Loosen restriction on open_tree so that this would open all CDMs

Project.toml

@@ -4,9 +4,9 @@ authors = ["Felix Cremer <[email protected]> and contributors"]
 version = "0.1.0-DEV"
 
 [deps]
+CFTime = "179af706-886a-5703-950a-314cd64e0468"
 CommonDataModel = "1fbeeb36-5f17-413c-809b-666fb144f157"
 DimensionalData = "0703355e-b756-11e9-17c0-8b28908087d0"
-DiskArrayTools = "fcd2136c-9f69-4db6-97e5-f31981721d63"
 DiskArrays = "3c3547ce-8d99-4f5e-a174-61eb10b00ae3"
 Rasters = "a3a2b9e3-a471-40c9-b274-f788e487c689"
 YAXArrayBase = "90b8fcef-0c2d-428d-9c56-5f86629e9d14"
@@ -15,13 +15,13 @@ Zarr = "0a941bbe-ad1d-11e8-39d9-ab76183a1d99"
 ZarrDatasets = "519a4cdf-1362-424a-9ea1-b1d782dbb24b"
 
 [compat]
-CommonDataModel = "0.3.8"
+CFTime = "0.2.1"
+CommonDataModel = "0.3.8, 0.4"
 DimensionalData = "0.29.12"
-DiskArrayTools = "0.1.12"
 DiskArrays = "0.4.11"
 Rasters = "0.14.4"
 YAXArrayBase = "0.7.5"
 YAXArrays = "0.6.1"
 Zarr = "0.9.4"
 ZarrDatasets = "0.1.3"
-julia = "1.6.7"
+julia = "1.6.7"

docs/introduction.qmd

@@ -0,0 +1,57 @@
+# Introduction to the SentinelDataSource julia package
+
+A user friendly way to open the EOPF Zarr products in Julia.
+
+
+## Introduction
+
+SentinelDataSource is a julia package that extends the DimensionalData.jl ecosystem to enable seamless access to ESA EOPF data products stored in the Zarr format. 
+This notebook demonstrates how to use SentinelDataSource.jl to explore and analyse EOPF Zarr datasets. 
+It highlights the key features currently supported. 
+
+## Install SentinelDataSource.jl
+
+To install the SentinelDataSource.jl package use the julia package manager. 
+
+In the julia REPL first press `]` to enter the pkg mode and then do
+
+```
+add SentinelDataSource
+```
+
+This will install SentinelDataSource into your current environment. 
+
+## Import Modules
+
+```{julia}
+using Pkg
+Pkg.activate(".")
+Pkg.instantiate()
+```
+
+```{julia}
+using SentinelDataSource: SentinelDataSource as SDS
+using ZarrDatasets
+```
+
+
+# Open the product in Native Mode
+
+## Sentinel-2 Level-2A
+
+```{julia}
+path ="https://objectstore.eodc.eu:2222/e05ab01a9d56408d82ac32d69a5aae2a:202505-s02msil2a/18/products/cpm_v256/S2B_MSIL2A_20250518T112119_N0511_R037_T29RLL_20250518T140519.zarr"
+```
+
+```{julia}
+dt = SDS.open_tree(path)
+```
+
+```{julia}
+dt.quality.l2a_quicklook.r60m[:tci]
+```
+
+```{julia}
+using GLMakie
+plot()
+```

src/SentinelDataSource.jl

@@ -5,18 +5,22 @@ using ZarrDatasets: ZarrDataset
 using CommonDataModel: CommonDataModel as CDM
 using Rasters:Raster
 
-open_tree(path::AbstractString) = open_tree(ZarrDataset(path))
+export open_tree
 
