add_annotation automatically compiles annotations from template if …

…missing

CHANGELOG.md

@@ -1,6 +1,6 @@
 ## Changes since last CRAN release
-* `27324b88 (HEAD -> master)` [_`dipterix`_]: Fixing the side panels so the background color is always black
-* `ad4633fe (origin/master, origin/HEAD)` [_`dipterix`_]: Canvas and screenshot is transparent when background is `#ffffff`
+* `dd4b0b0a (HEAD -> master, origin/master, origin/HEAD)` [_`dipterix`_]: Fixing the side panels so the background color is always black
+* `ad4633fe` [_`dipterix`_]: Canvas and screenshot is transparent when background is `#ffffff`
 * `ff5eca46` [_`dipterix`_]: Fixed shader ignoring always-depth flag when outline is off; updated `jsPDF` to the 2.5.2 build
 * `ad202235` [_`dipterix`_]: Transition animation allows video recording
 * `94ec004f` [_`dipterix`_]: Fixed screenshot button and improved video quality

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: threeBrain
 Type: Package
 Title: Your Advanced 3D Brain Visualization
-Version: 1.2.0.9009
+Version: 1.2.0.9010
 Authors@R: c(
     person("Zhengjia", "Wang", email = "[email protected]", role = c("aut", "cre", "cph")),
     person("John", "Magnotti", email = "[email protected]", role = c("ctb", "res")),

NAMESPACE

@@ -47,6 +47,7 @@ export(freeserfer_colormap)
 export(freesurfer_brain)
 export(freesurfer_brain2)
 export(freesurfer_lut)
+export(generate_cortical_parcellation)
 export(generate_smooth_envelope)
 export(generate_subcortical_surface)
 export(geom_freemesh)

R/class_brain.R

@@ -271,12 +271,15 @@ Brain2 <- R6::R6Class(
 
     },
 
-    add_annotation = function(annotation, surface_type = "pial") {
+    add_annotation = function(annotation, surface_type = "pial", template_subject = "fsaverage") {
       if(tolower(surface_type) == "pial.t1") {
         surface_type <- "pial"
       }
       if(!surface_type %in% self$surface_types) {
-        return(invisible())
+        self$add_surface(surface_type)
+        if(!surface_type %in% self$surface_types) {
+          return(invisible())
+        }
       }
       annot_dir <- dirname(annotation)
       annot_fname <- filename(annotation)
@@ -294,6 +297,22 @@ Brain2 <- R6::R6Class(
 
       surface_instance <- self$surfaces[[surface_type]]
 
+      if(!length(lh_path) || !length(rh_path)) {
+        # annot file is missing; generate one on the fly
+        tryCatch({
+          generate_cortical_parcellation(brain = self,
+                                         template_subject = template_subject,
+                                         annotation = annot_fname,
+                                         add_annotation = FALSE)
+          lh_path <- file.path(label_path, sprintf(c("lh.%s.annot", "lh.%s"), annot_fname))
+          lh_path <- lh_path[file.exists(lh_path)]
+          rh_path <- file.path(label_path, sprintf(c("rh.%s.annot", "rh.%s"), annot_fname))
+          rh_path <- rh_path[file.exists(rh_path)]
+        }, error = function(e) {
+          warning(e)
+        })
+      }
+
       if(length(lh_path)) {
         surface_instance$left_hemisphere$set_annotation(annotation, lh_path[[1]])
       }

R/class_brainatlas.R

@@ -248,3 +248,5 @@ create_voxel_cube <- function(mni_ras, value, colormap,
   }
   re
 }
+
+

