From 5f1a040439533c9ca28c1c6849809d2ebe8e5c29 Mon Sep 17 00:00:00 2001
From: alexanderbates <alexander.shakeel.bates@gmail.com>
Date: Thu, 12 Dec 2024 18:39:29 -0500
Subject: [PATCH] Update root IDs using CAVE tables and joining up supervoxel
 IDs

---
 R/ids.R              | 30 ++++++++++++++++++++++++++++++
 man/banc_latestid.Rd |  3 +++
 2 files changed, 33 insertions(+)

diff --git a/R/ids.R b/R/ids.R
index d3b70d6..a824ca4 100644
--- a/R/ids.R
+++ b/R/ids.R
@@ -159,6 +159,7 @@ banc_islatest <- function(x, timestamp=NULL, ...) {
 #' @param root.column when `x` is a `data.frame`, the `root_id` column you wish to update
 #' @param supervoxel.column when `x` is a `data.frame`, the `supervoxel_id` column you wish to use to update `root.column`
 #' @param position.column when `x` is a `data.frame`, the `position` column with xyz values you wish to use to update `supervoxel.column`
+#' @param use.cave read from the best established CAVE tables and join by `pt_supervoxel_id` to update `root_id`
 #' @param serial if TRUE and x is a vector, calls `banc_updateids` on each ID in sequence to bufffer against connection failures. Slower.
 #' @export
 #' @seealso \code{\link{banc_islatest}}
@@ -177,10 +178,38 @@ banc_updateids <- function(x,
                            root.column = "root_id",
                            supervoxel.column = "supervoxel_id",
                            position.column = "position",
+                           use.cave = TRUE,
                            serial = FALSE,
                            ...){
   if(is.data.frame(x)){
 
+    # Use CAVE tables to join by supervoxel_id
+    if(use.cave&!is.null(supervoxel.column)){
+      if(supervoxel.column%in%colnames(x)){
+        cat('joining to CAVE tables ...\n')
+        proofed <- banc_backbone_proofread() %>% dplyr::distinct(pt_root_id, pt_supervoxel_id)
+        info <- banc_cell_info()  %>% dplyr::distinct(pt_root_id, pt_supervoxel_id)
+        nuclei <- banc_nuclei()  %>% dplyr::distinct(pt_root_id = root_id, pt_supervoxel_id)
+        nerves <- banc_peripheral_nerves() %>% dplyr::distinct(pt_root_id, pt_supervoxel_id)
+        seeds <- banc_neck_connective_neurons() %>% dplyr::distinct(pt_root_id, pt_supervoxel_id)
+        cave.tables <- proofed %>%
+          rbind(info) %>%
+          rbind(nuclei) %>%
+          rbind(nerves) %>%
+          rbind(seeds) %>%
+          dplyr::mutate(cave_pt_root_id=as.character(pt_root_id),
+                        cave_pt_supervoxel_id=as.character(pt_supervoxel_id)) %>%
+          dplyr::distinct(cave_pt_root_id, cave_pt_supervoxel_id) %>%
+          as.data.frame()
+        x$cave_pt_supervoxel_id = x[[supervoxel.column]]
+        x <- x %>%
+          dplyr::left_join(cave.tables, by = "cave_pt_supervoxel_id")
+        x[[root.column]] <- ifelse(is.na(x$cave_pt_root_id)|x$cave_pt_root_id=="0",x[[root.column]],x$cave_pt_root_id)
+        x <- x %>%
+          dplyr::select(-cave_pt_root_id, -cave_pt_supervoxel_id)
+      }
+    }
+
     # Update supervoxel IDs
     if(!is.null(position.column)){
       if(all(c(position.column,supervoxel.column)%in%colnames(x))){
@@ -206,6 +235,7 @@ banc_updateids <- function(x,
       old <- rep(TRUE,nrow(x))
     }
     old[is.na(old)] <- TRUE
+    message("old root_ids: ",sum(old),"\n")
     if(!sum(old)){
       return(x)
     }
diff --git a/man/banc_latestid.Rd b/man/banc_latestid.Rd
index fb38b71..7c57bb4 100644
--- a/man/banc_latestid.Rd
+++ b/man/banc_latestid.Rd
@@ -18,6 +18,7 @@ banc_updateids(
   root.column = "root_id",
   supervoxel.column = "supervoxel_id",
   position.column = "position",
+  use.cave = TRUE,
   serial = FALSE,
   ...
 )
@@ -48,6 +49,8 @@ Else a vector of \code{BANC} root IDs.}
 
 \item{position.column}{when \code{x} is a \code{data.frame}, the \code{position} column with xyz values you wish to use to update \code{supervoxel.column}}
 
+\item{use.cave}{read from the best established CAVE tables and join by \code{pt_supervoxel_id} to update \code{root_id}}
+
 \item{serial}{if TRUE and x is a vector, calls \code{banc_updateids} on each ID in sequence to bufffer against connection failures. Slower.}
 }
 \description{