spatialdata
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Image2DModel.parse() forgetting about scale_factors if chunking
Recommendation: attach a minimal working example Generally, the easier it is for us to reproduce the issue, the faster we can work on it. It is not required, but if you can, please:
- Reproduce using the
blobsdataset
from spatialdata.datasets import blobs
sdata = blobs()
image = sdata['blobs_image'].values
sdata['image_chunk_downscale'] = spatialdata.models.Image2DModel.parse(
data=image,
dims=['c', 'y', 'x'],
transformations=None,
scale_factors=[2,2],
method="nearest",
chunks=(1,100,100))
sdata
SpatialData object
├── Images
│ ├── 'blobs_image': DataArray[cyx] (3, 512, 512)
│ ├── 'blobs_multiscale_image': DataTree[cyx] (3, 512, 512), (3, 256, 256), (3, 128, 128)
│ └── 'image_chunk_downscale': DataTree[cyx] (3, 512, 512)
├── Labels
│ ├── 'blobs_labels': DataArray[yx] (512, 512)
│ └── 'blobs_multiscale_labels': DataTree[yx] (512, 512), (256, 256), (128, 128)
├── Points
│ └── 'blobs_points': DataFrame with shape: (<Delayed>, 4) (2D points)
├── Shapes
│ ├── 'blobs_circles': GeoDataFrame shape: (5, 2) (2D shapes)
│ ├── 'blobs_multipolygons': GeoDataFrame shape: (2, 1) (2D shapes)
│ └── 'blobs_polygons': GeoDataFrame shape: (5, 1) (2D shapes)
└── Tables
└── 'table': AnnData (26, 3)
with coordinate systems:
▸ 'global', with elements:
blobs_image (Images), blobs_multiscale_image (Images), image_chunk_downscale (Images), blobs_labels (Labels), blobs_multiscale_labels (Labels), blobs_points (Points), blobs_circles (Shapes), blobs_multipolygons (Shapes), blobs_polygons (Shapes)
Describe the bug
Want to parse a array (dask_array is my aim) to a multiscale chunked xarray.DataTree for my image.
When using both scale_factors and chunking, chunking works, but multiscale image is not created...
Not sure if intentional..
Expected behavior Expect multiscale chunked image.
Desktop (optional):
- OS: macOS
- Version 14.0.0
packages
# packages in environment at /opt/homebrew/Caskroom/mambaforge/base/envs/spatialdata:
#
# Name Version Build Channel
aiobotocore 2.5.4 pypi_0 pypi
aiohappyeyeballs 2.4.6 pyhd8ed1ab_0 conda-forge
aiohttp 3.11.13 py312h998013c_0 conda-forge
aioitertools 0.12.0 pypi_0 pypi
aiosignal 1.3.2 pyhd8ed1ab_0 conda-forge
alabaster 1.0.0 pyhd8ed1ab_1 conda-forge
anndata 0.11.3 pyhd8ed1ab_0 conda-forge
annotated-types 0.7.0 pyhd8ed1ab_1 conda-forge
aom 3.9.1 h7bae524_0 conda-forge
app-model 0.3.0 pyhd8ed1ab_0 conda-forge
appdirs 1.4.4 pyhd8ed1ab_1 conda-forge
appnope 0.1.4 pyhd8ed1ab_1 conda-forge
array-api-compat 1.10.0 pyhd8ed1ab_0 conda-forge
asciitree 0.3.3 py_2 conda-forge
asttokens 3.0.0 pyhd8ed1ab_1 conda-forge
attrs 25.1.0 pyh71513ae_0 conda-forge
aws-c-auth 0.8.1 hfc2798a_0 conda-forge
aws-c-cal 0.8.1 hc8a0bd2_3 conda-forge
aws-c-common 0.10.6 h5505292_0 conda-forge
aws-c-compression 0.3.0 hc8a0bd2_5 conda-forge
aws-c-event-stream 0.5.0 h54f970a_11 conda-forge