-function open_tree(dataset::ZarrDataset)
+open_tree(path::AbstractString;kwargs...) = open_tree(ZarrDataset(path);kwargs...)
+
+function open_tree(dataset; prefer_datetime=true)
     stem = DimTree()
     groupnames = CDM.groupnames(dataset)
     varnames = CDM.varnames(dataset)
     alldimnames = nesteddimnames(dataset)
+    @show varnames
     for v in setdiff(varnames, alldimnames)
-        setindex!(stem, Raster(CDM.variable(dataset, v), lazy=true),Symbol(v))
+        r = Raster(CDM.variable(dataset, v); lazy=true, prefer_datetime)
+        setindex!(stem, r,Symbol(v))
     end
     for g in groupnames
-        setindex!(stem,  open_tree(CDM.group(dataset, g)),Symbol(g))
+        setindex!(stem,  open_tree(CDM.group(dataset, g);prefer_datetime),Symbol(g))
     end
     stem
 end

test/Project.toml

@@ -1,4 +1,5 @@
 [deps]
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
+DimensionalData = "0703355e-b756-11e9-17c0-8b28908087d0"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Zarr = "0a941bbe-ad1d-11e8-39d9-ab76183a1d99"

test/runtests.jl

@@ -2,7 +2,7 @@ using SentinelDataSource
 using Test
 using Aqua
 using Zarr
-using ZarrDatasets
+using DimensionalData
 
 @testset "SentinelDataSource.jl" begin
     @testset "Code quality (Aqua.jl)" begin
@@ -12,33 +12,33 @@ using ZarrDatasets
 
     @testset "S1 L1 GRD" begin
         s1grdpath = "https://objectstore.eodc.eu:2222/e05ab01a9d56408d82ac32d69a5aae2a:sample-data/tutorial_data/cpm_v253/S1A_IW_GRDH_1SDV_20240201T164915_20240201T164940_052368_065517_750E.zarr"
-        s1grd = ZarrDataset(s1grdpath)
-        s1grdtree = SentinelDataSource.open_tree(s1grd)
+        s1grdtree = open_tree(s1grdpath)
+        @test s1grdtree isa DimTree
     end
     @testset "S1 L1 SLC" begin
         s1slcpath = "https://objectstore.eodc.eu:2222/e05ab01a9d56408d82ac32d69a5aae2a:sample-data/tutorial_data/cpm_v253/S1A_IW_SLC__1SDV_20231119T170635_20231119T170702_051289_063021_178F.zarr"
-        s1slc = zopen(s1slcpath)
-        @test s1slc isa ZGroup
+        s1slc = open_tree(s1slcpath)
+        @test s1slc isa DimTree
     end
     @testset "S1 L1 NRB" begin
         s1nrbpath = "https://objectstore.eodc.eu:2222/e05ab01a9d56408d82ac32d69a5aae2a:sample-data/tutorial_data/cpm_v253/S1A_IW_SLC__1SDV_20240106T170607_20240106T170635_051989_064848_04A6.zarr"
-        s1nrb = zopen(s1nrbpath)
-        @test s1nrb isa ZGroup
+        s1nrb = open_tree(s1nrbpath)
+        @test s1nrb isa DimTree
     end
     @testset "S1 L2 OCN" begin
         s1ocnpath = "https://objectstore.eodc.eu:2222/e05ab01a9d56408d82ac32d69a5aae2a:sample-data/tutorial_data/cpm_v253/S1A_IW_OCN__2SDV_20250224T054940_20250224T055005_058034_072A26_160E.zarr"
-        s1ocn = zopen(s1ocnpath)
-        @test s1ocn isa ZGroup
+        s1ocn = open_tree(s1ocnpath)
+        @test s1ocn isa DimTree
     end
     @testset "S2 L1C MSI" begin
         s2l1cpath = "https://objectstore.eodc.eu:2222/e05ab01a9d56408d82ac32d69a5aae2a:sample-data/tutorial_data/cpm_v253/S2B_MSIL1C_20250113T103309_N0511_R108_T32TLQ_20250113T122458.zarr"
-        s2l1c = zopen(s2l1cpath)
-        @test s2l1c isa ZGroup
+        s2l1c = open_tree(s2l1cpath)
+        @test s2l1c isa DimTree
     end
     @testset "S2 L2A MSI" begin
         s2l2apath = "https://objectstore.eodc.eu:2222/e05ab01a9d56408d82ac32d69a5aae2a:sample-data/tutorial_data/cpm_v253/S2A_MSIL2A_20240101T102431_N0510_R065_T32TNT_20240101T144052.zarr"
-        s2l2a = zopen(s2l2apath)
-        @test s2l2a isa ZGroup
+        s2l2a = open_tree(s2l2apath)
+        @test s2l2a isa DimTree
     end
 
 end