to FALSE.
 #'
 #' @keywords internal
-#' @importFrom rgl open3d bg3d rgl.viewpoint
+#' @importFrom rgl open3d bg3d view3d
 brainview.sd <- function(coloredmeshes, view_angle, background="white", skip_all_na=TRUE, style="default", rgloptions = rglo(), rglactions = list(), draw_colorbar = FALSE) {
 
 
@@ -614,42 +614,42 @@ brainview.sd <- function(coloredmeshes, view_angle, background="white", skip_all
     if(view_angle == "lateral_lh") {
         vis.rotated.coloredmeshes(lh_meshes, pi/2, 1, 0, 0, style=style);
         handle.rglactions.highlight.points(rglactions, pi/2, 1, 0, 0, hemi = "lh");
-        rgl::rgl.viewpoint(-90, 0, fov=0, interactive=FALSE);
+        rgl::view3d(-90, 0, fov=0, interactive=FALSE);
         if(is.function(callback_after_render)) { callback_after_render('lateral_lh'); }
     } else if (view_angle == "dorsal") {
         vis.rotated.coloredmeshes(coloredmeshes, 0, 1, 0, 0, style=style);
         handle.rglactions.highlight.points(rglactions, 0, 1, 0, 0, hemi = "both");
-        rgl::rgl.viewpoint(0, 0, fov=0, interactive=FALSE);
+        rgl::view3d(0, 0, fov=0, interactive=FALSE);
         if(is.function(callback_after_render)) { callback_after_render('dorsal'); }
     } else if(view_angle == "lateral_rh") {
         vis.rotated.coloredmeshes(rh_meshes, pi/2, 1, 0, 0, style=style);
         handle.rglactions.highlight.points(rglactions, pi/2, 1, 0, 0, hemi = "rh");
-        rgl::rgl.viewpoint(90, 0, fov=0, interactive=FALSE);
+        rgl::view3d(90, 0, fov=0, interactive=FALSE);
         if(is.function(callback_after_render)) { callback_after_render('lateral_lh'); }
     } else if(view_angle == "medial_lh") {
         vis.rotated.coloredmeshes(lh_meshes, pi/2, 1, 0, 0, style=style);
         handle.rglactions.highlight.points(rglactions, pi/2, 1, 0, 0, hemi = "lh");
-        rgl::rgl.viewpoint(90, 0, fov=0, interactive=FALSE);
+        rgl::view3d(90, 0, fov=0, interactive=FALSE);
         if(is.function(callback_after_render)) { callback_after_render('medial_lh'); }
     } else if(view_angle == "ventral") {
         vis.rotated.coloredmeshes(coloredmeshes, pi, 1, 0, 0, style=style);
         handle.rglactions.highlight.points(rglactions, pi/2, 1, 0, 0, hemi = "both");
-        rgl::rgl.viewpoint(0, 0, fov=0, interactive=FALSE);
+        rgl::view3d(0, 0, fov=0, interactive=FALSE);
         if(is.function(callback_after_render)) { callback_after_render('ventral'); }
     } else if(view_angle == "medial_rh") {
         vis.rotated.coloredmeshes(rh_meshes, pi/2, 1, 0, 0, style=style);
         handle.rglactions.highlight.points(rglactions, pi/2, 1, 0, 0, hemi = "rh");
-        rgl::rgl.viewpoint(-90, 0, fov=0, interactive=FALSE);
+        rgl::view3d(-90, 0, fov=0, interactive=FALSE);
         if(is.function(callback_after_render)) { callback_after_render('medial_rh'); }
     } else if(view_angle == "rostral") {
         vis.rotated.coloredmeshes(coloredmeshes, pi/2, 1, 0, 0, style=style);
         handle.rglactions.highlight.points(rglactions, pi/2, 1, 0, 0, hemi = "both");
-        rgl.viewpoint(0, 0, fov=0, interactive=FALSE);
+        view3d(0, 0, fov=0, interactive=FALSE);
         if(is.function(callback_after_render)) { callback_after_render('rostral'); }
     } else if(view_angle == "caudal") {
         vis.rotated.coloredmeshes(coloredmeshes, pi/2, 1, 0, 0, style=style);
         handle.rglactions.highlight.points(rglactions, pi/2, 1, 0, 0, hemi = "both");
-        rgl::rgl.viewpoint(180, 0, fov=0, interactive=FALSE);
+        rgl::view3d(180, 0, fov=0, interactive=FALSE);
         if(is.function(callback_after_render)) { callback_after_render('caudal'); }
     } else {
         stop(sprintf("Invalid view_angle '%s'. Must be one of 'lateral_lh', 'dorsal', 'lateral_rh', 'medial_lh', 'ventral', 'medial_rh', 'rostral' or 'caudal'.\n", view_angle));

R/vis_volume_3d.R

@@ -81,7 +81,7 @@ volvis.voxels <- function(volume, render_every=1, voxelcol=NULL, ...) {
             row_idx = rendered_voxels[idx];
             surface_ras[idx,] = (vox2surface_ras_matrix %*% voxel_crs[row_idx,])[1:3];
         }
-        #rgl::rgl.spheres(surface_ras, r = 0.5, ...);
+        #rgl::spheres3d(surface_ras, r = 0.5, ...);
         return(invisible(rglvoxels(surface_ras, r = 1.0, voxelcol=voxelcol, ...)));
     } else {
         warning("No foreground voxels in volume, nothing to visualize.");
@@ -339,7 +339,7 @@ apply.transform <- function(object, matrix_fun) {
 
 #' @title Draw 3D boxes at locations using rgl.
 #'
-#' @description Draw 3D boxes at all given coordinates using rgl, analogous to \code{\link{rgl.spheres}}. Constructs the coordinates for triangles making up the boxes, then uses \code{\link{triangles3d}} to render them.
+#' @description Draw 3D boxes at all given coordinates using rgl, analogous to \code{\link{spheres3d}}. Constructs the coordinates for triangles making up the boxes, then uses \code{\link{triangles3d}} to render them.
 #'
 #' @param centers numerical matrix with 3 columns. Each column represents the x, y, z coordinates of a center at which to create a cube.
 #'

tests/testthat/helper-functions.R

@@ -129,8 +129,8 @@ get.demo.volume <- function(vd = 30L, bg = NA, num_centers = 8L) {
 
 #' @title Close rgl windows after test.
 close.all.rgl.windows <- function() {
-  while (rgl::rgl.cur() > 0) {
-    rgl::rgl.close();
+  while (rgl::cur3d() > 0) {
+    rgl::close3d();
   }
 }