aws-c-http 0.9.2 h96aa502_4 conda-forge
aws-c-io 0.15.3 haba67d1_6 conda-forge
aws-c-mqtt 0.11.0 h24f418c_12 conda-forge
aws-c-s3 0.7.9 hf37e03c_1 conda-forge
aws-c-sdkutils 0.2.2 hc8a0bd2_0 conda-forge
aws-checksums 0.2.2 hc8a0bd2_4 conda-forge
aws-crt-cpp 0.29.9 ha81f72f_2 conda-forge
aws-sdk-cpp 1.11.489 h0e5014b_0 conda-forge
azure-core-cpp 1.14.0 hd50102c_0 conda-forge
azure-identity-cpp 1.10.0 hc602bab_0 conda-forge
azure-storage-blobs-cpp 12.13.0 h7585a09_1 conda-forge
azure-storage-common-cpp 12.8.0 h9ca1f76_1 conda-forge
azure-storage-files-datalake-cpp 12.12.0 hcdd55da_1 conda-forge
babel 2.17.0 pyhd8ed1ab_0 conda-forge
backports 1.0 pyhd8ed1ab_5 conda-forge
backports.tarfile 1.2.0 pyhd8ed1ab_1 conda-forge
blosc 1.21.6 h7dd00d9_1 conda-forge
bokeh 3.6.3 pyhd8ed1ab_0 conda-forge
botocore 1.31.17 pypi_0 pypi
branca 0.8.1 pyhd8ed1ab_0 conda-forge
brotli 1.1.0 hd74edd7_2 conda-forge
brotli-bin 1.1.0 hd74edd7_2 conda-forge
brotli-python 1.1.0 py312hde4cb15_2 conda-forge
brunsli 0.1 h9f76cd9_0 conda-forge
bzip2 1.0.8 h99b78c6_7 conda-forge
c-ares 1.34.4 h5505292_0 conda-forge
c-blosc2 2.15.2 h9cbb436_1 conda-forge
ca-certificates 2025.1.31 hf0a4a13_0 conda-forge
cachecontrol 0.14.2 pyha770c72_0 conda-forge
cachecontrol-with-filecache 0.14.2 pyhd8ed1ab_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cachey 0.2.1 pyh9f0ad1d_0 conda-forge
cachy 0.3.0 pyhd8ed1ab_2 conda-forge
certifi 2025.1.31 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py312h0fad829_0 conda-forge
charls 2.4.2 h13dd4ca_0 conda-forge
charset-normalizer 3.4.1 pyhd8ed1ab_0 conda-forge
click 8.1.8 pyh707e725_0 conda-forge
click-default-group 1.2.4 pyhd8ed1ab_1 conda-forge
clikit 0.6.2 pyhd8ed1ab_3 conda-forge
cloudpickle 3.1.1 pyhd8ed1ab_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_1 conda-forge
colorcet 3.1.0 pyhd8ed1ab_1 conda-forge
comm 0.2.2 pyhd8ed1ab_1 conda-forge
conda-lock 2.5.7 pyhd8ed1ab_1 conda-forge
contourpy 1.3.1 py312hb23fbb9_0 conda-forge
cpython 3.12.9 py312hd8ed1ab_0 conda-forge
crashtest 0.4.1 pyhd8ed1ab_1 conda-forge
cycler 0.12.1 pyhd8ed1ab_1 conda-forge
cytoolz 1.0.1 py312hea69d52_0 conda-forge
dask 2024.11.2 pypi_0 pypi
dask-expr 1.1.19 pypi_0 pypi
dask-image 2024.5.3 pyhd8ed1ab_0 conda-forge
datashader 0.17.0 pyhd8ed1ab_0 conda-forge
dav1d 1.2.1 hb547adb_0 conda-forge
debugpy 1.8.12 py312hd8f9ff3_0 conda-forge
decorator 5.2.1 pyhd8ed1ab_0 conda-forge
deprecated 1.2.18 pyhd8ed1ab_0 conda-forge
distlib 0.3.9 pyhd8ed1ab_1 conda-forge
distributed 2024.11.2 pypi_0 pypi
docstring_parser 0.16 pyhd8ed1ab_0 conda-forge
docutils 0.21.2 pyhd8ed1ab_1 conda-forge
ensureconda 1.4.4 pyhd8ed1ab_1 conda-forge
exceptiongroup 1.2.2 pyhd8ed1ab_1 conda-forge
executing 2.1.0 pyhd8ed1ab_1 conda-forge
fasteners 0.19 pyhd8ed1ab_1 conda-forge
fcsparser 0.2.8 pyhd8ed1ab_0 conda-forge
filelock 3.17.0 pyhd8ed1ab_0 conda-forge
flexcache 0.3 pyhd8ed1ab_1 conda-forge