R/template_cortical-annotation.R

@@ -0,0 +1,147 @@
+#' Generate cortical annotations from template using surface mapping
+#' @description
+#' This is a low-level function. Use \code{brain$add_annotation} instead.
+#'
+#' @param brain Brain object
+#' @param template_subject template subject where the annotation is stored
+#' @param annotation annotation name in the label folder; default is
+#' \code{'Yeo2011_7Networks_N1000'}, standing for
+#' \code{'lh.Yeo2011_7Networks_N1000.annot'} and
+#' \code{'rh.Yeo2011_7Networks_N1000.annot'}.
+#' @param add_annotation whether to add annotation to \code{brain}
+#' @returns \code{brain} with the annotation added if \code{add_annotation}
+#' is true
+#'
+#' @export
+generate_cortical_parcellation <- function(
+    brain, template_subject = "fsaverage", annotation = "Yeo2011_7Networks_N1000",
+    add_annotation = TRUE) {
+
+  # DIPSAUS DEBUG START
+  # devtools::load_all()
+  # brain <- raveio::rave_brain("demo/DemoSubject")
+  # template_subject <- "fsaverage"
+  # annotation <- "Yeo2011_17Networks_N1000"
+
+  if(is.null(brain$surfaces$sphere.reg)) {
+    brain$add_surface("sphere.reg")
+    on.exit({
+      brain$surfaces$sphere.reg <- NULL
+    })
+  }
+
+  if(!length(brain$surfaces$sphere.reg)) {
+    stop("The FreeSurfer brain object does not have `sphere.reg` surface. Did you finish `recon-all`?")
+  }
+  # make sure fsaverage is present
+  tempolate_path <- file.path(default_template_directory(), template_subject)
+  if(!dir.exists(tempolate_path)) {
+    message("Template `", template_subject, "` is missing. Downloading it from RAVE (this is one-time procedure).")
+    message(sprintf("Running `threeBrain::download_template_subject(subject_code = '%s')`", template_subject))
+    download_template_subject(subject_code = template_subject)
+  }
+
+  # check if the annoations are available
+  lh_annot_path <- file.path(tempolate_path, "label", sprintf("lh.%s.annot", annotation))
+  rh_annot_path <- file.path(tempolate_path, "label", sprintf("rh.%s.annot", annotation))
+
+  if(!file.exists(lh_annot_path)) {
+    stop(sprintf("Template `%s` does not have FreeSurfer annotation `%s` for the left hemisphere (%s is missing).", template_subject, annotation, basename(lh_annot_path)))
+  }
+  if(!file.exists(rh_annot_path)) {
+    stop(sprintf("Template `%s` does not have FreeSurfer annotation `%s` for the right hemisphere (%s is missing).", template_subject, annotation, basename(rh_annot_path)))
+  }
+
+  # sphere.reg for template
+  lh_sphere_reg_path_template <- file.path(tempolate_path, "surf", "lh.sphere.reg")
+  rh_sphere_reg_path_template <- file.path(tempolate_path, "surf", "rh.sphere.reg")
+
+  # read sphere.reg for native
+  lh_sphere_reg_path <- file.path(brain$base_path, "surf", "lh.sphere.reg")
+  rh_sphere_reg_path <- file.path(brain$base_path, "surf", "rh.sphere.reg")
+
+  # build mapping for each native node
+
+  # left
+  sphere_reg <- freesurferformats::read.fs.surface(lh_sphere_reg_path)
+  sphere_reg_template <- freesurferformats::read.fs.surface(lh_sphere_reg_path_template)
+  annot_template <- freesurferformats::read.fs.annot(lh_annot_path)
+
+  kdtree <- ravetools::vcg_kdtree_nearest(
