Merge

R/array-nested.R

@@ -239,24 +239,27 @@ NestedArray <- R6::R6Class("NestedArray",
         message(value)
         stop("Got unexpected type for value in NestedArray$set()")
       }
-
-      # Cannot figure out how to dynamically set values in an array
-      # of arbitrary dimensions.
-      # Tried: abind::afill <- but it doesn't seem to work with arbitrary dims or do.call
-      if(length(selection_list) == 1) {
-        self$data[selection_list[[1]]] <- value_data
-      } else if(length(selection_list) == 2) {
-        self$data[selection_list[[1]], selection_list[[2]]] <- value_data
-      } else if(length(selection_list) == 3) {
-        self$data[selection_list[[1]], selection_list[[2]], selection_list[[3]]] <- value_data
-      } else if(length(selection_list) == 4) {
-        self$data[selection_list[[1]], selection_list[[2]], selection_list[[3]], selection_list[[4]]] <- value_data
-      } else if(length(selection_list) == 5) {
-        self$data[selection_list[[1]], selection_list[[2]], selection_list[[3]], selection_list[[4]], selection_list[[5]]] <- value_data
-      } else if(length(selection_list) == 6) {
-        self$data[selection_list[[1]], selection_list[[2]], selection_list[[3]], selection_list[[4]], selection_list[[5]], selection_list[[6]]] <- value_data
-      } else {
-        stop("NestedArray$set() can only handle up to 6D arrays at the moment. Please make a feature request if you need to handle more dims.")
+
+      # Only set values if the array is not meant to be empty.
+      if(sum(length(value_data)) > 0 || sum(dim(value_data)) > 0) {
+        # Cannot figure out how to dynamically set values in an array
+        # of arbitrary dimensions.
+        # Tried: abind::afill <- but it doesn't seem to work with arbitrary dims or do.call
+        if(length(selection_list) == 1) {
+          self$data[selection_list[[1]]] <- value_data
+        } else if(length(selection_list) == 2) {
+          self$data[selection_list[[1]], selection_list[[2]]] <- value_data
+        } else if(length(selection_list) == 3) {
+          self$data[selection_list[[1]], selection_list[[2]], selection_list[[3]]] <- value_data
+        } else if(length(selection_list) == 4) {
+          self$data[selection_list[[1]], selection_list[[2]], selection_list[[3]], selection_list[[4]]] <- value_data
+        } else if(length(selection_list) == 5) {
+          self$data[selection_list[[1]], selection_list[[2]], selection_list[[3]], selection_list[[4]], selection_list[[5]]] <- value_data
+        } else if(length(selection_list) == 6) {
+          self$data[selection_list[[1]], selection_list[[2]], selection_list[[3]], selection_list[[4]], selection_list[[5]], selection_list[[6]]] <- value_data
+        } else {
+          stop("NestedArray$set() can only handle up to 6D arrays at the moment. Please make a feature request if you need to handle more dims.")
+        }
       }
     },
     #' @description

R/normalize.R

@@ -180,7 +180,7 @@ guess_chunks <- function(shape, typesize) {
         break  # Element size larger than CHUNK_MAX
       }
 
-      chunks[idx %% ndims] <- ceiling(chunks[idx %% ndims] / 2.0)
+      chunks[idx %% ndims + 1] <- ceiling(chunks[idx %% ndims + 1] / 2.0)
       idx <- idx + 1
   }
 

R/slicing.R

@@ -119,7 +119,7 @@ slice <- function(start, stop = NA, step = NA, zero_based = FALSE) {
   ))
 }
 
-#' Convenience function for the internal Sliceclass constructor 
+#' Convenience function for the internal Slice class constructor 
 #' with zero-based indexing and exclusive stop index.
 #' @param start The start index.
 #' @param stop The stop index.

