ported multiple dipsaus package (plan to remove this dep in the next …

…3 versions); bump the version for CRAN

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: threeBrain
 Type: Package
 Title: 3D Brain Visualization
-Version: 0.2.4.9003
+Version: 0.2.5
 Authors@R: c(
     person("Zhengjia", "Wang", email = "[email protected]", role = c("aut", "cre", "cph")),
     person("John", "Magnotti", email = "[email protected]", role = c("aut")),
@@ -15,19 +15,20 @@ Description: A fast, interactive cross-platform, and easy to share
     'WebGL'-based 3D brain viewer that visualizes 'FreeSurfer' and/or
     'AFNI/SUMA' surfaces. The viewer widget can be either standalone or 
     embedded into 'R-shiny' applications. The standalone version only require
-    a web browser with 'WebGL2' support (for example, 'Chrome'). It can be
-    inserted into any websites; see <https://dipterix.org/project/threebrain/>).
-    as an example. The 'R-shiny' support allows the 3D viewer to be dynamically 
-    generated from reactive user inputs. This feature has been fully adopted by
-    'RAVE' <https://openwetware.org/wiki/RAVE>, an interactive toolbox to 
-    analyze 'iEEG/eCoG' data. Documentation about 'threeBrain' is provided
+    a web browser with 'WebGL2' support (for example, 'Chrome', 'Firefox', 
+    'Safari'). It can be inserted into any websites; see 
+    <https://dipterix.org/project/threebrain/>) as an example. The 'R-shiny' 
+    support allows the 3D viewer to be dynamically generated from reactive user 
+    inputs. This feature 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
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.0
 Roxygen: list(r6 = FALSE)
 Language: en-US
 URL: https://dipterix.org/threeBrain/ https://github.com/dipterix/threeBrain

NEWS.md

@@ -9,6 +9,7 @@ threeBrain 0.2.5
 * Volume `fragmentShader` uses non-linear function to calculate fragment colors combined with face normal; this will create smoother results
 * `DataCube2` geometry uses `ConvexHull` instead of box/sphere to improve the performance
 * `DataCube2` are no longer hidden when `sync from voxels` is on: users can use shortcuts `l` and `k` to easily control the visibility.
+* `download_template_subject` can download other templates such as `fsaverage`, `cvs_avg35`, `bert`.
 
 ## Bug fixes
 

R/aaa.R

@@ -121,3 +121,43 @@ get_os <- function(){
   }
   return('unknown')
 }
+
+package_installed <- function(pkgs, all = FALSE){
+  re <- sapply(pkgs, function(p){
+    system.file('', package = p) != ''
+  })
+  if(all){
+    re <- all(re)
+  }
+  re
+}
+
+col2hexStr <- function(col, alpha = NULL, prefix = '#', ...){
+  if(is.null(alpha)){
+    alpha <- 1
+    transparent <- FALSE
+  }else{
+    transparent <- TRUE
+  }
+  re <- grDevices::adjustcolor(col, alpha.f = alpha)
+  if(!transparent){
+    re <- substr(re, start = 1L, stop = 7L)
+  }
+  gsub('^[^0-9A-F]*', replacement = prefix, x = re)
+}
+
+rs_avail <- function(){
+  tryCatch({
+    spath <- search()
+    if('tools:rstudio' %in% spath) {
+      rs_ver <- get("RStudio.Version", inherits = TRUE, envir = parent.env(globalenv()))
+      if(is.function(rs_ver)) {
+        rs_ver()
+        return(TRUE)
+      }
+    }
+    return(FALSE)
+  }, error = function(e){
+    return(FALSE)
+  })
+}

