Merge branch 'master' into drop_prefix

# Conflicts:
#	R/name.R

R/connectivity.R

@@ -25,7 +25,7 @@ neuprint_get_adjacency_matrix <- function(bodyids, dataset = NULL, all_segments
     namefield,
     namefield
   )
-  nc = neuprint_fetch_custom(cypher=cypher, conn = conn, ...)
+  nc = neuprint_fetch_custom(cypher=cypher, conn = conn, dataset = dataset, ...)
   m = matrix(0,nrow = length(bodyids),ncol = length(bodyids))
   rownames(m) = colnames(m) = bodyids
   for(i in 1:length(nc$data)){
@@ -86,7 +86,7 @@ neuprint_connection_table <- function(bodyids, prepost = c("PRE","POST"), roi =
                    ifelse(prepost=="POST","bodyid","partner"),
                    ifelse(prepost=="POST","partner","bodyid")
                   )
-  nc = neuprint_fetch_custom(cypher=cypher, conn = conn)
+  nc = neuprint_fetch_custom(cypher=cypher, conn = conn, dataset = dataset, ...)
   ## Filter out the rare cases where PSDs and tbars are in different ROIs (hence post is null)
   nc$data <- nc$data[sapply(nc$data,function(x) !is.null(x[[4]]))]
   d <-  data.frame(do.call(rbind,lapply(nc$data,unlist)),stringsAsFactors = FALSE)
@@ -265,7 +265,7 @@ neuprint_get_paths <- function(body_pre,body_post,n,weightT=5,roi=NULL,dataset =
   ifelse(is.null(roi),"",roi)
   )
 
-  nc <-  neuprint_fetch_custom(cypher=cypher, conn = conn)
+  nc <-  neuprint_fetch_custom(cypher=cypher, conn = conn, dataset = dataset, ...)
 
   connTable <- dplyr::bind_rows(lapply(nc$data, function(d){
                   l <- d[[1]]
@@ -331,7 +331,7 @@ neuprint_get_shortest_paths <- function(body_pre,body_post,weightT=5,roi=NULL,da
   ifelse(is.null(roi),"",roi)
   )
 
-  nc <-  neuprint_fetch_custom(cypher=cypher, conn = conn)
+  nc <-  neuprint_fetch_custom(cypher=cypher, conn = conn, dataset=dataset, ...)
 
   connTable <- dplyr::bind_rows(lapply(nc$data, function(d){
     l <- d[[1]]

R/dump.R

@@ -17,7 +17,7 @@
 #' @rdname neuprint_dump
 #' @importFrom nat write.neurons
 neuprint_dump <- function(dir, bodyids = NULL, roi = NULL, preprocess = NULL, connectivity = TRUE, volumes = TRUE,
-                          meta = TRUE, nat = TRUE, drvid = TRUE, flow.centrality = FALSE, soma = TRUE, estimate.soma = FALSE,
+                          meta = TRUE, nat = TRUE, drvid = FALSE, flow.centrality = FALSE, soma = TRUE, estimate.soma = FALSE,
                           heal = TRUE, connectors = TRUE, all_segments = TRUE, resample = FALSE,
                           scale = 4, voxel.thresh = 1e+07, split = c("postsynapses","presynapses","distance"),
                           dataset = NULL, conn=NULL, OmitFailures = TRUE, ...){

R/fetch.R

@@ -92,15 +92,15 @@ neuprint_list2df <- function(x, cols=NULL, return_empty_df=FALSE, ...) {
 }
 
 #' @importFrom memoise memoise
-neuprint_name_field <- memoise(function(conn=NULL) {
+neuprint_name_field <- memoise(function(conn=NULL, dataset = NULL) {
   if (is.null(conn))
     stop(
       "You must do\n  conn = neuprint_login(conn)\n",
       "before using neuprint_name_field(conn) in your function!",
       call. = FALSE
     )
   q="MATCH (n :hemibrain_Neuron) WHERE exists(n.instance) RETURN count(n)"
-  n=unlist(neuprint_fetch_custom(q, include_headers=F)[['data']])
+  n=unlist(neuprint_fetch_custom(q, dataset = dataset, include_headers=F)[['data']])
   return(ifelse(n>0, "instance", "name"))
 })
 
@@ -113,7 +113,7 @@ neuprint_dataset_prefix <- memoise(function(dataset, conn=NULL) {
       call. = FALSE
     )
   # q=sprintf("MATCH (n:`%s_Segment`) RETURN count(n)", dataset)
-  # n=unlist(neuprint_fetch_custom(q, include_headers=F)[['data']])
+  # n=unlist(neuprint_fetch_custom(q, dataset = dataset, include_headers=F)[['data']])
   #paste0(dataset, ifelse(n>0, "_", "-")) # I think we no longer need to specify the dataset. Might be good to keep this function in place though, in case situation changes
   ""
 })
@@ -126,7 +126,7 @@ check_dataset <- function(dataset=NULL) {   # Get a default dataset if none spec
       warning("Please supply a dataset or set a default one using the ",
            "neuprint_dataset environment variable! See ?neuprint_login for details.
            For now we will use hemibrain:v1.0")
-    dataset = "hemibrain:1.0"
+    dataset = "hemibrain:v1.0"
     }
   }
   dataset