flexparser 0.4 pyhd8ed1ab_1 conda-forge
folium 0.19.4 pyhd8ed1ab_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_3 conda-forge
fontconfig 2.15.0 h1383a14_1 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.56.0 py312h998013c_0 conda-forge
freetype 2.12.1 hadb7bae_2 conda-forge
freetype-py 2.5.1 pyhd8ed1ab_1 conda-forge
freexl 2.0.0 h3ab3353_2 conda-forge
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fsspec 2023.6.0 pyh1a96a4e_0 conda-forge
geopandas 1.0.1 pyhd8ed1ab_3 conda-forge
geopandas-base 1.0.1 pyha770c72_3 conda-forge
geos 3.13.0 hf9b8971_0 conda-forge
geotiff 1.7.4 hbef4fa4_0 conda-forge
gflags 2.2.2 hf9b8971_1005 conda-forge
giflib 5.2.2 h93a5062_0 conda-forge
gitdb 4.0.12 pyhd8ed1ab_0 conda-forge
gitpython 3.1.44 pyhff2d567_0 conda-forge
glog 0.7.1 heb240a5_0 conda-forge
gmp 6.3.0 h7bae524_2 conda-forge
gmpy2 2.1.5 py312h524cf62_3 conda-forge
h2 4.2.0 pyhd8ed1ab_0 conda-forge
h5py 3.13.0 nompi_py312hd7c5113_100 conda-forge
hdf5 1.14.3 nompi_ha698983_109 conda-forge
heapdict 1.0.1 pyhd8ed1ab_2 conda-forge
hpack 4.1.0 pyhd8ed1ab_0 conda-forge
hsluv 5.0.4 pyhd8ed1ab_1 conda-forge
html5lib 1.1 pyhd8ed1ab_2 conda-forge
hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge
icu 75.1 hfee45f7_0 conda-forge
idna 3.10 pyhd8ed1ab_1 conda-forge
imagecodecs 2024.12.30 py312h8857d0e_0 conda-forge
imageio 2.37.0 pyhfb79c49_0 conda-forge
imagesize 1.4.1 pyhd8ed1ab_0 conda-forge
importlib-metadata 8.6.1 pyha770c72_0 conda-forge
importlib_resources 6.5.2 pyhd8ed1ab_0 conda-forge
in-n-out 0.2.1 pyhd8ed1ab_1 conda-forge
ipykernel 6.29.5 pyh57ce528_0 conda-forge
ipython 8.32.0 pyh907856f_0 conda-forge
jaraco.classes 3.4.0 pyhd8ed1ab_2 conda-forge
jaraco.context 6.0.1 pyhd8ed1ab_0 conda-forge
jaraco.functools 4.1.0 pyhd8ed1ab_0 conda-forge
jedi 0.19.2 pyhd8ed1ab_1 conda-forge
jinja2 3.1.5 pyhd8ed1ab_0 conda-forge
jmespath 1.0.1 pypi_0 pypi
joblib 1.4.2 pyhd8ed1ab_1 conda-forge
json-c 0.18 he4178ee_0 conda-forge
jsonschema 4.23.0 pyhd8ed1ab_1 conda-forge
jsonschema-specifications 2024.10.1 pyhd8ed1ab_1 conda-forge
jupyter_client 8.6.3 pyhd8ed1ab_1 conda-forge
jupyter_core 5.7.2 pyh31011fe_1 conda-forge
jxrlib 1.1 h93a5062_3 conda-forge
keyring 25.6.0 pyh534df25_0 conda-forge
kiwisolver 1.4.8 py312h2c4a281_0 conda-forge
krb5 1.21.3 h237132a_0 conda-forge
lamin_utils 0.13.10 pyhd8ed1ab_0 conda-forge
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libarrow 19.0.1 h0945df6_0_cpu conda-forge
libarrow-acero 19.0.1 hf07054f_0_cpu conda-forge
libarrow-dataset 19.0.1 hf07054f_0_cpu conda-forge
libarrow-substrait 19.0.1 h4239455_0_cpu conda-forge
libavif16 1.1.1 hf9d1e0e_3 conda-forge
libblas 3.9.0 31_h10e41b3_openblas conda-forge
libbrotlicommon 1.1.0 hd74edd7_2 conda-forge
libbrotlidec 1.1.0 hd74edd7_2 conda-forge
libbrotlienc 1.1.0 hd74edd7_2 conda-forge
libcblas 3.9.0 31_hb3479ef_openblas conda-forge
libcrc32c 1.1.2 hbdafb3b_0 conda-forge
libcurl 8.12.1 h73640d1_0 conda-forge