R/class_proxy.R

@@ -68,7 +68,7 @@ ViewerProxy <- R6::R6Class(
     },
 
     set_background = function(col){
-      private$set_value('background', dipsaus::col2hexStr(col))
+      private$set_value('background', col2hexStr(col))
     },
 
     set_zoom_level = function( zoom ){

R/loaders.R

@@ -18,15 +18,27 @@
 NULL
 
 #' @rdname template_subject
-#' @param subject_code character with only letters and numbers (Important). Default is `N27`
-#' @param url zip file address
+#' @param subject_code character with only letters and numbers (Important); default is `N27`
+#' @param url zip file address; must be specified if \code{subject_code} is not from the followings: \code{'bert'}, \code{'cvs_avg35'}, \code{'cvs_avg35_inMNI152'}, \code{'fsaverage'}, \code{'fsaverage_sym'}, or \code{'N27'}
 #' @param template_dir parent directory where subject's `FreeSurfer` folder should be stored
 #' @export
 download_template_subject <- function(
-  subject_code = 'N27',
-  url = 'https://github.com/dipterix/threeBrain-sample/releases/download/1.0.0/N27.zip',
+  subject_code = 'N27', url,
   template_dir = default_template_directory()
 ){
+
+  force(subject_code)
+  if(missing(url) || is.null(url)) {
+    avails <- available_templates()
+    if(!subject_code %in% names(avails)) {
+      stop("`download_template_subject`: please specify the url for your template if subject code is not from the followings: ", paste(names(avails), collapse = ", "))
+    }
+    url <- avails[[subject_code]]
+  }
+
+  # = 'https://github.com/dipterix/threeBrain-sample/releases/download/1.0.0/N27.zip'
+
+
   dir_create(template_dir)
   dir <- normalizePath(template_dir)
 
@@ -131,15 +143,22 @@ threebrain_finalize_installation <- function(upgrade = c('ask', 'always', 'never
   })
 
   if(has_n27 && upgrade %in% c('never')){
-    dipsaus::cat2('N27 brain has been installed', level = 'DEFAULT')
+    cat2('N27 brain has been installed', level = 'DEFAULT')
     return(invisible())
   }
 
   if(has_n27 && upgrade %in% c('ask')){
     if(interactive()){
       reinst <- tryCatch({
-        dipsaus::ask_yesno('N27 template brain detected at \n  ', template_dir,
-                           '\nDo you want to reinstall?', error_if_canceled = FALSE)
+        if(package_installed("dipsaus")) {
+          dipsaus::ask_yesno('N27 template brain detected at \n  ', template_dir,
+                             '\nDo you want to reinstall?', error_if_canceled = FALSE)
+        } else {
+          utils::askYesNo(msg = paste0(
+            'N27 template brain detected at `', template_dir,
+            '`. Do you want to reinstall? '
+          ), default = FALSE)
+        }
       }, error = function(e){
         FALSE
       })
@@ -148,31 +167,31 @@ threebrain_finalize_installation <- function(upgrade = c('ask', 'always', 'never
     }
 
     if(!isTRUE(reinst)){
-      dipsaus::cat2('N27 template brain... skip', level = 'DEFAULT')
+      cat2('N27 template brain... skip', level = 'DEFAULT')
       return(invisible())
     }
   }
 
   # install N27 brain
 
-  if( async ){
+  if( async && package_installed("dipsaus") ){
     code <- sprintf(
       "{
-  dipsaus::cat2('Installing N27 template brain...', level = 'INFO')
+  threeBrain:::cat2('Installing N27 template brain...', level = 'INFO')
   threeBrain::download_N27(template_dir = '%s')
 
   # load N27
-  dipsaus::cat2('Expand the template, creating cache...', level = 'INFO')
+  threeBrain:::cat2('Expand the template, creating cache...', level = 'INFO')
   threeBrain::merge_brain(template_subject = 'N27')
   }", template_dir)
 
     dipsaus::rs_exec(parse(text = code)[[1]], name = 'Finalize threeBrain N27 installation', quoted = TRUE)
   } else {
-    dipsaus::cat2('Installing N27 template brain...', level = 'INFO')
-    threeBrain::download_N27(template_dir = template_dir)
+    cat2('Installing N27 template brain...', level = 'INFO')
+    download_N27(template_dir = template_dir)
     # load N27
-    dipsaus::cat2('Expand the template, creating cache...', level = 'INFO')
-    threeBrain::merge_brain(template_subject = 'N27', template_dir = template_dir)
+    cat2('Expand the template, creating cache...', level = 'INFO')
+    merge_brain(template_subject = 'N27', template_dir = template_dir)
   }
 
