From 8406792023c9a049ed143098c687d18212177e3c Mon Sep 17 00:00:00 2001
From: Gregory Jefferis <jefferis@gmail.com>
Date: Fri, 22 Nov 2024 13:46:43 +0000
Subject: [PATCH 1/2] handle variations in encoding of source URL
* for yakuba they were $source not $source$url for some reason ...
---
R/datasets.R | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/R/datasets.R b/R/datasets.R
index 875a0d5..07024fe 100644
--- a/R/datasets.R
+++ b/R/datasets.R
@@ -100,7 +100,7 @@ flyem_scene4dataset <- memoise::memoise(function(dataset=NULL) {
flyem_servers4dataset <- memoise::memoise(function(dataset=NULL) {
sc=flyem_scene4dataset(dataset)
dl=flyem_dvidlayer4scene(sc)
- u=dl$source$url
+ u=if(is.character(dl$source)) dl$source else dl$source$url
dvid=sub("dvid-service=.*", "", u)
dvid=sub("dvid://", "", dvid)
dvid=sub("(https://[^/]+).*", "\\1", dvid)
@@ -112,7 +112,10 @@ flyem_servers4dataset <- memoise::memoise(function(dataset=NULL) {
flyem_dvidlayer4scene <- function(sc) {
dvidlayer <- sapply(sc$layers, function(x) isTRUE(try(grepl("dvid", x$source$url), silent = T)))
- # if(sum(dvidlayer)!=1)
+ if(sum(dvidlayer)<1) {
+ # try again just with source
+ dvidlayer <- sapply(sc$layers, function(x) isTRUE(try(grepl("dvid", x$source), silent = T)))
+ }
# warning("Unable to extract a unique DVID layer!")
dl=sc$layers[[min(which(dvidlayer))]]
dl
From fafddcc62bbd4c57428727f1b6c6cdc0788d710c Mon Sep 17 00:00:00 2001
From: Gregory Jefferis <jefferis@gmail.com>
Date: Fri, 22 Nov 2024 13:47:45 +0000
Subject: [PATCH 2/2] respect the ordering of layers in clio
* there is a property orderedLayers that I hadn't previously used
* for yakuba it was important because the supervoxel layer came before the agglomeration layer
---
R/datasets.R | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/R/datasets.R b/R/datasets.R
index 07024fe..9fcae4d 100644
--- a/R/datasets.R
+++ b/R/datasets.R
@@ -93,6 +93,10 @@ flyem_scene4dataset <- memoise::memoise(function(dataset=NULL) {
# there are some key layers here
sc2=fafbseg::ngl_decode_scene(ds$versions[[1]]$neuroglancer)
ll=c(sc$layers[1], sc2$layers[1], sc$layers[-1], sc2$layers[-1])
+ if(!is.null(ds$orderedLayers) && all(ds$orderedLayers %in% names(ll))) {
+ # reorder layers based on clio config information putting preferred ones first
+ ll=ll[union(ds$orderedLayers, names(ll))]
+ }
fafbseg::ngl_layers(sc) <- ll
sc
})