Merge pull request #35 from dipterix/custom-electrode-geom

added custom electrode shape support
dipterix · Mar 19, 2024 · 7a59b8b · 7a59b8b
2 parents fe5f2c8 + b53c072
commit 7a59b8b
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -23,6 +23,7 @@
 ^inst/threeBrainJS/package
 ^inst/threeBrainJS/webpack
 ^inst/threeBrainJS/\.npmignore$
+^inst/prototypes/.*\.R$
 ^build\.sh$
 ^CRAN-RELEASE$
 ^\.travis\.yml$

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -38,6 +38,8 @@ jobs:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
+          extra-repositories: |
+            https://rave-ieeg.r-universe.dev
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -27,6 +27,8 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
+          extra-repositories: |
+            https://rave-ieeg.r-universe.dev
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: threeBrain
 Type: Package
-Title: 3D Brain Visualization
-Version: 1.0.1.9109
+Title: Your Advanced 3D Brain Visualization
+Version: 1.0.1.9200
 Authors@R: c(
     person("Zhengjia", "Wang", email = "[email protected]", role = c("aut", "cre", "cph")),
     person("John", "Magnotti", email = "[email protected]", role = c("aut", "res")),
@@ -18,14 +18,14 @@ Description: A fast, interactive cross-platform, and easy to share
     a web browser with 'WebGL2' support (for example, 'Chrome', 'Firefox', 
     'Safari'), and can be inserted into any websites. The 'R-shiny' 
     support allows the 3D viewer to be dynamically generated from reactive user 
-    inputs. This feature has been fully adopted by 'RAVE' 
+    inputs. Please check the publication by Wang, Magnoti, Zhang,
+    and Beauchamp (2023, <doi:10.1523/ENEURO.0328-23.2023>) for electrode 
+    localization. This viewer has been fully adopted by 'RAVE' 
     <https://openwetware.org/wiki/RAVE>, an interactive toolbox to 
-    analyze 'iEEG' data. Documentation about 'threeBrain' is provided
-    by <https://dipterix.org/threeBrain/> and several vignettes included 
-    in this package. To cite the package, please check our 'NeuroImage' paper 
-    by Magnotti, Wang, and Beauchamp (2020, <doi:10.1016/j.neuroimage.2020.117341>),
-    or see 'citation("threeBrain")' for details.
-License: GPL-3 | file LICENSE
+    analyze 'iEEG' data by Magnotti, Wang, and Beauchamp (2020, 
+    <doi:10.1016/j.neuroimage.2020.117341>). Please check 
+    'citation("threeBrain")' for details.
+License: MPL-2.0 | file LICENSE
 Encoding: UTF-8
 RoxygenNote: 7.3.1
 Roxygen: list(r6 = FALSE)
@@ -38,7 +38,6 @@ Imports:
     grDevices,
     graphics,
     dipsaus,
-    ravetools,
     xml2,
     servr,
     png,
@@ -55,5 +54,6 @@ Suggests:
     knitr,
     rmarkdown,
     DT,
+    ravetools,
     htmltools
 VignetteBuilder: knitr
diff --git a/LICENSE b/LICENSE
diff --git a/NAMESPACE b/NAMESPACE
@@ -52,6 +52,7 @@ export(get_ijk2ras)
 export(import_from_freesurfer)
 export(import_fs)
 export(import_suma)
+export(list_electrode_prototypes)
 export(load_colormap)
 export(localization_module)
 export(merge_brain)

diff --git a/R/aaa.R b/R/aaa.R
@@ -88,6 +88,24 @@ freesurferformats::write.nifti2
 
 cache_version <- 0.1
 
+DEFAULT_COLOR_DISCRETE <- c(
+  # default RAVE colors
+  "orange", "dodgerblue3", "darkgreen", "orangered", "brown", "purple3",
+
+  # polychrome
+  "#5A5156", "#E4E1E3", "#F6222E", "#FE00FA", "#16FF32", "#3283FE",
+  "#FEAF16", "#B00068", "#1CFFCE", "#90AD1C", "#2ED9FF", "#DEA0FD",
+  "#AA0DFE", "#F8A19F", "#325A9B", "#C4451C", "#1C8356", "#85660D",
+  "#B10DA1", "#FBE426", "#1CBE4F", "#FA0087", "#FC1CBF", "#F7E1A0",
+  "#C075A6", "#782AB6", "#AAF400", "#BDCDFF", "#822E1C", "#B5EFB5",
+  "#7ED7D1", "#1C7F93", "#D85FF7", "#683B79", "#66B0FF", "#3B00FB"
+)
+
+DEFAULT_COLOR_CONTINUOUS <- c(
+  "#053061", "#2166ac", "#4393c3", "#92c5de", "#d1e5f0",
+  "#ffffff", "#fddbc7", "#f4a582", "#d6604d", "#b2182b", "#67001f"
+)
+
 #' @title Setup Package, Install Environment
 #' @author Zhengjia Wang
 #' @param continued logical, there are two phases of setting up environment. You