 

R/shiny-localization.R

@@ -38,7 +38,7 @@ localization_module <- function(
   ..., control_presets = NULL, side_display = FALSE, controllers = list()
 ){
 
-  if(!dipsaus::package_installed("DT")){
+  if(!package_installed("DT")){
     stop("Package `DT` is needed to run this module. Please install it by running\n  ",
          "install.packages('DT')")
   }

R/threejs_brain.R

@@ -265,8 +265,8 @@ threejs_brain <- function(
   }
 
   # backgrounds
-  background <- dipsaus::col2hexStr(background)
-  # side_background = dipsaus::col2hexStr(side_background)
+  background <- col2hexStr(background)
+  # side_background = col2hexStr(side_background)
 
 
 
@@ -519,7 +519,7 @@ save_brain <- function(widget, directory, filename = 'index.html', assetpath = '
 }
 
 grey_col <- function(...){
-  if( dipsaus::rs_avail() ){
+  if( rs_avail() ){
     cat("\033[38;5;246m", paste(..., sep = " ", collapse = "\n"),
         "\033[39m", sep = "")
   } else {
@@ -528,7 +528,7 @@ grey_col <- function(...){
 }
 
 green_col <- function(...){
-  if( dipsaus::rs_avail() ){
+  if( rs_avail() ){
     cat("\033[38;5;35m", paste(..., sep = " ", collapse = "\n"),
         "\033[39m", sep = "")
   } else {
@@ -537,7 +537,7 @@ green_col <- function(...){
 }
 
 red_col <- function(...){
-  if( dipsaus::rs_avail() ){
+  if( rs_avail() ){
     cat("\033[38;5;215m", paste(..., sep = " ", collapse = "\n"),
         "\033[39m", sep = "")
   } else {

R/utils.R

@@ -54,7 +54,7 @@ cat2 <- function(
     'WARNING' = '#ec942c',
     'ERROR' = '#f02c2c',
     'FATAL' = '#763053',
-    'DEFAULT' = '#000000'
+    'DEFAULT' = 'grey60'
   )
 ){
   level <- toupper(level)
@@ -63,11 +63,11 @@ cat2 <- function(
   }
   .col <- pal[[level]]
   if(is.null(.col)){
-    .col <- '#000000'
+    .col <- 'grey60'
   }
 
   # check if interactive
-  if(dipsaus::rs_avail() && !nzchar(file)){
+  if(rs_avail() && !nzchar(file)){
     if(print_level){
       base::cat('[', level, ']: ', sep = '')
     }
@@ -79,10 +79,10 @@ cat2 <- function(
       'WARNING' = '\033[38;5;215m',
       'ERROR' = '\033[38;5;203m',
       'FATAL' = '\033[38;5;95m',
-      'DEFAULT' = '\033[38;5;232m'
+      'DEFAULT' = '\033[38;5;246m'
     )[[level]]
     if(is.null(prefix)){
-      prefix <- '\033[38;5;232m'
+      prefix <- '\033[38;5;246m'
     }
     s <- paste(..., sep = sep)
     base::cat(prefix, s, "\033[39m", end, file = file, fill = fill, labels = labels, append = append, sep = '')

cran-comments.md

@@ -1,7 +1,7 @@
 # Update logs (for R-cran only)
 
-## 2021-12-02
-**Version 0.2.4 (current)**
+## 2022-05-29
+**Version 0.2.5 (current)**
 
 Self check: 0 errors | 0 warnings | 1 notes
 
@@ -10,6 +10,16 @@ checking installed package size ... NOTE
   installed size is  5.3Mb
 ```
 
+## 2021-12-02
+**Version 0.2.4 (passed)**
+
+Starting from this version, the package size will be greater than `5Mb`, which will trigger the check note. However, I can't reduce the size since most are from the `JavaScript` engine.
+
+```
+checking installed package size ... NOTE
+  installed size is  5.3Mb
+```
+
 ## 2021-10-13
 **Version 0.2.3 (passed)**