R/zarr-array.R

@@ -434,41 +434,41 @@ ZarrArray <- R6::R6Class("ZarrArray",
 
       selection_shape <- indexer$shape
       selection_shape_vec <- ensure_integer_vec(indexer$shape)
-
-      # Check value shape
-      if (length(selection_shape) == 0) {
-        # Setting a single value
-      } else if (is_scalar(value)) {
-        # Setting a scalar value
-      } else if("array" %in% class(value)) {
-        if (!all(ensure_integer_vec(dim(value)) == selection_shape_vec)) {
-          stop("Shape mismatch in source array and set selection: ${dim(value)} and ${selectionShape}")
-        }
-        value <- NestedArray$new(value, shape = selection_shape_vec, dtype=private$dtype, order = private$order)
-      } else if ("NestedArray" %in% class(value)) {
-        if (!all(ensure_integer_vec(value$shape) == selection_shape_vec)) {
-          stop("Shape mismatch in source NestedArray and set selection: ${value.shape} and ${selectionShape}")
-        }
-      } else {
-        # // TODO(zarr.js) support TypedArrays, buffers, etc
-        stop("Unknown data type for setting :(")
-      }
 
-      if(getOption("pizzarr.parallel_write_enabled")) {
-        if(!requireNamespace("foreach", quietly=TRUE)) {
-          stop("Parallel writing requires the 'foreach' package.")
-        }
-        # If optional package "foreach" is installed, try to run in parallel.
-        foreach::foreach(proj=indexer$iter(), .combine = c, .inorder = FALSE, .init = NULL) %dopar% {
-          chunk_value <- private$get_chunk_value(proj, indexer, value, selection_shape)
-          private$chunk_setitem(proj$chunk_coords, proj$chunk_sel, chunk_value)
-          NULL # return null since we are not using the combined result
+      if(sum(as.numeric(selection_shape)) > 0) {
+        # Check value shape
+        if (length(selection_shape) == 0) {
+          # Setting a single value
+        } else if (is_scalar(value)) {
+          # Setting a scalar value
+        } else if("array" %in% class(value)) {
+          if (!all(ensure_integer_vec(dim(value)) == selection_shape_vec)) {
+            stop("Shape mismatch in source array and set selection: ${dim(value)} and ${selectionShape}")
+          }
+          value <- NestedArray$new(value, shape = selection_shape_vec, dtype=private$dtype, order = private$order)
+        } else if ("NestedArray" %in% class(value)) {
+          if (!all(ensure_integer_vec(value$shape) == selection_shape_vec)) {
+            stop("Shape mismatch in source NestedArray and set selection: ${value.shape} and ${selectionShape}")
+          }
+        } else {
+          # // TODO(zarr.js) support TypedArrays, buffers, etc
+          stop("Unknown data type for setting :(")
         }
-      } else {
-        # Foreach package was not installed, instead use a normal for loop.
-        for (proj in indexer$iter()) {
-          chunk_value <- private$get_chunk_value(proj, indexer, value, selection_shape)
-          private$chunk_setitem(proj$chunk_coords, proj$chunk_sel, chunk_value)
+
+        if(getOption("pizzarr.parallel_write_enabled")) {
+          if(!requireNamespace("foreach", quietly=TRUE)) {
+            stop("Parallel writing requires the 'foreach' package.")
+          }
+          foreach::foreach(proj=indexer$iter(), .combine = c, .inorder = FALSE, .init = NULL) %dopar% {
+            chunk_value <- private$get_chunk_value(proj, indexer, value, selection_shape)
+            private$chunk_setitem(proj$chunk_coords, proj$chunk_sel, chunk_value)
+            NULL # return null since we are not using the combined result
+          }
+        } else {
+          for (proj in indexer$iter()) {
+            chunk_value <- private$get_chunk_value(proj, indexer, value, selection_shape)
+            private$chunk_setitem(proj$chunk_coords, proj$chunk_sel, chunk_value)
+          }
         }
       }
     },

tests/testthat/helper-vcr.R

@@ -1,6 +1,5 @@
 library("vcr") # *Required* as vcr is set up on loading
 invisible(vcr::vcr_configure(
-  dir = vcr::vcr_test_path("fixtures"),
-  log = TRUE
+  dir = vcr::vcr_test_path("fixtures")
 ))
 vcr::check_cassette_names()

tests/testthat/test-chunks.R

@@ -1,5 +1,18 @@
 library(pizzarr)
 
+test_that("no infinite loop", {
+    shape <- c(27557749)
+    dtype <- "<i4"
+    chunks <- NA
+
+    dtype <- normalize_dtype(dtype, object_codec = NA)
+    shape <- normalize_shape(shape)
+
+    dtype_itemsize <- dtype$num_bytes
+    chunks <- normalize_chunks(chunks, shape, dtype_itemsize)
+    expect_equal(chunks, c(215295))
+})
+
 test_that("can get array that spans multiple chunks", {
     a <- array(data=1:100, dim=c(10, 10))
     #      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]