+combine

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: SpatialData
 Title: Representation of Python's SpatialData in R
 Depends: R (>= 4.6)
-Version: 0.99.29
+Version: 0.99.30
 Description: Interface to Python's 'SpatialData', currently including:
     reticulate-based use of 'spatialdata-io' for reading of manufacturer
     data and writing to .zarr, on-disk representation of images/labels as
@@ -12,18 +12,34 @@ Authors@R: c(
 	    role=c("aut", "cre"),
 	    email="helena@crowell.eu", 
 	    comment=c(ORCID="0000-0002-4801-1767")),
+    person("Artür", "Manukyan",
+        role=c("aut"),
+        email="artur-man@hotmail.com",
+        comment=c(ORCID="0000-0002-0441-9517")),
+    person("Hugo", "Gruson",
+        role=c("aut"),
+        email="charlotte.soneson@fmi.ch",
+        comment=c(ORCID="0000-0002-4094-1476")),
     person("Vince", "Carey",
         role=c("aut"),
-        email="stvjc@channing.harvard.edu",
+        email="hugo.gruson@embl.de",
         comment=c(ORCID="0000-0003-4046-0063")),
+    person("Charlotte", "Soneson",
+        role=c("aut"),
+        email="charlotte.soneson@fmi.ch",
+        comment=c(ORCID="0000-0003-3833-2169")),
+    person("Michael", "Stadler",
+        role=c("aut"),
+        email="michael.stadler@fmi.ch",
+        comment=c(ORCID="0000-0002-2269-4934")),
+    person("Samuel", "Gunz",
+        role=c("aut"),
+        email="samuel.gunz@uzh.ch",
+        comment=c(ORCID="0000-0002-8909-0932")),
     person("Yixing E.", "Dong",
         role=c("aut"),
         email="estelladong729@gmail.com",
         comment=c(ORCID="0009-0003-5115-5686")),
-    person("Artür", "Manukyan",
-        role=c("aut"),
-        email="artur-man@hotmail.com",
-        comment=c(ORCID="0000-0002-0441-9517")),
     person("Dario", "Righelli", 
         role=c("aut"), 
         email="dario.righelli@gmail.com",
@@ -33,11 +49,12 @@ Authors@R: c(
         email="louise.deconinck@gmail.com",
         comment=c(ORCID="0000-0001-8100-6823")))
 Imports:
-    arrow,
+    anndataR,
     basilisk,
     BiocGenerics,
     DelayedArray,
     dplyr,
+    duckspatial,
     EBImage,
     geoarrow,
     graph,
@@ -47,7 +64,7 @@ Imports:
     Rarr,
     RBGL,
     reticulate,
-    anndataR,
+    rlang,
     sf,
     S4Arrays,
     S4Vectors,

