Catmaidserver

NAMESPACE

@@ -25,6 +25,7 @@ export(catmaid_connection)
 export(catmaid_connection_getenv)
 export(catmaid_connection_setenv)
 export(catmaid_connection_unsetenv)
+export(catmaid_connector_nodes)
 export(catmaid_entities_from_models)
 export(catmaid_fetch)
 export(catmaid_get_all_labels)
@@ -38,9 +39,11 @@ export(catmaid_get_contributor_stats)
 export(catmaid_get_label_stats)
 export(catmaid_get_labels)
 export(catmaid_get_meta_annotations)
+export(catmaid_get_neuronid)
 export(catmaid_get_neuronnames)
 export(catmaid_get_node_count)
 export(catmaid_get_review_status)
+export(catmaid_get_server)
 export(catmaid_get_time_invested)
 export(catmaid_get_treenode_table)
 export(catmaid_get_treenodes_detail)
@@ -49,6 +52,7 @@ export(catmaid_get_volume)
 export(catmaid_get_volumelist)
 export(catmaid_lock_neurons)
 export(catmaid_login)
+export(catmaid_node_time)
 export(catmaid_parse_url)
 export(catmaid_query_by_annotation)
 export(catmaid_query_by_name)
@@ -61,6 +65,7 @@ export(catmaid_rename_neuron)
 export(catmaid_set_annotations_for_skeletons)
 export(catmaid_set_labels)
 export(catmaid_set_meta_annotations)
+export(catmaid_skeletons_in_bbx)
 export(catmaid_skids)
 export(catmaid_unlock_neurons)
 export(catmaid_user_history)

R/catmaid_connection.R

@@ -557,3 +557,18 @@ catmaid_envstr <- function(){
   else stop(paste("\ncatmaid error: Only found the environment variable -- ", matchvalues))
 }
 
+
+#' Get the CATMAID server in use
+#'
+#' @description shows the URL for a connection object in use (see \code{catmaid_login})
+#' @param conn CATMAID connection object, see ?catmaid::catmaid_login for details
+#' @param ... methods passed to catmaid::catmaid_login
+#' @seealso \code{\link{catmaid_login}}
+#' @export
+#' @rdname catmaid_get_server
+catmaid_get_server<-function(conn=NULL,...){
+  if(is.null(conn)){
+    conn = catmaid::catmaid_login()
+  }
+  conn$server
+}

R/catmaid_search.R

@@ -0,0 +1,53 @@
+# Searching for CATMAID neurons
+
+#' Search for CATMAID skeletons within a volume
+#'
+#' @description  Programmatically search for skeleton IDs pertaining to neurons within a search volume defined by a bounding box.
+#' @param bbx the bounding box (a matrix of 2 rows and 3 columns) describing a search volume
+#' @param min_nodes the minimum number of nodes a neuron in the search area must have (includes nodes outside search area)
+#' @param pid project id. Defaults to 1
+#' @param conn CATMAID connection object, see ?catmaid::catmaid_login for details
+#' @param ... methods passed to catmaid::catmaid_fetch
+#' @export
+#' @rdname catmaid_skeletons_in_bbx
+catmaid_skeletons_in_bbx <- function(bbx, min_nodes = 2, pid = 1, conn = NULL, ...){
+  post_data = list()
+  post_data["minx"] = bbx[1,1]
+  post_data["miny"] = bbx[1,2]
+  post_data["minz"] = bbx[1,3]
+  post_data["maxx"] = bbx[2,1]
+  post_data["maxy"] = bbx[2,2]
+  post_data["maxz"] = bbx[2,3]
+  post_data["min_nodes"] = min_nodes
+  path = sprintf("/%d/skeletons/in-bounding-box", pid)
+  res = catmaid::catmaid_fetch(path, body = post_data, include_headers = F,
+                               simplifyVector = T, conn = conn, ...)
+  res
+}
+
+
+#' Get the CATMAID neuron ID that corresponds to the skeleton ID
+#'
+#' @description Retrieve the neuron IDs for given skeleton IDs. This is typically the skeleton ID + 1, and is often, but not always accurately, kept by CATMAID tracers in the name of a neuron.
+#' @param skids a vector of skeleton IDs or argument applicable to \code{catmaid_get_neuronid}
+#' @param pid project id. Defaults to 1
+#' @param conn CATMAID connection object, see \code{catmaid::catmaid_login} for details
+#' @param ... methods passed to  \code{catmaid_fetch}
+#' @export
+#' @rdname catmaid_get_neuronid
+catmaid_get_neuronid <- function(skids, pid = 1, conn = NULL, ...){
+  skids = catmaid_skids(skids, conn = conn, pid = pid, ...)
+  if (any(duplicated(skids))) {
+    uskids = unique(skids)
+    unids = catmaid_get_neuronid(uskids, pid = pid, conn = conn,...)
+    res = unids[match(skids, uskids)]
+    return(res)
+  }
+  skids[is.na(skids)] = -1L
+  res = lapply(skids,function(skid)
+    catmaid::catmaid_fetch(sprintf("/%d/skeleton/%s/neuronname", pid, skid), body = NULL, include_headers = F,
+                           conn = conn, ...)$neuronid)
+  res = sapply(res,function(r) ifelse(is.null(r),NA,r))
+  names(res) = skids
+  res
+}

