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sdImage/Label and OME versioning #249

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66 changes: 58 additions & 8 deletions R/sdAttrs.R
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Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,7 @@
#'
#' @export
SpatialDataAttrs <- \(x, type=c("image", "label", "frame"),
trans=NULL, ver="0.4", dim=2, nch=3, ...)
trans=NULL, ver="0.3", dim=2, nch=3, ...)
{
stopifnot(
length(dim) == 1, is.numeric(dim), dim %in% seq(2, 4),
Expand All @@ -72,16 +72,29 @@ SpatialDataAttrs <- \(x, type=c("image", "label", "frame"),
ax <- .default_ax(type, dim)
# transformations:
ct <- trans %||% .default_ct(ax)
# datasets:
ds <- .default_ds(.ax_names(ax))
# .zattrs list:
if (type != "frame") {
# default structure
res <- list(
omero=list(channels=list(label=letters[seq_len(nch)])),
multiscales=list(list(
axes=ax,
version="0.4",
coordinateTransformations=ct,
datasets=list(list(path="0", coordinateTransformations=list(list(type="scale", scale=list(1, 1))))))))
res <- list()
if(type != "label")
res <- c(res,
list(omero=list(channels=lapply(letters[seq_len(nch)],
\(.) list(label = .)))))
res <- c(res,
list(
version=.get_ome_version(ver),
multiscales=
list(
list(
axes=ax,
coordinateTransformations=ct,
datasets=ds
)
)
)
)
if (ver == "0.3") res <- list(ome=res)
} else {
# points/shapes
Expand Down Expand Up @@ -120,13 +133,41 @@ SpatialDataAttrs <- \(x, type=c("image", "label", "frame"),
return(ax)
}

# Internal helper to get axes names
.ax_names <- function(ax){
if (is.character(ax[[1]])) {
unlist(ax)
} else {
vapply(ax, \(.) .$name, character(1))
}
}

# Internal helper to generate coordinate transformations
.default_ct <- \(axes, name="global", type="identity", data=NULL) {
ct <- list(input=axes, output=list(name=name), type=type)
if (!is.null(data)) ct[[type]] <- data
list(ct)
}

# Internal helper to generate datasets
.default_ds <- function(axes, scale_factors = NULL){
scale_factors <- cumprod(c(1,scale_factors))
paths <- paste0(seq_along(scale_factors) - 1)
mapply(\(p,s) {
list(
coordinateTransformations = list(
list(
scale = lapply(
axes,
\(.) if(. == "c") 1 else s),
type = "scale"
)
),
path = p
)
}, paths, scale_factors, USE.NAMES = FALSE, SIMPLIFY = FALSE)
}

#' @export
#' @importFrom utils .DollarNames
.DollarNames.SpatialDataAttrs <- \(x, pattern="") names(x)
Expand All @@ -147,6 +188,15 @@ setMethod("$", "SpatialDataAttrs", \(x, name) x[[name]])
return(v)
}

.get_ome_version <- \(x){
switch(as.character(x),
"0.1" = "0.4",
"0.2" = "0.4-dev-spatialdata",
"0.3" = "0.5-dev-spatialdata",
stop("Invalid SpatialDataImage/Label format! ",
"Must be 0.1, 0.2, or 0.3"))
}

# internal use only!
#' @noRd
setMethod("multiscales", "list", \(x) {
Expand Down
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