diff --git a/R/class_animations.R b/R/class_animations.R
@@ -16,10 +16,13 @@ KeyFrame <- R6::R6Class(
     target = '.material.color',
 
     initialize = function(name, time, value, dtype = 'continuous', target = '.material.color', ...){
+      value <- unname(value)
 
       if( dtype == 'continuous' ){
         private$.dtype <- 'continuous'
-        value <- as.numeric(value)
+        if( !is.list(value) ) {
+          value <- as.numeric(value)
+        }
         sel <- !is.na(value)
         time <- time[ sel ]
         value <- value[ sel ]
@@ -28,8 +31,27 @@ KeyFrame <- R6::R6Class(
         private$.dtype <- 'discrete'
 
         # If is factor, then do not remake factor as we need to keep the levels
-        if(!is.factor(value)){
-          value <- factor(value, ...)
+        if( is.list(value) ) {
+          if(length(value)) {
+
+            # get levels
+            lv <- lapply(unname(value), function(v) {
+              if(is.factor(v)) {
+                return(levels(v))
+              }
+              unique(as.character(unlist(v)))
+            })
+            lv <- sort(unique(unlist(lv)))
+            lv <- lv[!is.na(lv)]
+
+            value <- lapply(unname(value), function(v) {
+              factor(as.character(v), levels = lv)
+            })
+          }
+        } else {
+          if(!is.factor(value)){
+            value <- factor(value, levels = as.character(sort(unique(value), decreasing = FALSE)))
+          }
         }
       }
 
@@ -61,7 +83,7 @@ KeyFrame <- R6::R6Class(
 
       json_cache(path = path, data = structure(list(self$to_list()), names = name), ...)
       if(self$is_continuous){
-        private$.values <- range(private$.values)
+        private$.values <- range(unlist(private$.values))
       }else{
         private$.values <- unique(private$.values)
       }
@@ -82,10 +104,14 @@ KeyFrame <- R6::R6Class(
       return(rg)
     },
     value_range = function(){
-      if( self$is_continuous ){ range(private$.values) }else{ NULL }
+      if( self$is_continuous ){ range(unlist(private$.values), na.rm = TRUE) }else{ NULL }
     },
     value_names = function(){
-      if( !self$is_continuous ){ levels(private$.values) }else{ NULL }
+      if( self$is_continuous ) { return(NULL) }
+      if(is.list(private$.values) && length(private$.values) >= 1) {
+        return( levels(private$.values[[1]]) )
+      }
+      return(levels(private$.values))
     }
   )
 )
@@ -154,7 +180,7 @@ ColorMap <- R6::R6Class(
     hard_range = numeric(0),
     value_names = NULL,
     n_colors = 64,
-    colors = c('navyblue', '#e2e2e2', 'red'),
+    colors = DEFAULT_COLOR_CONTINUOUS,
 
     initialize = function(name, ..., .list = NULL, symmetric = NULL, alias = NULL){
 
@@ -197,10 +223,10 @@ ColorMap <- R6::R6Class(
 
       if( length(self$value_names) ){
         self$value_type <- 'discrete'
-        self$colors <- grDevices::palette()
+        self$colors <- DEFAULT_COLOR_DISCRETE
       }else{
         self$value_type <- 'continuous'
-        self$colors <- c('navyblue', '#e2e2e2', 'red')
+        self$colors <- DEFAULT_COLOR_CONTINUOUS
       }
 
       self$set_colors()
@@ -218,10 +244,9 @@ ColorMap <- R6::R6Class(
         # discrete, ncolors must equals to number of colors must equal to value_names
         self$n_colors <- length( self$value_names )
         if( self$n_colors > length(colors) ){
-          self$colors <- grDevices::colorRampPalette(colors)(self$n_colors)
-        }else{
-          self$colors <- colors[seq_len(self$n_colors)]
+          colors <- rep(colors, ceiling(self$n_colors / length(colors)))
         }
+        self$colors <- colors[seq_len(self$n_colors)]
       }
     },
 