R/catmaid_stats.R

@@ -598,3 +598,69 @@ process_one_user_history <- function(x) {
   df$date=rep(dates, sapply(x, function(x) length(x)>0))
   df
 }
+
+
+
+#' Get meta information on nodes connected to a CATMAID connector node
+#'
+#' @description Get information on a CATMAID connector node
+#' @param connector_id the ID for a connector of interest
+#' @param node whether the connector is pre- or post-synaptic to the node of interest
+#' @param pid project id. Defaults to 1
+#' @param conn CATMAID connection object, see ?catmaid_login for details
+#' @param ... methods passed to \code{catmaid_fetch} and \code{catmaid_get_treenode_detail}
+#' @export
+#' @rdname catmaid_connector_nodes
+catmaid_connector_nodes <- function(connector_id, node = c("presynaptic","postsynaptic"),
+                                    pid=1, conn = conn, ...){
+  node = match.arg(node)
+  connector_id = as.numeric(connector_id)
+  if(length(connector_id)!=1){
+    stop("connector_id must be a single connector_id")
+  }
+  post_data = list()
+  post_data["connector_ids[0]"] = connector_id
+  path = sprintf("/%d/connector/skeletons", pid)
+  res = catmaid_fetch(path, body = post_data, include_headers = F,
+                               simplifyVector = T, conn = conn,...)
+  tnids = res[[1]][[2]][[paste0(node,"_to_node")]]
+  detail = catmaid_get_treenodes_detail (tnids=tnids, pid = pid, conn = conn, ...)
+  detail$connector_id = connector_id
+  detail
+}
+
+
+### Added to rcatmaid ###
+#' Get the UTC creation / edit time for a CATMAID node
+#'
+#' @description Get the UTC creation / edit time for a CATMAID treenode or connector. 
+#' Useful for making 'state' arguments to be passed to other functions that edit data on a CATMAID server.
+#' @param id a treenode or connector ID
+#' @param time whether to return the creation_time or edition_time
+#' @param pid project id. Defaults to 1
+#' @param conn CATMAID connection object, see ?catmaid_login for details
+#' @param ... methods passed to catmaid_set_labels
+#' @export
+#' @rdname catmaid_node_time
+catmaid_node_time <- function(id, time = c("creation_time", "edition_time"), pid = 1, conn = NULL, ...){
+  time = match.arg(time)
+  id = as.numeric(id)
+  post_data = list()
+  post_data["node_ids"] = id
+  path = sprintf("/%d/node/user-info", pid)
+  res = catmaid_fetch(path, body = post_data, include_headers = F,
+                               simplifyVector = T, conn = conn, ...)
+  if(!is.null(res$error)){
+    stop(res$error)
+  }else{
+    res[[1]][[time]]
+  }
+}
+
+# A helper function, not exported
+catmaid_convert_time <- function(utc){
+  t = format(as.POSIXlt(utc,tz="GMT",origin="1970-01-01"), "%Y-%m-%d %H:%M:%OS3")
+  s = unlist(strsplit(t," "))
+  t = paste0(s[1],"T",s[2],"Z")
+}
+