R/name.R

@@ -16,7 +16,8 @@ neuprint_get_neuron_names <- function(bodyids, dataset = NULL, all_segments = TR
   cypher = sprintf("WITH %s AS bodyIds UNWIND bodyIds AS bodyId MATCH (n:`%s`) WHERE n.bodyId=bodyId RETURN n.instance AS name",
                    jsonlite::toJSON(as.numeric(unlist(bodyids))),
                    all_segments.json)
-  nc = neuprint_fetch_custom(cypher=cypher, conn = conn, ...)
+
+  nc = neuprint_fetch_custom(cypher=cypher, conn = conn, dataset = dataset, ...)
   d =  unlist(lapply(nc$data,nullToNA))
   names(d) = bodyids
   d
@@ -47,7 +48,7 @@ neuprint_get_meta <- function(bodyids, dataset = NULL, all_segments = TRUE, conn
     all_segments,
     neuprint_name_field(conn)
   )
-  nc = neuprint_fetch_custom(cypher=cypher, conn = conn, include_headers = FALSE, ...)
+  nc = neuprint_fetch_custom(cypher=cypher, conn = conn, dataset = dataset, include_headers = FALSE, ...)
   neuprint_list2df(nc, return_empty_df = TRUE)
 }
 
@@ -71,7 +72,7 @@ neuprint_get_roiInfo <- function(bodyids, dataset = NULL, all_segments = TRUE, c
     jsonlite::toJSON(as.numeric(unlist(bodyids))),
     all_segments
   )
-  nc = neuprint_fetch_custom(cypher=cypher, conn = conn, ...)
+  nc = neuprint_fetch_custom(cypher=cypher, dataset = dataset, conn = conn, ...)
   lc <-  lapply(nc$data,function(x){cbind(bodyid=x[[1]],as.data.frame(t(unlist(jsonlite::fromJSON(x[[2]])))))})
   d <- dplyr::bind_rows(lc)
   d
@@ -103,7 +104,7 @@ neuprint_search <- function(search, meta = TRUE, all_segments = TRUE, dataset =
                    all_segments.cypher,
                    neuprint_name_field(conn),
                    search)
-  nc = neuprint_fetch_custom(cypher=cypher, ...)
+  nc = neuprint_fetch_custom(cypher=cypher, dataset = dataset, ...)
   foundbodyids=unlist(nc$data)
   if(meta && isTRUE(length(foundbodyids)>0)){
     neuprint_get_meta(bodyids = foundbodyids, dataset = dataset, all_segments = all_segments, conn = conn, ...)

R/neurons.R

@@ -105,7 +105,7 @@ neuprint_read_neuron <- function(bodyid,
     n = drvid::read.neuron.dvid(bodyid)
     d = n$d
   }else{
-    n = neuprint_read_neuron_simple(as.numeric(bodyid),dataset=dataset,conn = conn,heal = FALSE,...)
+    n = neuprint_read_neuron_simple(as.numeric(bodyid),dataset=dataset,conn = conn, heal = FALSE,...)
   }
   if(heal|flow.centrality){
     n = suppressWarnings( heal_skeleton(x = n) )

R/roi.R

@@ -60,7 +60,7 @@ neuprint_bodies_in_ROI <- function(roi, dataset = NULL, all_segments = FALSE, co
                 roi,
                 roi,
                 roi)
-  nc = neuprint_fetch_custom(cypher=cypher, conn = conn, ...)
+  nc = neuprint_fetch_custom(cypher=cypher, conn = conn, dataset = dataset, ...)
   d = data.frame(do.call(rbind,lapply(nc$data,unlist)))
   colnames(d) = unlist(nc$columns)
   d

R/soma.R

@@ -18,7 +18,7 @@ neuprint_locate_soma <- function(bodyids, dataset = NULL, all_segments = TRUE, c
   cypher = sprintf("WITH %s AS bodyIds UNWIND bodyIds AS bodyId MATCH (n:`%s`) WHERE n.bodyId=bodyId RETURN n.bodyId AS bodyId, n.somaLocation AS soma",
                    jsonlite::toJSON(as.numeric(unique(bodyids))),
                    paste0(dp, all_segments.json))
-  nc = neuprint_fetch_custom(cypher=cypher, conn = conn, ...)
+  nc = neuprint_fetch_custom(cypher=cypher, conn = conn, dataset = dataset, ...)
   if(length(nc$data)==0){
     coordinates = matrix(c(NA,NA,NA),nrow=length(bodyids),ncol=3)
     coordinates = cbind(data.frame(bodyid=bodyids),coordinates)

R/synapses.R

@@ -75,7 +75,7 @@ neuprint_get_synapses <- function(bodyids, roi = NULL, progress = FALSE, dataset
                         prefixed_seg,
                         prefixed_seg,
                         roi)
-  nc.post = neuprint_fetch_custom(cypher=cypher.post, conn = conn, ...)
+  nc.post = neuprint_fetch_custom(cypher=cypher.post, conn = conn, dataset = dataset, ...)
   nc.pre = neuprint_fetch_custom(cypher=cypher.pre, conn = conn, ...)
   m = rbind(do.call(rbind,nc.post$data),do.call(rbind,nc.pre$data))
   colnames(m) =  nc.post$columns