+    target = sphere_reg_template$vertices[, 1:3, drop = FALSE],
+    query = sphere_reg$vertices[, 1:3, drop = FALSE],
+    k = 1
+  )
+  new_label_codes <- annot_template$label_codes[kdtree$index[, 1]]
+
+  annot_path <- file.path(brain$base_path, "label", sprintf("lh.%s.annot", annotation))
+  freesurferformats::write.fs.annot(
+    filepath = annot_path, num_vertices = as.integer(length(new_label_codes)),
+    colortable = annot_template$colortable_df, labels_as_colorcodes = new_label_codes)
+
+
+  # pial_annotated <- merge(
+  #   ieegio::read_surface(file.path(brain$base_path, "surf", "lh.pial")),
+  #   ieegio::read_surface(annot_path)
+  # ); plot(pial_annotated)
+
+  # right
+  sphere_reg <- freesurferformats::read.fs.surface(rh_sphere_reg_path)
+  sphere_reg_template <- freesurferformats::read.fs.surface(rh_sphere_reg_path_template)
+  annot_template <- freesurferformats::read.fs.annot(rh_annot_path)
+
+  kdtree <- ravetools::vcg_kdtree_nearest(
+    target = sphere_reg_template$vertices[, 1:3, drop = FALSE],
+    query = sphere_reg$vertices[, 1:3, drop = FALSE],
+    k = 1
+  )
+  new_label_codes <- annot_template$label_codes[kdtree$index[, 1]]
+
+  annot_path <- file.path(brain$base_path, "label", sprintf("rh.%s.annot", annotation))
+  freesurferformats::write.fs.annot(
+    filepath = annot_path, num_vertices = as.integer(length(new_label_codes)),
+    colortable = annot_template$colortable_df, labels_as_colorcodes = new_label_codes)
+
+  # pial_annotated <- merge(
+  #   ieegio::read_surface(file.path(brain$base_path, "surf", "rh.pial")),
+  #   ieegio::read_surface(annot_path)
+  # ); plot(pial_annotated)
+
+
+  # # right
+  # rh_sphere_reg <- ieegio::read_surface(rh_sphere_reg_path)
+  # rh_sphere_reg_template <- ieegio::read_surface(rh_sphere_reg_path_template)
+  # rh_annot_template <- ieegio::read_surface(rh_annot_path)
+  #
+  # kdtree <- ravetools::vcg_kdtree_nearest(
+  #   t(rh_sphere_reg_template$geometry$vertices[1:3, , drop = FALSE]),
+  #   t(rh_sphere_reg$geometry$vertices[1:3, , drop = FALSE]),
+  #   1
+  # )
+  # mapping_index <- as.vector(kdtree$index)
+  #
+  # # mapping_index <- apply(rh_sphere_reg$geometry$vertices, 2, function(p) {
+  # #   which.min(colSums((rh_sphere_reg_template$geometry$vertices - p)^2))
+  # # })
+  # annot_name <- names(rh_annot_template$annotations$data_table)[[1]]
+  # new_annot <- rh_annot_template$annotations$data_table[[1]][mapping_index]
+  #
+  # rh_annot <- rh_annot_template
+  # rh_annot$sparse_node_index <- structure(seq_along(new_annot), start_index = 1L)
+  # annot_table <- structure(list(as.integer(new_annot)), names = annot_name)
+  # rh_annot$annotations$data_table <- data.table::as.data.table(annot_table)
+  #
+  # pial_annotated <- merge(
+  #   ieegio::read_surface(file.path(brain$base_path, "surf", "rh.pial")),
+  #   rh_annot)
+  # plot(pial_annotated, method = "r3js")
+
+  # # save
+  # ieegio::write_surface(x = rh_annot, con = file.path(brain$base_path, "label", sprintf("rh.%s.annot", annotation)), format = "freesurfer", type = "annotations")
+
+  if( add_annotation ) {
+    brain$add_annotation(sprintf("label/%s", annotation))
+  }
+  invisible(brain)
+
+}