libcxx 19.1.7 ha82da77_0 conda-forge
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libgoogle-cloud 2.35.0 hdbe95d5_0 conda-forge
libgoogle-cloud-storage 2.35.0 h7081f7f_0 conda-forge
libgrpc 1.67.1 h0a426d6_1 conda-forge
libheif 1.19.5 gpl_h297b2c4_100 conda-forge
libhwloc 2.11.2 default_hbce5d74_1001 conda-forge
libhwy 1.1.0 h2ffa867_0 conda-forge
libiconv 1.18 hfe07756_1 conda-forge
libjpeg-turbo 3.0.0 hb547adb_1 conda-forge
libjxl 0.11.1 h562e088_0 conda-forge
libkml 1.3.0 he250239_1021 conda-forge
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libnghttp2 1.64.0 h6d7220d_0 conda-forge
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libparquet 19.0.1 h636d7b7_0_cpu conda-forge
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matplotlib-base 3.10.0 py312hdbc7e53_0 conda-forge
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minizip 4.0.7 hff1a8ea_3 conda-forge
more-itertools 10.6.0 pyhd8ed1ab_0 conda-forge
mpc 1.3.1 h8f1351a_1 conda-forge
mpfr 4.2.1 hb693164_3 conda-forge
mpmath 1.3.0 pyhd8ed1ab_1 conda-forge
msgpack-python 1.1.0 py312h6142ec9_0 conda-forge
multidict 6.1.0 py312hdb8e49c_1 conda-forge
multipledispatch 0.6.0 pyhd8ed1ab_1 conda-forge
multiscale-spatial-image 2.0.2 pypi_0 pypi
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
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napari-matplotlib 3.0.0 pyh73487a3_0 conda-forge
napari-plugin-engine 0.2.0 pyha07c04f_3 conda-forge
napari-plugin-manager 0.1.4 pyha07c04f_0 conda-forge
napari-spatialdata 0.5.5 pypi_0 pypi
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readfcs 1.1.8 pyhd8ed1ab_0 conda-forge
readline 8.2 h1d1bf99_2 conda-forge
referencing 0.36.2 pyh29332c3_0 conda-forge
requests 2.32.3 pyhd8ed1ab_1 conda-forge
rich 13.9.4 pyhd8ed1ab_1 conda-forge
roman-numerals-py 3.1.0 pyhd8ed1ab_0 conda-forge
rpds-py 0.23.1 py312hd60eec9_0 conda-forge
ruamel.yaml 0.18.10 py312hea69d52_0 conda-forge
ruamel.yaml.clib 0.2.8 py312h0bf5046_1 conda-forge
s3fs 2023.6.0 pypi_0 pypi
scanpy 1.10.4 pyhd8ed1ab_0 conda-forge
scikit-image 0.25.2 py312hcb1e3ce_0 conda-forge
scikit-learn 1.6.1 py312h39203ce_0 conda-forge
scipy 1.15.2 py312h99a188d_0 conda-forge
seaborn 0.13.2 hd8ed1ab_3 conda-forge
seaborn-base 0.13.2 pyhd8ed1ab_3 conda-forge
session-info 1.0.0 pyhd8ed1ab_0 conda-forge
setuptools 75.8.0 pyhff2d567_0 conda-forge
shapely 2.0.7 py312ha6455e5_0 conda-forge
shellingham 1.5.4 pyhd8ed1ab_1 conda-forge
six 1.17.0 pyhd8ed1ab_0 conda-forge
sleef 3.8 h8391f65_0 conda-forge
slicerator 1.1.0 pyhd8ed1ab_1 conda-forge
smmap 5.0.2 pyhd8ed1ab_0 conda-forge
snappy 1.2.1 h98b9ce2_1 conda-forge
snowballstemmer 2.2.0 pyhd8ed1ab_0 conda-forge
sortedcontainers 2.4.0 pyhd8ed1ab_1 conda-forge
spatial-image 1.1.0 pyhd8ed1ab_1 conda-forge
spatialdata 0.3.0 pypi_0 pypi
spatialdata-io 0.1.5 pyhd8ed1ab_0 conda-forge
spatialdata-plot 0.2.7 pyhd8ed1ab_1 conda-forge
sphinx 8.2.1 pyhd8ed1ab_0 conda-forge
