Corrected example root IDs

R/cloudvolume.R

@@ -43,7 +43,7 @@ banc_token_available <- function() {
   !inherits(try(banc_token(), silent = TRUE), 'try-error')
 }
 
-#' Print information about your banc setup including tokens and python modules
+#' Print information about your BANC setup including tokens and python modules
 #'
 #' @export
 #' @seealso \code{\link{dr_fafbseg}}
@@ -61,13 +61,13 @@ dr_banc <- function() {
 }
 
 # hidden
-banc_api_report <- function() {
-  message("BANC Neuroglancer / CAVE API access\n----")
+banc_api_report <- function(with_dataset = bancr::with_banc) {
+  message("Neuroglancer / CAVE API access\n----")
   token=try(banc_token(cached = F), silent = FALSE)
   if(inherits(token, "try-error")) {
     FUN=if(requireNamespace('usethis', quietly = T)) usethis::ui_todo else message
     FUN(paste('No valid banc API token found. Set your token by doing:\n',
-                  "{ui_code('banc_set_token()')}"))
+                  "{ui_code('*_set_token()')}"))
   } else{
     cat("Valid banc API ChunkedGraph token is set!\n")
   }
@@ -77,7 +77,7 @@ banc_api_report <- function() {
         fafbseg:::cv_secretdir(),"\n")
     print(ff)
   }
-  u=with_banc(fafbseg:::check_cloudvolume_url(set = F))
+  u=with_dataset(fafbseg:::check_cloudvolume_url(set = F))
   cat("\nZetta cloudvolume URL:", u)
 }
 

R/ggplot2.R

@@ -41,9 +41,9 @@
 #'
 #' # Get some neurons to plot
 #' banc.meta.dnao1 <- subset(banc.meta, cell_type=="DNa01")
-#' dna01 <- banc_read_neuron_meshes(banc.meta.dnao1$root_id)
+#' dna01 <- banc_read_neuron_meshes(unique(banc.meta.dnao1$root_id))
 #' banc.meta.dnao2 <- subset(banc.meta, cell_type=="DNa02")
-#' dna02 <- banc_read_neuron_meshes(banc.meta.dnao2$root_id)
+#' dna02 <- banc_read_neuron_meshes(unique(banc.meta.dnao2$root_id))
 #'
 #' # Simplify neurons to make them easier to plot
 #' dna01 <- nat::nlapply(dna01,Rvcg::vcgQEdecim,percent = 0.1)
@@ -136,7 +136,7 @@ banc_neuron_comparison_plot <- function(neuron1 = NULL,
 
     # Work out colours
     if(length(neuron1)==1){
-      cols1 <- c("blue", "navy")
+      cols1 <- c("darkblue", "navy")
     }else{
       cols1 <- grDevices::colorRampPalette(c("#00008B","#0000CD","#4169E1","#1E90FF","#87CEEB", "#B0E0E6"))(length(neuron1))
     }

R/ids.R

@@ -144,7 +144,7 @@ banc_supervoxels <- function(x, voxdims=c(4,4,45)) {
 #' @export
 #' @family banc-ids
 #' @examples
-#' banc_islatest("648518346473954669")
+#' banc_islatest("720575941520182775")
 banc_islatest <- function(x, timestamp=NULL, ...) {
   with_banc(flywire_islatest(x=x, timestamp = timestamp, ...))
 }
@@ -163,7 +163,7 @@ banc_islatest <- function(x, timestamp=NULL, ...) {
 #' @family banc-ids
 #' @examples
 #' \dontrun{
-#' banc_latestid("648518346473954669")
+#' banc_latestid("720575941520182775")
 #' }
 banc_latestid <- function(rootid, sample=1000L, cloudvolume.url=NULL, Verbose=FALSE, ...) {
   with_banc(fafbseg::flywire_latestid(rootid=rootid, sample = sample, Verbose=Verbose, ...))
@@ -387,3 +387,13 @@ banc_cellid_table <- memoise::memoise(function(fac=banc_cave_client()) {
   seltable=rev(sort(grep("^cell_info", tablenames, value = T)))[1]
   return(seltable)
 })
+
+# hideen
+banc_nucelus_id_to_rootid <- function(nucleus_ids){
+  nuclei <- banc_nuclei()
+  nuclei$root_id <- as.character(nuclei$root_id)
+  nuclei$nucleus_id <- as.character(nuclei$nucleus_id)
+  ids <- nuclei$root_id[match(nucleus_ids, nuclei$nucleus_id)]
+  ids[is.na(ids)] <- "0"
+  ids
+}

R/urls.R

@@ -1,4 +1,4 @@
-#' Return a sample Neuroglancer scene URL for banc dataset
+#' Return a sample Neuroglancer scene URL for BANC dataset
 #'
 #' @details See
 #'   \href{https://banc-reconstruction.slack.com/archives/C01RZP5JH9C/p1616522511001900}{banc

R/utils.R

@@ -18,7 +18,7 @@ euclidean_distances <- function(A, B) {
 }
 
 # Helper
-express_lane <- function(base_dir) {
+express_lane <- function(base_dir, symlink = TRUE) {
   todo_dir <- base_dir #fs::path(base_dir, "todo")
   if (fs::dir_exists(todo_dir)) {
     express_dir <- fs::path(base_dir, "express")
@@ -48,7 +48,11 @@ express_lane <- function(base_dir) {
       }
 
       # Create symlink
-      fs::link_create(file, symlink_path)
+      if(symlink){
+        fs::link_create(file, symlink_path)
+      }else{
+        fs::file_copy(file,symlink_path)
+      }
       cat("Created symlink:", symlink_path, "->", file, "\n")
     })
     remove_empty_dirs(base_dir)