adhoc/cortical_mapping.R

@@ -0,0 +1,126 @@
+
+
+
+generate_cortical_parcellation <- function(
+    brain, template_subject = "fsaverage", annotation = "Yeo2011_7Networks_N1000") {
+
+  # DIPSAUS DEBUG START
+  # devtools::load_all()
+  # brain <- raveio::rave_brain("demo/DemoSubject")
+  # template_subject <- "fsaverage"
+  # annotation <- "Yeo2011_17Networks_N1000"
+
+  if(is.null(brain$surfaces$sphere.reg)) {
+    brain$add_surface("sphere.reg")
+    on.exit({
+      brain$surfaces$sphere.reg <- NULL
+    })
+  }
+
+  if(!length(brain$surfaces$sphere.reg)) {
+    stop("The FreeSurfer brain object does not have `sphere.reg` surface. Did you finish `recon-all`?")
+  }
+  # make sure fsaverage is present
+  tempolate_path <- file.path(default_template_directory(), template_subject)
+  if(!dir.exists(tempolate_path)) {
+    message("Template `", template_subject, "` is missing. Downloading it from RAVE (this is one-time procedure).")
+    message(sprintf("Running `threeBrain::download_template_subject(subject_code = '%s')`", template_subject))
+    download_template_subject(subject_code = template_subject)
+  }
+
+  # check if the annoations are available
+  lh_annot_path <- file.path(tempolate_path, "label", sprintf("lh.%s.annot", annotation))
+  rh_annot_path <- file.path(tempolate_path, "label", sprintf("rh.%s.annot", annotation))
+
+  if(!file.exists(lh_annot_path)) {
+    stop(sprintf("Template `%s` does not have FreeSurfer annotation `%s` for the left hemisphere (%s is missing).", template_subject, annotation, basename(lh_annot_path)))
+  }
+  if(!file.exists(rh_annot_path)) {
+    stop(sprintf("Template `%s` does not have FreeSurfer annotation `%s` for the right hemisphere (%s is missing).", template_subject, annotation, basename(rh_annot_path)))
+  }
+
+  # sphere.reg for template
+  lh_sphere_reg_path_template <- file.path(tempolate_path, "surf", "lh.sphere.reg")
+  rh_sphere_reg_path_template <- file.path(tempolate_path, "surf", "rh.sphere.reg")
+
+  # read sphere.reg for native
+  lh_sphere_reg_path <- file.path(brain$base_path, "surf", "lh.sphere.reg")
+  rh_sphere_reg_path <- file.path(brain$base_path, "surf", "rh.sphere.reg")
+
+  # build mapping for each native node
+
+  # left
+  sphere_reg <- freesurferformats::read.fs.surface(lh_sphere_reg_path)
+  sphere_reg_template <- freesurferformats::read.fs.surface(lh_sphere_reg_path_template)
+  annot_template <- freesurferformats::read.fs.annot(lh_annot_path)
+
+  kdtree <- ravetools::vcg_kdtree_nearest(
+    target = sphere_reg_template$vertices[, 1:3, drop = FALSE],
+    query = sphere_reg$vertices[, 1:3, drop = FALSE],
+    k = 1
+  )
+  new_label_codes <- annot_template$label_codes[kdtree$index[, 1]]
+
+  annot_path <- file.path(brain$base_path, "label", sprintf("lh.%s.annot", annotation))
+  freesurferformats::write.fs.annot(
+    filepath = annot_path, num_vertices = as.integer(length(new_label_codes)),
+    colortable = annot_template$colortable_df, labels_as_colorcodes = new_label_codes)
+
+
+  # pial_annotated <- merge(
+  #   ieegio::read_surface(file.path(brain$base_path, "surf", "lh.pial")),
+  #   ieegio::read_surface(annot_path)
+  # ); plot(pial_annotated)
+
+  # right
+  sphere_reg <- freesurferformats::read.fs.surface(rh_sphere_reg_path)
+  sphere_reg_template <- freesurferformats::read.fs.surface(rh_sphere_reg_path_template)
+  annot_template <- freesurferformats::read.fs.annot(rh_annot_path)
+
+  kdtree <- ravetools::vcg_kdtree_nearest(
+    target = sphere_reg_template$vertices[, 1:3, drop = FALSE],
+    query = sphere_reg$vertices[, 1:3, drop = FALSE],
+    k = 1
+  )
+  new_label_codes <- annot_template$label_codes[kdtree$index[, 1]]
+
+  annot_path <- file.path(brain$base_path, "label", sprintf("rh.%s.annot", annotation))
+  freesurferformats::write.fs.annot(
+    filepath = annot_path, num_vertices = as.integer(length(new_label_codes)),
+    colortable = annot_template$colortable_df, labels_as_colorcodes = new_label_codes)
+
+  # pial_annotated <- merge(
+  #   ieegio::read_surface(file.path(brain$base_path, "surf", "rh.pial")),
+  #   ieegio::read_surface(annot_path)
+  # ); plot(pial_annotated)
+
+#
+#   # right
+#   rh_sphere_reg <- ieegio::read_surface(rh_sphere_reg_path)
+#   rh_sphere_reg_template <- ieegio::read_surface(rh_sphere_reg_path_template)
+#   rh_annot_template <- ieegio::read_surface(rh_annot_path)
+#
+#   kdtree <- ravetools::vcg_kdtree_nearest(
+#     t(rh_sphere_reg_template$geometry$vertices[1:3, , drop = FALSE]),
+#     t(rh_sphere_reg$geometry$vertices[1:3, , drop = FALSE]),
+#     1
+#   )
+#   mapping_index <- as.vector(kdtree$index)
+#   annot_name <- names(rh_annot_template$annotations$data_table)[[1]]
+#   new_annot <- rh_annot_template$annotations$data_table[[1]][mapping_index]
+#
+#   rh_annot <- rh_annot_template
+#   rh_annot$sparse_node_index <- structure(seq_along(new_annot), start_index = 1L)
+#   annot_table <- structure(list(as.integer(new_annot)), names = annot_name)
+#   rh_annot$annotations$data_table <- data.table::as.data.table(annot_table)
+#
+#   # pial_annotated <- merge(ieegio::read_surface(file.path(brain$base_path, "surf", "rh.pial")), rh_annot)
+#   # plot(pial_annotated, method = "r3js")
+#
+#   # save
+#   ieegio::write_surface(x = rh_annot, con = file.path(brain$base_path, "label", sprintf("rh.%s.annot", annotation)), format = "freesurfer", type = "annotations")
+
+  brain$add_annotation(sprintf("label/%s", annotation))
+  invisible(annotation)
+
+}