NAMESPACE

@@ -28,14 +28,19 @@ exportMethods("[")
 exportMethods("[[")
 exportMethods("[[<-")
 exportMethods("image<-")
+exportMethods("imageNames<-")
 exportMethods("images<-")
 exportMethods("label<-")
+exportMethods("labelNames<-")
 exportMethods("labels<-")
 exportMethods("point<-")
+exportMethods("pointNames<-")
 exportMethods("points<-")
 exportMethods("shape<-")
+exportMethods("shapeNames<-")
 exportMethods("shapes<-")
 exportMethods("table<-")
+exportMethods("tableNames<-")
 exportMethods("tables<-")
 exportMethods(CTdata)
 exportMethods(CTgraph)
@@ -49,6 +54,7 @@ exportMethods(axes)
 exportMethods(centroids)
 exportMethods(channels)
 exportMethods(colnames)
+exportMethods(combine)
 exportMethods(data)
 exportMethods(data_type)
 exportMethods(dim)
@@ -64,6 +70,7 @@ exportMethods(image)
 exportMethods(imageNames)
 exportMethods(images)
 exportMethods(instance_key)
+exportMethods(instances)
 exportMethods(label)
 exportMethods(labelNames)
 exportMethods(labels)
@@ -83,31 +90,31 @@ exportMethods(rmvCT)
 exportMethods(rotate)
 exportMethods(rownames)
 exportMethods(scale)
+exportMethods(sequence)
 exportMethods(setTable)
 exportMethods(shape)
 exportMethods(shapeNames)
 exportMethods(shapes)
 exportMethods(table)
 exportMethods(tableNames)
 exportMethods(tables)
+exportMethods(transform)
 exportMethods(translation)
-exportMethods(valTable)
 import(anndataR)
 import(geoarrow)
 importClassesFrom(S4Arrays,Array)
 importClassesFrom(S4Vectors,DFrame)
 importFrom(BiocGenerics,as.data.frame)
 importFrom(BiocGenerics,colnames)
+importFrom(BiocGenerics,combine)
 importFrom(BiocGenerics,rownames)
 importFrom(DelayedArray,DelayedArray)
 importFrom(EBImage,resize)
 importFrom(EBImage,rotate)
 importFrom(EBImage,translate)
-importFrom(Matrix,rowSums)
 importFrom(Matrix,sparseMatrix)
 importFrom(Matrix,sparseVector)
 importFrom(Matrix,summary)
-importFrom(Matrix,t)
 importFrom(RBGL,sp.between)
 importFrom(Rarr,read_zarr_attributes)
 importFrom(Rarr,zarr_overview)
@@ -130,17 +137,26 @@ importFrom(SummarizedExperiment,colData)
 importFrom(ZarrArray,ZarrArray)
 importFrom(ZarrArray,path)
 importFrom(ZarrArray,type)
-importFrom(arrow,open_dataset)
 importFrom(basilisk,BasiliskEnvironment)
 importFrom(basilisk,basiliskRun)
 importFrom(basilisk,basiliskStart)
 importFrom(basilisk,basiliskStop)
 importFrom(dplyr,all_of)
 importFrom(dplyr,collect)
+importFrom(dplyr,count)
 importFrom(dplyr,filter)
+importFrom(dplyr,inner_join)
+importFrom(dplyr,join_by)
 importFrom(dplyr,mutate)
 importFrom(dplyr,pull)
+importFrom(dplyr,row_number)
 importFrom(dplyr,select)
+importFrom(dplyr,slice)
+importFrom(dplyr,sql)
+importFrom(dplyr,tally)
+importFrom(duckspatial,as_duckspatial_df)
+importFrom(duckspatial,ddbs_intersects)
+importFrom(duckspatial,ddbs_open_dataset)
 importFrom(graph,"edgeData<-")
 importFrom(graph,"edgeDataDefaults<-")
 importFrom(graph,"nodeData<-")
@@ -160,16 +176,20 @@ importFrom(methods,new)
 importFrom(methods,setClassUnion)
 importFrom(methods,setReplaceMethod)
 importFrom(reticulate,import)
+importFrom(rlang,"!!")
+importFrom(rlang,":=")
+importFrom(rlang,.data)
 importFrom(sf,"st_geometry<-")
 importFrom(sf,st_as_sf)
+importFrom(sf,st_as_sfc)
 importFrom(sf,st_bbox)
 importFrom(sf,st_coordinates)
-importFrom(sf,st_crop)
-importFrom(sf,st_distance)
 importFrom(sf,st_geometry)
 importFrom(sf,st_geometry_type)
 importFrom(sf,st_intersects)
 importFrom(sf,st_polygon)
+importFrom(sf,st_sf)
+importFrom(sf,st_sfc)
 importFrom(utils,.DollarNames)
 importFrom(utils,head)
 importFrom(utils,tail)

R/AllClasses.R

@@ -3,7 +3,7 @@
     contains="list")
 
 #' @importFrom methods setClassUnion
-#' @importClassesFrom S4Arrays Array 
+#' @importClassesFrom S4Arrays Array
 setClassUnion(
     "array_OR_df",
     c("Array", "array", "data.frame"))
@@ -22,15 +22,17 @@ setClassUnion(
 # this somehow does the trick...
 setClass("FileSystemDataset", "VIRTUAL")
 setClass("arrow_dplyr_query", "VIRTUAL")
+setClass("tbl_duckdb_connection", "VIRTUAL")
+setClass("duckspatial_df", "VIRTUAL")
 setClass("Table", "VIRTUAL")
 
 # TODO: this isn't great... arrow::open_dataset gives a FileSystemDataset,
-# read_parquet gives a Table, dplyr calls give a query, but also wanna 
+# read_parquet gives a Table, dplyr calls give a query, but also wanna
 # be able to store a normal data.frame, maybe?
 #' @importFrom methods setClassUnion
 setClassUnion(
     "arrow_OR_df",
-    c("FileSystemDataset", "Table", "arrow_dplyr_query", "data.frame"))
+    c("tbl_duckdb_connection", "duckspatial_df", "FileSystemDataset", "Table", "arrow_dplyr_query", "data.frame"))
 
 .PointFrame <- setClass(
     Class="PointFrame",
@@ -43,9 +45,8 @@ setClassUnion(
     contains=c("Annotated"),
     slots=list(data="arrow_OR_df", meta="Zattrs"))
 
-setClassUnion(
-  "sdArray",
-  c("ImageArray", "LabelArray"))
+setClassUnion("sdArray", c("ImageArray", "LabelArray"))
+setClassUnion("sdFrame", c("PointFrame", "ShapeFrame"))
 
 setClassUnion(
     "SpatialDataElement",

R/AllGenerics.R

@@ -22,15 +22,23 @@ setGeneric("shapeNames", \(x, ...) standardGeneric("shapeNames"))
 setGeneric("pointNames", \(x, ...) standardGeneric("pointNames"))
 setGeneric("tableNames", \(x, ...) standardGeneric("tableNames"))
 
