Pass attributes from consolidated metadata

for better performance

Author: Bisaloo

R/read.R

@@ -44,8 +44,8 @@ NULL
 
 #' @importFrom Rarr read_zarr_attributes
 #' @importFrom ZarrArray ZarrArray
-.readArray <- function(x, ...) {
-    md <- read_zarr_attributes(x)
+.readArray <- function(x, md = NULL, ...) {
+    md <- md %||% read_zarr_attributes(x)
     mdattr <- SpatialDataAttrs(md)
     # TODO: paths to datasets have to be validated properly in the future
     # https://ngff.openmicroscopy.org/specifications/0.5/index.html#images
@@ -66,15 +66,15 @@ NULL
 
 #' @rdname readSpatialData
 #' @export
-readImage <- function(x, ...) {
-    l <- .readArray(x, ...)
+readImage <- function(x, md = NULL, ...) {
+    l <- .readArray(x, md = md, ...)
     SpatialDataImage(data=l$array, meta=l$mdattr, ...)
 }
 
 #' @rdname readSpatialData
 #' @export
-readLabel <- function(x, ...) {
-    l <- .readArray(x, ...)
+readLabel <- function(x, md = NULL, ...) {
+    l <- .readArray(x, md = md, ...)
     SpatialDataLabel(data=l$array, meta=l$mdattr, ...)
 }
 
@@ -83,9 +83,9 @@ readLabel <- function(x, ...) {
 #' @importFrom Rarr read_zarr_attributes
 #' @importFrom dplyr sql
 #' @export
-readPoint <- function(x, ...) {
+readPoint <- function(x, md = NULL, ...) {
     pq <- paste0(x, file.path("points.parquet", "part.0.parquet"))
-    md <- read_zarr_attributes(x)
+    md <- md %||% read_zarr_attributes(x)
     ax <- unlist(md$axes)
     df <- ddbs_open_dataset(pq, conn=.conn()) |>
         mutate(geometry=sql(sprintf("ST_Point(%s, %s)", ax[1], ax[2]))) |>
@@ -112,8 +112,8 @@ readPoint <- function(x, ...) {
 #' @importFrom duckspatial ddbs_open_dataset
 #' @import geoarrow
 #' @export
-readShape <- function(x, ...) {
-    md <- read_zarr_attributes(x)
+readShape <- function(x, md = NULL, ...) {
+    md <- md %||% read_zarr_attributes(x)
     # "shapes.parquet" currently hardcoded in SpatialData.io
     pq <- paste0(x, "shapes.parquet")
     df <- ddbs_open_dataset(pq, conn=.conn(), crs=NA_character_)
@@ -126,7 +126,7 @@ readShape <- function(x, ...) {
 #' @importFrom S4Vectors metadata metadata<-
 #' @importFrom SummarizedExperiment colData colData<-
 #' @importFrom SingleCellExperiment int_colData int_colData<- int_metadata int_metadata<-
-readTable <- function(x) {
+readTable <- function(x, ...) {
     suppressWarnings({ # suppress warnings related to hidden files
       sce <- anndataR::read_zarr(x, as="SingleCellExperiment")
     })
@@ -164,10 +164,7 @@ readSpatialData <- function(x,
     .readLayer <- \(l) {
         message("  reading ", l, "...")
         j <- store_groups[startsWith(store_groups, paste0(l, "/"))]
-        j <- setNames(
-            paste0(x, j, "/", recycle0 = TRUE),
-            basename(j)
-        )
+        names(j) <- basename(j)
 
         opt <- args[[l]]
         if (!isTRUE(opt)) {
@@ -178,7 +175,11 @@ readSpatialData <- function(x,
             j <- j[opt]
         }
         reader <- get(paste0("read", toupper(substr(l, 1, 1)), substr(l, 2, nchar(l)-1)))
-        lapply(j, reader)
+        lapply(j, function(el) {
+            md <- store_meta[[el]]$attributes
+            el <- paste0(x, el, "/", recycle0 = TRUE)
+            reader(el, md=md)
+        })
     }
 
     names(ls) <- ls <- .LAYERS[!skip]