@@ -231,9 +256,13 @@ ColorMap <- R6::R6Class(
       ncols <- max(16 , 2^ceiling(log2(self$n_colors)) )
       if( self$value_type == 'continuous' ){
         colors <- grDevices::colorRampPalette(self$colors)(ncols)
-        color_keys <- seq( self$value_range[1], self$value_range[2], length.out = ncols )
+        value_range <- self$value_range
+        if(!all(is.finite(value_range))) {
+          value_range <- c(-1, 1)
+        }
+        color_keys <- seq( value_range[1], value_range[2], length.out = ncols )
       }else{
-        colors <- grDevices::colorRampPalette(self$colors)( self$n_colors )
+        colors <- col2hexStr(self$colors)
         if(length(colors) < ncols) {
           colors <- c(colors, rep("#000000", ncols - length(colors)))
         }

diff --git a/R/class_brain.R b/R/class_brain.R
@@ -40,7 +40,7 @@ Brain2 <- R6::R6Class(
     Norig = diag(rep(1, 4)),
     Torig = diag(rep(1, 4)),
 
-    initialize = function(subject_code, xfm, Norig, Torig){
+    initialize = function(subject_code, xfm, Norig, Torig, base_path = NULL){
       stopifnot2( length(xfm) == 16 && length(dim(xfm)) == 2 && sum(dim(xfm)) == 8,
                   msg = 'xfm must be 4x4 matrix')
       stopifnot2( length(Norig) == 16 && length(dim(Norig)) == 2 && sum(dim(Norig)) == 8,
@@ -66,6 +66,11 @@ Brain2 <- R6::R6Class(
         group = GeomGroup$new(name = sprintf('_internal_group_data_%s', subject_code)),
         name = sprintf('_misc_%s', subject_code)
       )
+
+      if(length(base_path) == 1 && !is.na(base_path) && is.character(base_path) &&
+         file.exists(base_path)) {
+        self$base_path <- base_path
+      }
     },
 
     add_surface = function(
@@ -229,14 +234,22 @@ Brain2 <- R6::R6Class(
       if(!inherits(atlas, 'brain-atlas')) {
 
         stopifnot2(is.character(atlas), msg = 'atlas must be a brain-atlas object or valid atlas name from FreeSurfer folder')
-        atlas <- gsub("_", "+", atlas)
         path_atlases <- file.path( self$base_path, "mri", as.vector(rbind(
           sprintf("%s.mgz", atlas),
           sprintf("%s.nii.gz", atlas),
           sprintf("%s.nii", atlas)
         )) )
         atlas_path <- path_atlases[file.exists(path_atlases)]
-        if(!length(atlas_path)) { return() }
+        if(!length(atlas_path)) {
+          atlas <- gsub("_", "+", atlas)
+          path_atlases <- file.path( self$base_path, "mri", as.vector(rbind(
+            sprintf("%s.mgz", atlas),
+            sprintf("%s.nii.gz", atlas),
+            sprintf("%s.nii", atlas)
+          )) )
+          atlas_path <- path_atlases[file.exists(path_atlases)]
+          if(!length(atlas_path)) { return() }
+        }
         atlas_path <- atlas_path[[ 1 ]]
 
         atlas_geom <- VolumeGeom2$new(
@@ -276,13 +289,18 @@ Brain2 <- R6::R6Class(
       )
     },
 
-    set_electrodes = function(electrodes, coord_sys = c("tkrRAS", "scannerRAS", "MNI305", "MNI152"), ...){
+    set_electrodes = function(electrodes, coord_sys = c("tkrRAS", "scannerRAS", "MNI305", "MNI152"), ...,
+                              priority = c("prototype", "sphere", "both")){
       coord_sys <- match.arg(coord_sys)
+      priority <- match.arg(priority)
+      if( missing(electrodes) ) {
+        electrodes <- self$electrodes$raw_table
+      }
       if( R6::is.R6(electrodes) && 'brain-electrodes' %in% class(electrodes)){
         self$electrodes <- electrodes
         self$electrodes$set_brain( self )
       }else{
-        self$electrodes$set_electrodes( electrodes, coord_sys = coord_sys, ... )
+        self$electrodes$set_electrodes( electrodes, coord_sys = coord_sys, priority = priority, ... )
       }
     },
 
@@ -440,7 +458,7 @@ Brain2 <- R6::R6Class(
 
       if( isTRUE(electrodes) && !is.null(self$electrodes) ){
         # self$electrodes$set_values()
-        geoms <- c(geoms, self$electrodes$objects)
+        geoms <- c(geoms, unique(unlist(self$electrodes$objects)), unique(unlist(self$electrodes$objects2)))
       }
 
       geoms <- c(geoms, self$misc)