-# set one -----
+# set nms ----
+
+setGeneric("imageNames<-", \(x, ..., value) standardGeneric("imageNames<-"))
+setGeneric("labelNames<-", \(x, ..., value) standardGeneric("labelNames<-"))
+setGeneric("shapeNames<-", \(x, ..., value) standardGeneric("shapeNames<-"))
+setGeneric("pointNames<-", \(x, ..., value) standardGeneric("pointNames<-"))
+setGeneric("tableNames<-", \(x, ..., value) standardGeneric("tableNames<-"))
+
+# set one ----
 
 setGeneric("image<-", \(x, i, ..., value) standardGeneric("image<-"))
 setGeneric("shape<-", \(x, i, ..., value) standardGeneric("shape<-"))
 setGeneric("label<-", \(x, i, ..., value) standardGeneric("label<-"))
 setGeneric("point<-", \(x, i, ..., value) standardGeneric("point<-"))
 setGeneric("table<-", \(x, i, ..., value) standardGeneric("table<-"))
 
-# set all -----
+# set all ----
 
 setGeneric("images<-", \(x, value) standardGeneric("images<-"))
 setGeneric("labels<-", \(x, value) standardGeneric("labels<-"))
@@ -53,7 +61,8 @@ setGeneric("addCT", \(x, ...) standardGeneric("addCT"))
 
 setGeneric("scale", \(x, t, ...) standardGeneric("scale"))
 setGeneric("rotate", \(x, t, ...) standardGeneric("rotate"))
-setGeneric("transform", \(x, ...) standardGeneric("transform"))
+setGeneric("sequence", \(x, t, ...) standardGeneric("sequence"))
+setGeneric("transform", \(x, i, ...) standardGeneric("transform"))
 setGeneric("translation", \(x, t, ...) standardGeneric("translation"))
 
 setGeneric("flip", \(x, ...) standardGeneric("flip"))
@@ -63,6 +72,11 @@ setGeneric("mirror", \(x, ...) standardGeneric("mirror"))
 # sda ----
 
 setGeneric("region", \(x, ...) standardGeneric("region"))
+setGeneric("region<-", \(x, ..., value) standardGeneric("region<-"))
+
+setGeneric("regions", \(x, ...) standardGeneric("regions"))
+setGeneric("instances", \(x, ...) standardGeneric("instances"))
+
 setGeneric("region_key", \(x, ...) standardGeneric("region_key"))
 setGeneric("feature_key", \(x, ...) standardGeneric("feature_key"))
 setGeneric("instance_key", \(x, ...) standardGeneric("instance_key"))
@@ -91,4 +105,3 @@ setGeneric("multiscales", \(x, ...) standardGeneric("multiscales"))
 setGeneric("hasTable", \(x, i, ...) standardGeneric("hasTable"))
 setGeneric("getTable", \(x, i, ...) standardGeneric("getTable"))
 setGeneric("setTable", \(x, i, ...) standardGeneric("setTable"))
-setGeneric("valTable", \(x, i, ...) standardGeneric("valTable"))

R/CTgraph.R

@@ -77,11 +77,12 @@ setMethod("CTgraph", "ANY", \(x) stop("'x' should be a",
     g <- .init_g()
     for (l in names(md)) for (e in names(md[[l]])) {
         .md <- md[[l]][[e]]
-        ms <- .md$multiscales
+        ms <- multiscales(.md)
         if (!is.null(ms)) .md <- ms[[1]]
+        .e <- paste0("_", e)
+        g <- addNode(.e, g)
+        nodeData(g, .e, "type") <- "element"
         ct <- .md$coordinateTransformations
-        g <- addNode(e, g)
-        nodeData(g, e, "type") <- "element"
         for (i in seq_along(ct)) {
             n <- ct[[i]]$output$name
             if (!n %in% nodes(g)) {
@@ -91,7 +92,7 @@ setMethod("CTgraph", "ANY", \(x) stop("'x' should be a",
             t <- ct[[i]]$type
             if (t == "sequence") {
                 sq <- ct[[i]]$transformations
-                . <- e
+                . <- .e
                 for (j in seq_along(sq)) {
                     if (j == length(sq)) {
                         m <- n
@@ -108,10 +109,10 @@ setMethod("CTgraph", "ANY", \(x) stop("'x' should be a",
                     . <- m
                 }
             } else {
-                g <- addEdge(e, n, g)
+                g <- addEdge(.e, n, g)
                 d <- ct[[i]][[ct[[i]]$type]]
-                edgeData(g, e, n, "type") <- t
-                edgeData(g, e, n, "data") <- list(d)
+                edgeData(g, .e, n, "type") <- t
+                edgeData(g, .e, n, "data") <- list(d)
             }
         }
     }
@@ -123,6 +124,7 @@ setMethod("CTgraph", "ANY", \(x) stop("'x' should be a",
 #' @importFrom graph edgeData
 #' @importFrom RBGL sp.between
 .path_ij <- \(g, i, j) {
+    i <- paste0("_", i)
     p <- sp.between(g, i, j)
     p <- p[[1]]$path_detail
     n <- length(p)-1