Added brain$electrodes$fix_electrode_color to fix contacts to a color…

… for given clip names; added electrode visibility mode: use threshold only to show contacts that pass threhsold but have no values

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: threeBrain
 Type: Package
 Title: 3D Brain Visualization
-Version: 1.0.1.9103
+Version: 1.0.1.9104
 Authors@R: c(
     person("Zhengjia", "Wang", email = "dipterix.wang@gmail.com", role = c("aut", "cre", "cph")),
     person("John", "Magnotti", email = "John.Magnotti@Pennmedicine.upenn.edu", role = c("aut", "res")),

R/class_brainelectrodes.R

@@ -449,6 +449,21 @@ BrainElectrodes <- R6::R6Class(
       }
     },
 
+    fix_electrode_color = function(number, color, names = NULL, inclusive = TRUE) {
+      names <- as.character(names)
+      inclusive <- as.logical(inclusive)[[1]]
+      el <- self$objects[[ number ]]
+      if(!is.null(el)) {
+        el$fixed_color <- list(
+          color[[1]],
+          names,
+          inclusive
+        )
+        return(TRUE)
+      }
+      return(FALSE)
+    },
+
     # function to set values to electrodes
     set_values = function(table_or_path){
       if( missing(table_or_path) ){

R/geom_electrode.R

@@ -22,12 +22,36 @@ ElectrodeGeom <- R6::R6Class(
     sphere_position = c(0,0,0),
     number = NULL,
 
+    # case 1: hex color, then will show in all values
+    # case 2: list(color, names, [true/false]): colors that will only be activated
+    # when names in(true) or not in(false) given names
+    fixed_color = NULL,
+
     # ------------ for sub cortical electrodes only ------------
 
     # Not yet implemented
 
     # ------------ G ------------
     to_list = function(){
+      fixed_color <- self$fixed_color
+      if( !length( fixed_color ) ) {
+        fixed_color <- NULL
+      } else if(is.list(fixed_color) && length(fixed_color) > 1) {
+        if(length(fixed_color) < 3) {
+          fixed_color[[3]] <- TRUE
+        }
+        fixed_color <- list(
+          color = dipsaus::col2hexStr(fixed_color[[1]]),
+          names = as.character(fixed_color[[2]]),
+          inclusive = isTRUE(as.logical(fixed_color[[3]]))
+        )
+      } else {
+        fixed_color <- list(
+          color = dipsaus::col2hexStr(fixed_color[[1]]),
+          names = character(0L),
+          inclusive = FALSE
+        )
+      }
       re <- c(
         super$to_list(),
         list(
@@ -41,7 +65,8 @@ ElectrodeGeom <- R6::R6Class(
           sphere_position = self$sphere_position,
           sub_cortical = !self$is_surface_electrode,
           search_geoms = self$hemisphere,
-          number = c(self$number, NA)[[1]]
+          number = c(self$number, NA)[[1]],
+          fixed_color = fixed_color
         )
       )
       return( re )

build.sh

@@ -1,5 +1,22 @@
 #/bin/bash
 
+########## Use the following command to register shortcut ######################
+# dipsaus::rs_add_shortcut(5, {
+#   dipsaus::rs_focus_console()
+#   cwd <- getwd()
+#   on.exit({
+#     setwd(cwd)
+#   })
+#   proj_dir <- .rs.getProjectDirectory()
+#   build_sh <- file.path(proj_dir, "build.sh")
+#   if(file.exists(build_sh)) {
+#     system2("bash", shQuote(build_sh), env = c("USE_DIPSAUS=1"))
+#   }
+#   devtools::load_all(proj_dir)
+#   setwd(cwd)
+# }, force = TRUE)
+################################################################################
+
 cd inst/three-brain-js
 
 npm run build
@@ -9,7 +26,8 @@ cd ../../
 cp -r inst/three-brain-js/dist inst/threeBrainJS
 
 # git submodule update --recursive --remote
-
-Rscript -e "devtools::document(roclets = c('rd', 'collate', 'namespace', 'vignette'))"
-source_file=$(Rscript -e "cat(devtools::build(vignettes = FALSE, manual = FALSE, path = './adhoc/', quiet = TRUE))")
-R CMD INSTALL --preclean --no-multiarch --with-keep.source "$source_file"
+if [[ "$USE_DIPSAUS" != "1" ]]; then
+  Rscript -e "devtools::document(roclets = c('rd', 'collate', 'namespace', 'vignette'))"
+  source_file=$(Rscript -e "cat(devtools::build(vignettes = FALSE, manual = FALSE, path = './adhoc/', quiet = TRUE))")
+  R CMD INSTALL --preclean --no-multiarch --with-keep.source "$source_file"
+fi