sphinxcontrib-applehelp 2.0.0 pyhd8ed1ab_1 conda-forge
sphinxcontrib-devhelp 2.0.0 pyhd8ed1ab_1 conda-forge
sphinxcontrib-htmlhelp 2.1.0 pyhd8ed1ab_1 conda-forge
sphinxcontrib-jsmath 1.0.1 pyhd8ed1ab_1 conda-forge
sphinxcontrib-qthelp 2.0.0 pyhd8ed1ab_1 conda-forge
sphinxcontrib-serializinghtml 1.1.10 pyhd8ed1ab_1 conda-forge
sqlite 3.49.1 hd7222ec_1 conda-forge
stack_data 0.6.3 pyhd8ed1ab_1 conda-forge
statsmodels 0.14.4 py312h755e627_0 conda-forge
stdlib-list 0.11.1 pyhd8ed1ab_0 conda-forge
superqt 0.7.0 pyhb6d5dde_0 conda-forge
svt-av1 3.0.0 h8ab69cd_0 conda-forge
sympy 1.13.3 pyh2585a3b_105 conda-forge
tabulate 0.9.0 pyhd8ed1ab_2 conda-forge
tbb 2022.0.0 h0cbf7ec_0 conda-forge
tblib 3.0.0 pyhd8ed1ab_1 conda-forge
threadpoolctl 3.5.0 pyhc1e730c_0 conda-forge
tifffile 2025.2.18 pyhd8ed1ab_0 conda-forge
tinycss2 1.4.0 pyhd8ed1ab_0 conda-forge
tk 8.6.13 h5083fa2_1 conda-forge
tomli 2.2.1 pyhd8ed1ab_1 conda-forge
tomli-w 1.2.0 pyhd8ed1ab_0 conda-forge
tomlkit 0.13.2 pyha770c72_1 conda-forge
toolz 0.12.1 pyhd8ed1ab_0 conda-forge
tornado 6.4.2 py312hea69d52_0 conda-forge
tqdm 4.67.1 pyhd8ed1ab_1 conda-forge
traitlets 5.14.3 pyhd8ed1ab_1 conda-forge
typer 0.15.1 pyhd8ed1ab_0 conda-forge
typer-slim 0.15.1 pyhd8ed1ab_0 conda-forge
typer-slim-standard 0.15.1 hd8ed1ab_0 conda-forge
typing-extensions 4.12.2 hd8ed1ab_1 conda-forge
typing_extensions 4.12.2 pyha770c72_1 conda-forge
tzdata 2025a h78e105d_0 conda-forge
umap-learn 0.5.7 py312h81bd7bf_1 conda-forge
unicodedata2 16.0.0 py312hea69d52_0 conda-forge
uriparser 0.9.8 h00cdb27_0 conda-forge
urllib3 1.26.20 pypi_0 pypi
virtualenv 20.29.2 pyhd8ed1ab_0 conda-forge
vispy 0.14.3 py312h9179848_1 conda-forge
wcwidth 0.2.13 pyhd8ed1ab_1 conda-forge
webencodings 0.5.1 pyhd8ed1ab_3 conda-forge
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
wrapt 1.17.2 py312hea69d52_0 conda-forge
x265 3.5 hbc6ce65_3 conda-forge
xarray 2024.11.0 pypi_0 pypi
xarray-dataclasses 1.9.1 pypi_0 pypi
xarray-datatree 0.0.14 pyhd8ed1ab_0 conda-forge
xarray-schema 0.0.3 pyhd8ed1ab_0 conda-forge
xarray-spatial 0.4.0 pyhd8ed1ab_1 conda-forge
xerces-c 3.2.5 h92fc2f4_2 conda-forge
xorg-libxau 1.0.12 h5505292_0 conda-forge
xorg-libxdmcp 1.1.5 hd74edd7_0 conda-forge
xyzservices 2025.1.0 pyhd8ed1ab_0 conda-forge
yaml 0.2.5 h3422bc3_2 conda-forge
yarl 1.18.3 py312h998013c_1 conda-forge
zarr 2.18.4 pyhd8ed1ab_0 conda-forge
zeromq 4.3.5 hc1bb282_7 conda-forge
zfp 1.0.1 h1c5d8ea_2 conda-forge
zict 3.0.0 pyhd8ed1ab_1 conda-forge
zipp 3.21.0 pyhd8ed1ab_1 conda-forge
zlib 1.3.1 h8359307_2 conda-forge
zlib-ng 2.2.4 h13dfb9a_0 conda-forge
zstandard 0.23.0 py312h15fbf35_1 conda-forge
zstd 1.5.6 hb46c0d2_0 conda-forge
as additional context: when I run
sdata4['image'] = spatialdata.models.Image2DModel.parse(
data=dask_image.imread.imread(path_to_image),
dims=['c', 'y', 'x'],
transformations=None,
scale_factors=[2,2])
The chunking is defaulted to (256,256) for all scales (see image below).
Here is just scale0