Add an argument to bypass roi checks

R/info.R

@@ -54,11 +54,25 @@ neuprint_version <- function(conn = NULL, ...){
 #' @description Get the regions of interest (ROIs) used in a neuPrint project
 #' @param superLevel whether not to show 'superlevel' ROIs - ROIs composed of other ROIs.
 #' If set to NULL, both low-level and superlevel ROIs are returned.
+#' @param fromNeuronFields : Whether to use fields of :Neuron nodes to fetch the ROIs. If
+#' FALSE (the default), use the dataset metadata instead. If TRUE, the \code{superLevel} argument
+#' is ignored
 #' @param ... methods passed to \code{neuprint_login}
 #' @inheritParams neuprint_fetch_custom
 #' @seealso \code{\link{neuprint_login}}, \code{\link{neuprint_datasets}}
 #' @export
-neuprint_ROIs <- function(superLevel = FALSE, dataset = NULL, conn = NULL, ...){
+neuprint_ROIs <- function(superLevel = FALSE, dataset = NULL, fromNeuronFields= FALSE,conn = NULL, ...){
+  if (fromNeuronFields){
+    rois <- neuprint_get_fields(possibleFields = c("bodyId", "pre", "post",
+                                                   "upstream", "downstream",
+                                                   "status", "statusLabel",
+                                                   "cropped", "instance", "name",
+                                                   "size", "type", "cellBodyFiber",
+                                                   "somaLocation", "somaRadius","roiInfo"),
+                                limit=200,
+                                negateFields=TRUE,
+                                dataset = NULL, conn = NULL, ...)
+  }else{
   ds = neuprint_datasets(conn=conn, ...)
   conn=neuprint_login(conn)
   dataset = check_dataset(dataset, conn=conn)
@@ -77,7 +91,7 @@ neuprint_ROIs <- function(superLevel = FALSE, dataset = NULL, conn = NULL, ...){
     if(is.null(rois)){
       rois = ds[[1]]$ROIs
     }
-  }
+  }}
   sort(rois)
 }
 

R/name.R

@@ -356,6 +356,8 @@ neuprint_ids <- function(x, mustWork=TRUE, unique=TRUE, fixed=TRUE, conn=NULL, d
 #' @title Get available metadata fields for Neuron nodes
 #' @return a vector of available fields
 #' @param possibleFields : field names to choose from
+#' @param limit : Max length of the server's response (used to speed up the query/adapt to different scenarios)
+#' @param negateFields : Whether to include (FALSE, the default) or exclude \code{possibleFields}
 #' @inheritParams neuprint_ROI_hierarchy
 #' @export
 #' @examples
@@ -368,9 +370,12 @@ neuprint_get_fields <- function(possibleFields = c("bodyId", "pre", "post",
                                                    "cropped", "instance", "name",
                                                    "size", "type", "cellBodyFiber",
                                                    "somaLocation", "somaRadius"),
+                                limit=20,
+                                negateFields=FALSE,
                                 dataset = NULL, conn = NULL, ...){
-  cypher <- sprintf("MATCH (n :`Neuron`) UNWIND KEYS(n) AS k RETURN DISTINCT k AS neuron_fields LIMIT 20")
+  cypher <- sprintf("MATCH (n :`Neuron`) UNWIND KEYS(n) AS k RETURN DISTINCT k AS neuron_fields LIMIT %s",limit)
   fields <- unlist(neuprint_fetch_custom(cypher=cypher, cache=TRUE, conn=conn, dataset = dataset, ...)$data)
+  if (negateFields){return(fields[!(fields %in% possibleFields)])}
   return(fields[fields %in% possibleFields])
 }
 

R/roi.R

@@ -201,8 +201,8 @@ neuprint_ROI_mesh <- function(roi, dataset = NULL, conn = NULL, ...){
 }
 
 # hidden
-neuprint_check_roi <- function(rois, superLevel = NULL, dataset = NULL, conn = NULL, ...){
-  possible.rois = neuprint_ROIs(dataset=dataset,conn=conn, superLevel = superLevel, ...)
+neuprint_check_roi <- function(rois, superLevel = NULL, fromNeuronFields = TRUE,dataset = NULL, conn = NULL, ...){
+  possible.rois = neuprint_ROIs(dataset=dataset,conn=conn, fromNeuronFields = fromNeuronFields, superLevel = superLevel, ...)
   if(!all(rois%in%possible.rois)){
     stop("Regions of interest provided that are not demarcated in dataset ", dataset, " for server ", neuprint_login(conn)$server,
          ". Please call neuprint_ROIs(superLevel = NULL) to see the available ROIs.")