From 04dd43eedbdd8fc9fd6945c1958f0927b11c2ea6 Mon Sep 17 00:00:00 2001
From: Nathan Zimmerberg <39104088+nhz2@users.noreply.github.com>
Date: Mon, 27 Nov 2023 12:01:23 -0500
Subject: [PATCH] Change saving order from F to C (#42)

---
 Project.toml   | 4 ++--
 src/loading.jl | 2 +-
 src/saving.jl  | 7 ++++---
 3 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/Project.toml b/Project.toml
index 6e355e7..464b71e 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,7 +1,7 @@
 name = "SmallZarrGroups"
 uuid = "d423b6e5-1c84-4ae2-8d2d-b903aee15ac7"
 authors = ["nhz2 <nhz2@cornell.edu>"]
-version = "0.7.1"
+version = "0.8.0"
 
 [deps]
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
@@ -25,5 +25,5 @@ DataStructures = "0.18"
 JSON3 = "1"
 StructArrays = "0.6"
 TranscodingStreams = "0.9, 0.10"
-ZipArchives = "0.3, 0.4, 0.5, 1"
+ZipArchives = "1"
 julia = "1.8"
diff --git a/src/loading.jl b/src/loading.jl
index cd941db..5012141 100644
--- a/src/loading.jl
+++ b/src/loading.jl
@@ -108,7 +108,7 @@ function load_dir(reader::AbstractReader)::ZGroup
                 end
             end
 
-            zarray = if metadata.is_column_major
+            zarray = if metadata.is_column_major || ndims(array) ≤ 1
                 ZArray(array;
                     chunks = Tuple(chunks),
                     compressor = metadata.compressor,
diff --git a/src/saving.jl b/src/saving.jl
index cbab9f9..35c3122 100644
--- a/src/saving.jl
+++ b/src/saving.jl
@@ -89,7 +89,8 @@ function _save_zarray(writer::AbstractWriter, key_prefix::String, z::ZArray)
     if zarr_size != 0 && !any(iszero, shape)
         chunks = Tuple(z.chunks)
         # store chunks
-        shaped_chunkdata = zeros(UInt8, zarr_size, chunks...)
+        shaped_chunkdata = zeros(UInt8, zarr_size, reverse(chunks)...)
+        permuted_shaped_chunkdata = PermutedDimsArray(shaped_chunkdata, (1, ndims(z)+1:-1:2...))
         shaped_array = if dtype.julia_size == 1
             reshape(reinterpret(reshape, UInt8, data), 1, shape...)
         else
@@ -102,7 +103,7 @@ function _save_zarray(writer::AbstractWriter, key_prefix::String, z::ZArray)
             real_chunksize = chunkstop .- chunkstart .+ 1
             # now create overlapping views
             array_view = view(shaped_array, :, (range.(chunkstart, chunkstop))...)
-            chunk_view = view(shaped_chunkdata, :, (range.(1, real_chunksize))...)
+            chunk_view = view(permuted_shaped_chunkdata, :, (range.(1, real_chunksize))...)
             # TODO check if the data can just be directly copied.
             for (zarr_byte, julia_byte) in enumerate(dtype.byteorder)
                 selectdim(chunk_view, 1, zarr_byte) .= selectdim(array_view, 1, julia_byte)
@@ -122,7 +123,7 @@ function _save_zarray(writer::AbstractWriter, key_prefix::String, z::ZArray)
             "dtype": $dtype_str,
             "fill_value": null,
             "filters": null,
-            "order": "F",
+            "order": "C",
             "shape": [$(join(shape, ", "))],
             "zarr_format": 2
         }